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Articles published in PLoS Comput Biol

Retrieve available abstracts of 92 articles:
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    February 2019
  1. GRYTTEN I, Rand KD, Nederbragt AJ, Storvik GO, et al
    Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.
    PLoS Comput Biol. 2019;15:e1006731.
    PubMed     Text format     Abstract available


  2. FRANZ NM, Musher LJ, Brown JW, Yu S, et al
    Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion.
    PLoS Comput Biol. 2019;15:e1006493.
    PubMed     Text format     Abstract available


  3. LAFITA A, Bliven S, Prlic A, Guzenko D, et al
    BioJava 5: A community driven open-source bioinformatics library.
    PLoS Comput Biol. 2019;15:e1006791.
    PubMed     Text format     Abstract available


  4. DUNN NA, Unni DR, Diesh C, Munoz-Torres M, et al
    Apollo: Democratizing genome annotation.
    PLoS Comput Biol. 2019;15:e1006790.
    PubMed     Text format     Abstract available


  5. KOCH S, Kohrs F, Lahmann P, Bissinger T, et al
    RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion.
    PLoS Comput Biol. 2019;15:e1006759.
    PubMed     Text format     Abstract available


    January 2019
  6. BRUBAKER DK, Proctor EA, Haigis KM, Lauffenburger DA, et al
    Computational translation of genomic responses from experimental model systems to humans.
    PLoS Comput Biol. 2019;15:e1006286.
    PubMed     Text format     Abstract available


    December 2018
  7. BROWN AV, Campbell JD, Assefa T, Grant D, et al
    Ten quick tips for sharing open genomic data.
    PLoS Comput Biol. 2018;14:e1006472.
    PubMed     Text format     Abstract available


  8. TARKOWSKA A, Carvalho-Silva D, Cook CE, Turner E, et al
    Eleven quick tips to build a usable REST API for life sciences.
    PLoS Comput Biol. 2018;14:e1006542.
    PubMed     Text format    


  9. PABON NA, Xia Y, Estabrooks SK, Ye Z, et al
    Predicting protein targets for drug-like compounds using transcriptomics.
    PLoS Comput Biol. 2018;14:e1006651.
    PubMed     Text format     Abstract available


    November 2018
  10. BUTLER BM, Kazan IC, Kumar A, Ozkan SB, et al
    Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs.
    PLoS Comput Biol. 2018;14:e1006626.
    PubMed     Text format     Abstract available


  11. KELLEHER J, Thornton KR, Ashander J, Ralph PL, et al
    Efficient pedigree recording for fast population genetics simulation.
    PLoS Comput Biol. 2018;14:e1006581.
    PubMed     Text format     Abstract available


  12. SHOKO R, Manasa J, Maphosa M, Mbanga J, et al
    Strategies and opportunities for promoting bioinformatics in Zimbabwe.
    PLoS Comput Biol. 2018;14:e1006480.
    PubMed     Text format    


  13. CROOK OM, Mulvey CM, Kirk PDW, Lilley KS, et al
    A Bayesian mixture modelling approach for spatial proteomics.
    PLoS Comput Biol. 2018;14:e1006516.
    PubMed     Text format     Abstract available


  14. VOLZ EM, Siveroni I
    Bayesian phylodynamic inference with complex models.
    PLoS Comput Biol. 2018;14:e1006546.
    PubMed     Text format     Abstract available


    October 2018
  15. RAZZAQ M, Pauleve L, Siegel A, Saez-Rodriguez J, et al
    Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data.
    PLoS Comput Biol. 2018;14:e1006538.
    PubMed     Text format     Abstract available


  16. AUN E, Brauer A, Kisand V, Tenson T, et al
    A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria.
    PLoS Comput Biol. 2018;14:e1006434.
    PubMed     Text format     Abstract available


  17. SKINNIDER MA, Stacey RG, Foster LJ
    Genomic data integration systematically biases interactome mapping.
    PLoS Comput Biol. 2018;14:e1006474.
    PubMed     Text format     Abstract available


  18. HUH I, Mendizabal I, Park T, Yi SV, et al
    Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals.
    PLoS Comput Biol. 2018;14:e1006451.
    PubMed     Text format     Abstract available


  19. CHEN L, Fish AE, Capra JA
    Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties.
    PLoS Comput Biol. 2018;14:e1006484.
    PubMed     Text format     Abstract available


    September 2018
  20. HUNT KA, Jennings RM, Inskeep WP, Carlson RP, et al
    Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community.
    PLoS Comput Biol. 2018;14:e1006431.
    PubMed     Text format     Abstract available


  21. CASCARINA SM, Ross ED
    Proteome-scale relationships between local amino acid composition and protein fates and functions.
    PLoS Comput Biol. 2018;14:e1006256.
    PubMed     Text format     Abstract available


  22. TITUS AJ, Flower A, Hagerty P, Gamble P, et al
    SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases.
    PLoS Comput Biol. 2018;14:e1006454.
    PubMed     Text format     Abstract available


    August 2018
  23. CHEN X, Yin J, Qu J, Huang L, et al
    MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction.
    PLoS Comput Biol. 2018;14:e1006418.
    PubMed     Text format     Abstract available


  24. GARRIDO-MARTIN D, Palumbo E, Guigo R, Breschi A, et al
    ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization.
    PLoS Comput Biol. 2018;14:e1006360.
    PubMed     Text format     Abstract available


  25. VLACHOS C, Kofler R
    MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies.
    PLoS Comput Biol. 2018;14:e1006413.
    PubMed     Text format     Abstract available


  26. LEE K, Famiglietti ML, McMahon A, Wei CH, et al
    Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
    PLoS Comput Biol. 2018;14:e1006390.
    PubMed     Text format     Abstract available


  27. BRADLEY PH, Nayfach S, Pollard KS
    Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.
    PLoS Comput Biol. 2018;14:e1006242.
    PubMed     Text format     Abstract available


  28. TSE MJ, Chu BK, Gallivan CP, Read EL, et al
    Rare-event sampling of epigenetic landscapes and phenotype transitions.
    PLoS Comput Biol. 2018;14:e1006336.
    PubMed     Text format     Abstract available


    July 2018
  29. CHAI H, Jiang H, Lin L, Liu L, et al
    A marginalized two-part Beta regression model for microbiome compositional data.
    PLoS Comput Biol. 2018;14:e1006329.
    PubMed     Text format     Abstract available


  30. DE WECK A, Golji J, Jones MD, Korn JM, et al
    Correction of copy number induced false positives in CRISPR screens.
    PLoS Comput Biol. 2018;14:e1006279.
    PubMed     Text format     Abstract available


    June 2018
  31. HIGASHI K, Suzuki S, Kurosawa S, Mori H, et al
    Latent environment allocation of microbial community data.
    PLoS Comput Biol. 2018;14:e1006143.
    PubMed     Text format     Abstract available


  32. LU J, Salzberg SL
    Removing contaminants from databases of draft genomes.
    PLoS Comput Biol. 2018;14:e1006277.
    PubMed     Text format     Abstract available


    May 2018
  33. MACGILVRAY ME, Shishkova E, Chasman D, Place M, et al
    Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response.
    PLoS Comput Biol. 2018;13:e1006088.
    PubMed     Text format     Abstract available


  34. GHOSH SK, Jost D
    How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes.
    PLoS Comput Biol. 2018;14:e1006159.
    PubMed     Text format     Abstract available


  35. AITE M, Chevallier M, Frioux C, Trottier C, et al
    Traceability, reproducibility and wiki-exploration for "a-la-carte" reconstructions of genome-scale metabolic models.
    PLoS Comput Biol. 2018;14:e1006146.
    PubMed     Text format     Abstract available


    April 2018
  36. FETROW JS, Babbitt PC
    New computational approaches to understanding molecular protein function.
    PLoS Comput Biol. 2018;14:e1005756.
    PubMed     Text format    


  37. KIM JS, Gao X, Rzhetsky A
    RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning.
    PLoS Comput Biol. 2018;14:e1006106.
    PubMed     Text format     Abstract available


  38. BUCKLEY RM, Kortschak RD, Adelson DL
    Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse.
    PLoS Comput Biol. 2018;14:e1006091.
    PubMed     Text format     Abstract available


  39. HANNIGAN GD, Duhaime MB, Koutra D, Schloss PD, et al
    Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.
    PLoS Comput Biol. 2018;14:e1006099.
    PubMed     Text format     Abstract available


    March 2018
  40. CORPAS M, Kovalevskaya NV, McMurray A, Nielsen FGG, et al
    A FAIR guide for data providers to maximise sharing of human genomic data.
    PLoS Comput Biol. 2018;14:e1005873.
    PubMed     Text format     Abstract available


  41. BAADEN M, Delalande O, Ferey N, Pasquali S, et al
    Ten simple rules to create a serious game, illustrated with examples from structural biology.
    PLoS Comput Biol. 2018;14:e1005955.
    PubMed     Text format    


  42. BAILLIE JK, Bretherick A, Haley CS, Clohisey S, et al
    Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.
    PLoS Comput Biol. 2018;14:e1005934.
    PubMed     Text format     Abstract available


  43. SAMADIAN S, Bruce JP, Pugh TJ
    Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.
    PLoS Comput Biol. 2018;14:e1006080.
    PubMed     Text format     Abstract available


  44. EDGINGTON MP, Alphey LS
    Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors.
    PLoS Comput Biol. 2018;14:e1006059.
    PubMed     Text format     Abstract available


  45. LUO Y, He J, Xu X, Sun MA, et al
    Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells.
    PLoS Comput Biol. 2018;14:e1006034.
    PubMed     Text format     Abstract available


  46. PITA-JUAREZ Y, Altschuler G, Kariotis S, Wei W, et al
    The Pathway Coexpression Network: Revealing pathway relationships.
    PLoS Comput Biol. 2018;14:e1006042.
    PubMed     Text format     Abstract available


  47. DING J, Hagood JS, Ambalavanan N, Kaminski N, et al
    iDREM: Interactive visualization of dynamic regulatory networks.
    PLoS Comput Biol. 2018;14:e1006019.
    PubMed     Text format     Abstract available


  48. IRASTORZA-AZCARATE I, Acemel RD, Tena JJ, Maeso I, et al
    4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data.
    PLoS Comput Biol. 2018;14:e1006030.
    PubMed     Text format     Abstract available


    February 2018
  49. MOXLEY MA, Vinnakota KC, Bazil JN, Qi NR, et al
    Systems-level computational modeling demonstrates fuel selection switching in high capacity running and low capacity running rats.
    PLoS Comput Biol. 2018;14:e1005982.
    PubMed     Text format     Abstract available


  50. QI F, Motz M, Jung K, Lassak J, et al
    Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation.
    PLoS Comput Biol. 2018;14:e1005987.
    PubMed     Text format     Abstract available


  51. SUN JX, He Y, Sanford E, Montesion M, et al
    A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal.
    PLoS Comput Biol. 2018;14:e1005965.
    PubMed     Text format     Abstract available


  52. COLLINS C, Didelot X
    A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination.
    PLoS Comput Biol. 2018;14:e1005958.
    PubMed     Text format     Abstract available


    January 2018
  53. KOPLEV S, Lin K, Dohlman AB, Ma'ayan A, et al
    Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition.
    PLoS Comput Biol. 2018;14:e1005911.
    PubMed     Text format     Abstract available


  54. MARCAIS G, Delcher AL, Phillippy AM, Coston R, et al
    MUMmer4: A fast and versatile genome alignment system.
    PLoS Comput Biol. 2018;14:e1005944.
    PubMed     Text format     Abstract available


    November 2017
  55. FERNANDEZ-DE-COSSIO-DIAZ J, Leon K, Mulet R
    Characterizing steady states of genome-scale metabolic networks in continuous cell cultures.
    PLoS Comput Biol. 2017;13:e1005835.
    PubMed     Text format     Abstract available


  56. LIU R, Dickerson J
    Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.
    PLoS Comput Biol. 2017;13:e1005851.
    PubMed     Text format     Abstract available


  57. ROHART F, Gautier B, Singh A, Le Cao KA, et al
    mixOmics: An R package for 'omics feature selection and multiple data integration.
    PLoS Comput Biol. 2017;13:e1005752.
    PubMed     Text format     Abstract available


    October 2017
  58. PULLER V, Neher R, Albert J
    Estimating time of HIV-1 infection from next-generation sequence diversity.
    PLoS Comput Biol. 2017;13:e1005775.
    PubMed     Text format     Abstract available


  59. DREW K, Muller CL, Bonneau R, Marcotte EM, et al
    Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.
    PLoS Comput Biol. 2017;13:e1005625.
    PubMed     Text format     Abstract available


  60. VERNY L, Sella N, Affeldt S, Singh PP, et al
    Learning causal networks with latent variables from multivariate information in genomic data.
    PLoS Comput Biol. 2017;13:e1005662.
    PubMed     Text format     Abstract available


    September 2017
  61. MURRAY KD, Webers C, Ong CS, Borevitz J, et al
    kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.
    PLoS Comput Biol. 2017;13:e1005727.
    PubMed     Text format     Abstract available


  62. KIM M, Eetemadi A, Tagkopoulos I
    DeepPep: Deep proteome inference from peptide profiles.
    PLoS Comput Biol. 2017;13:e1005661.
    PubMed     Text format     Abstract available


  63. DUMEAUX V, Fjukstad B, Fjosne HE, Frantzen JO, et al
    Interactions between the tumor and the blood systemic response of breast cancer patients.
    PLoS Comput Biol. 2017;13:e1005680.
    PubMed     Text format     Abstract available


  64. LABHSETWAR P, Melo MCR, Cole JA, Luthey-Schulten Z, et al
    Population FBA predicts metabolic phenotypes in yeast.
    PLoS Comput Biol. 2017;13:e1005728.
    PubMed     Text format     Abstract available


  65. GRITSENKO AA, Weingarten-Gabbay S, Elias-Kirma S, Nir R, et al
    Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity.
    PLoS Comput Biol. 2017;13:e1005734.
    PubMed     Text format     Abstract available


    August 2017
  66. MONTI R, Barozzi I, Osterwalder M, Lee E, et al
    Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.
    PLoS Comput Biol. 2017;13:e1005720.
    PubMed     Text format     Abstract available


  67. AMAR D, Shamir R, Yekutieli D
    Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.
    PLoS Comput Biol. 2017;13:e1005700.
    PubMed     Text format     Abstract available


  68. FUKUYAMA J, Rumker L, Sankaran K, Jeganathan P, et al
    Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
    PLoS Comput Biol. 2017;13:e1005706.
    PubMed     Text format     Abstract available


  69. BASSANI-STERNBERG M, Chong C, Guillaume P, Solleder M, et al
    Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity.
    PLoS Comput Biol. 2017;13:e1005725.
    PubMed     Text format     Abstract available


    July 2017
  70. SHAO B, Yuan H, Zhang R, Wang X, et al
    Reconstructing the regulatory circuit of cell fate determination in yeast mating response.
    PLoS Comput Biol. 2017;13:e1005671.
    PubMed     Text format     Abstract available


  71. ATAMAN M, Hatzimanikatis V
    lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites.
    PLoS Comput Biol. 2017;13:e1005513.
    PubMed     Text format     Abstract available


  72. LI Y, Jourdain AA, Calvo SE, Liu JS, et al
    CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets.
    PLoS Comput Biol. 2017;13:e1005653.
    PubMed     Text format     Abstract available


  73. GURSOY G, Xu Y, Liang J
    Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model.
    PLoS Comput Biol. 2017;13:e1005658.
    PubMed     Text format     Abstract available


  74. GILPIN W, Feldman MW
    A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape.
    PLoS Comput Biol. 2017;13:e1005644.
    PubMed     Text format     Abstract available


    June 2017
  75. G C C L CARDENAS R, D Linhares N, L Ferreira R, Pena SDJ, et al
    Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders.
    PLoS Comput Biol. 2017;13:e1005520.
    PubMed     Text format     Abstract available


  76. JONGENEEL CV, Achinike-Oduaran O, Adebiyi E, Adebiyi M, et al
    Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.
    PLoS Comput Biol. 2017;13:e1005419.
    PubMed     Text format     Abstract available


  77. LAI EY, Chen YH, Wu KP
    A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data.
    PLoS Comput Biol. 2017;13:e1005601.
    PubMed     Text format     Abstract available


  78. HU Y, Lu Q, Powles R, Yao X, et al
    Leveraging functional annotations in genetic risk prediction for human complex diseases.
    PLoS Comput Biol. 2017;13:e1005589.
    PubMed     Text format     Abstract available


    May 2017
  79. SUOMI T, Seyednasrollah F, Jaakkola MK, Faux T, et al
    ROTS: An R package for reproducibility-optimized statistical testing.
    PLoS Comput Biol. 2017;13:e1005562.
    PubMed     Text format     Abstract available


  80. CHAN SHJ, Simons MN, Maranas CD
    SteadyCom: Predicting microbial abundances while ensuring community stability.
    PLoS Comput Biol. 2017;13:e1005539.
    PubMed     Text format     Abstract available


  81. LI Y, Zhou X, Zhai Z, Li T, et al
    Co-occurring protein phosphorylation are functionally associated.
    PLoS Comput Biol. 2017;13:e1005502.
    PubMed     Text format     Abstract available


    March 2017
  82. BASILE W, Sachenkova O, Light S, Elofsson A, et al
    High GC content causes orphan proteins to be intrinsically disordered.
    PLoS Comput Biol. 2017;13:e1005375.
    PubMed     Text format     Abstract available


    February 2017
  83. MAGEE D, Suchard MA, Scotch M
    Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.
    PLoS Comput Biol. 2017;13:e1005389.
    PubMed     Text format     Abstract available


    January 2017
  84. WU T, Wang L, Fu F
    Coevolutionary dynamics of phenotypic diversity and contingent cooperation.
    PLoS Comput Biol. 2017;13:e1005363.
    PubMed     Text format     Abstract available


  85. HWANG HY, Wang J
    Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans.
    PLoS Comput Biol. 2017;13:e1005369.
    PubMed     Text format     Abstract available


  86. SAEEDGHALATI M, Farahpour F, Budeus B, Lange A, et al
    Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes.
    PLoS Comput Biol. 2017;13:e1005362.
    PubMed     Text format     Abstract available


  87. PRIGENT S, Frioux C, Dittami SM, Thiele S, et al
    Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.
    PLoS Comput Biol. 2017;13:e1005276.
    PubMed     Text format     Abstract available


    June 2016
  88. BRANKOVICS B, Zhang H, van Diepeningen AD, van der Lee TA, et al
    GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.
    PLoS Comput Biol. 2016;12:e1004753.
    PubMed     Text format     Abstract available


    May 2016
  89. BENDL J, Musil M, Stourac J, Zendulka J, et al
    PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
    PLoS Comput Biol. 2016;12:e1004962.
    PubMed     Text format     Abstract available


  90. BOHLER A, Wu G, Kutmon M, Pradhana LA, et al
    Reactome from a WikiPathways Perspective.
    PLoS Comput Biol. 2016;12:e1004941.
    PubMed     Text format     Abstract available


  91. BRECKELS LM, Holden SB, Wojnar D, Mulvey CM, et al
    Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.
    PLoS Comput Biol. 2016;12:e1004920.
    PubMed     Text format     Abstract available


  92. KELLEHER J, Etheridge AM, McVean G
    Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.
    PLoS Comput Biol. 2016;12:e1004842.
    PubMed     Text format     Abstract available


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