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COVID-19: Daily Top 10 Papers


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Articles published in PLoS Comput Biol

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    December 2020
  1. 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
  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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
  10. 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

  11. 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

  12. 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

  13. 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

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

  15. 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

  16. 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

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

  18. 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

  19. 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

  20. 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

  21. 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
  22. 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

  23. 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

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

  25. 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
  26. 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

  27. 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

  28. 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
    Cross-species regulatory sequence activity prediction.
    PLoS Comput Biol. 2020;16:e1008050.
    PubMed     Abstract available

  30. 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
  31. 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

  32. 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
  33. 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

  34. 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

  35. 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
  36. 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

  37. 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

  38. 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

  39. 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

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

    March 2020
  41. 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

  42. 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

  43. 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

  44. 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
  45. 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

  46. 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

  47. 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

  48. 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
  49. 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

  50. 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
  51. 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

  52. 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
  53. 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

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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

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

  60. 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

  61. 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
  62. 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

  63. 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

  64. 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

  65. 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
  66. 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
  67. 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

  68. 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

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

  70. 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
  71. 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
  72. 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

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

    May 2019
  74. 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

  75. 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

  76. 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
  77. 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

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

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

  80. 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

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

  82. 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

  83. 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

  84. 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

  85. 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

  86. 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

  87. 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
  88. 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

  89. 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

  90. 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
  91. 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     Abstract available

  92. 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     Abstract available

  93. 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     Abstract available

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

  95. 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     Abstract available

  96. 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.
    PubMed     Abstract available

    January 2019
  97. 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     Abstract available

    December 2018
  98. 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     Abstract available

  99. 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.

  100. 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     Abstract available

    November 2018
  101. 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     Abstract available

  102. 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     Abstract available

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

  104. 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

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

    October 2018
  106. 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     Abstract available

  107. 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     Abstract available

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

  109. 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

  110. 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
  111. 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

  112. 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

  113. 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     Abstract available

    August 2018
  114. 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     Abstract available

  115. 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

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

  117. 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

  118. 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

  119. 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
  120. 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

  121. 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
  122. 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

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

    May 2018
  124. 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

  125. 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

  126. 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     Abstract available

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

  128. 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

  129. 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     Abstract available

  130. 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
  131. 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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  132. 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.

  133. 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.
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  134. 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

  135. 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

  136. 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     Abstract available

  137. 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     Abstract available

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

  139. 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
  140. 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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  141. 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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  142. 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

  143. 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     Abstract available

    January 2018
  144. 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     Abstract available

  145. 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     Abstract available

    November 2017
    Characterizing steady states of genome-scale metabolic networks in continuous cell cultures.
    PLoS Comput Biol. 2017;13:e1005835.
    PubMed     Abstract available

  147. 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

  148. 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     Abstract available

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

  150. 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.
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    Learning causal networks with latent variables from multivariate information in genomic data.
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    September 2017
  152. MURRAY KD, Webers C, Ong CS, Borevitz J, et al
    kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.
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  153. KIM M, Eetemadi A, Tagkopoulos I
    DeepPep: Deep proteome inference from peptide profiles.
    PLoS Comput Biol. 2017;13:e1005661.
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  154. 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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  155. LABHSETWAR P, Melo MCR, Cole JA, Luthey-Schulten Z, et al
    Population FBA predicts metabolic phenotypes in yeast.
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  156. 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
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    Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.
    PLoS Comput Biol. 2017;13:e1005720.
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  158. 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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  159. FUKUYAMA J, Rumker L, Sankaran K, Jeganathan P, et al
    Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
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  160. 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
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    Reconstructing the regulatory circuit of cell fate determination in yeast mating response.
    PLoS Comput Biol. 2017;13:e1005671.
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  162. 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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  163. 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.
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  164. 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.
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  165. 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
  166. 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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    Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.
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  168. LAI EY, Chen YH, Wu KP
    A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data.
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  169. HU Y, Lu Q, Powles R, Yao X, et al
    Leveraging functional annotations in genetic risk prediction for human complex diseases.
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    May 2017
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    ROTS: An R package for reproducibility-optimized statistical testing.
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  171. CHAN SHJ, Simons MN, Maranas CD
    SteadyCom: Predicting microbial abundances while ensuring community stability.
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  172. LI Y, Zhou X, Zhai Z, Li T, et al
    Co-occurring protein phosphorylation are functionally associated.
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    March 2017
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    High GC content causes orphan proteins to be intrinsically disordered.
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    February 2017
  174. 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
  175. WU T, Wang L, Fu F
    Coevolutionary dynamics of phenotypic diversity and contingent cooperation.
    PLoS Comput Biol. 2017;13:e1005363.
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  176. 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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  177. 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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    Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.
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    June 2016
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    GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.
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    May 2016
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    PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
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  181. BOHLER A, Wu G, Kutmon M, Pradhana LA, et al
    Reactome from a WikiPathways Perspective.
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    Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.
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  183. 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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