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Genetics

Free Subscription Articles published in PLoS Comput Biol Retrieve available abstracts of 165 articles: HTML format

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October 2026
1. HUTTON A, Meyer JG
   Omics data discovery agents: Agent-supported retrieval, reanalysis, and synthesis of published omics data.
   PLoS Comput Biol. 2026;22:e1014822.
   PubMed     Abstract available
   
   
   
2. CHAI L, Gao J, Guo T, Ba T, et al
   DeCTCF: Decoding CTCF binding sequences by leveraging predicted epigenomic features.
   PLoS Comput Biol. 2026;22:e1014848.
   PubMed     Abstract available
   
   
   
3. WICAKSONO A, Parikesit AA
   From prompts to genomes: A constraint-first framework for AI-driven sequence design across life and viruses.
   PLoS Comput Biol. 2026;22:e1014865.
   PubMed     Abstract available
   
   
   
4. CONCEICAO EC, Sharma A, Marcon DJ, Ribeiro LR, et al
   Ten simple rules to build genomics capacity for routine laboratory practice in the Global South.
   PLoS Comput Biol. 2026;22:e1014863.
   PubMed     Abstract available
   
   
   
5. RIUDAVETS PUIG R, O'Mahony DG, Brorson IS, Sokolova K, et al
   HiFIseek: Gene-specific enrichment of high-impact mutations in associated genomic regions.
   PLoS Comput Biol. 2026;22:e1014842.
   PubMed     Abstract available
   
   
   September 2026
6. LAN Y, Wu CY, Lin HH, Cohen T, et al
   Comparing subsampling strategies for efficient pairwise analysis of large pathogen genomic and spatial datasets: An application to Mycobacterium tuberculosis transmission.
   PLoS Comput Biol. 2026;22:e1014353.
   PubMed     Abstract available
   
   
   
7. CHION M, Leroy A
   A Bayesian framework for multivariate differential analysis.
   PLoS Comput Biol. 2026;22:e1014637.
   PubMed     Abstract available
   
   
   
8. KUROGI N, Shimbara K, Koreeda T, Tsuyuzaki K, et al
   Ten quick tips for spatial transcriptomics analysis.
   PLoS Comput Biol. 2026;22:e1014757.
   PubMed     Abstract available
   
   
   
9. KRONENBERG Z, Yoo B, Chua KP, Chaisson MJP, et al
   Hunting for microsatellite instability in long-read data with Owl.
   PLoS Comput Biol. 2026;22:e1014423.
   PubMed     Abstract available
   
   
   
10. MATSUI Y
    Glycan reachability analysis: A bottleneck-aware framework for inferring tissue-specific glycan biosynthetic potential from transcriptomics.
    PLoS Comput Biol. 2026;22:e1014655.
    PubMed     Abstract available
    
    
    
11. ZENG D, Wang Y, Wang Y, Li G, et al
    Per- and polyfluoroalkyl substances and kidney disease: Genetic associations and computational prioritization of candidate toxicogenomic pathways.
    PLoS Comput Biol. 2026;22:e1014665.
    PubMed     Abstract available
    
    
    
12. COLLI S, Maresi E, Bonnici V
    PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis.
    PLoS Comput Biol. 2026;22:e1014724.
    PubMed     Abstract available
    
    
    
13. GUNZ S, Crowell HL, Robinson MD
    Analysis of multicellular anatomical structures from spatial omics data using sosta.
    PLoS Comput Biol. 2026;22:e1014551.
    PubMed     Abstract available
    
    
    
14. MADEN G, Baysan M, Aydin N
    Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.
    PLoS Comput Biol. 2026;22:e1014824.
    PubMed     Abstract available
    
    
    August 2026
15. GRAVEL N, Zhou Z, Fang R, Downes A, et al
    CLASPP: A unified model for predicting post-translational modifications.
    PLoS Comput Biol. 2026;22:e1014616.
    PubMed     Abstract available
    
    
    
16. FELLOWS YATES JA, Hubner A, Borry M, Warinner C, et al
    De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.
    PLoS Comput Biol. 2026;22:e1014591.
    PubMed     Abstract available
    
    
    
17. VONKAENEL ED, Bramer LM, Flores JE, Metz TO, et al
    A benchmarking study of feature screening approaches across type 1 diabetes omics studies classification settings.
    PLoS Comput Biol. 2026;22:e1014625.
    PubMed     Abstract available
    
    
    
18. LEE H, Kim S, Sunartha MA, Lee CY, et al
    A portable recalibration workflow for reference-based variant calling in non-human genomes.
    PLoS Comput Biol. 2026;22:e1014603.
    PubMed     Abstract available
    
    
    
19. RAMIREZ-RAFAEL JA, Korchmaros A, Avina-Padilla K, Lopez-Sanchez A, et al
    REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.
    PLoS Comput Biol. 2026;22:e1013017.
    PubMed     Abstract available
    
    
    
20. SUN A, Hao Y, Ding Y, Chen J, et al
    GPCR-GO: Relation-aware graph learning for predicting Gene Ontology terms of G protein-coupled receptors.
    PLoS Comput Biol. 2026;22:e1014718.
    PubMed     Abstract available
    
    
    
21. SEEGER L, Pinheiro F, Lassig M
    Enzyme kinetics shapes the growth response of metabolic networks.
    PLoS Comput Biol. 2026;22:e1014642.
    PubMed     Abstract available
    
    
    July 2026
22. FAN J
    Another 10 years of PLOS Computational Biology: A data-driven reflection on trends in genomics research.
    PLoS Comput Biol. 2026;22:e1014471.
    PubMed     Abstract available
    
    
    
23. LI W, Yu S, Cheng Y, Wang S, et al
    DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotation.
    PLoS Comput Biol. 2026;22:e1014476.
    PubMed     Abstract available
    
    
    
24. ARNOUX J, Mainguy J, Bry L, Fernandez de Grado Q, et al
    Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.
    PLoS Comput Biol. 2026;22:e1013856.
    PubMed     Abstract available
    
    
    
25. ZONG L, Friedler SA, Mathieson S
    Popformer: Learning general signatures of positive selection with a self-supervised transformer.
    PLoS Comput Biol. 2026;22:e1014492.
    PubMed     Abstract available
    
    
    
26. EASWAR A, Narayanan M
    NLCD: A method to discover nonlinear causal relations among genes.
    PLoS Comput Biol. 2026;22:e1014570.
    PubMed     Abstract available
    
    
    June 2026
27. MAHMUD A, Huang C
    IsoPepTracker: An interactive web application for peptide-driven isoform analysis.
    PLoS Comput Biol. 2026;22:e1014324.
    PubMed     Abstract available
    
    
    
28. WITCZAK D, Sychla K, Wysocka J, Laskowski A, et al
    GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.
    PLoS Comput Biol. 2026;22:e1014406.
    PubMed     Abstract available
    
    
    
29. GUNTHER E, Camara PG
    Exploring the structural lexicon of the Proteome via Metric Geometry.
    PLoS Comput Biol. 2026;22:e1014487.
    PubMed     Abstract available
    
    
    May 2026
30. KWON J, Li K, Warren JL, Pandya S, et al
    Utilizing virus genomic surveillance to predict vaccine effectiveness.
    PLoS Comput Biol. 2026;22:e1014329.
    PubMed     Abstract available
    
    
    
31. HUANG Y, Gan Y, Gong X
    scHG: A supercell framework with high-order graph learning enables scalable multi-omics analysis.
    PLoS Comput Biol. 2026;22:e1013851.
    PubMed     Abstract available
    
    
    
32. MOTH CW, Sheehan JH, Al Mamun A, Sivley RM, et al
    VUStruct: A compute pipeline for high throughput and personalized structural biology.
    PLoS Comput Biol. 2026;22:e1014183.
    PubMed     Abstract available
    
    
    
33. PETROVSKIY DV, Nikolsky KS, Rudnev VR, Kulikova LI, et al
    PowerNovo2: A generative flow-based approach to non-autoregressive de novo peptide sequencing.
    PLoS Comput Biol. 2026;22:e1014298.
    PubMed     Abstract available
    
    
    
34. KAZEMI P, Sanchez Olivares I, Warren RL, Coombe L, et al
    AIEdit: Alignment-free genome assembly polisher trained on spaced seed match patterns.
    PLoS Comput Biol. 2026;22:e1014245.
    PubMed     Abstract available
    
    
    
35. TEYSSIER N, Dobin A
    BINSEQ: A family of high-performance binary formats for nucleotide sequences.
    PLoS Comput Biol. 2026;22:e1014181.
    PubMed     Abstract available
    
    
    April 2026
36. ZHANG W, Yu Y, Zheng X, Shen J, et al
    Clustering single-cell multi-omics data via weighted distance penalty and adaptive consistent graph regularization.
    PLoS Comput Biol. 2026;22:e1014110.
    PubMed     Abstract available
    
    
    
37. KAZEMI P, Coombe L, Warren RL, Birol I, et al
    ntStat: k-mer characterization using occurrence statistics in raw sequencing data.
    PLoS Comput Biol. 2026;22:e1014158.
    PubMed     Abstract available
    
    
    
38. BORA A, McKenzie M, Ziemann M
    Ten common mistakes that could ruin your enrichment analysis.
    PLoS Comput Biol. 2026;22:e1014122.
    PubMed     Abstract available
    
    
    
39. LI G, Jianhan F, Gu J, Wang Y, et al
    Systematic prioritization of potential therapeutic targets for glomerulonephritis using multi-omics Mendelian randomization.
    PLoS Comput Biol. 2026;22:e1014174.
    PubMed     Abstract available
    
    
    
40. LI H, Lin C, Liu L, Lyu J, et al
    CASER: A semi-supervised model with multi-omics data integration prioritizes cancer-associated epigenetic regulator genes.
    PLoS Comput Biol. 2026;22:e1014253.
    PubMed     Abstract available
    
    
    
41. AHN S, Fu W, van Gerwen M, Liu L, et al
    A multi-omics framework for survival mediation analysis of high-dimensional proteogenomic data.
    PLoS Comput Biol. 2026;22:e1014217.
    PubMed     Abstract available
    
    
    March 2026
42. LIAO K, Du D, Li J, Huang J, et al
    Interpretable integration of unpaired multi-omics for Alzheimer's diagnosis via cross-modal transformer reconstruction.
    PLoS Comput Biol. 2026;22:e1014074.
    PubMed     Abstract available
    
    
    
43. ZHAO M, Tang X, Li J, Liang C, et al
    MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.
    PLoS Comput Biol. 2026;22:e1014054.
    PubMed     Abstract available
    
    
    
44. PUCCI N, Kaan AM, Ujcic-Voortman J, Verhoeff AP, et al
    Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.
    PLoS Comput Biol. 2026;22:e1013185.
    PubMed     Abstract available
    
    
    
45. YANG M, Huang ZA, Zheng Z, Liu Y, et al
    HiCMamba: Enhancing Hi-C resolution and identifying 3D genome structures with state space modeling.
    PLoS Comput Biol. 2026;22:e1014057.
    PubMed     Abstract available
    
    
    
46. SOLEYMANI F, Razaghi-Moghadam Z, Nikoloski Z
    Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks.
    PLoS Comput Biol. 2026;22:e1014066.
    PubMed     Abstract available
    
    
    
47. ANTONOPOULOS K, Nordenstorm O, Nilsson A
    Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries.
    PLoS Comput Biol. 2026;22:e1014100.
    PubMed     Abstract available
    
    
    
48. MARTIN EA, Patchigolla V, Fu AQ
    Approximate Bayesian inference of directed acyclic graphs in biology with flexible priors on edge states.
    PLoS Comput Biol. 2026;22:e1014039.
    PubMed     Abstract available
    
    
    February 2026
49. GUO Y, Mallona I, Robinson MD, Li L, et al
    BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration.
    PLoS Comput Biol. 2026;22:e1013932.
    PubMed     Abstract available
    
    
    
50. HARTMAN E, Malmstrom J, Wallin J
    Degradation graphs reveal hidden proteolytic activity in peptidomes.
    PLoS Comput Biol. 2026;22:e1013972.
    PubMed     Abstract available
    
    
    
51. BACON WA, Batut B, Srikakulam SK, Zierep P, et al
    Ten common misconceptions about Galaxy (and why they are wrong!).
    PLoS Comput Biol. 2026;22:e1013869.
    PubMed     Abstract available
    
    
    
52. CHANTZI N, Mouratidis I, Georgakopoulos-Soares I
    Zimin patterns in genomes.
    PLoS Comput Biol. 2026;22:e1013909.
    PubMed     Abstract available
    
    
    
53. BALOYAN A, Konecny T, Hovhannisyan E, Zadirako N, et al
    A topological map of the genetic components of grapevine-Admixture meets SOMmelier machine learning.
    PLoS Comput Biol. 2026;22:e1013882.
    PubMed     Abstract available
    
    
    
54. COLBY JM, Krantz BA
    A dynamical anthrax toxin nanopore biosensor for high-fidelity single-peptide classification.
    PLoS Comput Biol. 2026;22:e1014019.
    PubMed     Abstract available
    
    
    
55. ZHANG S, Lu Y, Li P, Wu J, et al
    CA-CAE: A deep learning-based multi-omics model for pan-cancer subtype classification and prognosis prediction.
    PLoS Comput Biol. 2026;22:e1014015.
    PubMed     Abstract available
    
    
    
56. ZHOU H, Edelman B, Skolnick J
    MENDELSEEK: An algorithm that predicts mendelian genes and elucidates what makes them special.
    PLoS Comput Biol. 2026;22:e1013992.
    PubMed     Abstract available
    
    
    January 2026
57. BURKE D, Raychaudhuri J, Chuong E, Taylor W, et al
    TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.
    PLoS Comput Biol. 2026;22:e1013122.
    PubMed     Abstract available
    
    
    
58. KARAGIANNIS TT, Chen Y, Bald S, Tai A, et al
    Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.
    PLoS Comput Biol. 2026;22:e1013883.
    PubMed     Abstract available
    
    
    
59. PELLOW R, Comeron JM
    A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights.
    PLoS Comput Biol. 2026;22:e1013887.
    PubMed     Abstract available
    
    
    
60. ROY A, Zhang X
    Powerful large scale inference in high dimensional mediation analysis.
    PLoS Comput Biol. 2026;22:e1013880.
    PubMed     Abstract available
    
    
    
61. MIAO J, Li D
    TEvarSim: A genome simulator for transposable element (TE) variants.
    PLoS Comput Biol. 2026;22:e1013933.
    PubMed     Abstract available
    
    
    
62. KRZYNOWEK A, Snoeks J, Faust K
    PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets.
    PLoS Comput Biol. 2026;22:e1013892.
    PubMed     Abstract available
    
    
    
63. WEN G, Li L
    CoFormerSurv: Collaborative transformer for multi-omics survival analysis.
    PLoS Comput Biol. 2026;22:e1013875.
    PubMed     Abstract available
    
    
    December 2025
64. CHICCO D, Jurman G
    Comment on "Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper".
    PLoS Comput Biol. 2025;21:e1013673.
    PubMed     Abstract available
    
    
    
65. REYNOLDS J, Pan C
    Benchmarking interpretability of deep learning for predictive genomics: Recall, precision, and variability of feature attribution.
    PLoS Comput Biol. 2025;21:e1013784.
    PubMed     Abstract available
    
    
    
66. DODERO-ROJAS E, Mendieta A, Fehlis Y, Mayala N, et al
    Epigenetics is all you need: A transformer to decode chromatin structural compartments from the epigenome.
    PLoS Comput Biol. 2025;21:e1012326.
    PubMed     Abstract available
    
    
    
67. COLEMAN S, Breckels L, Waller RF, Lilley KS, et al
    Semi-supervised Bayesian integration of multiple spatial proteomics datasets.
    PLoS Comput Biol. 2025;21:e1013799.
    PubMed     Abstract available
    
    
    
68. CHEN D, Storey JD
    Coancestry superposed on admixed populations yields measures of relatedness at individual-level resolution.
    PLoS Comput Biol. 2025;21:e1013848.
    PubMed     Abstract available
    
    
    November 2025
69. YIN Y, Zhuang L, Wang Y, Shi Y, et al
    Branch-specific gene discovery in cell differentiation using multi-omics graph attention.
    PLoS Comput Biol. 2025;21:e1013664.
    PubMed     Abstract available
    
    
    October 2025
70. MI Y, Cahill B, Yallapragada VVB, Rotem R, et al
    AI-driven discovery of novel extracellular matrix biomarkers in pelvic organ prolapse.
    PLoS Comput Biol. 2025;21:e1013483.
    PubMed     Abstract available
    
    
    
71. LIANG X, Xiao S, Ba L, Feng Y, et al
    Spatial domain identification method based on multi-view graph convolutional network and contrastive learning.
    PLoS Comput Biol. 2025;21:e1013369.
    PubMed     Abstract available
    
    
    September 2025
72. MULLER NF, Bouckaert RR, Wu CH, Bedford T, et al
    MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.
    PLoS Comput Biol. 2025;21:e1013421.
    PubMed     Abstract available
    
    
    
73. 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.
    PubMed     Abstract available
    
    
    
74. 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.
    PubMed     Abstract available
    
    
    
75. YANG J, Grant GR, Brooks TG
    Generating correlated data for omics simulation.
    PLoS Comput Biol. 2025;21:e1013392.
    PubMed     Abstract available
    
    
    
76. TRUONG L, Truong T, Nguyen H
    OmnibusX: A unified platform for accessible multi-omics analysis.
    PLoS Comput Biol. 2025;21:e1013480.
    PubMed     Abstract available
    
    
    
77. 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.
    PubMed     Abstract available
    
    
    
78. MA Z, Chen R, Feng Z
    Exploration of potential novel drug targets for rheumatoid arthritis by plasma proteome screening.
    PLoS Comput Biol. 2025;21:e1013333.
    PubMed     Abstract available
    
    
    
79. GAO C, Yang C, Zhang L
    A graph neural network-based spatial multi-omics data integration method for deciphering spatial domains.
    PLoS Comput Biol. 2025;21:e1013546.
    PubMed     Abstract available
    
    
    
80. YUAN R, Rong Z, Hu H, Liu T, et al
    Harmony-based data integration for distributed single-cell multi-omics data.
    PLoS Comput Biol. 2025;21:e1013526.
    PubMed     Abstract available
    
    
    
81. LUCAS A, Schaffer DE, Wickramasinghe J, Auslander N, et al
    kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies.
    PLoS Comput Biol. 2025;21:e1013470.
    PubMed     Abstract available
    
    
    August 2025
82. ROBERTSON J, Consul S, Vikalo H
    NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.
    PLoS Comput Biol. 2025;21:e1013360.
    PubMed     Abstract available
    
    
    
83. 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.
    PubMed     Abstract available
    
    
    July 2025
84. DONG X, Jiao D, Xue H, Fan S, et al
    APAV: An advanced pangenome analysis and visualization toolkit.
    PLoS Comput Biol. 2025;21:e1013288.
    PubMed     Abstract available
    
    
    June 2025
85. WADDEL H, Koelle K, Lau MSY
    ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.
    PLoS Comput Biol. 2025;21:e1012657.
    PubMed     Abstract available
    
    
    May 2025
86. 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.
    PubMed     Abstract available
    
    
    April 2025
87. 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.
    PubMed     Abstract available
    
    
    
88. 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.
    PubMed     Abstract available
    
    
    
89. 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.
    PubMed     Abstract available
    
    
    
90. 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.
    PubMed     Abstract available
    
    
    March 2025
91. RYAN B, Marioni R, Simpson TI
    An integrative network approach for longitudinal stratification in Parkinson's disease.
    PLoS Comput Biol. 2025;21:e1012857.
    PubMed     Abstract available
    
    
    
92. 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.
    PubMed     Abstract available
    
    
    
93. 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.
    PubMed     Abstract available
    
    
    February 2025
94. 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.
    PubMed     Abstract available
    
    
    
95. 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.
    PubMed     Abstract available
    
    
    January 2025
96. 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.
    PubMed     Abstract available
    
    
    
97. 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.
    PubMed     Abstract available
    
    
    
98. FANG M, Gorin G, Pachter L
    Trajectory inference from single-cell genomics data with a process time model.
    PLoS Comput Biol. 2025;21:e1012752.
    PubMed     Abstract available
    
    
    
99. GORSTEIN E, Aghdam R, Solis-Lemus C
    HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data.
    PLoS Comput Biol. 2025;21:e1012143.
    PubMed     Abstract available
    
    
    December 2024
100. 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.
     PubMed     Abstract available
     
     
     
101. 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.
     PubMed     Abstract available
     
     
     
102. 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.
     PubMed     Abstract available
     
     
     
103. ABHARI N, Colijn C, Mooers A, Tupper P, et al
     Measuring genetic diversity across populations.
     PLoS Comput Biol. 2024;20:e1012651.
     PubMed     Abstract available
     
     
     
104. 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.
     PubMed     Abstract available
     
     
     
105. 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.
     PubMed     Abstract available
     
     
     
106. 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.
     PubMed     Abstract available
     
     
     November 2024
107. 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.
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108. CHEN L, Huang ZH, Sun Y, Domaratzki M, et al
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109. ROCHA U, Kasmanas JC, Toscan R, Sanches DS, et al
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113. LE SUEUR C, Rattray M, Savitski M
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114. AMARAL AS, Devos DP
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115. NEY A, Nene NR, Sedlak E, Acedo P, et al
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116. RINTALA TJ, Fortino V
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117. SHI P, Han J, Zhang Y, Li G, et al
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119. BERGMAN S, Tuller T
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120. ABDENNUR N, Abraham S, Fudenberg G, Flyamer IM, et al
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121. GORMAN ED, Lladser ME
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122. CASCARINA SM, Ross ED
     Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life.
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123. WANG M, Yan X, Dong Y, Li X, et al
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124. GIUDICE L, Mohamed A, Malm T
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125. MARTIN NS, Camargo CQ, Louis AA
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127. LIU X, Gillis N, Jiang C, McCofie A, et al
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130. MUKHERJEE A, Chang YF, Huang Y, Benites NC, et al
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131. PFLUG FG, Bhat D, Pigolotti S
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135. SINGH A, Chakrabarti S
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136. VASILEIOU D, Karapiperis C, Baltsavia I, Chasapi A, et al
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137. SCHMIDT H, Sashittal P, Raphael BJ
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138. KIPEN J, Jalden J
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139. HEUPINK TH, Verboven L, Sharma A, Rennie V, et al
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140. BRUNNER JD, Gallegos-Graves LA, Kroeger ME
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141. CECIL RM, Sugden LA
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142. GAO Y, Sun F
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143. KOSINSKI JG, Zywicki M
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144. YELMEN B, Decelle A, Boulos LL, Szatkownik A, et al
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146. HUANG Z, Cui X, Xia Y, Zhao K, et al
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147. TCHOUNKE B, Sanchez L, Bell JM, Cros D, et al
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149. CHARI T, Pachter L
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150. WANG N, Khan S, Elo LL
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152. CHICCO D, Cumbo F, Angione C
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154. KAHANE I, Leiserson MDM, Sharan R
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155. MINEEVA O, Danciu D, Scholkopf B, Ley RE, et al
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161. CAPPELLO L, Kim J, Palacios JA
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162. GUO A, Salzberg SL, Zimin AV
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