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  • 1
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    RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-27
    Description: Motivation: Ancestral character state reconstruction describes a set of techniques for estimating phenotypic or genetic features of species or related individuals that are the predecessors of those present today. Such reconstructions can reach into the distant past and can provide insights into the history of a population or a set of species when fossil data are not available, or they can be used to test evolutionary hypotheses, e.g. on the co-evolution of traits. Typical methods for ancestral character state reconstruction of continuous characters consider the phylogeny of the underlying data and estimate the ancestral process along the branches of the tree. They usually assume a Brownian motion model of character evolution or extensions thereof, requiring specific assumptions on the rate of phenotypic evolution. Results: We suggest using ridge regression to infer rates for each branch of the tree and the ancestral values at each inner node. We performed extensive simulations to evaluate the performance of this method and have shown that the accuracy of its reconstructed ancestral values is competitive to reconstructions using other state-of-the-art software. Using a hierarchical clustering of gene mutation profiles from an ovarian cancer dataset, we demonstrate the use of the method as a feature selection tool. Availability and implementation: The algorithm described here is implemented in C++ as a stand-alone program, and the source code is freely available at http://algbio.cs.uni-duesseldorf.de/software/RidgeRace.tar.gz . Contact: mchardy@hhu.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-02
    Description: The Tammar wallaby (Macropus eugenii) harbors unique gut bacteria and produces only one-fifth the amount of methane produced by ruminants per unit of digestible energy intake. We have isolated a dominant bacterial species (WG-1) from the wallaby microbiota affiliated with the family Succinivibrionaceae and implicated in lower methane emissions from starch-containing diets. This was achieved by using a partial reconstruction of the bacterium's metabolism from binned metagenomic data (nitrogen and carbohydrate utilization pathways and antibiotic resistance) to devise cultivation-based strategies that produced axenic WG-1 cultures. Pure-culture studies confirm that the bacterium is capnophilic and produces succinate, further explaining a microbiological basis for lower methane emissions from macropodids. This knowledge also provides new strategic targets for redirecting fermentation and reducing methane production in livestock.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pope, P B -- Smith, W -- Denman, S E -- Tringe, S G -- Barry, K -- Hugenholtz, P -- McSweeney, C S -- McHardy, A C -- Morrison, M -- New York, N.Y. -- Science. 2011 Jul 29;333(6042):646-8. doi: 10.1126/science.1205760. Epub 2011 Jun 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia 4067, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21719642" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carbohydrate Metabolism ; Digestive System/*microbiology ; Female ; Fermentation ; Genome, Bacterial ; Macropodidae/*microbiology ; Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; Starch/metabolism ; Succinic Acid/*metabolism ; Succinivibrionaceae/genetics/growth & development/*isolation & ; purification/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Functional overlap of the Arabidopsis leaf and root microbiota (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-12-04
    Description: Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive taxonomic overlap between the leaf and root microbiota. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf- and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization. While this raises the possibility of reciprocal relocation between root and leaf microbiota members, genome information and recolonization experiments also provide evidence for microbiota specialization to their respective niche.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bai, Yang -- Muller, Daniel B -- Srinivas, Girish -- Garrido-Oter, Ruben -- Potthoff, Eva -- Rott, Matthias -- Dombrowski, Nina -- Munch, Philipp C -- Spaepen, Stijn -- Remus-Emsermann, Mitja -- Huttel, Bruno -- McHardy, Alice C -- Vorholt, Julia A -- Schulze-Lefert, Paul -- England -- Nature. 2015 Dec 17;528(7582):364-9. doi: 10.1038/nature16192. Epub 2015 Dec 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. ; Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland. ; Department of Algorithmic Bioinformatics, Heinrich Heine University Dusseldorf, 40225 Dusseldorf, Germany. ; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. ; Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany. ; Max-von-Pettenkofer Institute, Ludwig Maximilian University, German Center for Infection Research (DZIF), partner site LMU Munich, 80336 Munich, Germany. ; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany. ; Max Planck Genome Center, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26633631" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*microbiology ; Bacteria/classification/genetics/isolation & purification ; Genome, Bacterial/genetics ; Germ-Free Life ; Microbiota/genetics/*physiology ; Plant Leaves/*microbiology ; Plant Roots/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores (2010)
    National Academy of Sciences
    Details
    Publication Date: 2010-07-28
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Thaumarchaeotal diversification [Evolution] (2015)
    National Academy of Sciences
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    Publication Date: 2015-07-29
    Description: The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins (2010)
    National Academy of Sciences
    Details
    Publication Date: 2010-04-02
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Snowball: strain aware gene assembly of metagenomes (2016)
    Oxford University Press
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    Publication Date: 2016-09-02
    Description: Motivation: Gene assembly is an important step in functional analysis of shotgun metagenomic data. Nonetheless, strain aware assembly remains a challenging task, as current assembly tools often fail to distinguish among strain variants or require closely related reference genomes of the studied species to be available. Results: We have developed Snowball , a novel strain aware gene assembler for shotgun metagenomic data that does not require closely related reference genomes to be available. It uses profile hidden Markov models (HMMs) of gene domains of interest to guide the assembly. Our assembler performs gene assembly of individual gene domains based on read overlaps and error correction using read quality scores at the same time, which results in very low per-base error rates. Availability and Implementation: The software runs on a user-defined number of processor cores in parallel, runs on a standard laptop and is available under the GPL 3.0 license for installation under Linux or OS X at https://github.com/hzi-bifo/snowball . Contact: AMC14@helmholtz-hzi.de , a.schoenhuth@cwi.nl Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 8
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    Denoising DNA deep sequencing data--high-throughput sequencing errors and their correction (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-21
    Description: Characterizing the errors generated by common high-throughput sequencing platforms and telling true genetic variation from technical artefacts are two interdependent steps, essential to many analyses such as single nucleotide variant calling, haplotype inference, sequence assembly and evolutionary studies. Both random and systematic errors can show a specific occurrence profile for each of the six prominent sequencing platforms surveyed here: 454 pyrosequencing, Complete Genomics DNA nanoball sequencing, Illumina sequencing by synthesis, Ion Torrent semiconductor sequencing, Pacific Biosciences single-molecule real-time sequencing and Oxford Nanopore sequencing. There is a large variety of programs available for error removal in sequencing read data, which differ in the error models and statistical techniques they use, the features of the data they analyse, the parameters they determine from them and the data structures and algorithms they use. We highlight the assumptions they make and for which data types these hold, providing guidance which tools to consider for benchmarking with regard to the data properties. While no benchmarking results are included here, such specific benchmarks would greatly inform tool choices and future software development. The development of stand-alone error correctors, as well as single nucleotide variant and haplotype callers, could also benefit from using more of the knowledge about error profiles and from (re)combining ideas from the existing approaches presented here.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 9
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    Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection (2012)
    Oxford University Press
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    Publication Date: 2012-07-31
    Description: Influenza A viruses are single-stranded RNA viruses capable of evolving rapidly to adapt to environmental conditions. Examples include the establishment of a virus in a novel host or an adaptation to increasing immunity within the host population due to prior infection or vaccination against a circulating strain. Knowledge of the viral protein regions under positive selection is therefore crucial for surveillance. We have developed a method for detecting positively selected patches of sites on the surface of viral proteins, which we assume to be relevant for adaptive evolution. We measure positive selection based on d N /d S ratios of genetic changes inferred by considering the phylogenetic structure of the data and suggest a graph-cut algorithm to identify such regions. Our algorithm searches for dense and spatially distinct clusters of sites under positive selection on the protein surface. For the hemagglutinin protein of human influenza A viruses of the subtypes H3N2 and H1N1, our predicted sites significantly overlap with known antigenic and receptor-binding sites. From the structure and sequence data of the 2009 swine-origin influenza A/H1N1 hemagglutinin and PB2 protein, we identified regions that provide evidence of evolution under positive selection since introduction of the virus into the human population. The changes in PB2 overlap with sites reported to be associated with mammalian adaptation of the influenza A virus. Application of our technique to the protein structures of viruses of yet unknown adaptive behavior could identify further candidate regions that are important for host–virus interaction.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Taxonomic binning of metagenome samples generated by next-generation sequencing technologies (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-23
    Description: Metagenome research uses random shotgun sequencing of microbial community DNA to study the genetic sequences of its members without cultivation. This development has been strongly supported by improvements in sequencing technologies, which have rendered sequencing cheaper than before. As a consequence, downstream computational analysis of metagenome sequence samples is now faced with large amounts of complex data. One of the essential steps in metagenome analysis is reconstruction of draft genomes for populations of a community or of draft ‘pan-genomes’ for higher level clades. ‘Taxonomic binning’ corresponds to the process of assigning a taxonomic identifier to sequence fragments, based on information such as sequence similarity, sequence composition or read coverage. This is used for draft genome reconstruction, if sequencing coverage is insufficient for reconstruction based on assembly information alone. Subsequent functional and metabolic annotation of draft genomes allows a genome-level analysis of novel uncultured microbial species and even inference of their cultivation requirements.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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