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Articles published in PLoS Comput Biol

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    August 2020
  1. 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

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

  3. 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
  4. 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

  5. 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
  6. 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

  7. 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

  8. 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
  9. 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

  10. 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

  11. 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

  12. 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

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

    March 2020
  14. 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

  15. 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

  16. 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

  17. 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
  18. 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

  19. 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

  20. 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

  21. 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
  22. 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

  23. 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
  24. 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

  25. 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
  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

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

  33. 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

  34. 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
  35. 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

  36. 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

  37. 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

  38. 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
  39. 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
  40. 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

  41. 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

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

  43. 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
  44. 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
  45. 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

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

    May 2019
  47. 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

  48. 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

  49. 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
  50. 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

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

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

  53. 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

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

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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

  60. 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
  61. 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

  62. 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

  63. 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
  64. 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

  65. 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

  66. 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

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

  68. 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

  69. 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
  70. 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
  71. 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

  72. 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.

  73. 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
  74. 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

  75. 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

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

  77. 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

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

    October 2018
  79. 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

  80. 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

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

  82. 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

  83. 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
  84. 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

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

  86. 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
  87. 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

  88. 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

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

  90. 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

  91. 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

  92. 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
  93. 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

  94. 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     Abstract available

    June 2018
  95. 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

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

    May 2018
  97. 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

  98. 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

  99. 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
  100. FETROW JS, Babbitt PC
    New computational approaches to understanding molecular protein function.
    PLoS Comput Biol. 2018;14:e1005756.

  101. 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

  102. 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

  103. 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     Abstract available

    March 2018
  104. 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     Abstract available

  105. 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.

  106. 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

  107. 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

  108. 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

  109. 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

  110. 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

  111. 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

  112. 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     Abstract available

    February 2018
  113. 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     Abstract available

  114. 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     Abstract available

  115. 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

  116. 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
  117. 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

  118. MARCAIS G, Delcher AL, Phillippy AM, Coston R, et al
    MUMmer4: A fast and versatile genome alignment system.
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    November 2017
    Characterizing steady states of genome-scale metabolic networks in continuous cell cultures.
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  120. LIU R, Dickerson J
    Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.
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    mixOmics: An R package for 'omics feature selection and multiple data integration.
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    Estimating time of HIV-1 infection from next-generation sequence diversity.
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    Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.
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    Learning causal networks with latent variables from multivariate information in genomic data.
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    kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.
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  126. KIM M, Eetemadi A, Tagkopoulos I
    DeepPep: Deep proteome inference from peptide profiles.
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  127. DUMEAUX V, Fjukstad B, Fjosne HE, Frantzen JO, et al
    Interactions between the tumor and the blood systemic response of breast cancer patients.
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    Population FBA predicts metabolic phenotypes in yeast.
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    Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity.
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    August 2017
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    Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.
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  131. AMAR D, Shamir R, Yekutieli D
    Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.
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  132. 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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  133. 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.
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    July 2017
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    Reconstructing the regulatory circuit of cell fate determination in yeast mating response.
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  135. ATAMAN M, Hatzimanikatis V
    lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites.
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    CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets.
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  137. 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.
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  138. GILPIN W, Feldman MW
    A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape.
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    June 2017
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    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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  141. LAI EY, Chen YH, Wu KP
    A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data.
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    Leveraging functional annotations in genetic risk prediction for human complex diseases.
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    SteadyCom: Predicting microbial abundances while ensuring community stability.
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    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
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    Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.
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    January 2017
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    Coevolutionary dynamics of phenotypic diversity and contingent cooperation.
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  149. HWANG HY, Wang J
    Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans.
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    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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    PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
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    Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.
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