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Genetics

Free Subscription Articles published in PLoS Comput Biol Retrieve available abstracts of 79 articles: HTML format

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April 2025
1. 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
   
   
   
2. 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
   
   
   
3. 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
   
   
   
4. 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
5. 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
   
   
   
6. 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
   
   
   
7. 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
8. 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
   
   
   
9. 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
10. 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
    
    
    
11. 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
    
    
    
12. 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
    
    
    
13. 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
14. 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
    
    
    
15. 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
    
    
    
16. 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
    
    
    
17. ABHARI N, Colijn C, Mooers A, Tupper P, et al
    Measuring genetic diversity across populations.
    PLoS Comput Biol. 2024;20:e1012651.
    PubMed     Abstract available
    
    
    
18. 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
    
    
    
19. 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
    
    
    
20. 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
21. 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
22. 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
    
    
    
23. 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
    
    
    
24. 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
25. 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
    
    
    
26. 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
    
    
    
27. 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
    
    
    
28. 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
29. 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
    
    
    
30. 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
    
    
    
31. 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
32. 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
33. 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
34. 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
    
    
    
35. GORMAN ED, Lladser ME
    Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance.
    PLoS Comput Biol. 2024;20:e1011543.
    PubMed     Abstract available
    
    
    
36. 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
    
    
    
37. 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
38. 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
39. 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
    
    
    
40. 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
41. 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
    
    
    
42. 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
43. 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
    
    
    
44. 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
    
    
    
45. PFLUG FG, Bhat D, Pigolotti S
    Genome replication in asynchronously growing microbial populations.
    PLoS Comput Biol. 2024;20:e1011753.
    PubMed     Abstract available
    
    
    
46. 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
    
    
    
47. 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
    
    
    
48. 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
49. 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
50. 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
    
    
    
51. 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
    
    
    
52. 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
    
    
    
53. 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
    
    
    
54. 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
    
    
    
55. 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
56. 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
    
    
    
57. KOSINSKI JG, Zywicki M
    AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals.
    PLoS Comput Biol. 2023;19:e1011527.
    PubMed     Abstract available
    
    
    
58. 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
59. 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
    
    
    
60. 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
    
    
    
61. 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
    
    
    
62. 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
63. CHARI T, Pachter L
    The specious art of single-cell genomics.
    PLoS Comput Biol. 2023;19:e1011288.
    PubMed     Abstract available
    
    
    
64. 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
    
    
    
65. 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
66. 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
    
    
    
67. 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
68. 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
69. 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
70. 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
    
    
    
71. 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
    
    
    
72. 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
73. 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
    
    
    
74. 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
    
    
    
75. 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
    
    
    
76. 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
    
    
    
77. 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
78. 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
    
    
    
79. 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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