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COVID-19: Daily Top 10 Papers


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Articles published in PLoS Comput Biol

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    March 2021
  1. MARCON Y, Bishop T, Avraam D, Escriba-Montagut X, et al
    Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD.
    PLoS Comput Biol. 2021;17:e1008880.
    PubMed     Abstract available


  2. PAVLOVA YS, Paez-Espino D, Morozov AY, Belalov IS, et al
    Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.
    PLoS Comput Biol. 2021;17:e1008841.
    PubMed     Abstract available


  3. SUN R, Nikolakopoulos AN
    Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors.
    PLoS Comput Biol. 2021;17:e1008838.
    PubMed     Abstract available


  4. BAK JH, Kim MH, Liu L, Hyeon C, et al
    A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C.
    PLoS Comput Biol. 2021;17:e1008834.
    PubMed     Abstract available


  5. SACHDEVA V, Mora T, Walczak AM, Palmer SE, et al
    Optimal prediction with resource constraints using the information bottleneck.
    PLoS Comput Biol. 2021;17:e1008743.
    PubMed     Abstract available


  6. LAM SD, Babu MM, Lees J, Orengo CA, et al
    Biological impact of mutually exclusive exon switching.
    PLoS Comput Biol. 2021;17:e1008708.
    PubMed     Abstract available


  7. CHELOSHKINA K, Poptsova M
    Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements.
    PLoS Comput Biol. 2021;17:e1008749.
    PubMed     Abstract available


    February 2021
  8. RATNIKOV BI, Cieplak P, Remacle AG, Nguyen E, et al
    Quantitative profiling of protease specificity.
    PLoS Comput Biol. 2021;17:e1008101.
    PubMed     Abstract available


  9. VEGA YON GG, Thomas DC, Morrison J, Mi H, et al
    Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.
    PLoS Comput Biol. 2021;17:e1007948.
    PubMed     Abstract available


  10. SOMMER MJ, Salzberg SL
    Balrog: A universal protein model for prokaryotic gene prediction.
    PLoS Comput Biol. 2021;17:e1008727.
    PubMed     Abstract available


  11. LLOYD JP, Soellner MB, Merajver SD, Li JZ, et al
    Impact of between-tissue differences on pan-cancer predictions of drug sensitivity.
    PLoS Comput Biol. 2021;17:e1008720.
    PubMed     Abstract available


  12. JACKSON M, Kavoussanakis K, Wallace EWJ
    Using prototyping to choose a bioinformatics workflow management system.
    PLoS Comput Biol. 2021;17:e1008622.
    PubMed     Abstract available


  13. TUNG HR, Durrett R
    Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective.
    PLoS Comput Biol. 2021;17:e1008701.
    PubMed     Abstract available


  14. GARRIDO-RODRIGUEZ M, Lopez-Lopez D, Ortuno FM, Pena-Chilet M, et al
    A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.
    PLoS Comput Biol. 2021;17:e1008748.
    PubMed     Abstract available


  15. VAN DAMME R, Holzer M, Viehweger A, Muller B, et al
    Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN).
    PLoS Comput Biol. 2021;17:e1008716.
    PubMed     Abstract available


  16. YU L, Wang M, Yang Y, Xu F, et al
    Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways.
    PLoS Comput Biol. 2021;17:e1008696.
    PubMed     Abstract available


  17. XUE B, Jordan B, Rizvi S, Naegle KM, et al
    KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions.
    PLoS Comput Biol. 2021;17:e1008681.
    PubMed     Abstract available


    January 2021
  18. VALIENTE-MULLOR C, Beamud B, Ansari I, Frances-Cuesta C, et al
    One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
    PLoS Comput Biol. 2021;17:e1008678.
    PubMed     Abstract available


  19. AVRAM O, Kigel A, Vaisman-Mentesh A, Kligsberg S, et al
    PASA: Proteomic analysis of serum antibodies web server.
    PLoS Comput Biol. 2021;17:e1008607.
    PubMed     Abstract available


  20. MARTINEZ-GARCIA PM, Garcia-Torres M, Divina F, Terron-Bautista J, et al
    Genome-wide prediction of topoisomerase IIbeta binding by architectural factors and chromatin accessibility.
    PLoS Comput Biol. 2021;17:e1007814.
    PubMed     Abstract available


  21. KHARERIN H, Bai L
    Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.
    PLoS Comput Biol. 2021;17:e1008560.
    PubMed     Abstract available


  22. TJARNBERG A, Mahmood O, Jackson CA, Saldi GA, et al
    Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data.
    PLoS Comput Biol. 2021;17:e1008569.
    PubMed     Abstract available


  23. KALKAUSKAS A, Perron U, Sun Y, Goldman N, et al
    Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.
    PLoS Comput Biol. 2021;17:e1008561.
    PubMed     Abstract available


  24. KOUKOULI E, Wang D, Dondelinger F, Park J, et al
    A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response.
    PLoS Comput Biol. 2021;17:e1008066.
    PubMed     Abstract available


  25. SCELSI MA, Napolioni V, Greicius MD, Altmann A, et al
    Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities.
    PLoS Comput Biol. 2021;17:e1008517.
    PubMed     Abstract available


  26. PATUMCHAROENPOL P, Nakphaichit M, Panagiotou G, Senavonge A, et al
    MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome.
    PLoS Comput Biol. 2021;17:e1008487.
    PubMed     Abstract available


    December 2020
  27. LIN D, Yalamanchili HB, Zhang X, Lewis NE, et al
    CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.
    PLoS Comput Biol. 2020;16:e1008498.
    PubMed     Abstract available


    November 2020
  28. TOWNES FW, Carr K, Miller JW
    Identifying longevity associated genes by integrating gene expression and curated annotations.
    PLoS Comput Biol. 2020;16:e1008429.
    PubMed     Abstract available


  29. THESSEN AE, Walls RL, Vogt L, Singer J, et al
    Transforming the study of organisms: Phenomic data models and knowledge bases.
    PLoS Comput Biol. 2020;16:e1008376.
    PubMed     Abstract available


  30. SETHI R, Becker J, Graaf J, Lower M, et al
    Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.
    PLoS Comput Biol. 2020;16:e1008397.
    PubMed     Abstract available


  31. KULMANOV M, Hoehndorf R
    DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier.
    PLoS Comput Biol. 2020;16:e1008453.
    PubMed     Abstract available


  32. JUNG H, Ventura T, Chung JS, Kim WJ, et al
    Twelve quick steps for genome assembly and annotation in the classroom.
    PLoS Comput Biol. 2020;16:e1008325.
    PubMed     Abstract available


  33. YANG H, Wei Q, Li D, Wang Z, et al
    Cancer classification based on chromatin accessibility profiles with deep adversarial learning model.
    PLoS Comput Biol. 2020;16:e1008405.
    PubMed     Abstract available


  34. CROOK OM, Geladaki A, Nightingale DJH, Vennard OL, et al
    A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection.
    PLoS Comput Biol. 2020;16:e1008288.
    PubMed     Abstract available


  35. KAVEH K, McAvoy A, Chatterjee K, Nowak MA, et al
    The Moran process on 2-chromatic graphs.
    PLoS Comput Biol. 2020;16:e1008402.
    PubMed     Abstract available


    October 2020
  36. RATHI KS, Arif S, Koptyra M, Naqvi AS, et al
    A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.
    PLoS Comput Biol. 2020;16:e1008263.
    PubMed     Abstract available


  37. CLIFF OM, McLean N, Sintchenko V, Fair KM, et al
    Inferring evolutionary pathways and directed genotype networks of foodborne pathogens.
    PLoS Comput Biol. 2020;16:e1008401.
    PubMed     Abstract available


  38. PEREIRA-SANTANA A, Gamboa-Tuz SD, Zhao T, Schranz ME, et al
    Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin.
    PLoS Comput Biol. 2020;16:e1008318.
    PubMed     Abstract available


  39. NGUYEN M, Olson R, Shukla M, VanOeffelen M, et al
    Predicting antimicrobial resistance using conserved genes.
    PLoS Comput Biol. 2020;16:e1008319.
    PubMed     Abstract available


  40. STEVENS I, Mukarram AK, Hortenhuber M, Meehan TF, et al
    Ten simple rules for annotating sequencing experiments.
    PLoS Comput Biol. 2020;16:e1008260.
    PubMed    


  41. RODRIGUEZ JM, Pozo F, di Domenico T, Vazquez J, et al
    An analysis of tissue-specific alternative splicing at the protein level.
    PLoS Comput Biol. 2020;16:e1008287.
    PubMed     Abstract available


  42. LAM TJ, Stamboulian M, Han W, Ye Y, et al
    Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species.
    PLoS Comput Biol. 2020;16:e1007951.
    PubMed     Abstract available


  43. MCCARTER C, Howrylak J, Kim S
    Learning gene networks underlying clinical phenotypes using SNP perturbation.
    PLoS Comput Biol. 2020;16:e1007940.
    PubMed     Abstract available


  44. KARCHER MD, Carvalho LM, Suchard MA, Dudas G, et al
    Estimating effective population size changes from preferentially sampled genetic sequences.
    PLoS Comput Biol. 2020;16:e1007774.
    PubMed     Abstract available


  45. MANOLOV A, Konanov D, Fedorov D, Osmolovsky I, et al
    Genome Complexity Browser: Visualization and quantification of genome variability.
    PLoS Comput Biol. 2020;16:e1008222.
    PubMed     Abstract available


  46. KOJIMA K, Tadaka S, Katsuoka F, Tamiya G, et al
    A genotype imputation method for de-identified haplotype reference information by using recurrent neural network.
    PLoS Comput Biol. 2020;16:e1008207.
    PubMed     Abstract available


  47. M A BASHER AR, McLaughlin RJ, Hallam SJ
    Metabolic pathway inference using multi-label classification with rich pathway features.
    PLoS Comput Biol. 2020;16:e1008174.
    PubMed     Abstract available


    September 2020
  48. ZHAO Z, Sokhansanj BA, Malhotra C, Zheng K, et al
    Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization.
    PLoS Comput Biol. 2020;16:e1008269.
    PubMed     Abstract available


  49. FIAUX PC, Chen HV, Chen PB, Chen AR, et al
    Discovering functional sequences with RELICS, an analysis method for CRISPR screens.
    PLoS Comput Biol. 2020;16:e1008194.
    PubMed     Abstract available


  50. RAPPOPORT N, Safra R, Shamir R
    MONET: Multi-omic module discovery by omic selection.
    PLoS Comput Biol. 2020;16:e1008182.
    PubMed     Abstract available


  51. POLITANO G, Benso A
    IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis.
    PLoS Comput Biol. 2020;16:e1008238.
    PubMed     Abstract available


    August 2020
  52. PEI J, Zhang Y, Nielsen R, Wu Y, et al
    Inferring the ancestry of parents and grandparents from genetic data.
    PLoS Comput Biol. 2020;16:e1008065.
    PubMed     Abstract available


  53. YAO E, Buels R, Stein L, Sen TZ, et al
    JBrowse Connect: A server API to connect JBrowse instances and users.
    PLoS Comput Biol. 2020;16:e1007261.
    PubMed     Abstract available


  54. CASEY JR, Follows MJ
    A steady-state model of microbial acclimation to substrate limitation.
    PLoS Comput Biol. 2020;16:e1008140.
    PubMed     Abstract available


    July 2020
  55. KELLEY DR
    Cross-species regulatory sequence activity prediction.
    PLoS Comput Biol. 2020;16:e1008050.
    PubMed     Abstract available


  56. KRIEGER MS, Denison CE, Anderson TL, Nowak MA, et al
    Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections.
    PLoS Comput Biol. 2020;16:e1008010.
    PubMed     Abstract available


    June 2020
  57. LAMPARTER D, Bhatnagar R, Hebestreit K, Belgard TG, et al
    A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data.
    PLoS Comput Biol. 2020;16:e1007770.
    PubMed     Abstract available


  58. SARGENT L, Liu Y, Leung W, Mortimer NT, et al
    G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation.
    PLoS Comput Biol. 2020;16:e1007863.
    PubMed     Abstract available


    May 2020
  59. BRUCKER A, Lu W, Marceau West R, Yu QY, et al
    Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis.
    PLoS Comput Biol. 2020;16:e1007797.
    PubMed     Abstract available


  60. YOUNG F, Rogers S, Robertson DL
    Predicting host taxonomic information from viral genomes: A comparison of feature representations.
    PLoS Comput Biol. 2020;16:e1007894.
    PubMed     Abstract available


  61. LE GOALLEC A, Tierney BT, Luber JM, Cofer EM, et al
    A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type.
    PLoS Comput Biol. 2020;16:e1007895.
    PubMed     Abstract available


    April 2020
  62. LUO C, Fa B, Yan Y, Wang Y, et al
    High-dimensional mediation analysis in survival models.
    PLoS Comput Biol. 2020;16:e1007768.
    PubMed     Abstract available


  63. JIANG Y, Giase G, Grennan K, Shieh AW, et al
    DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data.
    PLoS Comput Biol. 2020;16:e1007522.
    PubMed     Abstract available


  64. BUSTO-MONER L, Morival J, Ren H, Fahim A, et al
    Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation.
    PLoS Comput Biol. 2020;16:e1007195.
    PubMed     Abstract available


  65. KLEIN HU, Schafer M, Bennett DA, Schwender H, et al
    Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks.
    PLoS Comput Biol. 2020;16:e1007771.
    PubMed     Abstract available


  66. NGUYEN ND, Wang D
    Multiview learning for understanding functional multiomics.
    PLoS Comput Biol. 2020;16:e1007677.
    PubMed     Abstract available


    March 2020
  67. INBAR S, Cohen P, Yahav T, Privman E, et al
    Comparative study of population genomic approaches for mapping colony-level traits.
    PLoS Comput Biol. 2020;16:e1007653.
    PubMed     Abstract available


  68. GAUTREAU G, Bazin A, Gachet M, Planel R, et al
    PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
    PLoS Comput Biol. 2020;16:e1007732.
    PubMed     Abstract available


  69. KATHURIA K, Ratan A
    SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures.
    PLoS Comput Biol. 2020;16:e1007737.
    PubMed     Abstract available


  70. MOORADIAN AD, van der Post S, Naegle KM, Held JM, et al
    ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis.
    PLoS Comput Biol. 2020;16:e1007741.
    PubMed     Abstract available


    February 2020
  71. REIMERING S, Munoz S, McHardy AC
    Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.
    PLoS Comput Biol. 2020;16:e1007101.
    PubMed     Abstract available


  72. LIU C, Zhao J, Lu W, Dai Y, et al
    Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6,700 cancer genomes.
    PLoS Comput Biol. 2020;16:e1007701.
    PubMed     Abstract available


  73. LOVE MI, Soneson C, Hickey PF, Johnson LK, et al
    Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
    PLoS Comput Biol. 2020;16:e1007664.
    PubMed     Abstract available


  74. DEROUAULT P, Chauzeix J, Rizzo D, Miressi F, et al
    CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer.
    PLoS Comput Biol. 2020;16:e1007503.
    PubMed     Abstract available


    January 2020
  75. CASCARINA SM, Elder MR, Ross ED
    Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome.
    PLoS Comput Biol. 2020;16:e1007487.
    PubMed     Abstract available


  76. LAVENDER CA, Shapiro AJ, Day FS, Fargo DC, et al
    ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.
    PLoS Comput Biol. 2020;16:e1007571.
    PubMed     Abstract available


    December 2019
  77. JANDRASITS C, Kroger S, Haas W, Renard BY, et al
    Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.
    PLoS Comput Biol. 2019;15:e1007527.
    PubMed     Abstract available


  78. KOO PK, Eddy SR
    Representation learning of genomic sequence motifs with convolutional neural networks.
    PLoS Comput Biol. 2019;15:e1007560.
    PubMed     Abstract available


    November 2019
  79. GUO WF, Zhang SW, Zeng T, Li Y, et al
    A novel network control model for identifying personalized driver genes in cancer.
    PLoS Comput Biol. 2019;15:e1007520.
    PubMed     Abstract available


  80. WATTS GS, Thornton JE Jr, Youens-Clark K, Ponsero AJ, et al
    Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity.
    PLoS Comput Biol. 2019;15:e1006863.
    PubMed     Abstract available


  81. GOVEK KW, Yamajala VS, Camara PG
    Clustering-independent analysis of genomic data using spectral simplicial theory.
    PLoS Comput Biol. 2019;15:e1007509.
    PubMed     Abstract available


  82. ZHENG Y, Wiehe T
    Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps.
    PLoS Comput Biol. 2019;15:e1007426.
    PubMed     Abstract available


  83. PLYUSNIN I, Holm L, Toronen P
    Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
    PLoS Comput Biol. 2019;15:e1007419.
    PubMed     Abstract available


  84. JANSEN C, Ramirez RN, El-Ali NC, Gomez-Cabrero D, et al
    Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.
    PLoS Comput Biol. 2019;15:e1006555.
    PubMed     Abstract available


  85. ZHANG Y, Mahony S
    Direct prediction of regulatory elements from partial data without imputation.
    PLoS Comput Biol. 2019;15:e1007399.
    PubMed     Abstract available


  86. ST JOHN PC, Strutz J, Broadbelt LJ, Tyo KEJ, et al
    Bayesian inference of metabolic kinetics from genome-scale multiomics data.
    PLoS Comput Biol. 2019;15:e1007424.
    PubMed     Abstract available


  87. VIJAYABASKAR MS, Goode DK, Obier N, Lichtinger M, et al
    Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.
    PLoS Comput Biol. 2019;15:e1007337.
    PubMed     Abstract available


    October 2019
  88. WOOTEN DJ, Groves SM, Tyson DR, Liu Q, et al
    Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers.
    PLoS Comput Biol. 2019;15:e1007343.
    PubMed     Abstract available


  89. GAO T, Qian J
    EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions.
    PLoS Comput Biol. 2019;15:e1007436.
    PubMed     Abstract available


  90. GOMEZ-SCHIAVON M, Buchler NE
    Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise.
    PLoS Comput Biol. 2019;15:e1007364.
    PubMed     Abstract available


  91. XAVIER A, Scott RJ, Talseth-Palmer BA
    TAPES: A tool for assessment and prioritisation in exome studies.
    PLoS Comput Biol. 2019;15:e1007453.
    PubMed     Abstract available


    September 2019
  92. MCCLURE RS, Wendler JP, Adkins JN, Swanstrom J, et al
    Unified feature association networks through integration of transcriptomic and proteomic data.
    PLoS Comput Biol. 2019;15:e1007241.
    PubMed     Abstract available


    August 2019
  93. GHURYE J, Rhie A, Walenz BP, Schmitt A, et al
    Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
    PLoS Comput Biol. 2019;15:e1007273.
    PubMed     Abstract available


  94. HERRERIAS-AZCUE F, Perez-Munuzuri V, Galla T
    Motion, fixation probability and the choice of an evolutionary process.
    PLoS Comput Biol. 2019;15:e1007238.
    PubMed     Abstract available


  95. TAN G, Polychronopoulos D, Lenhard B
    CNEr: A toolkit for exploring extreme noncoding conservation.
    PLoS Comput Biol. 2019;15:e1006940.
    PubMed     Abstract available


  96. YANG J, Muller NF, Bouckaert R, Xu B, et al
    Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration.
    PLoS Comput Biol. 2019;15:e1007189.
    PubMed     Abstract available


    July 2019
  97. SEILER E, Trappe K, Renard BY
    Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.
    PLoS Comput Biol. 2019;15:e1007208.
    PubMed     Abstract available


    June 2019
  98. LIM H, He D, Qiu Y, Krawczuk P, et al
    Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology.
    PLoS Comput Biol. 2019;15:e1006619.
    PubMed     Abstract available


  99. GHURYE J, Pop M
    Modern technologies and algorithms for scaffolding assembled genomes.
    PLoS Comput Biol. 2019;15:e1006994.
    PubMed     Abstract available


    May 2019
  100. OHAYON S, Girsault A, Nasser M, Shen-Orr S, et al
    Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification.
    PLoS Comput Biol. 2019;15:e1007067.
    PubMed     Abstract available


  101. KNOWLES DA, Bouchard G, Plevritis S
    Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features.
    PLoS Comput Biol. 2019;15:e1006743.
    PubMed     Abstract available


  102. SARTO BASSO R, Hochbaum DS, Vandin F
    Efficient algorithms to discover alterations with complementary functional association in cancer.
    PLoS Comput Biol. 2019;15:e1006802.
    PubMed     Abstract available


    April 2019
  103. JURIC I, Yu M, Abnousi A, Raviram R, et al
    MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.
    PLoS Comput Biol. 2019;15:e1006982.
    PubMed     Abstract available


  104. NUISMER SL, Week B
    Approximate Bayesian estimation of coevolutionary arms races.
    PLoS Comput Biol. 2019;15:e1006988.
    PubMed     Abstract available


  105. SALVADORES M, Mas-Ponte D, Supek F
    Passenger mutations accurately classify human tumors.
    PLoS Comput Biol. 2019;15:e1006953.
    PubMed     Abstract available


  106. FLAGEL LE, Blackman BK, Fishman L, Monnahan PJ, et al
    GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity.
    PLoS Comput Biol. 2019;15:e1006949.
    PubMed     Abstract available


  107. MARTI JM
    Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.
    PLoS Comput Biol. 2019;15:e1006967.
    PubMed     Abstract available


  108. LAU MSY, Grenfell BT, Worby CJ, Gibson GJ, et al
    Model diagnostics and refinement for phylodynamic models.
    PLoS Comput Biol. 2019;15:e1006955.
    PubMed     Abstract available


  109. CANINO-KONING R, Wiser MJ, Ofria C
    Fluctuating environments select for short-term phenotypic variation leading to long-term exploration.
    PLoS Comput Biol. 2019;15:e1006445.
    PubMed     Abstract available


  110. BENSTEAD-HUME G, Chen X, Hopkins SR, Lane KA, et al
    Predicting synthetic lethal interactions using conserved patterns in protein interaction networks.
    PLoS Comput Biol. 2019;15:e1006888.
    PubMed     Abstract available


  111. RICHELLE A, Chiang AWT, Kuo CC, Lewis NE, et al
    Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions.
    PLoS Comput Biol. 2019;15:e1006867.
    PubMed     Abstract available


  112. HOSMANI PS, Shippy T, Miller S, Benoit JB, et al
    A quick guide for student-driven community genome annotation.
    PLoS Comput Biol. 2019;15:e1006682.
    PubMed     Abstract available


  113. LACHANCE JC, Lloyd CJ, Monk JM, Yang L, et al
    BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
    PLoS Comput Biol. 2019;15:e1006971.
    PubMed     Abstract available


    March 2019
  114. LI W, Lin L, Malhotra R, Yang L, et al
    A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations.
    PLoS Comput Biol. 2019;15:e1006564.
    PubMed     Abstract available


  115. BRODIE NI, Popov KI, Petrotchenko EV, Dokholyan NV, et al
    Conformational ensemble of native alpha-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.
    PLoS Comput Biol. 2019;15:e1006859.
    PubMed     Abstract available


  116. NOROY C, Lefrancois T, Meyer DF
    Searching algorithm for Type IV effector proteins (S4TE) 2.0: Improved tools for Type IV effector prediction, analysis and comparison in proteobacteria.
    PLoS Comput Biol. 2019;15:e1006847.
    PubMed     Abstract available


    February 2019
  117. 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.
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  118. 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.
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  119. 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.
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  120. DUNN NA, Unni DR, Diesh C, Munoz-Torres M, et al
    Apollo: Democratizing genome annotation.
    PLoS Comput Biol. 2019;15:e1006790.
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  121. 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.
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  122. DAMIANI C, Maspero D, Di Filippo M, Colombo R, et al
    Integration of single-cell RNA-seq data into population models to characterize cancer metabolism.
    PLoS Comput Biol. 2019;15:e1006733.
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    January 2019
  123. 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.
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    December 2018
  124. BROWN AV, Campbell JD, Assefa T, Grant D, et al
    Ten quick tips for sharing open genomic data.
    PLoS Comput Biol. 2018;14:e1006472.
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  125. 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    


  126. 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.
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    November 2018
  127. 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.
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  128. KELLEHER J, Thornton KR, Ashander J, Ralph PL, et al
    Efficient pedigree recording for fast population genetics simulation.
    PLoS Comput Biol. 2018;14:e1006581.
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  129. 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    


  130. 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     Abstract available


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


    October 2018
  132. 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.
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  133. 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.
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  134. SKINNIDER MA, Stacey RG, Foster LJ
    Genomic data integration systematically biases interactome mapping.
    PLoS Comput Biol. 2018;14:e1006474.
    PubMed     Abstract available


  135. 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     Abstract available


  136. 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     Abstract available


    September 2018
  137. 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     Abstract available


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


  139. 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.
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    August 2018
  140. 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.
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  141. 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     Abstract available


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


  143. 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     Abstract available


  144. 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     Abstract available


  145. 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     Abstract available


    July 2018
  146. 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     Abstract available


  147. 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.
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    June 2018
  148. HIGASHI K, Suzuki S, Kurosawa S, Mori H, et al
    Latent environment allocation of microbial community data.
    PLoS Comput Biol. 2018;14:e1006143.
    PubMed     Abstract available


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


    May 2018
  150. 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     Abstract available


  151. 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     Abstract available


  152. 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.
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    April 2018
  153. FETROW JS, Babbitt PC
    New computational approaches to understanding molecular protein function.
    PLoS Comput Biol. 2018;14:e1005756.
    PubMed    


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


  155. 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.
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  156. 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.
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    March 2018
  157. 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.
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  158. 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    


  159. 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     Abstract available


  160. 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     Abstract available


  161. 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     Abstract available


  162. 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.
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  163. PITA-JUAREZ Y, Altschuler G, Kariotis S, Wei W, et al
    The Pathway Coexpression Network: Revealing pathway relationships.
    PLoS Comput Biol. 2018;14:e1006042.
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  164. DING J, Hagood JS, Ambalavanan N, Kaminski N, et al
    iDREM: Interactive visualization of dynamic regulatory networks.
    PLoS Comput Biol. 2018;14:e1006019.
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  165. 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.
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    February 2018
  166. 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.
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  167. 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.
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  168. 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     Abstract available


  169. 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.
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    January 2018
  170. 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.
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  171. MARCAIS G, Delcher AL, Phillippy AM, Coston R, et al
    MUMmer4: A fast and versatile genome alignment system.
    PLoS Comput Biol. 2018;14:e1005944.
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    November 2017
  172. 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     Abstract available


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


  174. 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.
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    October 2017
  175. PULLER V, Neher R, Albert J
    Estimating time of HIV-1 infection from next-generation sequence diversity.
    PLoS Comput Biol. 2017;13:e1005775.
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  176. DREW K, Muller CL, Bonneau R, Marcotte EM, et al
    Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.
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  177. VERNY L, Sella N, Affeldt S, Singh PP, et al
    Learning causal networks with latent variables from multivariate information in genomic data.
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    September 2017
  178. 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.
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  179. KIM M, Eetemadi A, Tagkopoulos I
    DeepPep: Deep proteome inference from peptide profiles.
    PLoS Comput Biol. 2017;13:e1005661.
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  180. 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.
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  181. LABHSETWAR P, Melo MCR, Cole JA, Luthey-Schulten Z, et al
    Population FBA predicts metabolic phenotypes in yeast.
    PLoS Comput Biol. 2017;13:e1005728.
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  182. 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.
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    August 2017
  183. 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.
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  184. 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.
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  185. 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.
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  186. 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.
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    July 2017
  187. 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.
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  188. 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.
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  189. 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.
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  190. 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     Abstract available


  191. 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.
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    June 2017
  192. 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.
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  193. 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.
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  194. 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.
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  195. 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.
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    May 2017
  196. 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.
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  197. CHAN SHJ, Simons MN, Maranas CD
    SteadyCom: Predicting microbial abundances while ensuring community stability.
    PLoS Comput Biol. 2017;13:e1005539.
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  198. LI Y, Zhou X, Zhai Z, Li T, et al
    Co-occurring protein phosphorylation are functionally associated.
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    March 2017
  199. 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.
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    February 2017
  200. 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.
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    January 2017
  201. WU T, Wang L, Fu F
    Coevolutionary dynamics of phenotypic diversity and contingent cooperation.
    PLoS Comput Biol. 2017;13:e1005363.
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  202. HWANG HY, Wang J
    Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans.
    PLoS Comput Biol. 2017;13:e1005369.
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  203. 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.
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  204. PRIGENT S, Frioux C, Dittami SM, Thiele S, et al
    Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.
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    June 2016
  205. 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.
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    May 2016
  206. 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.
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  207. BOHLER A, Wu G, Kutmon M, Pradhana LA, et al
    Reactome from a WikiPathways Perspective.
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  208. BRECKELS LM, Holden SB, Wojnar D, Mulvey CM, et al
    Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.
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  209. KELLEHER J, Etheridge AM, McVean G
    Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.
    PLoS Comput Biol. 2016;12:e1004842.
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