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  • 1
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    MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-12
    Description: : MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a fourfold improvement. Availability and implementation: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license. Contact: rb@l3-bioinfo.com or twlam@cs.hku.hk 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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    Mid-infrared luminous quasars in the GOODS-Herschel fields: a large population of heavily obscured, Compton-thick quasars at z {approx} 2 (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-01
    Description: We present the infrared (IR) and X-ray properties of a sample of 33 mid-IR luminous quasars ( L 6 μm ≥ 6 x 10 44 erg s –1 ) at redshift z 1–3, identified through detailed spectral energy distribution analyses of distant star-forming galaxies, using the deepest IR data from Spitzer and Herschel in the GOODS– Herschel fields. The aim is to constrain the fraction of obscured, and Compton-thick (CT, N H 〉 1.5 x 10 24 cm –2 ) quasars at the peak era of nuclear and star formation activities. Despite being very bright in the mid-IR band, 30 per cent of these quasars are not detected in the extremely deep 2 and 4 Ms Chandra X-ray data available in these fields. X-ray spectral analysis of the detected sources reveals that the majority (67 per cent) are obscured by column densities N H 〉 10 22 cm –2 ; this fraction reaches 80 per cent when including the X-ray-undetected sources (9 out of 33), which are likely to be the most heavily obscured, CT quasars. We constrain the fraction of CT quasars in our sample to be 24–48 per cent, and their space density to be = (6.7 ± 2.2) x 10 –6 Mpc –3 . From the investigation of the quasar host galaxies in terms of star formation rates (SFRs) and morphological distortions, as a sign of galaxy mergers/interactions, we do not find any direct relation between SFRs and quasar luminosity or X-ray obscuration. On the other hand, there is tentative evidence that the most heavily obscured quasars have, on average, more disturbed morphologies than the unobscured/moderately obscured quasar hosts, which preferentially live in undisturbed systems. However, the fraction of quasars with disturbed morphology amongst the whole sample is 40 per cent, suggesting that galaxy mergers are not the main fuelling mechanism of quasars at z 2.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm (2016)
    Oxford University Press
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    Publication Date: 2016-09-02
    Description: Motivation: Drug repositioning, which aims to identify new indications for existing drugs, offers a promising alternative to reduce the total time and cost of traditional drug development. Many computational strategies for drug repositioning have been proposed, which are based on similarities among drugs and diseases. Current studies typically use either only drug-related properties (e.g. chemical structures) or only disease-related properties (e.g. phenotypes) to calculate drug or disease similarity, respectively, while not taking into account the influence of known drug–disease association information on the similarity measures. Results: In this article, based on the assumption that similar drugs are normally associated with similar diseases and vice versa, we propose a novel computational method named MBiRW, which utilizes some comprehensive similarity measures and Bi-Random walk (BiRW) algorithm to identify potential novel indications for a given drug. By integrating drug or disease features information with known drug–disease associations, the comprehensive similarity measures are firstly developed to calculate similarity for drugs and diseases. Then drug similarity network and disease similarity network are constructed, and they are incorporated into a heterogeneous network with known drug–disease interactions. Based on the drug–disease heterogeneous network, BiRW algorithm is adopted to predict novel potential drug–disease associations. Computational experiment results from various datasets demonstrate that the proposed approach has reliable prediction performance and outperforms several recent computational drug repositioning approaches. Moreover, case studies of five selected drugs further confirm the superior performance of our method to discover potential indications for drugs practically. Availability and Implementation: http://github.com//bioinfomaticsCSU/MBiRW . Contact: jxwang@mail.csu.edu.cn 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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  • 4
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    SIFTER search: a web server for accurate phylogeny-based protein function prediction (2015)
    Oxford University Press
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    Publication Date: 2015-07-02
    Description: We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-01
    Description: Homologous recombination of single-stranded oligonucleotides is a highly efficient process for introducing precise mutations into the genome of E. coli and other organisms when mismatch repair (MMR) is disabled. This can result in the rapid accumulation of off-target mutations that can mask desired phenotypes, especially when selections need to be employed following the generation of combinatorial libraries. While the use of inducible mutator phenotypes or other MMR evasion tactics have proven useful, reported methods either require non-mobile genetic modifications or costly oligonucleotides that also result in reduced efficiencies of replacement. Therefore a new system was developed, Transient Mutator Multiplex Automated Genome Engineering (TM-MAGE), that solves problems encountered in other methods for oligonucleotide-mediated recombination. TM-MAGE enables nearly equivalent efficiencies of allelic replacement to the use of strains with fully disabled MMR and with an approximately 12- to 33-fold lower off-target mutation rate. Furthermore, growth temperatures are not restricted and a version of the plasmid can be readily removed by sucrose counterselection. TM-MAGE was used to combinatorially reconstruct mutations found in evolved salt-tolerant strains, enabling the identification of causative mutations and isolation of strains with up to 75% increases in growth rate and greatly reduced lag times in 0.6 M NaCl.
    Keywords: Recombination, Targeted gene modification
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Efficient comparison of sets of intervals with NC-lists (2013)
    Oxford University Press
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    Publication Date: 2013-03-23
    Description: Motivation: High-throughput sequencing produces in a small amount of time a large amount of data, which are usually difficult to analyze. Mapping the reads to the transcripts they originate from, to quantify the expression of the genes, is a simple, yet time demanding, example of analysis. Fast genomic comparison algorithms are thus crucial for the analysis of the ever-expanding number of reads sequenced. Results: We used NC-lists to implement an algorithm that compares a set of query intervals with a set of reference intervals in two steps. The first step, a pre-processing done once for all, requires time , where Q and R are the sets of query and reference intervals. The search phase requires constant space, and time , where M is the set of overlaps. We showed that our algorithm compares favorably with five other algorithms, especially when several comparisons are performed. Availability: The algorithm has been included to S–MART, a versatile tool box for RNA-Seq analysis, freely available at http://urgi.versailles.inra.fr/Tools/S-Mart . The algorithm can be used for many kinds of data (sequencing reads, annotations, etc.) in many formats (GFF3, BED, SAM, etc.), on any operating system. It is thus readily useable for the analysis of next-generation sequencing data. Contact: matthias.zytnicki@versailles.inra.fr 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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  • 7
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    In silico site of metabolism prediction for human UGT-catalyzed reactions (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-29
    Description: Motivation:  The human uridine diphosphate-glucuronosyltransferase enzyme family catalyzes the glucuronidation of the glycosyl group of a nucleotide sugar to an acceptor compound (substrate), which is the most common conjugation pathway that serves to protect the organism from the potential toxicity of xenobiotics. Moreover, it could affect the pharmacological profile of a drug. Therefore, it is important to identify the metabolically labile sites for glucuronidation. Results:  In the present study, we developed four in silico models to predict sites of glucuronidation, for four major sites of metabolism functional groups, i.e. aliphatic hydroxyl, aromatic hydroxyl, carboxylic acid or amino nitrogen, respectively. According to the mechanism of glucuronidation, a series of ‘local’ and ‘global’ molecular descriptors characterizing the atomic reactivity, bonding strength and physical–chemical properties were calculated and selected with a genetic algorithm-based feature selection approach. The constructed support vector machine classification models show good prediction performance, with the balanced accuracy ranging from 0.88 to 0.96 on test set. For further validation, our models can successfully identify 84% of experimentally observed sites of metabolisms for an external test set containing 54 molecules. Availability and implementation:  The software somugt based on our models is available at www.dddc.ac.cn/adme/jlpeng/somugt_win32.zip . Contact:   xmluo@simm.ac.cn or myzheng@mail.shcnc.ac.cn 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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    Nucleocapsid protein structures from orthobunyaviruses reveal insight into ribonucleoprotein architecture and RNA polymerization (2013)
    Oxford University Press
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    Publication Date: 2013-06-08
    Description: All orthobunyaviruses possess three genome segments of single-stranded negative sense RNA that are encapsidated with the virus-encoded nucleocapsid (N) protein to form a ribonucleoprotein (RNP) complex, which is uncharacterized at high resolution. We report the crystal structure of both the Bunyamwera virus (BUNV) N–RNA complex and the unbound Schmallenberg virus (SBV) N protein, at resolutions of 3.20 and 2.75 Å, respectively. Both N proteins crystallized as ring-like tetramers and exhibit a high degree of structural similarity despite classification into different orthobunyavirus serogroups. The structures represent a new RNA-binding protein fold. BUNV N possesses a positively charged groove into which RNA is deeply sequestered, with the bases facing away from the solvent. This location is highly inaccessible, implying that RNA polymerization and other critical base pairing events in the virus life cycle require RNP disassembly. Mutational analysis of N protein supports a correlation between structure and function. Comparison between these crystal structures and electron microscopy images of both soluble tetramers and authentic RNPs suggests the N protein does not bind RNA as a repeating monomer; thus, it represents a newly described architecture for bunyavirus RNP assembly, with implications for many other segmented negative-strand RNA viruses.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    A single leaf of Camellia oleifera has two types of carbon assimilation pathway, C3 and crassulacean acid metabolism (2012)
    Oxford University Press
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    Publication Date: 2012-03-02
    Description: The C 4 plants, whose first product of photosynthetic CO 2 fixation is a four-carbon acid, have evolved independently many times. Crassulacean acid metabolism (CAM) is a biological mechanism known to exhibit some C 4 characteristics such as the C 3 cycle during daylight and demonstrates the C 4 cycle at night. There are also various C 3 -CAM intermediates, whose CAM pathway can be induced by environmental changes. However, neither fungus-induced CAM nor Theaceae CAM have been reported previously. Here, we show that CAM could be generated by fungus infection in Camellia oleifera Abel. young leaves, even at a location of a single leaf where the upper part had been transformed into a succulent one, while the lower part remained unchanged. The early photosynthetic products of dark-grown C. oleifera succulent leaves were malate, whereas C. oleifera normal leaves and light-grown succulent leaves incorporated most of 14 C into the primary photosynthetic product 3-phosphoglycerate. Camellia oleifera succulent leaves have a lower absolute 13 C value, much lower photorespiration rates and lower transpiration rates during the day than those of C. oleifera normal leaves. Like a typical CAM plant, stomata of C. oleifera succulent leaves closed during the daylight, but opened at night, and therefore had a detectable CO 2 compensation point in darkness. Net photosynthetic rates ( P n ) fluctuated diurnally and similarly with stomatal aperture. No light intensity saturation could be defined for C. oleifera succulent leaves. C 4 key enzymes in C. oleifera succulent leaves were increased at both the transcriptional/translational levels as well as at the enzyme activity level.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 10
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    Sex differences in alarm response and predation risk in the fresh water snail Pomacea canaliculata (2014)
    Oxford University Press
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    Publication Date: 2014-04-29
    Description: Many animals show alarm responses (ARs) to chemical cues released from predators or injured conspecifics. However, the prey often makes a trade-off between predation avoidance and reproduction, resulting in pronounced sex differences in AR and in sex-biased predation. This phenomenon has rarely been investigated in snails. The freshwater snail Pomacea canaliculata is reported to exhibit an AR to chemical cues released from predators or injured conspecifics. Here, we investigate the sex differences in AR in the snail to chemical cues released from its predator turtle Chinemys reevesii and injured conspecifics. By exposing adult females and males of equivalent size to turtles, we also evaluate the sex-biased predation in the snail. We find that females respond to chemical cues significantly more strongly than males. The predation experiment shows that more females survived than males after a week of predation. These results suggest that males may reduce their antipredator behaviour in order to increase the chance of mating, suggesting a trade-off between predation avoidance and reproduction.
    Print ISSN: 0260-1230
    Electronic ISSN: 1464-3766
    Topics: Biology
    Published by Oxford University Press
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