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Articles published in
PLoS Comput Biol
    September 2025
  1. XIAO T, Liu Y, Hu K, Guo K, et al
    Drug-induced liver injury prediction based on graph convolutional networks and toxicogenomics.
    PLoS Comput Biol. 2025;21:e1013423.
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  2. ZAK J, Newman I, Montiel Garcia DJ, Parisi D, et al
    Catalyzing computational biology research at an academic institute through an interest network.
    PLoS Comput Biol. 2025;21:e1013453.
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  3. YANG J, Grant GR, Brooks TG
    Generating correlated data for omics simulation.
    PLoS Comput Biol. 2025;21:e1013392.
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  4. TRUONG L, Truong T, Nguyen H
    OmnibusX: A unified platform for accessible multi-omics analysis.
    PLoS Comput Biol. 2025;21:e1013480.
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  5. WANG X, Guan Y, Gao W, Lai X, et al
    MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection.
    PLoS Comput Biol. 2025;21:e1013443.
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    August 2025
  6. ROBERTSON J, Consul S, Vikalo H
    NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.
    PLoS Comput Biol. 2025;21:e1013360.
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  7. YUAN H, Liu M, Qiu Y, Ching WK, et al
    PLNMFG: Pseudo-label guided non-negative matrix factorization model with graph constraint for single-cell multi-omics data clustering.
    PLoS Comput Biol. 2025;21:e1013375.
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    July 2025
  8. DONG X, Jiao D, Xue H, Fan S, et al
    APAV: An advanced pangenome analysis and visualization toolkit.
    PLoS Comput Biol. 2025;21:e1013288.
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    June 2025
  9. WADDEL H, Koelle K, Lau MSY
    ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.
    PLoS Comput Biol. 2025;21:e1012657.
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    May 2025
  10. GOLDMAN M, Zhao C, Pollard KS
    Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).
    PLoS Comput Biol. 2025;21:e1012277.
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    April 2025
  11. SHEN C, Wedell E, Pop M, Warnow T, et al
    TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics.
    PLoS Comput Biol. 2025;21:e1012593.
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  12. LIU W, Pratte KA, Castaldi PJ, Hersh C, et al
    A generalized higher-order correlation analysis framework for multi-omics network inference.
    PLoS Comput Biol. 2025;21:e1011842.
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  13. ROBERTS I, Everitt RG, Koskela J, Didelot X, et al
    Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model.
    PLoS Comput Biol. 2025;21:e1012995.
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  14. NOURBAKHSH M, Zheng Y, Noor H, Chen H, et al
    Revealing cancer driver genes through integrative transcriptomic and epigenomic analyses with Moonlight.
    PLoS Comput Biol. 2025;21:e1012999.
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    March 2025
  15. RYAN B, Marioni R, Simpson TI
    An integrative network approach for longitudinal stratification in Parkinson's disease.
    PLoS Comput Biol. 2025;21:e1012857.
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  16. HAIMAN ZB, Key A, D'Alessandro A, Palsson BO, et al
    RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell.
    PLoS Comput Biol. 2025;21:e1012109.
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  17. WU Y, Chen M, Qin Y
    Anticancer drug response prediction integrating multi-omics pathway-based difference features and multiple deep learning techniques.
    PLoS Comput Biol. 2025;21:e1012905.
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    February 2025
  18. KHODASEVICH D, Holland N, van der Laan L, Cardenas A, et al
    A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits.
    PLoS Comput Biol. 2025;21:e1012768.
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  19. MIAO R, Yu HY, Zhong BJ, Sun HX, et al
    AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis.
    PLoS Comput Biol. 2025;21:e1012773.
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    January 2025
  20. PAN L, Gao Q, Wei K, Yu Y, et al
    A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data.
    PLoS Comput Biol. 2025;21:e1012739.
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  21. DAOUD A, Ben-Hur A
    The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.
    PLoS Comput Biol. 2025;21:e1012755.
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  22. FANG M, Gorin G, Pachter L
    Trajectory inference from single-cell genomics data with a process time model.
    PLoS Comput Biol. 2025;21:e1012752.
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  23. GORSTEIN E, Aghdam R, Solis-Lemus C
    HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data.
    PLoS Comput Biol. 2025;21:e1012143.
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    December 2024
  24. LAN W, Ling T, Chen Q, Zheng R, et al
    scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis.
    PLoS Comput Biol. 2024;20:e1012679.
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  25. ESCRIBA-MONTAGUT X, Marcon Y, Anguita-Ruiz A, Avraam D, et al
    Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform.
    PLoS Comput Biol. 2024;20:e1012626.
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  26. CICCOLELLA S, Cozzi D, Della Vedova G, Kuria SN, et al
    Differential quantification of alternative splicing events on spliced pangenome graphs.
    PLoS Comput Biol. 2024;20:e1012665.
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  27. ABHARI N, Colijn C, Mooers A, Tupper P, et al
    Measuring genetic diversity across populations.
    PLoS Comput Biol. 2024;20:e1012651.
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  28. ZUNIGA NR, Earls NE, Denos AEA, Elison JM, et al
    Quantitative and Kinetic Proteomics Reveal ApoE Isoform-dependent Proteostasis Adaptations in Mouse Brain.
    PLoS Comput Biol. 2024;20:e1012407.
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  29. ORCALES F, Moctezuma Tan L, Johnson-Hagler M, Suntay JM, et al
    Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper.
    PLoS Comput Biol. 2024;20:e1012579.
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  30. BU Y, Liang J, Li Z, Wang J, et al
    Cancer molecular subtyping using limited multi-omics data with missingness.
    PLoS Comput Biol. 2024;20:e1012710.
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    November 2024
  31. LI S, Gulisija D, Carja O
    The evolutionary cost of homophily: Social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens.
    PLoS Comput Biol. 2024;20:e1012619.
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    October 2024
  32. CHEN L, Huang ZH, Sun Y, Domaratzki M, et al
    Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer.
    PLoS Comput Biol. 2024;20:e1012490.
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  33. ROCHA U, Kasmanas JC, Toscan R, Sanches DS, et al
    Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.
    PLoS Comput Biol. 2024;20:e1012530.
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  34. SILVA GAA, Harder AM, Kirksey KB, Mathur S, et al
    Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.
    PLoS Comput Biol. 2024;20:e1012566.
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    September 2024
  35. PLAISIER SB, Alarid DO, Denning JA, Brownell SE, et al
    Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics.
    PLoS Comput Biol. 2024;20:e1012384.
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  36. ABBARA A, Pagani L, Garcia-Pareja C, Bitbol AF, et al
    Mutant fate in spatially structured populations on graphs: Connecting models to experiments.
    PLoS Comput Biol. 2024;20:e1012424.
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  37. LE SUEUR C, Rattray M, Savitski M
    GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments.
    PLoS Comput Biol. 2024;20:e1011632.
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  38. AMARAL AS, Devos DP
    The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.
    PLoS Comput Biol. 2024;20:e1012459.
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    August 2024
  39. NEY A, Nene NR, Sedlak E, Acedo P, et al
    Identification of a serum proteomic biomarker panel using diagnosis specific ensemble learning and symptoms for early pancreatic cancer detection.
    PLoS Comput Biol. 2024;20:e1012408.
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  40. RINTALA TJ, Fortino V
    COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms.
    PLoS Comput Biol. 2024;20:e1012275.
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  41. SHI P, Han J, Zhang Y, Li G, et al
    IMI-driver: Integrating multi-level gene networks and multi-omics for cancer driver gene identification.
    PLoS Comput Biol. 2024;20:e1012389.
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    July 2024
  42. CHEN AA, Clark K, Dewey BE, DuVal A, et al
    PARE: A framework for removal of confounding effects from any distance-based dimension reduction method.
    PLoS Comput Biol. 2024;20:e1012241.
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    June 2024
  43. BERGMAN S, Tuller T
    Strong association between genomic 3D structure and CRISPR cleavage efficiency.
    PLoS Comput Biol. 2024;20:e1012214.
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    May 2024
  44. ABDENNUR N, Abraham S, Fudenberg G, Flyamer IM, et al
    Cooltools: Enabling high-resolution Hi-C analysis in Python.
    PLoS Comput Biol. 2024;20:e1012067.
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  45. GORMAN ED, Lladser ME
    Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance.
    PLoS Comput Biol. 2024;20:e1011543.
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  46. CASCARINA SM, Ross ED
    Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life.
    PLoS Comput Biol. 2024;20:e1011372.
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  47. WANG M, Yan X, Dong Y, Li X, et al
    Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment.
    PLoS Comput Biol. 2024;20:e1012113.
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    April 2024
  48. GIUDICE L, Mohamed A, Malm T
    StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling.
    PLoS Comput Biol. 2024;20:e1012022.
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    March 2024
  49. MARTIN NS, Camargo CQ, Louis AA
    Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs.
    PLoS Comput Biol. 2024;20:e1011893.
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  50. WIEDER C, Cooke J, Frainay C, Poupin N, et al
    PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.
    PLoS Comput Biol. 2024;20:e1011814.
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    February 2024
  51. LIU X, Gillis N, Jiang C, McCofie A, et al
    An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.
    PLoS Comput Biol. 2024;20:e1011873.
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  52. DALL'OLIO D, Strang E, Turki AT, Tettero JM, et al
    Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology.
    PLoS Comput Biol. 2024;20:e1011299.
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    January 2024
  53. ROBLES J, Prakash A, Vizcaino JA, Casal JI, et al
    Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation.
    PLoS Comput Biol. 2024;20:e1011828.
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  54. MUKHERJEE A, Chang YF, Huang Y, Benites NC, et al
    Plasticity of growth laws tunes resource allocation strategies in bacteria.
    PLoS Comput Biol. 2024;20:e1011735.
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  55. PFLUG FG, Bhat D, Pigolotti S
    Genome replication in asynchronously growing microbial populations.
    PLoS Comput Biol. 2024;20:e1011753.
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  56. LOUARN M, Collet G, Barre E, Fest T, et al
    Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints.
    PLoS Comput Biol. 2024;20:e1011816.
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  57. MANCUSO CA, Johnson KA, Liu R, Krishnan A, et al
    Joint representation of molecular networks from multiple species improves gene classification.
    PLoS Comput Biol. 2024;20:e1011773.
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  58. EL BOUHADDANI S, Hollerhage M, Uh HW, Moebius C, et al
    Statistical integration of multi-omics and drug screening data from cell lines.
    PLoS Comput Biol. 2024;20:e1011809.
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    December 2023
  59. SINGH A, Chakrabarti S
    Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture.
    PLoS Comput Biol. 2023;19:e1011725.
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    November 2023
  60. VASILEIOU D, Karapiperis C, Baltsavia I, Chasapi A, et al
    CGG toolkit: Software components for computational genomics.
    PLoS Comput Biol. 2023;19:e1011498.
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  61. SCHMIDT H, Sashittal P, Raphael BJ
    A zero-agnostic model for copy number evolution in cancer.
    PLoS Comput Biol. 2023;19:e1011590.
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  62. KIPEN J, Jalden J
    Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data.
    PLoS Comput Biol. 2023;19:e1011345.
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  63. HEUPINK TH, Verboven L, Sharma A, Rennie V, et al
    The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples.
    PLoS Comput Biol. 2023;19:e1011648.
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  64. BRUNNER JD, Gallegos-Graves LA, Kroeger ME
    Inferring microbial interactions with their environment from genomic and metagenomic data.
    PLoS Comput Biol. 2023;19:e1011661.
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  65. CECIL RM, Sugden LA
    On convolutional neural networks for selection inference: Revealing the effect of preprocessing on model learning and the capacity to discover novel patterns.
    PLoS Comput Biol. 2023;19:e1010979.
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    October 2023
  66. GAO Y, Sun F
    Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies.
    PLoS Comput Biol. 2023;19:e1010608.
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  67. KOSINSKI JG, Zywicki M
    AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals.
    PLoS Comput Biol. 2023;19:e1011527.
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  68. YELMEN B, Decelle A, Boulos LL, Szatkownik A, et al
    Deep convolutional and conditional neural networks for large-scale genomic data generation.
    PLoS Comput Biol. 2023;19:e1011584.
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    September 2023
  69. ZHANG Y, Zhou R, Liu L, Chen L, et al
    Trackplot: A flexible toolkit for combinatorial analysis of genomic data.
    PLoS Comput Biol. 2023;19:e1011477.
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  70. HUANG Z, Cui X, Xia Y, Zhao K, et al
    Pathfinder: Protein folding pathway prediction based on conformational sampling.
    PLoS Comput Biol. 2023;19:e1011438.
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  71. TCHOUNKE B, Sanchez L, Bell JM, Cros D, et al
    Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding.
    PLoS Comput Biol. 2023;19:e1010290.
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  72. BOUTRY S, Helaers R, Lenaerts T, Vikkula M, et al
    Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data.
    PLoS Comput Biol. 2023;19:e1011488.
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    August 2023
  73. CHARI T, Pachter L
    The specious art of single-cell genomics.
    PLoS Comput Biol. 2023;19:e1011288.
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  74. WANG N, Khan S, Elo LL
    VarSCAT: A computational tool for sequence context annotations of genomic variants.
    PLoS Comput Biol. 2023;19:e1010727.
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  75. ECKENRODE KB, Righelli D, Ramos M, Argelaguet R, et al
    Curated single cell multimodal landmark datasets for R/Bioconductor.
    PLoS Comput Biol. 2023;19:e1011324.
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    July 2023
  76. CHICCO D, Cumbo F, Angione C
    Ten quick tips for avoiding pitfalls in multi-omics data integration analyses.
    PLoS Comput Biol. 2023;19:e1011224.
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  77. BAUR B, Shin J, Schreiber J, Zhang S, et al
    Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation.
    PLoS Comput Biol. 2023;19:e1011286.
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    June 2023
  78. KAHANE I, Leiserson MDM, Sharan R
    A mutation-level covariate model for mutational signatures.
    PLoS Comput Biol. 2023;19:e1011195.
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    May 2023
  79. MINEEVA O, Danciu D, Scholkopf B, Ley RE, et al
    ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.
    PLoS Comput Biol. 2023;19:e1011001.
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    April 2023
  80. CUMSILLE A, Duran RE, Rodriguez-Delherbe A, Saona-Urmeneta V, et al
    GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.
    PLoS Comput Biol. 2023;19:e1010998.
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  81. DWIVEDI-YU JA, Oppler ZJ, Mitchell MW, Song YS, et al
    A fast machine-learning-guided primer design pipeline for selective whole genome amplification.
    PLoS Comput Biol. 2023;19:e1010137.
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  82. REKENA A, Pinheiro MJ, Bonturi N, Belouah I, et al
    Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides.
    PLoS Comput Biol. 2023;19:e1011009.
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    March 2023
  83. NANJALA R, Nyasimi F, Masiga D, Kibet CK, et al
    A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya.
    PLoS Comput Biol. 2023;19:e1010904.
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  84. PENG H, Wong L, Goh WWB
    ProInfer: An interpretable protein inference tool leveraging on biological networks.
    PLoS Comput Biol. 2023;19:e1010961.
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  85. CAPPELLO L, Kim J, Palacios JA
    adaPop: Bayesian inference of dependent population dynamics in coalescent models.
    PLoS Comput Biol. 2023;19:e1010897.
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  86. GUO A, Salzberg SL, Zimin AV
    JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.
    PLoS Comput Biol. 2023;19:e1011032.
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  87. BARSHAI M, Engel B, Haim I, Orenstein Y, et al
    G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data.
    PLoS Comput Biol. 2023;19:e1010948.
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    February 2023
  88. NIELSEN BF, Saad-Roy CM, Li Y, Sneppen K, et al
    Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2.
    PLoS Comput Biol. 2023;19:e1010896.
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  89. BERGINSKI ME, Joisa CU, Golitz BT, Gomez SM, et al
    Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types.
    PLoS Comput Biol. 2023;19:e1010888.
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