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  • Genomics
  • American Association for the Advancement of Science (AAAS)  (168)
  • Oxford University Press  (47)
  • BioMed Central  (2)
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  • 1
    Publikationsdatum: 2022-10-18
    Beschreibung: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Beschreibung: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Beschreibung: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Schlagwort(e): Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
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  • 2
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 14, doi:10.1186/s13742-016-0118-5.
    Beschreibung: Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.
    Beschreibung: Work was supported in part by: the Institute of Theoretical Physics and the Pauli Center at ETH Zurich; the US National Science Foundation (NSF Moorea Coral Reef Long Term Ecological Research Site, OCE-1236905; Socio-Ecosystem Dynamics of Natural-Human Networks on Model Islands, CNH-1313830; Coastal SEES: Adaptive Capacity, Resilience, and Coral Reef State Shifts in Social-ecological Systems, OCE-1325652, OCE-1325554); the Gordon and Betty Moore Foundation (Berkeley Initiative in Global Change Biology; Genomic Standards Consortium); Courtney Ross and the Ross Institute; UC Berkeley Vice Chancellor for Research; CRIOBE; and the France Berkeley Fund (FBF 2014-0015).
    Schlagwort(e): Computational ecology ; Biodiversity ; Genomics ; Biocode ; Earth observations ; Social-ecological system ; Ecosystem dynamics ; Climate change scenarios ; Predictive modeling
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 3
    Publikationsdatum: 2015-09-19
    Beschreibung: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 4
    Publikationsdatum: 2015-08-29
    Beschreibung: Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 5
    Publikationsdatum: 2015-05-29
    Beschreibung: A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines G enomic O rigins T hrough T axonomic CHA llenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 6
    Publikationsdatum: 2016-07-09
    Beschreibung: Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 7
    Publikationsdatum: 2016-07-28
    Beschreibung: Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 8
    Publikationsdatum: 2013-06-08
    Beschreibung: DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging owing to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of cytosine–guanine dinucleotide islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared with adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 9
    Publikationsdatum: 2014-12-17
    Beschreibung: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 10
    Publikationsdatum: 2014-12-17
    Beschreibung: Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro . Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 11
    Publikationsdatum: 2015-04-02
    Beschreibung: With read lengths of currently up to 2 x 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 12
    Publikationsdatum: 2015-04-02
    Beschreibung: RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se , other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 13
    Publikationsdatum: 2016-01-09
    Beschreibung: Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 14
    Publikationsdatum: 2015-08-29
    Beschreibung: Any given human individual carries multiple genetic variants that disrupt protein-coding genes, through structural variation, as well as nucleotide variants and indels. Predicting the phenotypic consequences of a gene disruption remains a significant challenge. Current approaches employ information from a range of biological networks to predict which human genes are haploinsufficient (meaning two copies are required for normal function) or essential (meaning at least one copy is required for viability). Using recently available study gene sets, we show that these approaches are strongly biased towards providing accurate predictions for well-studied genes. By contrast, we derive a haploinsufficiency score from a combination of unbiased large-scale high-throughput datasets, including gene co-expression and genetic variation in over 6000 human exomes. Our approach provides a haploinsufficiency prediction for over twice as many genes currently unassociated with papers listed in Pubmed as three commonly-used approaches, and outperforms these approaches for predicting haploinsufficiency for less-studied genes. We also show that fine-tuning the predictor on a set of well-studied ‘gold standard’ haploinsufficient genes does not improve the prediction for less-studied genes. This new score can readily be used to prioritize gene disruptions resulting from any genetic variant, including copy number variants, indels and single-nucleotide variants.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 15
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    Oxford University Press
    Publikationsdatum: 2015-07-12
    Beschreibung: Meta-analysis of gene expression has enabled numerous insights into biological systems, but current methods have several limitations. We developed a method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. To demonstrate the utility of our method, we conducted a meta-analysis of lung cancer gene expression based on publicly available data. Using 629 samples from five data sets, we trained a multinomial classifier to distinguish between four lung cancer subtypes. Our meta-analysis-derived classifier included 58 genes and achieved 91% accuracy on leave-one-study-out cross-validation and on three independent data sets. Our method makes meta-analysis of gene expression more systematic and expands the range of questions that a meta-analysis can be used to address. As the amount of publicly available gene expression data continues to grow, our method will be an effective tool to help distill these data into knowledge.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 16
    Publikationsdatum: 2016-08-20
    Beschreibung: Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an i ntegrative and d iscriminative e pigenome a nnotation s ystem, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 17
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publikationsdatum: 2016-06-10
    Beschreibung: Early data-sharing efforts have led to improved variant interpretation and development of treatments for rare diseases and some cancer types (1–3). However, such benefits will only be available to the general population if researchers and clinicians can access and make comparisons across data from millions of individuals. Author:
    Schlagwort(e): Genomics
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 18
    Publikationsdatum: 2016-09-03
    Beschreibung: A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 x 10 –4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 x 10 –5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS 1 , IS 2 , IS 5 and IS 186 . Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS 186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 19
    Publikationsdatum: 2015-04-21
    Beschreibung: Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact .
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 20
    Publikationsdatum: 2015-05-20
    Beschreibung: Analysis of rewired upstream subnetworks impacting downstream differential gene expression aids the delineation of evolving molecular mechanisms. Cumulative statistics based on conventional differential correlation are limited for subnetwork rewiring analysis since rewiring is not necessarily equivalent to change in correlation coefficients. Here we present a computational method ChiNet to quantify subnetwork rewiring by statistical heterogeneity that enables detection of potential genotype changes causing altered transcription regulation in evolving organisms. Given a differentially expressed downstream gene set, ChiNet backtracks a rewired upstream subnetwork from a super-network including gene interactions known to occur under various molecular contexts. We benchmarked ChiNet for its high accuracy in distinguishing rewired artificial subnetworks, in silico yeast transcription-metabolic subnetworks, and rewired transcription subnetworks for Candida albicans versus Saccharomyces cerevisiae , against two differential-correlation based subnetwork rewiring approaches. Then, using transcriptome data from tolerant S. cerevisiae strain NRRL Y-50049 and a wild-type intolerant strain, ChiNet identified 44 metabolic pathways affected by rewired transcription subnetworks anchored to major adaptively activated transcription factor genes YAP1 , RPN4 , SFP1 and ROX1 , in response to toxic chemical challenges involved in lignocellulose-to-biofuels conversion. These findings support the use of ChiNet in rewiring analysis of subnetworks where differential interaction patterns resulting from divergent nonlinear dynamics abound.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 21
    Publikationsdatum: 2015-06-24
    Beschreibung: Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein–RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein–rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a ‘proof of concept’ that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 22
    Publikationsdatum: 2015-02-18
    Beschreibung: The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins , implemented in Python and C and supported on Linux and Mac OS X.
    Schlagwort(e): Genomics
    Print ISSN: 0305-1048
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 23
    Publikationsdatum: 2015-02-18
    Beschreibung: Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.
    Schlagwort(e): Genomics
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  • 24
    Publikationsdatum: 2016-02-20
    Beschreibung: Genetic variants in or near miRNA genes can have profound effects on miRNA expression and targeting. As user-friendly software for the impact prediction of miRNA variants on a large scale is still lacking, we created a tool called miRVaS. miRVaS automates this prediction by annotating the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) and by annotating all predicted structural changes within the miRNA due to the variant. In addition, the tool defines the most important region that is predicted to have structural changes and calculates a conservation score that is indicative of the reliability of the structure prediction. The output is presented in a tab-separated file, which enables fast screening, and in an html file, which allows visual comparison between wild-type and variant structures. All separate images are provided for downstream use. Finally, we tested two different approaches on a small test set of published functionally validated genetic variants for their capacity to predict the impact of variants on miRNA expression.
    Schlagwort(e): Genomics
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  • 25
    Publikationsdatum: 2016-02-20
    Beschreibung: Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts ( trans -spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (〉98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans -spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans -spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
    Schlagwort(e): Genomics
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    Publiziert von Oxford University Press
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  • 26
    Publikationsdatum: 2015-12-02
    Beschreibung: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.
    Schlagwort(e): Genomics
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  • 27
    Publikationsdatum: 2013-12-07
    Beschreibung: Identity by descent (IBD) can be reliably detected for long shared DNA segments, which are found in related individuals. However, many studies contain cohorts of unrelated individuals that share only short IBD segments. New sequencing technologies facilitate identification of short IBD segments through rare variants, which convey more information on IBD than common variants. Current IBD detection methods, however, are not designed to use rare variants for the detection of short IBD segments. Short IBD segments reveal genetic structures at high resolution. Therefore, they can help to improve imputation and phasing, to increase genotyping accuracy for low-coverage sequencing and to increase the power of association studies. Since short IBD segments are further assumed to be old, they can shed light on the evolutionary history of humans. We propose HapFABIA, a computational method that applies biclustering to identify very short IBD segments characterized by rare variants. HapFABIA is designed to detect short IBD segments in genotype data that were obtained from next-generation sequencing, but can also be applied to DNA microarray data. Especially in next-generation sequencing data, HapFABIA exploits rare variants for IBD detection. HapFABIA significantly outperformed competing algorithms at detecting short IBD segments on artificial and simulated data with rare variants. HapFABIA identified 160 588 different short IBD segments characterized by rare variants with a median length of 23 kb (mean 24 kb) in data for chromosome 1 of the 1000 Genomes Project. These short IBD segments contain 752 000 single nucleotide variants (SNVs), which account for 39% of the rare variants and 23.5% of all variants. The vast majority—152 000 IBD segments—are shared by Africans, while only 19 000 and 11 000 are shared by Europeans and Asians, respectively. IBD segments that match the Denisova or the Neandertal genome are found significantly more often in Asians and Europeans but also, in some cases exclusively, in Africans. The lengths of IBD segments and their sharing between continental populations indicate that many short IBD segments from chromosome 1 existed before humans migrated out of Africa. Thus, rare variants that tag these short IBD segments predate human migration from Africa. The software package HapFABIA is available from Bioconductor. All data sets, result files and programs for data simulation, preprocessing and evaluation are supplied at http://www.bioinf.jku.at/research/short-IBD .
    Schlagwort(e): Genomics
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  • 28
    Publikationsdatum: 2013-12-07
    Beschreibung: Glioma is the most common and fatal primary brain tumour with poor prognosis; however, the functional roles of miRNAs in glioma malignant progression are insufficiently understood. Here, we used an integrated approach to identify miRNA functional targets during glioma malignant progression by combining the paired expression profiles of miRNAs and mRNAs across 160 Chinese glioma patients, and further constructed the functional miRNA–mRNA regulatory network. As a result, most tumour-suppressive miRNAs in glioma progression were newly discovered, whose functions were widely involved in gliomagenesis. Moreover, three miRNA signatures, with different combinations of hub miRNAs (regulations≥30) were constructed, which could independently predict the survival of patients with all gliomas, high-grade glioma and glioblastoma. Our network-based method increased the ability to identify the prognostic biomarkers, when compared with the traditional method and random conditions. Hsa-miR-524-5p and hsa-miR-628-5p, shared by these three signatures, acted as protective factors and their expression decreased gradually during glioma progression. Functional analysis of these miRNA signatures highlighted their critical roles in cell cycle and cell proliferation in glioblastoma malignant progression, especially hsa-miR-524-5p and hsa-miR-628-5p exhibited dominant regulatory activities. Therefore, network-based biomarkers are expected to be more effective and provide deep insights into the molecular mechanism of glioma malignant progression.
    Schlagwort(e): Genomics
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    Thema: Biologie
    Publiziert von Oxford University Press
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  • 29
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    Oxford University Press
    Publikationsdatum: 2014-02-11
    Beschreibung: A major challenge in cancer genomics is uncovering genes with an active role in tumorigenesis from a potentially large pool of mutated genes across patient samples. Here we focus on the interactions that proteins make with nucleic acids, small molecules, ions and peptides, and show that residues within proteins that are involved in these interactions are more frequently affected by mutations observed in large-scale cancer genomic data than are other residues. We leverage this observation to predict genes that play a functionally important role in cancers by introducing a computational pipeline ( http://canbind.princeton.edu ) for mapping large-scale cancer exome data across patients onto protein structures, and automatically extracting proteins with an enriched number of mutations affecting their nucleic acid, small molecule, ion or peptide binding sites. Using this computational approach, we show that many previously known genes implicated in cancers are enriched in mutations within the binding sites of their encoded proteins. By focusing on functionally relevant portions of proteins—specifically those known to be involved in molecular interactions—our approach is particularly well suited to detect infrequent mutations that may nonetheless be important in cancer, and should aid in expanding our functional understanding of the genomic landscape of cancer.
    Schlagwort(e): Genomics
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  • 30
    Publikationsdatum: 2014-04-03
    Beschreibung: Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea ( Arabidopsis petraea subsp. umbrosa ), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica . The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated ( r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses.
    Schlagwort(e): Genomics
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    Publiziert von Oxford University Press
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  • 31
    Publikationsdatum: 2015-03-14
    Beschreibung: Methods to interpret personal genome sequences are increasingly required. Here, we report a novel framework (EvoTol) to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation of protein sequences and can incorporate tissue-specific gene expression data. We apply this framework to the analysis of whole-exome sequence data in epilepsy and congenital heart disease, and demonstrate EvoTol's ability to identify known disease-causing genes is unmatched by competing methods. Application of EvoTol to the human interactome revealed networks enriched for genes intolerant to protein sequence variation, informing novel polygenic contributions to human disease.
    Schlagwort(e): Genomics
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  • 32
    Publikationsdatum: 2015-03-14
    Beschreibung: Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo . However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. However, technical limitations of these methods prevent them from being applied broadly, especially in clinical settings. We conducted a comprehensive survey involving multiple cell lines, TFs, and methylation types and found that there are intimate relationships between TF binding and methylation level changes around the binding sites. Exploiting the connection between DNA methylation and TF binding, we proposed a novel supervised learning approach to predict TF–DNA interaction using data from base-resolution whole-genome methylation sequencing experiments. We devised beta-binomial models to characterize methylation data around TF binding sites and the background. Along with other static genomic features, we adopted a random forest framework to predict TF–DNA interaction. After conducting comprehensive tests, we saw that the proposed method accurately predicts TF binding and performs favorably versus competing methods.
    Schlagwort(e): Genomics
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  • 33
    Publikationsdatum: 2012-10-10
    Beschreibung: Enriching target sequences in sequencing libraries via capture hybridization to bait/probes is an efficient means of leveraging the capabilities of next-generation sequencing for obtaining sequence data from target regions of interest. However, homologous sequences from non-target regions may also be enriched by such methods. Here we investigate the fidelity of capture enrichment for complete mitochondrial DNA (mtDNA) genome sequencing by analyzing sequence data for nuclear copies of mtDNA (NUMTs). Using capture-enriched sequencing data from a mitochondria-free cell line and the parental cell line, and from samples previously sequenced from long-range PCR products, we demonstrate that NUMT alleles are indeed present in capture-enriched sequence data, but at low enough levels to not influence calling the authentic mtDNA genome sequence. However, distinguishing NUMT alleles from true low-level mutations (e.g. heteroplasmy) is more challenging. We develop here a computational method to distinguish NUMT alleles from heteroplasmies, using sequence data from artificial mixtures to optimize the method.
    Schlagwort(e): Genomics
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  • 34
    Publikationsdatum: 2012-10-10
    Beschreibung: Single nucleotide polymorphisms (SNPs) are increasingly used to tag genetic loci associated with phenotypes such as risk of complex diseases. Technically, this is done genome-wide without prior restriction or knowledge of biological feasibility in scans referred to as genome-wide association studies (GWAS). Depending on the linkage disequilibrium (LD) structure at a particular locus, such tagSNPs may be surrogates for many thousands of other SNPs, and it is difficult to distinguish those that may play a functional role in the phenotype from those simply genetically linked. Because a large proportion of tagSNPs have been identified within non-coding regions of the genome, distinguishing functional from non-functional SNPs has been an even greater challenge. A strategy was recently proposed that prioritizes surrogate SNPs based on non-coding chromatin and epigenomic mapping techniques that have become feasible with the advent of massively parallel sequencing. Here, we introduce an R/Bioconductor software package that enables the identification of candidate functional SNPs by integrating information from tagSNP locations, lists of linked SNPs from the 1000 genomes project and locations of chromatin features which may have functional significance. Availability: FunciSNP is available from Bioconductor (bioconductor.org).
    Schlagwort(e): Genomics
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  • 35
    Publikationsdatum: 2014-04-15
    Beschreibung: Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and analysis of a relatively small sample of marker genes. The selection of these phylogenetic markers should ideally be based on accurate predictions of their combined, rather than individual, potential to accurately resolve the phylogeny of interest. Here we present and validate a new phylogenomics strategy to efficiently select a minimal set of stable markers able to reconstruct the underlying species phylogeny. In contrast to previous approaches, our methodology does not only rely on the ability of individual genes to reconstruct a known phylogeny, but it also explores the combined power of sets of concatenated genes to accurately infer phylogenetic relationships of species not previously analyzed. We applied our approach to two broad sets of cyanobacterial and ascomycetous fungal species, and provide two minimal sets of six and four genes, respectively, necessary to fully resolve the target phylogenies. This approach paves the way for the informed selection of phylogenetic markers in the effort of reconstructing the tree of life.
    Schlagwort(e): Genomics
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  • 36
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    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-08-10
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lynch, Michael -- New York, N.Y. -- Science. 2002 Aug 9;297(5583):945-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Indiana University, Bloomington, IN 47405, USA. mlynch@bio.indiana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12169715" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Biological Evolution ; Caenorhabditis elegans/genetics ; Chromosomes/genetics ; Chromosomes, Human/genetics ; *Gene Duplication ; Gene Rearrangement ; Gene Silencing ; *Genes, Duplicate ; *Genome, Human ; Genomics ; Humans ; Mutation ; Selection, Genetic
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 37
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-06-01
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Copeland, Neal G -- Jenkins, Nancy A -- O'Brien, Stephen J -- New York, N.Y. -- Science. 2002 May 31;296(5573):1617-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, USA. copeland@ncifcrf.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12040165" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Base Composition ; Biological Evolution ; Chromosome Aberrations ; Chromosomes/*genetics ; Chromosomes, Human/genetics ; Computational Biology ; Conserved Sequence ; Evolution, Molecular ; Gene Duplication ; Gene Rearrangement ; Genes ; Genome ; *Genome, Human ; Genomics ; Humans ; Mice ; Mice, Inbred Strains/*genetics ; Multigene Family ; *Sequence Analysis, DNA ; Species Specificity ; Synteny
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 38
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    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2003-10-25
    Beschreibung: Noninvasive molecular-imaging technologies are providing researchers with exciting new opportunities to study small-animal models of human disease. With continued improvements in instrumentation, identification of better imaging targets by genome-based approaches, and design of better imaging probes by innovative chemistry, these technologies promise to play increasingly important roles in disease diagnosis and therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herschman, Harvey R -- P50 CA88306/CA/NCI NIH HHS/ -- R01 CA84572/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2003 Oct 24;302(5645):605-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, David Geffen School of Medicine at the University of California, Los Angeles, 341 Boyer Hall, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA. hherschman@mednet.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14576425" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Diagnostic Imaging/instrumentation/methods/trends ; *Disease Models, Animal ; Gene Expression ; Gene Expression Profiling ; Genes, Reporter ; Genomics ; Humans ; *Molecular Probe Techniques/instrumentation/trends ; Tomography, Emission-Computed ; Tomography, Emission-Computed, Single-Photon
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  • 39
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2003-02-22
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bray, Dennis -- New York, N.Y. -- Science. 2003 Feb 21;299(5610):1189-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. d.bray@zoo.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12595679" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Substitution ; Animals ; Antibody Diversity ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Evolution, Molecular ; Genetic Variation ; Genomics ; Histones/chemistry/genetics/metabolism ; Humans ; Methylation ; Phenotype ; Potassium Channels/chemistry/genetics/metabolism ; Protein Conformation ; Protein Isoforms/chemistry/metabolism ; Protein Processing, Post-Translational ; Proteins/*chemistry/genetics/*metabolism ; Proteomics ; RNA Splicing ; Receptors, Cell Surface/chemistry/genetics/metabolism ; Selection, Genetic ; Troponin T/chemistry/genetics/metabolism
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  • 40
    Publikationsdatum: 2003-09-27
    Beschreibung: A survey of the dog genome sequence (6.22 million sequence reads; 1.5x coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (〉25%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kirkness, Ewen F -- Bafna, Vineet -- Halpern, Aaron L -- Levy, Samuel -- Remington, Karin -- Rusch, Douglas B -- Delcher, Arthur L -- Pop, Mihai -- Wang, Wei -- Fraser, Claire M -- Venter, J Craig -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1898-903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Institute for Genomic Research, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512627" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Chromosomes, Mammalian/genetics ; Computational Biology ; Conserved Sequence ; Contig Mapping ; DNA, Intergenic ; Dogs/*genetics ; Genetic Variation ; *Genome ; Genome, Human ; Genomics ; Humans ; Long Interspersed Nucleotide Elements ; Male ; Mice/genetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Physical Chromosome Mapping ; Polymorphism, Single Nucleotide ; RNA, Messenger/genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; *Sequence Analysis, DNA ; Short Interspersed Nucleotide Elements ; Synteny
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  • 41
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-12-26
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 2001 Dec 21;294(5551):2458-60.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11752552" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Biological Evolution ; *Evolution, Molecular ; Fishes/genetics ; Gene Dosage ; *Gene Duplication ; *Genome ; Genome, Human ; Genomics ; Humans ; Invertebrates/genetics ; Multigene Family ; Polyploidy ; Vertebrates/genetics
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  • 42
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-03-17
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Springer, M S -- de Jong, W W -- New York, N.Y. -- Science. 2001 Mar 2;291(5509):1709-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California, Riverside, CA 92521 USA. springer@citrus.ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11253193" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; Genomics ; Humans ; Mammals/anatomy & histology/*classification/genetics ; Meta-Analysis as Topic ; Pedigree ; *Phylogeny ; Sequence Analysis, DNA
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 43
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-04-11
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Normile, D -- New York, N.Y. -- Science. 2001 Apr 6;292(5514):44-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11294209" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Biological Evolution ; Blood Cells/metabolism ; Bone and Bones/chemistry ; Cerebral Cortex/*metabolism ; Fossils ; *Gene Expression ; Gene Expression Profiling ; Genomics ; Humans ; Lectins/chemistry/metabolism ; Liver/metabolism ; Macaca mulatta/*genetics/metabolism ; Mixed Function Oxygenases/genetics/metabolism ; Mutation ; N-Acetylneuraminic Acid/metabolism ; Neuraminic Acids/metabolism ; Pan troglodytes/*genetics/metabolism ; Sialic Acids/metabolism ; Species Specificity
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    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 44
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-03-09
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Couzin, Jennifer -- New York, N.Y. -- Science. 2002 Mar 8;295(5561):1817.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11884730" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Computational Biology ; *Databases, Nucleic Acid ; *Genome, Human ; Genomics ; *Human Genome Project ; Humans ; Private Sector ; Public Sector ; Publishing ; *Sequence Analysis, DNA
    Print ISSN: 0036-8075
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 45
    Publikationsdatum: 2002-04-06
    Beschreibung: The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goff, Stephen A -- Ricke, Darrell -- Lan, Tien-Hung -- Presting, Gernot -- Wang, Ronglin -- Dunn, Molly -- Glazebrook, Jane -- Sessions, Allen -- Oeller, Paul -- Varma, Hemant -- Hadley, David -- Hutchison, Don -- Martin, Chris -- Katagiri, Fumiaki -- Lange, B Markus -- Moughamer, Todd -- Xia, Yu -- Budworth, Paul -- Zhong, Jingping -- Miguel, Trini -- Paszkowski, Uta -- Zhang, Shiping -- Colbert, Michelle -- Sun, Wei-lin -- Chen, Lili -- Cooper, Bret -- Park, Sylvia -- Wood, Todd Charles -- Mao, Long -- Quail, Peter -- Wing, Rod -- Dean, Ralph -- Yu, Yeisoo -- Zharkikh, Andrey -- Shen, Richard -- Sahasrabudhe, Sudhir -- Thomas, Alun -- Cannings, Rob -- Gutin, Alexander -- Pruss, Dmitry -- Reid, Julia -- Tavtigian, Sean -- Mitchell, Jeff -- Eldredge, Glenn -- Scholl, Terri -- Miller, Rose Mary -- Bhatnagar, Satish -- Adey, Nils -- Rubano, Todd -- Tusneem, Nadeem -- Robinson, Rosann -- Feldhaus, Jane -- Macalma, Teresita -- Oliphant, Arnold -- Briggs, Steven -- New York, N.Y. -- Science. 2002 Apr 5;296(5565):92-100.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA. stephen.goff@syngenta.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11935018" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Arabidopsis/genetics ; Chromosome Mapping ; Chromosomes/genetics ; Computational Biology ; Conserved Sequence ; DNA, Plant/genetics ; Databases, Nucleic Acid ; Edible Grain/genetics ; Gene Duplication ; Genes, Plant ; *Genome, Plant ; Genomics ; Oryza/*genetics/metabolism/physiology ; Phosphate Transport Proteins/genetics ; Plant Diseases ; Plant Proteins/chemistry/genetics ; Plant Structures/genetics ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Software ; Synteny ; Transcription Factors/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 46
    Publikationsdatum: 2002-03-02
    Beschreibung: Type III secreted "effector" proteins of bacterial pathogens play central roles in virulence, yet are notoriously difficult to identify. We used an in vivo genetic screen to identify 13 effectors secreted by the type III apparatus (called Hrp, for "hypersensitive response and pathogenicity") of the plant pathogen Pseudomonas syringae. Although sharing little overall homology, the amino-terminal regions of these effectors had strikingly similar amino acid compositions. This feature facilitated the bioinformatic prediction of 38 P. syringae effectors, including 15 previously unknown proteins. The secretion of two of these putative effectors was shown to be type III--dependent. Effectors showed high interstrain variation, supporting a role for some effectors in adaptation to different hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guttman, David S -- Vinatzer, Boris A -- Sarkar, Sara F -- Ranall, Max V -- Kettler, Gregory -- Greenberg, Jean T -- GM020024/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Mar 1;295(5560):1722-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada. guttman@botany.utoronto.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11872842" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Amino Acids/analysis ; Arabidopsis/genetics/metabolism/*microbiology ; *Arabidopsis Proteins ; Bacterial Proteins/chemistry/*genetics/*metabolism ; Computational Biology ; DNA Transposable Elements ; *Genes, Bacterial ; Genomics ; Molecular Sequence Data ; Plant Proteins/metabolism ; Promoter Regions, Genetic ; Proteome ; Pseudomonas/*genetics/*metabolism/pathogenicity ; Recombinant Fusion Proteins/metabolism ; Virulence
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 47
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-07-20
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Long, Carole A -- Hoffman, Stephen L -- New York, N.Y. -- Science. 2002 Jul 19;297(5580):345-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Malaria Vaccine Development Unit, National Institutes of Health, Rockville, MD 20852, USA. clong@niaid.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12130768" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Antibodies, Protozoan/immunology ; Antigens, Protozoan/immunology ; B-Lymphocytes/immunology ; Clinical Trials, Phase II as Topic ; Genes, Protozoan ; Genomics ; Host-Parasite Interactions ; Humans ; *Malaria/epidemiology/immunology/parasitology/prevention & control ; *Malaria Vaccines/immunology ; *Malaria, Falciparum/epidemiology/immunology/parasitology/prevention & control ; *Plasmodium/genetics/immunology/physiology ; *Plasmodium falciparum/immunology/physiology ; Proteome ; T-Lymphocytes/immunology
    Print ISSN: 0036-8075
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 48
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-10-20
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jain, K K -- New York, N.Y. -- Science. 2001 Oct 19;294(5542):621-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11641502" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Computational Biology ; DNA Probes ; DNA, Complementary ; Diagnosis ; *Gene Expression Profiling ; Genetic Testing ; Genetics, Medical ; Genome, Human ; Genomics ; Humans ; Miniaturization ; Nucleic Acid Hybridization ; *Oligonucleotide Array Sequence Analysis/instrumentation/methods ; Pharmacogenetics ; Polymorphism, Single Nucleotide ; RNA, Messenger/genetics/metabolism ; Software
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 49
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-12-12
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 2001 Dec 7;294(5549):2074-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11739930" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Automation ; Biotechnology/*methods ; Computers ; Crystallography, X-Ray ; Databases, Protein ; Drug Industry ; Electrophoresis, Gel, Two-Dimensional ; Genomics ; Private Sector ; *Proteins/chemistry/isolation & purification/physiology ; *Proteome ; Public Sector ; Research Support as Topic ; Robotics ; Two-Hybrid System Techniques ; Universities
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 50
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-03-10
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉New York, N.Y. -- Science. 2001 Feb 16;291(5507):1218.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11233443" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Chromosomes, Human ; Computational Biology ; Genes ; Genetic Variation ; Genetics, Medical ; *Genome, Human ; Genomics ; *Human Genome Project ; Humans ; *Sequence Analysis, DNA/methods
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 51
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-07-14
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kourilsky, P -- New York, N.Y. -- Science. 2001 Jul 13;293(5528):173.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11452085" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Allergy and Immunology/organization & administration/trends ; European Union ; Genome, Human ; Genomics ; Humans ; Research ; Research Support as Topic ; United States
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 52
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-04-27
    Beschreibung: Human disease phenotypes are controlled not only by genes but by lawful self-organizing networks that display system-wide dynamics. These networks range from metabolic pathways to signaling pathways that regulate hormone action. When perturbed, networks alter their output of matter and energy which, depending on the environmental context, can produce either a pathological or a normal phenotype. Study of the dynamics of these networks by approaches such as metabolic control analysis may provide new insights into the pathogenesis and treatment of complex diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strohman, Richard -- New York, N.Y. -- Science. 2002 Apr 26;296(5568):701-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, 229 Stanley Hall, No. 3206, University of California at Berkeley, Berkeley, CA 94720-3206, USA. E-mail: strohman@uclink4.berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11976445" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Alzheimer Disease/metabolism ; *Disease ; Genomics ; *Genotype ; Humans ; *Metabolism ; Molecular Biology ; Parkinson Disease/metabolism ; *Phenotype ; Proteins/metabolism ; Research Support as Topic ; Signal Transduction
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 53
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-07-20
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gelb, Michael H -- Hol, Wim G J -- New York, N.Y. -- Science. 2002 Jul 19;297(5580):343-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Chemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12130767" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Antimalarials/chemistry/pharmacology/therapeutic use ; *Antiprotozoal Agents/chemistry/pharmacology/therapeutic use ; Chagas Disease/drug therapy/parasitology ; Chemistry, Pharmaceutical ; Combinatorial Chemistry Techniques ; Computational Biology ; Databases, Factual ; Drug Design ; Drug Resistance ; Genomics ; Humans ; Leishmania/drug effects/genetics/metabolism ; Leishmaniasis/drug therapy/parasitology ; Malaria/drug therapy/parasitology ; Plasmodium falciparum/drug effects/genetics/metabolism ; Plasmodium vivax/drug effects/genetics ; *Trypanocidal Agents/chemistry/pharmacology/therapeutic use ; Trypanosoma brucei brucei/drug effects/genetics/metabolism ; Trypanosoma cruzi/drug effects/genetics/metabolism ; Trypanosomiasis, African/drug therapy/parasitology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 54
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-10-05
    Beschreibung: Insecticide resistance poses a serious threat to current malaria control efforts. The Anopheles gambiae genome will enable identification of new resistance genes and will provide new molecular targets for the design of more effective insecticides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hemingway, Janet -- Field, Linda -- Vontas, John -- New York, N.Y. -- Science. 2002 Oct 4;298(5591):96-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12364782" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Africa South of the Sahara ; Animals ; Anopheles/*genetics/metabolism/parasitology ; Gene Expression ; Gene Expression Profiling ; *Genes, Insect ; Genes, Regulator ; *Genome ; Genomics ; Host-Parasite Interactions ; Humans ; Insect Proteins/metabolism ; Insect Vectors/genetics/metabolism/parasitology ; *Insecticide Resistance ; Insecticides/metabolism ; Malaria/prevention & control/transmission ; Mutation ; Oxidative Stress ; Parasites/physiology ; Quantitative Trait, Heritable ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 55
    Publikationsdatum: 2002-06-01
    Beschreibung: The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mural, Richard J -- Adams, Mark D -- Myers, Eugene W -- Smith, Hamilton O -- Miklos, George L Gabor -- Wides, Ron -- Halpern, Aaron -- Li, Peter W -- Sutton, Granger G -- Nadeau, Joe -- Salzberg, Steven L -- Holt, Robert A -- Kodira, Chinnappa D -- Lu, Fu -- Chen, Lin -- Deng, Zuoming -- Evangelista, Carlos C -- Gan, Weiniu -- Heiman, Thomas J -- Li, Jiayin -- Li, Zhenya -- Merkulov, Gennady V -- Milshina, Natalia V -- Naik, Ashwinikumar K -- Qi, Rong -- Shue, Bixiong Chris -- Wang, Aihui -- Wang, Jian -- Wang, Xin -- Yan, Xianghe -- Ye, Jane -- Yooseph, Shibu -- Zhao, Qi -- Zheng, Liansheng -- Zhu, Shiaoping C -- Biddick, Kendra -- Bolanos, Randall -- Delcher, Arthur L -- Dew, Ian M -- Fasulo, Daniel -- Flanigan, Michael J -- Huson, Daniel H -- Kravitz, Saul A -- Miller, Jason R -- Mobarry, Clark M -- Reinert, Knut -- Remington, Karin A -- Zhang, Qing -- Zheng, Xiangqun H -- Nusskern, Deborah R -- Lai, Zhongwu -- Lei, Yiding -- Zhong, Wenyan -- Yao, Alison -- Guan, Ping -- Ji, Rui-Ru -- Gu, Zhiping -- Wang, Zhen-Yuan -- Zhong, Fei -- Xiao, Chunlin -- Chiang, Chia-Chien -- Yandell, Mark -- Wortman, Jennifer R -- Amanatides, Peter G -- Hladun, Suzanne L -- Pratts, Eric C -- Johnson, Jeffery E -- Dodson, Kristina L -- Woodford, Kerry J -- Evans, Cheryl A -- Gropman, Barry -- Rusch, Douglas B -- Venter, Eli -- Wang, Mei -- Smith, Thomas J -- Houck, Jarrett T -- Tompkins, Donald E -- Haynes, Charles -- Jacob, Debbie -- Chin, Soo H -- Allen, David R -- Dahlke, Carl E -- Sanders, Robert -- Li, Kelvin -- Liu, Xiangjun -- Levitsky, Alexander A -- Majoros, William H -- Chen, Quan -- Xia, Ashley C -- Lopez, John R -- Donnelly, Michael T -- Newman, Matthew H -- Glodek, Anna -- Kraft, Cheryl L -- Nodell, Marc -- Ali, Feroze -- An, Hui-Jin -- Baldwin-Pitts, Danita -- Beeson, Karen Y -- Cai, Shuang -- Carnes, Mark -- Carver, Amy -- Caulk, Parris M -- Center, Angela -- Chen, Yen-Hui -- Cheng, Ming-Lai -- Coyne, My D -- Crowder, Michelle -- Danaher, Steven -- Davenport, Lionel B -- Desilets, Raymond -- Dietz, Susanne M -- Doup, Lisa -- Dullaghan, Patrick -- Ferriera, Steven -- Fosler, Carl R -- Gire, Harold C -- Gluecksmann, Andres -- Gocayne, Jeannine D -- Gray, Jonathan -- Hart, Brit -- Haynes, Jason -- Hoover, Jeffery -- Howland, Tim -- Ibegwam, Chinyere -- Jalali, Mena -- Johns, David -- Kline, Leslie -- Ma, Daniel S -- MacCawley, Steven -- Magoon, Anand -- Mann, Felecia -- May, David -- McIntosh, Tina C -- Mehta, Somil -- Moy, Linda -- Moy, Mee C -- Murphy, Brian J -- Murphy, Sean D -- Nelson, Keith A -- Nuri, Zubeda -- Parker, Kimberly A -- Prudhomme, Alexandre C -- Puri, Vinita N -- Qureshi, Hina -- Raley, John C -- Reardon, Matthew S -- Regier, Megan A -- Rogers, Yu-Hui C -- Romblad, Deanna L -- Schutz, Jakob -- Scott, John L -- Scott, Richard -- Sitter, Cynthia D -- Smallwood, Michella -- Sprague, Arlan C -- Stewart, Erin -- Strong, Renee V -- Suh, Ellen -- Sylvester, Karena -- Thomas, Reginald -- Tint, Ni Ni -- Tsonis, Christopher -- Wang, Gary -- Wang, George -- Williams, Monica S -- Williams, Sherita M -- Windsor, Sandra M -- Wolfe, Keriellen -- Wu, Mitchell M -- Zaveri, Jayshree -- Chaturvedi, Kabir -- Gabrielian, Andrei E -- Ke, Zhaoxi -- Sun, Jingtao -- Subramanian, Gangadharan -- Venter, J Craig -- Pfannkoch, Cynthia M -- Barnstead, Mary -- Stephenson, Lisa D -- New York, N.Y. -- Science. 2002 May 31;296(5573):1661-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA. richard.mural@celera.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12040188" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Base Composition ; Chromosomes/*genetics ; Chromosomes, Human/genetics ; Computational Biology ; Conserved Sequence ; Databases, Nucleic Acid ; Evolution, Molecular ; Genes ; Genetic Markers ; *Genome ; *Genome, Human ; Genomics ; Humans ; Mice ; Mice, Inbred A/genetics ; Mice, Inbred DBA/genetics ; Mice, Inbred Strains/*genetics ; Molecular Sequence Data ; Physical Chromosome Mapping ; Proteins/chemistry/genetics ; Sequence Alignment ; *Sequence Analysis, DNA ; Species Specificity ; *Synteny
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 56
    Publikationsdatum: 2001-10-27
    Beschreibung: Listeria monocytogenes is a food-borne pathogen with a high mortality rate that has also emerged as a paradigm for intracellular parasitism. We present and compare the genome sequences of L. monocytogenes (2,944,528 base pairs) and a nonpathogenic species, L. innocua (3,011,209 base pairs). We found a large number of predicted genes encoding surface and secreted proteins, transporters, and transcriptional regulators, consistent with the ability of both species to adapt to diverse environments. The presence of 270 L. monocytogenes and 149 L. innocua strain-specific genes (clustered in 100 and 63 islets, respectively) suggests that virulence in Listeria results from multiple gene acquisition and deletion events.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Glaser, P -- Frangeul, L -- Buchrieser, C -- Rusniok, C -- Amend, A -- Baquero, F -- Berche, P -- Bloecker, H -- Brandt, P -- Chakraborty, T -- Charbit, A -- Chetouani, F -- Couve, E -- de Daruvar, A -- Dehoux, P -- Domann, E -- Dominguez-Bernal, G -- Duchaud, E -- Durant, L -- Dussurget, O -- Entian, K D -- Fsihi, H -- Garcia-del Portillo, F -- Garrido, P -- Gautier, L -- Goebel, W -- Gomez-Lopez, N -- Hain, T -- Hauf, J -- Jackson, D -- Jones, L M -- Kaerst, U -- Kreft, J -- Kuhn, M -- Kunst, F -- Kurapkat, G -- Madueno, E -- Maitournam, A -- Vicente, J M -- Ng, E -- Nedjari, H -- Nordsiek, G -- Novella, S -- de Pablos, B -- Perez-Diaz, J C -- Purcell, R -- Remmel, B -- Rose, M -- Schlueter, T -- Simoes, N -- Tierrez, A -- Vazquez-Boland, J A -- Voss, H -- Wehland, J -- Cossart, P -- New York, N.Y. -- Science. 2001 Oct 26;294(5543):849-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genomique des Microorganismes Pathogenes, Unite des Interactions Bacteries-Cellules, Service d'Informatique Scientifique, Institut Pasteur, 25-28 rue du Dr. Roux, 75724 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11679669" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Adaptation, Physiological ; Amino Acid Motifs ; Bacillus subtilis/genetics ; Bacterial Proteins/chemistry/*genetics/physiology ; Base Composition ; Carrier Proteins/chemistry/genetics ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/chemistry/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Listeria/chemistry/*genetics/physiology ; Listeria monocytogenes/chemistry/*genetics/pathogenicity/physiology ; Membrane Proteins/chemistry/genetics ; Sequence Analysis, DNA ; Staphylococcus aureus/genetics ; Transcription Factors/chemistry/genetics ; Virulence/genetics
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  • 57
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-06-26
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2273-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11423647" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Costs and Cost Analysis ; Expressed Sequence Tags ; Fungi/*genetics/*pathogenicity ; *Genome, Fungal ; Genomics ; Government Agencies ; Plant Diseases ; Plants/*microbiology ; Research Support as Topic ; *Sequence Analysis, DNA/economics ; United States ; United States Department of Agriculture
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  • 58
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-10-27
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Modlin, R L -- Bloom, B R -- New York, N.Y. -- Science. 2001 Oct 26;294(5543):799-801.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Dermatology and Department of Microbiology and Immunology, UCLA School of Medicine, Los Angeles, CA 90095, USA. rmodlin@mednet.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11679655" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Candida albicans/immunology ; Cells, Cultured ; Dendritic Cells/*immunology/*metabolism ; Escherichia coli/immunology ; *Gene Expression Profiling ; *Gene Expression Regulation ; Genomics ; Humans ; Immunity, Innate ; Influenza A virus/immunology ; Ligands ; Lipopolysaccharides/immunology ; Mannans/immunology ; Oligonucleotide Array Sequence Analysis ; RNA, Double-Stranded/immunology
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  • 59
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-11-10
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fishman, M C -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1290-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts General Hospital and Harvard Medical School, Cardiovascular Division, Boston, MA 02114, USA. mcfishman@partners.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11701913" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Behavior, Animal ; Body Patterning ; Central Nervous System/physiology ; Cloning, Molecular ; Embryo, Nonmammalian/physiology ; Evolution, Molecular ; *Genome ; Genomics ; Humans ; Mutation ; Phenotype ; Signal Transduction ; Synteny ; Zebrafish/*embryology/*genetics ; Zebrafish Proteins/genetics/physiology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 60
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-04-20
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mertl, Melissa -- New York, N.Y. -- Science. 2002 Apr 19;296(5567):453.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11964454" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Financing, Government ; Foundations/economics/history/*organization & administration ; Genomics ; Great Britain ; History, 21st Century ; Research ; Research Support as Topic
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 61
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-06-08
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2002 Jun 7;296(5574):1792-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12052937" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Biological Evolution ; Chiroptera/anatomy & histology/genetics/growth & development ; Computational Biology ; Genes, Homeobox ; *Genome ; Genomics ; Introns ; Invertebrates/*genetics ; Planarians/genetics/physiology ; Regeneration ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Urochordata/anatomy & histology/embryology/*genetics/growth & development ; Vertebrates/*genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 62
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-06-01
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2002 May 31;296(5573):1600-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12040162" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Centromere/genetics ; Chromosomes, Human/genetics ; Computational Biology ; *Genome, Human ; Genomics ; *Human Genome Project ; Humans ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Software ; Telomere/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 63
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-04-06
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cantrell, Ronald P -- Reeves, Timothy G -- New York, N.Y. -- Science. 2002 Apr 5;296(5565):53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines. r.cantrell@cgiar.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11935006" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Agriculture ; Computational Biology ; Crops, Agricultural/*genetics ; Developed Countries ; Developing Countries ; Edible Grain/*genetics ; *Genome, Plant ; Genomics ; Humans ; International Cooperation ; Nutritional Physiological Phenomena ; Oryza/*genetics ; Private Sector ; Public Sector ; Research ; *Sequence Analysis, DNA ; Technology Transfer
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 64
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2001-12-12
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 2001 Dec 7;294(5549):2082-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11739934" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Drug Industry ; *Genes ; Genome, Human ; Genomics ; Humans ; *Patents as Topic ; *Proteins ; *Proteome ; RNA Splicing
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 65
    Publikationsdatum: 2002-04-06
    Beschreibung: We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Jun -- Hu, Songnian -- Wang, Jun -- Wong, Gane Ka-Shu -- Li, Songgang -- Liu, Bin -- Deng, Yajun -- Dai, Li -- Zhou, Yan -- Zhang, Xiuqing -- Cao, Mengliang -- Liu, Jing -- Sun, Jiandong -- Tang, Jiabin -- Chen, Yanjiong -- Huang, Xiaobing -- Lin, Wei -- Ye, Chen -- Tong, Wei -- Cong, Lijuan -- Geng, Jianing -- Han, Yujun -- Li, Lin -- Li, Wei -- Hu, Guangqiang -- Huang, Xiangang -- Li, Wenjie -- Li, Jian -- Liu, Zhanwei -- Li, Long -- Liu, Jianping -- Qi, Qiuhui -- Liu, Jinsong -- Li, Li -- Li, Tao -- Wang, Xuegang -- Lu, Hong -- Wu, Tingting -- Zhu, Miao -- Ni, Peixiang -- Han, Hua -- Dong, Wei -- Ren, Xiaoyu -- Feng, Xiaoli -- Cui, Peng -- Li, Xianran -- Wang, Hao -- Xu, Xin -- Zhai, Wenxue -- Xu, Zhao -- Zhang, Jinsong -- He, Sijie -- Zhang, Jianguo -- Xu, Jichen -- Zhang, Kunlin -- Zheng, Xianwu -- Dong, Jianhai -- Zeng, Wanyong -- Tao, Lin -- Ye, Jia -- Tan, Jun -- Ren, Xide -- Chen, Xuewei -- He, Jun -- Liu, Daofeng -- Tian, Wei -- Tian, Chaoguang -- Xia, Hongai -- Bao, Qiyu -- Li, Gang -- Gao, Hui -- Cao, Ting -- Wang, Juan -- Zhao, Wenming -- Li, Ping -- Chen, Wei -- Wang, Xudong -- Zhang, Yong -- Hu, Jianfei -- Wang, Jing -- Liu, Song -- Yang, Jian -- Zhang, Guangyu -- Xiong, Yuqing -- Li, Zhijie -- Mao, Long -- Zhou, Chengshu -- Zhu, Zhen -- Chen, Runsheng -- Hao, Bailin -- Zheng, Weimou -- Chen, Shouyi -- Guo, Wei -- Li, Guojie -- Liu, Siqi -- Tao, Ming -- Wang, Jian -- Zhu, Lihuang -- Yuan, Longping -- Yang, Huanming -- 1 RO1 ES09909/ES/NIEHS NIH HHS/ -- New York, N.Y. -- Science. 2002 Apr 5;296(5565):79-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11935017" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Arabidopsis/genetics ; Base Composition ; Computational Biology ; Contig Mapping ; DNA Transposable Elements ; DNA, Intergenic ; DNA, Plant/chemistry/genetics ; Databases, Nucleic Acid ; Exons ; Gene Duplication ; Genes, Plant ; *Genome, Plant ; Genomics ; Introns ; Molecular Sequence Data ; Oryza/*genetics ; Plant Proteins/chemistry/genetics ; Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Software ; Species Specificity ; Synteny
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  • 66
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2002-04-27
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, Kathryn -- New York, N.Y. -- Science. 2002 Apr 26;296(5568):640-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11976420" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Botany ; Genomics ; Libraries ; *Museums ; New York City ; *Plants/genetics ; Research
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 67
    Publikationsdatum: 2002-05-11
    Beschreibung: Comparison of the whole-genome sequence of Bacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide polymorphisms (SNPs), inserted or deleted sequences, and tandem repeats. Genome comparison detected four high-quality SNPs between the two sequenced B. anthracis chromosomes and seven differences among different preparations of the reference genome. These markers have been tested on a collection of anthrax isolates and were found to divide these samples into distinct families. These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Read, Timothy D -- Salzberg, Steven L -- Pop, Mihai -- Shumway, Martin -- Umayam, Lowell -- Jiang, Lingxia -- Holtzapple, Erik -- Busch, Joseph D -- Smith, Kimothy L -- Schupp, James M -- Solomon, Daniel -- Keim, Paul -- Fraser, Claire M -- R01-LM06845/LM/NLM NIH HHS/ -- New York, N.Y. -- Science. 2002 Jun 14;296(5575):2028-33. Epub 2002 May 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA., Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12004073" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Anthrax/microbiology ; Bacillus anthracis/classification/*genetics/isolation & ; purification/pathogenicity ; Bacterial Typing Techniques ; Base Sequence ; Bioterrorism ; Chromosome Inversion ; Computational Biology ; Disease Outbreaks ; Genetic Markers ; *Genetic Variation ; *Genome, Bacterial ; Genomics ; Humans ; Minisatellite Repeats ; Molecular Sequence Data ; Mutation ; Phenotype ; Phylogeny ; Plasmids ; *Polymorphism, Single Nucleotide ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Sequence Deletion ; Species Specificity ; Transposases/genetics ; Virulence/genetics
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  • 68
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2006-05-27
    Beschreibung: The allure of the emerging genomic technologies in cancer is their ability to generate new biomarkers that predict how individual cancer patients will respond to various treatments. However, productive implementation of cancer biomarkers into patient care will require fundamental changes in how we consider approvals for cancer indications and how we track patient responses. Here we briefly describe ongoing efforts to identify and to validate cancer biomarkers, discuss the technological hurdles that lie ahead, and then focus on the more pressing political and cultural issues that, if left unheeded, could derail many of the anticipated benefits of biomarker research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, William S -- Friend, Stephen H -- New York, N.Y. -- Science. 2006 May 26;312(5777):1165-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉H. Lee Moffitt Cancer Center, University of South Florida, Tampa, FL 33613, USA. dalton@moffitt.usf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16728629" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Academies and Institutes ; *Biomarkers, Tumor ; Biotechnology ; Clinical Trials as Topic ; Databases, Factual ; Drug Industry ; Gene Expression Regulation, Neoplastic ; Genomics ; Humans ; Intellectual Property ; Interprofessional Relations ; Mutation ; Neoplasms/genetics/*therapy ; *Patient Care Management ; Private Sector ; Proteomics ; Public Sector
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  • 69
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2006-11-11
    Beschreibung: The sea urchin genome reveals large domains of biology heretofore unexplored at the genome level, as this is the first nonchordate deuterostome sequence. The sequence will accelerate progress toward complete understanding of the genomic regulatory system that controls developmental specification and morphogenetic function, thus illuminating basic developmental process in all animals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Eric H -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):939-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, 156-29, California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095689" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Biological Evolution ; Embryo, Nonmammalian/physiology ; Embryonic Development ; Gene Expression Regulation ; Genes, Regulator ; Genetic Speciation ; *Genome ; Genomics ; Male ; Morphogenesis ; Sequence Analysis, DNA ; Strongylocentrotus purpuratus/embryology/*genetics/physiology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 70
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2006-07-01
    Beschreibung: The fundamental challenge in the social sciences is moving from complicated correlations to useful prediction. Progress usually reflects an interplay between theory, data, and tools. Six areas of innovation, principally data and tools, are now pushing at the frontiers of these sciences: longitudinal data, laboratory experimentation, improved statistical methods, geographic information tools, biosocial science, and international replication. These innovations are gaining power as they cross disciplinary boundaries, helping to attribute causality to observed relationships, to understand their nature, and thereby to improve the accuracy and usefulness of predictions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butz, William P -- Torrey, Barbara Boyle -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1898-900.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Population Reference Bureau, 1875 Connecticut Avenue, Washington, DC 20009, USA. wbutz@prb.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809524" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Behavior, Animal ; Biological Evolution ; Genomics ; Geography ; Health Status ; Humans ; Interdisciplinary Communication ; Internationality ; Internet ; Longitudinal Studies ; Nervous System Physiological Phenomena ; Neurosciences ; Psychology, Social ; *Research ; *Social Behavior ; *Social Sciences/methods ; Statistics as Topic
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 71
    Publikationsdatum: 2006-07-22
    Beschreibung: Rice fields are a global source of the greenhouse gas methane, which is produced by methanogenic archaea, and by methanogens of Rice Cluster I (RC-I) in particular. RC-I methanogens are not yet available in pure culture, and the mechanistic reasons for their prevalence in rice fields are unknown. We reconstructed a complete RC-I genome (3.18 megabases) using a metagenomic approach. Sequence analysis demonstrated an aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for carbohydrate metabolism and assimilatory sulfate reduction, hitherto unknown among methanogens. These capacities and a unique set of antioxidant enzymes and DNA repair mechanisms as well as oxygen-insensitive enzymes provide RC-I with a selective advantage over other methanogens in its habitats, thereby explaining the prevalence of RC-I methanogens in the rice rhizosphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erkel, Christoph -- Kube, Michael -- Reinhardt, Richard -- Liesack, Werner -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):370-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857943" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Amino Acids/biosynthesis/metabolism ; Carbohydrate Metabolism ; DNA Repair ; Euryarchaeota/classification/*genetics/metabolism/physiology ; *Genome, Archaeal ; Genomics ; Glycolysis ; Methane/*biosynthesis ; Methanomicrobiales/classification/genetics/metabolism/physiology ; Methanosarcinales/classification/genetics/metabolism/physiology ; Molecular Sequence Data ; Oryza/*microbiology ; Oxidative Stress ; Pyruvic Acid/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfates/metabolism ; Sulfur/metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 72
    Publikationsdatum: 2006-07-29
    Beschreibung: Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the latter implicated putative proteins that mediate viral virulence differences. Analysis of the viral linear DNA genome suggests that its evolution involved direct descent and DNA end-region recombination events. Knowing the sequences will help understand the viral proteome and improve diagnostic test precision, therapeutics, and systems for their assessment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Esposito, Joseph J -- Sammons, Scott A -- Frace, A Michael -- Osborne, John D -- Olsen-Rasmussen, Melissa -- Zhang, Ming -- Govil, Dhwani -- Damon, Inger K -- Kline, Richard -- Laker, Miriam -- Li, Yu -- Smith, Geoffrey L -- Meyer, Hermann -- Leduc, James W -- Wohlhueter, Robert M -- G0501257/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):807-12. Epub 2006 Jul 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. jesposito@cdc.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16873609" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): DNA, Viral/*genetics ; Disease Outbreaks ; *Evolution, Molecular ; Gene Deletion ; *Genetic Variation ; *Genome, Viral ; Genomics ; Humans ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Proteome/analysis/genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; Smallpox/epidemiology/mortality/*virology ; Variola virus/classification/*genetics/isolation & purification/pathogenicity ; Viral Proteins/chemistry/genetics ; Virulence/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 73
    Publikationsdatum: 2006-02-14
    Beschreibung: Plants may "eavesdrop" on volatile organic compounds (VOCs) released by herbivore-attacked neighbors to activate defenses before being attacked themselves. Transcriptome and signal cascade analyses of VOC-exposed plants suggest that plants eavesdrop to prime direct and indirect defenses and to hone competitive abilities. Advances in research on VOC biosynthesis and perception have facilitated the production of plants that are genetically "deaf" to particular VOCs or "mute" in elements of their volatile vocabulary. Such plants, together with advances in VOC analytical instrumentation, will allow researchers to determine whether fluency enhances the fitness of plants in natural communities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baldwin, Ian T -- Halitschke, Rayko -- Paschold, Anja -- von Dahl, Caroline C -- Preston, Catherine A -- New York, N.Y. -- Science. 2006 Feb 10;311(5762):812-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans Knoll Strasse 8, Jena 07745, Germany. baldwin@ice.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16469918" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Adaptation, Physiological ; Diffusion ; Gene Expression Regulation, Plant ; Genomics ; Mutation ; Oligonucleotide Array Sequence Analysis ; Organic Chemicals/*metabolism ; Plant Leaves/metabolism ; *Plant Physiological Phenomena ; Plants/*genetics/metabolism ; Signal Transduction ; Volatilization
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  • 74
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2006-09-30
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2006 Sep 29;313(5795):1908-11.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17008520" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Biological Evolution ; *Brain/anatomy & histology/embryology/physiology ; Cerebral Cortex/embryology/metabolism ; Evolution, Molecular ; Gene Dosage ; Gene Expression Profiling ; Gene Expression Regulation ; Genome ; *Genome, Human ; Genomics ; Humans ; Microcephaly/genetics ; Oligonucleotide Array Sequence Analysis ; Pan troglodytes/genetics ; Primates/*genetics ; Proteins/genetics/physiology ; RNA/genetics/physiology ; Selection, Genetic
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 75
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2007-07-07
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2007 Jul 6;317(5834):27.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17615309" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Biological Evolution ; Genes ; *Genome ; Genome, Human ; Genomics ; Humans ; Introns ; Sea Anemones/*genetics ; Sequence Analysis, DNA
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 76
    Publikationsdatum: 2007-10-13
    Beschreibung: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merchant, Sabeeha S -- Prochnik, Simon E -- Vallon, Olivier -- Harris, Elizabeth H -- Karpowicz, Steven J -- Witman, George B -- Terry, Astrid -- Salamov, Asaf -- Fritz-Laylin, Lillian K -- Marechal-Drouard, Laurence -- Marshall, Wallace F -- Qu, Liang-Hu -- Nelson, David R -- Sanderfoot, Anton A -- Spalding, Martin H -- Kapitonov, Vladimir V -- Ren, Qinghu -- Ferris, Patrick -- Lindquist, Erika -- Shapiro, Harris -- Lucas, Susan M -- Grimwood, Jane -- Schmutz, Jeremy -- Cardol, Pierre -- Cerutti, Heriberto -- Chanfreau, Guillaume -- Chen, Chun-Long -- Cognat, Valerie -- Croft, Martin T -- Dent, Rachel -- Dutcher, Susan -- Fernandez, Emilio -- Fukuzawa, Hideya -- Gonzalez-Ballester, David -- Gonzalez-Halphen, Diego -- Hallmann, Armin -- Hanikenne, Marc -- Hippler, Michael -- Inwood, William -- Jabbari, Kamel -- Kalanon, Ming -- Kuras, Richard -- Lefebvre, Paul A -- Lemaire, Stephane D -- Lobanov, Alexey V -- Lohr, Martin -- Manuell, Andrea -- Meier, Iris -- Mets, Laurens -- Mittag, Maria -- Mittelmeier, Telsa -- Moroney, James V -- Moseley, Jeffrey -- Napoli, Carolyn -- Nedelcu, Aurora M -- Niyogi, Krishna -- Novoselov, Sergey V -- Paulsen, Ian T -- Pazour, Greg -- Purton, Saul -- Ral, Jean-Philippe -- Riano-Pachon, Diego Mauricio -- Riekhof, Wayne -- Rymarquis, Linda -- Schroda, Michael -- Stern, David -- Umen, James -- Willows, Robert -- Wilson, Nedra -- Zimmer, Sara Lana -- Allmer, Jens -- Balk, Janneke -- Bisova, Katerina -- Chen, Chong-Jian -- Elias, Marek -- Gendler, Karla -- Hauser, Charles -- Lamb, Mary Rose -- Ledford, Heidi -- Long, Joanne C -- Minagawa, Jun -- Page, M Dudley -- Pan, Junmin -- Pootakham, Wirulda -- Roje, Sanja -- Rose, Annkatrin -- Stahlberg, Eric -- Terauchi, Aimee M -- Yang, Pinfen -- Ball, Steven -- Bowler, Chris -- Dieckmann, Carol L -- Gladyshev, Vadim N -- Green, Pamela -- Jorgensen, Richard -- Mayfield, Stephen -- Mueller-Roeber, Bernd -- Rajamani, Sathish -- Sayre, Richard T -- Brokstein, Peter -- Dubchak, Inna -- Goodstein, David -- Hornick, Leila -- Huang, Y Wayne -- Jhaveri, Jinal -- Luo, Yigong -- Martinez, Diego -- Ngau, Wing Chi Abby -- Otillar, Bobby -- Poliakov, Alexander -- Porter, Aaron -- Szajkowski, Lukasz -- Werner, Gregory -- Zhou, Kemin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Grossman, Arthur R -- GM07185/GM/NIGMS NIH HHS/ -- GM42143/GM/NIGMS NIH HHS/ -- R01 GM032843/GM/NIGMS NIH HHS/ -- R01 GM042143/GM/NIGMS NIH HHS/ -- R01 GM042143-09/GM/NIGMS NIH HHS/ -- R01 GM060992/GM/NIGMS NIH HHS/ -- R01 GM062915-06/GM/NIGMS NIH HHS/ -- R37 GM030626/GM/NIGMS NIH HHS/ -- R37 GM042143/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):245-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932292" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Algal Proteins/*genetics/*physiology ; Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/*genetics/physiology ; Chloroplasts/metabolism ; Computational Biology ; DNA, Algal/genetics ; Flagella/metabolism ; Genes ; *Genome ; Genomics ; Membrane Transport Proteins/genetics/physiology ; Molecular Sequence Data ; Multigene Family ; Photosynthesis/genetics ; Phylogeny ; Plants/genetics ; Proteome ; Sequence Analysis, DNA
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 77
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2007-06-30
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Jon -- New York, N.Y. -- Science. 2007 Jun 29;316(5833):1836.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600195" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Biological Evolution ; Brain/metabolism ; Computational Biology ; Gene Deletion ; Gene Dosage ; Gene Duplication ; Gene Expression ; *Gene Regulatory Networks ; *Genome ; *Genome, Human ; Genomics ; Humans ; Pan troglodytes/*genetics ; Species Specificity
    Print ISSN: 0036-8075
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 78
    Publikationsdatum: 2007-07-07
    Beschreibung: Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Putnam, Nicholas H -- Srivastava, Mansi -- Hellsten, Uffe -- Dirks, Bill -- Chapman, Jarrod -- Salamov, Asaf -- Terry, Astrid -- Shapiro, Harris -- Lindquist, Erika -- Kapitonov, Vladimir V -- Jurka, Jerzy -- Genikhovich, Grigory -- Grigoriev, Igor V -- Lucas, Susan M -- Steele, Robert E -- Finnerty, John R -- Technau, Ulrich -- Martindale, Mark Q -- Rokhsar, Daniel S -- 5 P41 LM006252-09/LM/NLM NIH HHS/ -- THL007279F/PHS HHS/ -- New York, N.Y. -- Science. 2007 Jul 6;317(5834):86-94.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17615350" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; *Biological Evolution ; Cell Adhesion ; Evolution, Molecular ; Genes ; Genetic Linkage ; *Genome ; Genome, Human ; Genomics ; Humans ; Introns ; Metabolic Networks and Pathways ; Multigene Family ; Muscles/physiology ; Nervous System Physiological Phenomena ; Phylogeny ; Sea Anemones/*genetics/metabolism ; Sequence Analysis, DNA ; Signal Transduction ; Synteny
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 79
    Publikationsdatum: 2007-06-02
    Beschreibung: Leguminous plants (such as peas and soybeans) and rhizobial soil bacteria are symbiotic partners that communicate through molecular signaling pathways, resulting in the formation of nodules on legume roots and occasionally stems that house nitrogen-fixing bacteria. Nodule formation has been assumed to be exclusively initiated by the binding of bacterial, host-specific lipochito-oligosaccharidic Nod factors, encoded by the nodABC genes, to kinase-like receptors of the plant. Here we show by complete genome sequencing of two symbiotic, photosynthetic, Bradyrhizobium strains, BTAi1 and ORS278, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors are not required for symbiosis in some legumes. Mutational analyses indicated that these unique rhizobia use an alternative pathway to initiate symbioses, where a purine derivative may play a key role in triggering nodule formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giraud, Eric -- Moulin, Lionel -- Vallenet, David -- Barbe, Valerie -- Cytryn, Eddie -- Avarre, Jean-Christophe -- Jaubert, Marianne -- Simon, Damien -- Cartieaux, Fabienne -- Prin, Yves -- Bena, Gilles -- Hannibal, Laure -- Fardoux, Joel -- Kojadinovic, Mila -- Vuillet, Laurie -- Lajus, Aurelie -- Cruveiller, Stephane -- Rouy, Zoe -- Mangenot, Sophie -- Segurens, Beatrice -- Dossat, Carole -- Franck, William L -- Chang, Woo-Suk -- Saunders, Elizabeth -- Bruce, David -- Richardson, Paul -- Normand, Philippe -- Dreyfus, Bernard -- Pignol, David -- Stacey, Gary -- Emerich, David -- Vermeglio, Andre -- Medigue, Claudine -- Sadowsky, Michael -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1307-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Recherche pour le Developpement, Centre de Cooperation International en Recherche Agronomique pour le Developpement, Institut National de la Recherche Agronomique, Universite Montpellier 2, France. giraud@mpl.ird.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540897" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Acyltransferases/genetics/metabolism ; Amidohydrolases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Bradyrhizobium/*genetics/growth & development/*physiology ; Cytokinins/metabolism ; Fabaceae/*microbiology ; Genes, Bacterial ; Genome, Bacterial ; Genomics ; Lipopolysaccharides/metabolism ; Molecular Sequence Data ; Mutation ; N-Acetylglucosaminyltransferases/genetics/metabolism ; Photosynthesis ; Plant Roots/microbiology ; Plant Stems/*microbiology ; Purines/biosynthesis ; Root Nodules, Plant/microbiology/*physiology ; Signal Transduction ; *Symbiosis
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 80
    Publikationsdatum: 2007-07-28
    Beschreibung: Only five bacterial phyla with members capable of chlorophyll (Chl)-based phototrophy are presently known. Metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park revealed the existence of a distinctive bacteriochlorophyll (BChl)-synthesizing, phototrophic bacterium. A highly enriched culture of this bacterium grew photoheterotrophically, synthesized BChls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. "Candidatus Chloracidobacterium thermophilum" is a BChl-producing member of the poorly characterized phylum Acidobacteria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bryant, Donald A -- Costas, Amaya M Garcia -- Maresca, Julia A -- Chew, Aline Gomez Maqueo -- Klatt, Christian G -- Bateson, Mary M -- Tallon, Luke J -- Hostetler, Jessica -- Nelson, William C -- Heidelberg, John F -- Ward, David M -- New York, N.Y. -- Science. 2007 Jul 27;317(5837):523-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. dab14@psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17656724" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Bacteria, Aerobic/*classification/*isolation & ; purification/physiology/ultrastructure ; Bacterial Chromatophores/ultrastructure ; Bacteriochlorophylls/biosynthesis ; Computational Biology ; Ecosystem ; Genome, Bacterial ; Genomics ; Hot Springs/*microbiology ; Molecular Sequence Data ; Photosystem I Protein Complex/analysis ; *Phototrophic Processes ; RNA, Ribosomal, 16S/genetics ; Temperature ; Wyoming
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 81
    Publikationsdatum: 2007-04-28
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martin, William -- Dagan, Tal -- Koonin, Eugene V -- Dipippo, Jonathan L -- Gogarten, J Peter -- Lake, James A -- New York, N.Y. -- Science. 2007 Apr 27;316(5824):542-3; author reply 542-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17463271" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; *Biological Evolution ; *Eukaryotic Cells ; Evolution, Molecular ; Fungal Proteins/chemistry ; Genomics ; Humans ; Mitochondria ; Phagocytosis ; Prokaryotic Cells ; Proteins/*chemistry
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 82
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-05-24
    Beschreibung: The biogeographic variation of life has predominantly been studied using taxonomy, but this focus is changing. There is a resurging interest in understanding patterns in the distribution not only of taxa but also of the traits those taxa possess. Patterns of trait variation shed light on fundamental questions in biology, including why organisms live where they do and how they will respond to environmental change. Technological advances such as environmental genomics place microbial ecology in a unique position to move trait-based biogeography forward. We anticipate that as trait-based biogeography continues to evolve, micro- and macroorganisms will be studied in concert, establishing a science that is informed by and relevant to all domains of life.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Jessica L -- Bohannan, Brendan J M -- Whitaker, Rachel J -- New York, N.Y. -- Science. 2008 May 23;320(5879):1039-43. doi: 10.1126/science.1153475.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Ecology and Evolutionary Biology, Department of Biology, University of Oregon, Eugene, Oregon 97403, USA. jlgreen@uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497288" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Archaea/classification/genetics/metabolism/physiology ; Bacteria/*classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; DNA, Ribosomal/genetics ; Ecology ; *Ecosystem ; Environment ; Gene Dosage ; Genes, Bacterial ; Genomics ; Plant Physiological Phenomena
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 83
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-11-15
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grimm, David -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1046-7. doi: 10.1126/science.322.5904.1046.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008426" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Biodiversity ; Crops, Agricultural/genetics/growth & development/microbiology ; Fungi/pathogenicity ; *Genome, Plant ; Genomics ; Musa/*genetics/growth & development/microbiology ; Plant Diseases/microbiology ; Polyploidy ; *Sequence Analysis, DNA/economics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 84
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-11-15
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hauser, Marc D -- Bever, Thomas -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1057-9. doi: 10.1126/science.1167437.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Psychology, Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. mdh@wjh.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008433" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animal Communication ; Animals ; Biological Evolution ; Brain/*physiology ; Forkhead Transcription Factors/genetics ; Functional Laterality ; Genomics ; Humans ; *Language ; Language Disorders/genetics/physiopathology ; *Linguistics ; Semantics ; Vocabulary
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  • 85
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-12-20
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉New York, N.Y. -- Science. 2008 Dec 19;322(5909):1773. doi: 10.1126/science.322.5909.1773.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19095908" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Astronomical Phenomena ; Elementary Particles ; Forecasting ; Genetic Speciation ; Genome, Plant ; Genomics ; Greenhouse Effect ; Hydrogen-Ion Concentration ; Jurisprudence ; Neurosciences ; *Science ; Seawater/chemistry
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 86
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-07-16
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, Elizabeth -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):196-7. doi: 10.1126/science.321.5886.196.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621652" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Adaptation, Biological ; Animals ; *Biological Evolution ; Body Patterning ; DNA/chemistry/genetics ; Developmental Biology ; Environment ; Epigenesis, Genetic ; Gene Expression Regulation ; Genetics ; Genetics, Population ; Genomics ; Mutation ; Selection, Genetic
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 87
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-04-26
    Beschreibung: The promise that came with genome sequencing was that we would soon know what genes do, particularly genes involved in human diseases and those of importance to agriculture. We now have the full genomic sequence of human, chimpanzee, mouse, chicken, dog, worm, fly, rice, and cress, as well as those for a wide variety of other species, and yet we still have a lot of trouble figuring out what genes do. Mapping genes to their function is called the "genotype-to-phenotype problem," where phenotype is whatever is changed in the organism when a gene's function is altered.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727942/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727942/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benfey, Philip N -- Mitchell-Olds, Thomas -- P50 GM081883/GM/NIGMS NIH HHS/ -- P50 GM081883-01/GM/NIGMS NIH HHS/ -- P50 GM081883-010003/GM/NIGMS NIH HHS/ -- P50 GM081883-02/GM/NIGMS NIH HHS/ -- P50 GM081883-020003/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 25;320(5875):495-7. doi: 10.1126/science.1153716.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Duke University, Durham, NC 27708, USA. philip.benfey@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436781" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Epistasis, Genetic ; Gene Regulatory Networks ; Genetic Techniques ; *Genetic Variation ; Genomics ; *Genotype ; Humans ; Metabolic Networks and Pathways ; Models, Genetic ; *Phenotype ; Plants/*genetics ; Polymorphism, Genetic ; Quantitative Trait Loci ; *Systems Biology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 88
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-02-23
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frudakis, Tony -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1039-40; author reply 1039-40. doi: 10.1126/science.319.5866.1039b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18292323" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Continental Population Groups/*genetics ; Databases, Genetic ; Ethnic Groups/*genetics ; Gene Frequency ; *Genetics, Population ; Genomics ; Humans ; *Pedigree
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 89
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-05-24
    Beschreibung: The oceans harbor a tremendous diversity of marine microbes. Different functional groups of bacteria, archaea, and protists arise from this diversity to dominate various habitats and drive globally important biogeochemical cycles. Explanations for the distribution of microbial taxa and their associated activity often focus on resource availability and abiotic conditions. However, the continual reshaping of communities by mortality, allelopathy, symbiosis, and other processes shows that community interactions exert strong selective pressure on marine microbes. Deeper exploration of microbial interactions is now possible via molecular prospecting and taxon-specific experimental approaches. A holistic outlook that encompasses the full array of selective pressures on individuals will help elucidate the maintenance of microbial diversity and the regulation of biogeochemical reactions by planktonic communities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strom, Suzanne L -- New York, N.Y. -- Science. 2008 May 23;320(5879):1043-5. doi: 10.1126/science.1153527.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Shannon Point Marine Center, Western Washington University, Anacortes, WA 98221, USA. Suzanne.Strom@wwu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497289" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Antibiosis ; Archaea/genetics/growth & development/*physiology ; Bacteria/genetics/growth & development ; *Bacterial Physiological Phenomena ; *Ecosystem ; Genomics ; Geological Phenomena ; Geology ; Nitrogen/metabolism ; Oceans and Seas ; Plankton/physiology ; Seawater/*microbiology ; Sulfur/metabolism ; Surface Properties ; Symbiosis
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 90
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-09-06
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaiser, Jocelyn -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1280-1. doi: 10.1126/science.321.5894.1280a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772403" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Brain Neoplasms/*genetics ; Gene Dosage ; *Genes, Neoplasm ; Genome, Human ; Genomics ; Glioblastoma/*genetics ; Humans ; *Mutation ; Pancreatic Neoplasms/*genetics ; Signal Transduction/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 91
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2008-04-26
    Beschreibung: Angiosperms are a relatively recent evolutionary innovation, but their genome sizes have diversified remarkably since their origin, at a rate beyond that of most other taxa. Genome size is often correlated with plant growth and ecology, and extremely large genomes may be limited both ecologically and evolutionarily. Yet the relationship between genome size and natural selection remains poorly understood. The manifold cellular and physiological effects of large genomes may be a function of selection on the major components that contribute to genome size, such as transposable elements and gene duplication. To understand the nature of selection on these genomic components, both population-genetic and comparative approaches are needed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gaut, Brandon S -- Ross-Ibarra, Jeffrey -- New York, N.Y. -- Science. 2008 Apr 25;320(5875):484-6. doi: 10.1126/science.1153586.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California Irvine, Irvine, CA 92697-2525, USA. bgaut@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436777" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Angiosperms/*genetics/physiology ; DNA Transposable Elements ; Gene Duplication ; Genetic Variation ; Genetics, Population ; *Genome, Plant ; Genomics ; Phenotype ; *Selection, Genetic
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  • 92
    Publikationsdatum: 2008-11-29
    Beschreibung: Most children with acute lymphoblastic leukemia (ALL) can be cured, but the prognosis is dismal for the minority of patients who relapse after treatment. To explore the genetic basis of relapse, we performed genome-wide DNA copy number analyses on matched diagnosis and relapse samples from 61 pediatric patients with ALL. The diagnosis and relapse samples typically showed different patterns of genomic copy number abnormalities (CNAs), with the CNAs acquired at relapse preferentially affecting genes implicated in cell cycle regulation and B cell development. Most relapse samples lacked some of the CNAs present at diagnosis, which suggests that the cells responsible for relapse are ancestral to the primary leukemia cells. Backtracking studies revealed that cells corresponding to the relapse clone were often present as minor subpopulations at diagnosis. These data suggest that genomic abnormalities contributing to ALL relapse are selected for during treatment, and they point to new targets for therapeutic intervention.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746051/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746051/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mullighan, Charles G -- Phillips, Letha A -- Su, Xiaoping -- Ma, Jing -- Miller, Christopher B -- Shurtleff, Sheila A -- Downing, James R -- P30 CA021765/CA/NCI NIH HHS/ -- P30 CA021765-30/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1377-80. doi: 10.1126/science.1164266.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19039135" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): B-Lymphocytes ; Cell Cycle/genetics ; Child ; Cyclin-Dependent Kinase Inhibitor p15/genetics ; Gene Deletion ; *Gene Dosage ; Genes, p16 ; *Genome, Human ; Genomics ; Humans ; *Loss of Heterozygosity ; Lymphopoiesis ; Metabolic Networks and Pathways/genetics ; *Mutation ; Oligonucleotide Array Sequence Analysis ; *Polymorphism, Single Nucleotide ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/*genetics/pathology ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/*genetics/pathology ; Proto-Oncogene Proteins c-ets/genetics ; Recurrence ; Repressor Proteins/genetics
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 93
    Publikationsdatum: 2009-04-04
    Beschreibung: The basis of science is the hypothetico-deductive method and the recording of experiments in sufficient detail to enable reproducibility. We report the development of Robot Scientist "Adam," which advances the automation of both. Adam has autonomously generated functional genomics hypotheses about the yeast Saccharomyces cerevisiae and experimentally tested these hypotheses by using laboratory automation. We have confirmed Adam's conclusions through manual experiments. To describe Adam's research, we have developed an ontology and logical language. The resulting formalization involves over 10,000 different research units in a nested treelike structure, 10 levels deep, that relates the 6.6 million biomass measurements to their logical description. This formalization describes how a machine contributed to scientific knowledge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Ross D -- Rowland, Jem -- Oliver, Stephen G -- Young, Michael -- Aubrey, Wayne -- Byrne, Emma -- Liakata, Maria -- Markham, Magdalena -- Pir, Pinar -- Soldatova, Larisa N -- Sparkes, Andrew -- Whelan, Kenneth E -- Clare, Amanda -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2009 Apr 3;324(5923):85-9. doi: 10.1126/science.1165620.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science, Aberystwyth University, SY23 3DB, UK. rdk@aber.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19342587" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Artificial Intelligence ; *Automation ; *Computational Biology ; Computers ; Enzymes/*genetics ; *Genes, Fungal ; Genomics ; Programming Languages ; Robotics ; Saccharomyces cerevisiae/enzymology/*genetics/growth & development/metabolism ; Software
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 94
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2010-12-18
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉News Staff -- New York, N.Y. -- Science. 2010 Dec 17;330(6011):1612-3. doi: 10.1126/science.330.6011.1612.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21163985" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Computers ; Genomics ; Internet ; Microscopy/methods ; Remote Sensing Technology ; *Research ; *Science
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 95
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2010-12-18
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉New York, N.Y. -- Science. 2010 Dec 17;330(6011):1605-7. doi: 10.1126/science.330.6011.1605.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21163979" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Anti-HIV Agents/administration & dosage/therapeutic use ; Female ; Genetic Diseases, Inborn/genetics ; Genetic Engineering ; Genetic Techniques ; Genomics ; HIV Infections/prevention & control ; Hominidae/genetics ; Humans ; Induced Pluripotent Stem Cells ; Male ; Molecular Dynamics Simulation ; Physical Phenomena ; Rats/genetics ; *Science ; Sequence Analysis, DNA ; Synthetic Biology
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 96
    Publikationsdatum: 2010-04-03
    Beschreibung: Chromosome segregation and cell division are essential, highly ordered processes that depend on numerous protein complexes. Results from recent RNA interference screens indicate that the identity and composition of these protein complexes is incompletely understood. Using gene tagging on bacterial artificial chromosomes, protein localization, and tandem-affinity purification-mass spectrometry, the MitoCheck consortium has analyzed about 100 human protein complexes, many of which had not or had only incompletely been characterized. This work has led to the discovery of previously unknown, evolutionarily conserved subunits of the anaphase-promoting complex and the gamma-tubulin ring complex--large complexes that are essential for spindle assembly and chromosome segregation. The approaches we describe here are generally applicable to high-throughput follow-up analyses of phenotypic screens in mammalian cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989461/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989461/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hutchins, James R A -- Toyoda, Yusuke -- Hegemann, Bjorn -- Poser, Ina -- Heriche, Jean-Karim -- Sykora, Martina M -- Augsburg, Martina -- Hudecz, Otto -- Buschhorn, Bettina A -- Bulkescher, Jutta -- Conrad, Christian -- Comartin, David -- Schleiffer, Alexander -- Sarov, Mihail -- Pozniakovsky, Andrei -- Slabicki, Mikolaj Michal -- Schloissnig, Siegfried -- Steinmacher, Ines -- Leuschner, Marit -- Ssykor, Andrea -- Lawo, Steffen -- Pelletier, Laurence -- Stark, Holger -- Nasmyth, Kim -- Ellenberg, Jan -- Durbin, Richard -- Buchholz, Frank -- Mechtler, Karl -- Hyman, Anthony A -- Peters, Jan-Michael -- F 3407/Austrian Science Fund FWF/Austria -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):593-9. doi: 10.1126/science.1181348. Epub 2010 Apr 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360068" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Anaphase-Promoting Complex-Cyclosome ; Centrosome/metabolism ; *Chromosome Segregation ; Chromosomes, Artificial, Bacterial ; Databases, Genetic ; Genomics ; Green Fluorescent Proteins ; HeLa Cells ; Humans ; *Mitosis ; Multiprotein Complexes/*metabolism ; Open Reading Frames ; Protein Binding ; Protein Interaction Mapping ; Protein Subunits/metabolism ; RNA Interference ; Spindle Apparatus/*metabolism ; Tubulin/*metabolism ; Ubiquitin-Protein Ligase Complexes/*metabolism
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
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  • 97
    Publikationsdatum: 2011-04-23
    Beschreibung: The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus--occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131103/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131103/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rhind, Nicholas -- Chen, Zehua -- Yassour, Moran -- Thompson, Dawn A -- Haas, Brian J -- Habib, Naomi -- Wapinski, Ilan -- Roy, Sushmita -- Lin, Michael F -- Heiman, David I -- Young, Sarah K -- Furuya, Kanji -- Guo, Yabin -- Pidoux, Alison -- Chen, Huei Mei -- Robbertse, Barbara -- Goldberg, Jonathan M -- Aoki, Keita -- Bayne, Elizabeth H -- Berlin, Aaron M -- Desjardins, Christopher A -- Dobbs, Edward -- Dukaj, Livio -- Fan, Lin -- FitzGerald, Michael G -- French, Courtney -- Gujja, Sharvari -- Hansen, Klavs -- Keifenheim, Dan -- Levin, Joshua Z -- Mosher, Rebecca A -- Muller, Carolin A -- Pfiffner, Jenna -- Priest, Margaret -- Russ, Carsten -- Smialowska, Agata -- Swoboda, Peter -- Sykes, Sean M -- Vaughn, Matthew -- Vengrova, Sonya -- Yoder, Ryan -- Zeng, Qiandong -- Allshire, Robin -- Baulcombe, David -- Birren, Bruce W -- Brown, William -- Ekwall, Karl -- Kellis, Manolis -- Leatherwood, Janet -- Levin, Henry -- Margalit, Hanah -- Martienssen, Rob -- Nieduszynski, Conrad A -- Spatafora, Joseph W -- Friedman, Nir -- Dalgaard, Jacob Z -- Baumann, Peter -- Niki, Hironori -- Regev, Aviv -- Nusbaum, Chad -- BB/E023754/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- DP1 OD003958/OD/NIH HHS/ -- R01 GM069957/GM/NIGMS NIH HHS/ -- R01 GM076396/GM/NIGMS NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-06/HG/NHGRI NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA. nick.rhind@umassmed.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21511999" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Centromere/genetics/physiology/ultrastructure ; DNA Transposable Elements ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Genes, Mating Type, Fungal ; *Genome, Fungal ; Genomics ; Glucose/metabolism ; Meiosis ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; RNA, Antisense/genetics ; RNA, Fungal/genetics ; RNA, Small Interfering/genetics ; RNA, Untranslated/genetics ; Regulatory Elements, Transcriptional ; Schizosaccharomyces/*genetics/growth & development/metabolism ; Schizosaccharomyces pombe Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Species Specificity ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
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    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 98
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2011-10-01
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kupferschmidt, Kai -- New York, N.Y. -- Science. 2011 Sep 30;333(6051):1818-9. doi: 10.1126/science.333.6051.1818.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21960605" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Bacteria/drug effects/*genetics/pathogenicity ; Bacterial Infections/*epidemiology/microbiology ; *Computational Biology ; *Databases, Genetic ; Developing Countries ; *Disease Outbreaks ; *Genome, Bacterial ; Genomics ; Humans ; *Information Dissemination ; Molecular Epidemiology ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 99
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2012-12-22
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉New York, N.Y. -- Science. 2012 Dec 21;338(6114):1525-32. doi: 10.1126/science.338.6114.1525.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23258865" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Brain-Computer Interfaces ; Crystallography, X-Ray ; Elementary Particles ; Embryonic Stem Cells ; Fossils ; Genetic Engineering ; Genome, Human ; Genomics ; Hominidae/genetics ; Humans ; Lasers ; Mars ; Oocytes/cytology ; Protein Conformation ; Protozoan Proteins/chemistry ; *Science ; Sequence Analysis, DNA ; Spacecraft ; Trypanosoma brucei brucei/enzymology
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 100
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2012-06-08
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hood, Leroy -- New York, N.Y. -- Science. 2012 Jun 8;336(6086):1209. doi: 10.1126/science.1225475. Epub 2012 Jun 6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22674329" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Genomics ; Humans ; *Metagenome ; Microbial Consortia/physiology ; Proteomics ; Systems Biology/*methods
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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