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Genetics

Free Subscription Articles published in PLoS Comput Biol Retrieve available abstracts of 137 articles: HTML format

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June 2026
1. MAHMUD A, Huang C
   IsoPepTracker: An interactive web application for peptide-driven isoform analysis.
   PLoS Comput Biol. 2026;22:e1014324.
   PubMed     Abstract available
   
   
   May 2026
2. 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
   
   
   
3. 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
   
   
   
4. 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
   
   
   
5. 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
   
   
   
6. 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
   
   
   
7. 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
8. 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
   
   
   
9. 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
   
   
   
10. BORA A, McKenzie M, Ziemann M
    Ten common mistakes that could ruin your enrichment analysis.
    PLoS Comput Biol. 2026;22:e1014122.
    PubMed     Abstract available
    
    
    
11. 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
    
    
    
12. 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
    
    
    
13. 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
14. 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
    
    
    
15. 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
    
    
    
16. 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
    
    
    
17. 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
    
    
    
18. 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
    
    
    
19. 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
    
    
    
20. 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
21. 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
    
    
    
22. HARTMAN E, Malmstrom J, Wallin J
    Degradation graphs reveal hidden proteolytic activity in peptidomes.
    PLoS Comput Biol. 2026;22:e1013972.
    PubMed     Abstract available
    
    
    
23. 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
    
    
    
24. CHANTZI N, Mouratidis I, Georgakopoulos-Soares I
    Zimin patterns in genomes.
    PLoS Comput Biol. 2026;22:e1013909.
    PubMed     Abstract available
    
    
    
25. 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
    
    
    
26. 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
    
    
    
27. 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
    
    
    
28. 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
29. 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
    
    
    
30. 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
    
    
    
31. 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
    
    
    
32. ROY A, Zhang X
    Powerful large scale inference in high dimensional mediation analysis.
    PLoS Comput Biol. 2026;22:e1013880.
    PubMed     Abstract available
    
    
    
33. MIAO J, Li D
    TEvarSim: A genome simulator for transposable element (TE) variants.
    PLoS Comput Biol. 2026;22:e1013933.
    PubMed     Abstract available
    
    
    
34. 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
    
    
    
35. WEN G, Li L
    CoFormerSurv: Collaborative transformer for multi-omics survival analysis.
    PLoS Comput Biol. 2026;22:e1013875.
    PubMed     Abstract available
    
    
    December 2025
36. 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
    
    
    
37. 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
    
    
    
38. 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
    
    
    
39. 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
    
    
    
40. 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
41. 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
42. 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
    
    
    
43. 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
44. 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
    
    
    
45. 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
    
    
    
46. 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
    
    
    
47. YANG J, Grant GR, Brooks TG
    Generating correlated data for omics simulation.
    PLoS Comput Biol. 2025;21:e1013392.
    PubMed     Abstract available
    
    
    
48. TRUONG L, Truong T, Nguyen H
    OmnibusX: A unified platform for accessible multi-omics analysis.
    PLoS Comput Biol. 2025;21:e1013480.
    PubMed     Abstract available
    
    
    
49. 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
    
    
    
50. 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
    
    
    
51. 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
    
    
    
52. 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
    
    
    
53. 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
54. 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
    
    
    
55. 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
56. 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
57. 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
58. 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
59. 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
    
    
    
60. 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
    
    
    
61. 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
    
    
    
62. 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
63. 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
    
    
    
64. 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
    
    
    
65. 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
66. 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
    
    
    
67. 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
68. 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
    
    
    
69. 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
    
    
    
70. 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
    
    
    
71. 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
72. 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
    
    
    
73. 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
    
    
    
74. 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
    
    
    
75. ABHARI N, Colijn C, Mooers A, Tupper P, et al
    Measuring genetic diversity across populations.
    PLoS Comput Biol. 2024;20:e1012651.
    PubMed     Abstract available
    
    
    
76. 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
    
    
    
77. 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
    
    
    
78. 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
79. 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.
    PubMed     Abstract available
    
    
    October 2024
80. 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.
    PubMed     Abstract available
    
    
    
81. 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.
    PubMed     Abstract available
    
    
    
82. 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.
    PubMed     Abstract available
    
    
    September 2024
83. 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.
    PubMed     Abstract available
    
    
    
84. 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.
    PubMed     Abstract available
    
    
    
85. 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.
    PubMed     Abstract available
    
    
    
86. AMARAL AS, Devos DP
    The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.
    PLoS Comput Biol. 2024;20:e1012459.
    PubMed     Abstract available
    
    
    August 2024
87. 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.
    PubMed     Abstract available
    
    
    
88. 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.
    PubMed     Abstract available
    
    
    
89. 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.
    PubMed     Abstract available
    
    
    July 2024
90. 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.
    PubMed     Abstract available
    
    
    June 2024
91. BERGMAN S, Tuller T
    Strong association between genomic 3D structure and CRISPR cleavage efficiency.
    PLoS Comput Biol. 2024;20:e1012214.
    PubMed     Abstract available
    
    
    May 2024
92. 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.
    PubMed     Abstract available
    
    
    
93. GORMAN ED, Lladser ME
    Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance.
    PLoS Comput Biol. 2024;20:e1011543.
    PubMed     Abstract available
    
    
    
94. 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.
    PubMed     Abstract available
    
    
    
95. 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.
    PubMed     Abstract available
    
    
    April 2024
96. 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.
    PubMed     Abstract available
    
    
    March 2024
97. 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.
    PubMed     Abstract available
    
    
    
98. 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.
    PubMed     Abstract available
    
    
    February 2024
99. 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.
    PubMed     Abstract available
    
    
    
100. 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.
     PubMed     Abstract available
     
     
     January 2024
101. 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.
     PubMed     Abstract available
     
     
     
102. 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.
     PubMed     Abstract available
     
     
     
103. PFLUG FG, Bhat D, Pigolotti S
     Genome replication in asynchronously growing microbial populations.
     PLoS Comput Biol. 2024;20:e1011753.
     PubMed     Abstract available
     
     
     
104. 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.
     PubMed     Abstract available
     
     
     
105. 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.
     PubMed     Abstract available
     
     
     
106. 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.
     PubMed     Abstract available
     
     
     December 2023
107. SINGH A, Chakrabarti S
     Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture.
     PLoS Comput Biol. 2023;19:e1011725.
     PubMed     Abstract available
     
     
     November 2023
108. VASILEIOU D, Karapiperis C, Baltsavia I, Chasapi A, et al
     CGG toolkit: Software components for computational genomics.
     PLoS Comput Biol. 2023;19:e1011498.
     PubMed     Abstract available
     
     
     
109. SCHMIDT H, Sashittal P, Raphael BJ
     A zero-agnostic model for copy number evolution in cancer.
     PLoS Comput Biol. 2023;19:e1011590.
     PubMed     Abstract available
     
     
     
110. KIPEN J, Jalden J
     Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data.
     PLoS Comput Biol. 2023;19:e1011345.
     PubMed     Abstract available
     
     
     
111. 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.
     PubMed     Abstract available
     
     
     
112. BRUNNER JD, Gallegos-Graves LA, Kroeger ME
     Inferring microbial interactions with their environment from genomic and metagenomic data.
     PLoS Comput Biol. 2023;19:e1011661.
     PubMed     Abstract available
     
     
     
113. 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.
     PubMed     Abstract available
     
     
     October 2023
114. GAO Y, Sun F
     Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies.
     PLoS Comput Biol. 2023;19:e1010608.
     PubMed     Abstract available
     
     
     
115. KOSINSKI JG, Zywicki M
     AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals.
     PLoS Comput Biol. 2023;19:e1011527.
     PubMed     Abstract available
     
     
     
116. 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.
     PubMed     Abstract available
     
     
     September 2023
117. 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.
     PubMed     Abstract available
     
     
     
118. 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.
     PubMed     Abstract available
     
     
     
119. 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.
     PubMed     Abstract available
     
     
     
120. 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.
     PubMed     Abstract available
     
     
     August 2023
121. CHARI T, Pachter L
     The specious art of single-cell genomics.
     PLoS Comput Biol. 2023;19:e1011288.
     PubMed     Abstract available
     
     
     
122. WANG N, Khan S, Elo LL
     VarSCAT: A computational tool for sequence context annotations of genomic variants.
     PLoS Comput Biol. 2023;19:e1010727.
     PubMed     Abstract available
     
     
     
123. 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.
     PubMed     Abstract available
     
     
     July 2023
124. CHICCO D, Cumbo F, Angione C
     Ten quick tips for avoiding pitfalls in multi-omics data integration analyses.
     PLoS Comput Biol. 2023;19:e1011224.
     PubMed     Abstract available
     
     
     
125. 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.
     PubMed     Abstract available
     
     
     June 2023
126. KAHANE I, Leiserson MDM, Sharan R
     A mutation-level covariate model for mutational signatures.
     PLoS Comput Biol. 2023;19:e1011195.
     PubMed     Abstract available
     
     
     May 2023
127. 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.
     PubMed     Abstract available
     
     
     April 2023
128. 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.
     PubMed     Abstract available
     
     
     
129. 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.
     PubMed     Abstract available
     
     
     
130. 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.
     PubMed     Abstract available
     
     
     March 2023
131. 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.
     PubMed     Abstract available
     
     
     
132. PENG H, Wong L, Goh WWB
     ProInfer: An interpretable protein inference tool leveraging on biological networks.
     PLoS Comput Biol. 2023;19:e1010961.
     PubMed     Abstract available
     
     
     
133. CAPPELLO L, Kim J, Palacios JA
     adaPop: Bayesian inference of dependent population dynamics in coalescent models.
     PLoS Comput Biol. 2023;19:e1010897.
     PubMed     Abstract available
     
     
     
134. GUO A, Salzberg SL, Zimin AV
     JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.
     PLoS Comput Biol. 2023;19:e1011032.
     PubMed     Abstract available
     
     
     
135. 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.
     PubMed     Abstract available
     
     
     February 2023
136. 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.
     PubMed     Abstract available
     
     
     
137. 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.
     PubMed     Abstract available
     
     

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