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Genetics

Free Subscription Articles published in PLoS Comput Biol Retrieve available abstracts of 183 articles: HTML format

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May 2024
1. 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
   
   
   April 2024
2. 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
3. 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
   
   
   
4. 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
5. 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
   
   
   
6. 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
7. 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
   
   
   
8. 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
   
   
   
9. PFLUG FG, Bhat D, Pigolotti S
   Genome replication in asynchronously growing microbial populations.
   PLoS Comput Biol. 2024;20:e1011753.
   PubMed     Abstract available
   
   
   
10. 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
    
    
    
11. 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
    
    
    
12. 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
13. 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
14. 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
    
    
    
15. 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
    
    
    
16. 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
    
    
    
17. 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
    
    
    
18. 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
    
    
    
19. 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
20. 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
    
    
    
21. KOSINSKI JG, Zywicki M
    AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals.
    PLoS Comput Biol. 2023;19:e1011527.
    PubMed     Abstract available
    
    
    
22. 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
23. 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
    
    
    
24. 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
    
    
    
25. 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
    
    
    
26. 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
27. CHARI T, Pachter L
    The specious art of single-cell genomics.
    PLoS Comput Biol. 2023;19:e1011288.
    PubMed     Abstract available
    
    
    
28. 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
    
    
    
29. 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
30. 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
    
    
    
31. 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
32. 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
33. 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
34. 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
    
    
    
35. 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
    
    
    
36. 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
37. 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
    
    
    
38. 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
    
    
    
39. 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
    
    
    
40. 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
    
    
    
41. 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
42. 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
    
    
    
43. 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
    
    
    January 2023
44. GUETO-TETTAY C, Tang D, Happonen L, Heusel M, et al
    Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics.
    PLoS Comput Biol. 2023;19:e1010457.
    PubMed     Abstract available
    
    
    December 2022
45. VUONG P, Wise MJ, Whiteley AS, Kaur P, et al
    Ten simple rules for investigating (meta)genomic data from environmental ecosystems.
    PLoS Comput Biol. 2022;18:e1010675.
    PubMed    
    
    
    
46. ZHU YH, Zhang C, Yu DJ, Zhang Y, et al
    Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.
    PLoS Comput Biol. 2022;18:e1010793.
    PubMed     Abstract available
    
    
    
47. SOYLEV A, Cokoglu SS, Koptekin D, Alkan C, et al
    CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.
    PLoS Comput Biol. 2022;18:e1010788.
    PubMed     Abstract available
    
    
    November 2022
48. DURANT E, Rouard M, Ganko EW, Muller C, et al
    Ten simple rules for developing visualization tools in genomics.
    PLoS Comput Biol. 2022;18:e1010622.
    PubMed    
    
    
    
49. SRIVASTAVA H, Lippincott MJ, Currie J, Canfield R, et al
    Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners.
    PLoS Comput Biol. 2022;18:e1010702.
    PubMed     Abstract available
    
    
    October 2022
50. LOCARD-PAULET M, Palasca O, Jensen LJ
    Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies.
    PLoS Comput Biol. 2022;18:e1010604.
    PubMed     Abstract available
    
    
    
51. MALINA S, Cizin D, Knowles DA
    Deep mendelian randomization: Investigating the causal knowledge of genomic deep learning models.
    PLoS Comput Biol. 2022;18:e1009880.
    PubMed     Abstract available
    
    
    
52. ZHANG D, Li SH, King CG, Wingreen NS, et al
    Global and gene-specific translational regulation in Escherichia coli across different conditions.
    PLoS Comput Biol. 2022;18:e1010641.
    PubMed     Abstract available
    
    
    September 2022
53. SU R, Yang H, Wei L, Chen S, et al
    A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data.
    PLoS Comput Biol. 2022;18:e1010402.
    PubMed     Abstract available
    
    
    
54. UPADHYA G, Steinrucken M
    Robust inference of population size histories from genomic sequencing data.
    PLoS Comput Biol. 2022;18:e1010419.
    PubMed     Abstract available
    
    
    
55. DIMOPOULOS EA, Carmagnini A, Velsko IM, Warinner C, et al
    HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.
    PLoS Comput Biol. 2022;18:e1010493.
    PubMed     Abstract available
    
    
    August 2022
56. BURGER KE, Pfaffelhuber P, Baumdicker F
    Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown.
    PLoS Comput Biol. 2022;18:e1010407.
    PubMed     Abstract available
    
    
    
57. LI A, Mueller A, English B, Arena A, et al
    Novel feature selection methods for construction of accurate epigenetic clocks.
    PLoS Comput Biol. 2022;18:e1009938.
    PubMed     Abstract available
    
    
    
58. GUO F, Carbone I, Rasmussen DA
    Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination.
    PLoS Comput Biol. 2022;18:e1010422.
    PubMed     Abstract available
    
    
    
59. CHION M, Carapito C, Bertrand F
    Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics.
    PLoS Comput Biol. 2022;18:e1010420.
    PubMed     Abstract available
    
    
    
60. GIMBERNAT-MAYOL J, Dominguez Mantes A, Bustamante CD, Mas Montserrat D, et al
    Archetypal Analysis for population genetics.
    PLoS Comput Biol. 2022;18:e1010301.
    PubMed     Abstract available
    
    
    July 2022
61. LIU L, Meng Q, Weng C, Lu Q, et al
    Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data.
    PLoS Comput Biol. 2022;18:e1010328.
    PubMed     Abstract available
    
    
    June 2022
62. WANG S, Garcia-Seisdedos D, Prakash A, Kundu DJ, et al
    Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.
    PLoS Comput Biol. 2022;18:e1010174.
    PubMed     Abstract available
    
    
    
63. ALINEJAD-ROKNY H, Ghavami Modegh R, Rabiee HR, Ramezani Sarbandi E, et al
    MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments.
    PLoS Comput Biol. 2022;18:e1010241.
    PubMed     Abstract available
    
    
    May 2022
64. NGUYEN QP, Hoen AG, Frost HR
    CBEA: Competitive balances for taxonomic enrichment analysis.
    PLoS Comput Biol. 2022;18:e1010091.
    PubMed     Abstract available
    
    
    
65. LAI B, Qian S, Zhang H, Zhang S, et al
    Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning.
    PLoS Comput Biol. 2022;18:e1010011.
    PubMed     Abstract available
    
    
    
66. REIJNDERS MJMF, Waterhouse RM
    CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation.
    PLoS Comput Biol. 2022;18:e1010075.
    PubMed     Abstract available
    
    
    April 2022
67. BRUNO S, Williams RJ, Del Vecchio D
    Epigenetic cell memory: The gene's inner chromatin modification circuit.
    PLoS Comput Biol. 2022;18:e1009961.
    PubMed     Abstract available
    
    
    
68. DEFFNER D, Kandler A, Fogarty L
    Effective population size for culturally evolving traits.
    PLoS Comput Biol. 2022;18:e1009430.
    PubMed     Abstract available
    
    
    
69. LEE D, Wang D, Yang XR, Shi J, et al
    SUITOR: Selecting the number of mutational signatures through cross-validation.
    PLoS Comput Biol. 2022;18:e1009309.
    PubMed     Abstract available
    
    
    
70. GRAZIOLI F, Siarheyeu R, Alqassem I, Henschel A, et al
    Microbiome-based disease prediction with multimodal variational information bottlenecks.
    PLoS Comput Biol. 2022;18:e1010050.
    PubMed     Abstract available
    
    
    
71. OUELLETTE TW, Awadalla P
    Inferring ongoing cancer evolution from single tumour biopsies using synthetic supervised learning.
    PLoS Comput Biol. 2022;18:e1010007.
    PubMed     Abstract available
    
    
    March 2022
72. YAO K, Schaafsma E, Zhang B, Cheng C, et al
    Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer.
    PLoS Comput Biol. 2022;18:e1009495.
    PubMed     Abstract available
    
    
    
73. STAMBOULIAN M, Canderan J, Ye Y
    Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species.
    PLoS Comput Biol. 2022;18:e1009397.
    PubMed     Abstract available
    
    
    
74. WENDERING P, Nikoloski Z
    COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions.
    PLoS Comput Biol. 2022;18:e1009906.
    PubMed     Abstract available
    
    
    
75. APAOLAZA I, San Jose-Eneriz E, Valcarcel LV, Agirre X, et al
    A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism.
    PLoS Comput Biol. 2022;18:e1009395.
    PubMed     Abstract available
    
    
    
76. PICCOLO SR, Mecham A, Golightly NP, Johnson JL, et al
    The ability to classify patients based on gene-expression data varies by algorithm and performance metric.
    PLoS Comput Biol. 2022;18:e1009926.
    PubMed     Abstract available
    
    
    
77. KIESER S, Zdobnov EM, Trajkovski M
    Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart.
    PLoS Comput Biol. 2022;18:e1009947.
    PubMed     Abstract available
    
    
    February 2022
78. DI FILIPPO M, Pescini D, Galuzzi BG, Bonanomi M, et al
    INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation.
    PLoS Comput Biol. 2022;18:e1009337.
    PubMed     Abstract available
    
    
    
79. MOUTINHO TJ JR, Neubert BC, Jenior ML, Papin JA, et al
    Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions.
    PLoS Comput Biol. 2022;18:e1009341.
    PubMed     Abstract available
    
    
    
80. ROSENTHAL SB, Wang H, Shi D, Liu C, et al
    Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics.
    PLoS Comput Biol. 2022;18:e1009903.
    PubMed     Abstract available
    
    
    
81. ZAREBSKI AE, du Plessis L, Parag KV, Pybus OG, et al
    A computationally tractable birth-death model that combines phylogenetic and epidemiological data.
    PLoS Comput Biol. 2022;18:e1009805.
    PubMed     Abstract available
    
    
    
82. SUN Q, Nematbakhsh A, Kuntala PK, Kellogg G, et al
    STENCIL: A web templating engine for visualizing and sharing life science datasets.
    PLoS Comput Biol. 2022;18:e1009859.
    PubMed     Abstract available
    
    
    January 2022
83. WICK RR, Holt KE
    Polypolish: Short-read polishing of long-read bacterial genome assemblies.
    PLoS Comput Biol. 2022;18:e1009802.
    PubMed     Abstract available
    
    
    
84. PORTA-PARDO E, Ruiz-Serra V, Valentini S, Valencia A, et al
    The structural coverage of the human proteome before and after AlphaFold.
    PLoS Comput Biol. 2022;18:e1009818.
    PubMed     Abstract available
    
    
    
85. XU ZM, Rueger S, Zwyer M, Brites D, et al
    Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations.
    PLoS Comput Biol. 2022;18:e1009628.
    PubMed     Abstract available
    
    
    December 2021
86. ARON S, Jongeneel CV, Chauke PA, Chaouch M, et al
    Ten simple rules for developing bioinformatics capacity at an academic institution.
    PLoS Comput Biol. 2021;17:e1009592.
    PubMed    
    
    
    
87. LIU L, Zhang B, Hyeon C
    Extracting multi-way chromatin contacts from Hi-C data.
    PLoS Comput Biol. 2021;17:e1009669.
    PubMed     Abstract available
    
    
    
88. MCCALL MN, Chu CY, Wang L, Benoodt L, et al
    A systems genomics approach uncovers molecular associates of RSV severity.
    PLoS Comput Biol. 2021;17:e1009617.
    PubMed     Abstract available
    
    
    
89. MOTTES F, Villa C, Osella M, Caselle M, et al
    The impact of whole genome duplications on the human gene regulatory networks.
    PLoS Comput Biol. 2021;17:e1009638.
    PubMed     Abstract available
    
    
    November 2021
90. KING SB, Singh M
    Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections.
    PLoS Comput Biol. 2021;17:e1009560.
    PubMed     Abstract available
    
    
    
91. SARMASHGHI S, Balaban M, Rachtman E, Touri B, et al
    Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.
    PLoS Comput Biol. 2021;17:e1009449.
    PubMed     Abstract available
    
    
    
92. CHARMPI K, Chokkalingam M, Johnen R, Beyer A, et al
    Optimizing network propagation for multi-omics data integration.
    PLoS Comput Biol. 2021;17:e1009161.
    PubMed     Abstract available
    
    
    
93. ROBESON MS 2ND, O'Rourke DR, Kaehler BD, Ziemski M, et al
    RESCRIPt: Reproducible sequence taxonomy reference database management.
    PLoS Comput Biol. 2021;17:e1009581.
    PubMed     Abstract available
    
    
    
94. MADSSEN TS, Giskeodegard GF, Smilde AK, Westerhuis JA, et al
    Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data.
    PLoS Comput Biol. 2021;17:e1009585.
    PubMed     Abstract available
    
    
    October 2021
95. PENEV PI, Alvarez-Carreno C, Smith E, Petrov AS, et al
    TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
    PLoS Comput Biol. 2021;17:e1009541.
    PubMed     Abstract available
    
    
    
96. RAMSEY J, McIntosh B, Renfro D, Aleksander SA, et al
    Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).
    PLoS Comput Biol. 2021;17:e1009463.
    PubMed     Abstract available
    
    
    
97. SU S, Gouil Q, Blewitt ME, Cook D, et al
    NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.
    PLoS Comput Biol. 2021;17:e1009524.
    PubMed     Abstract available
    
    
    
98. SUGIMOTO R, Nishimura L, Nguyen PT, Ito J, et al
    Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more.
    PLoS Comput Biol. 2021;17:e1009428.
    PubMed     Abstract available
    
    
    
99. JOHNSON R, Burch KS, Hou K, Paciuc M, et al
    Estimation of regional polygenicity from GWAS provides insights into the genetic architecture of complex traits.
    PLoS Comput Biol. 2021;17:e1009483.
    PubMed     Abstract available
    
    
    
100. LIBBRECHT MW, Chan RCW, Hoffman MM
     Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.
     PLoS Comput Biol. 2021;17:e1009423.
     PubMed     Abstract available
     
     
     
101. ZHANG YZ, Imoto S, Miyano S, Yamaguchi R, et al
     Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers.
     PLoS Comput Biol. 2021;17:e1009186.
     PubMed     Abstract available
     
     
     
102. DEMAERE MZ, Darling AE
     qc3C: Reference-free quality control for Hi-C sequencing data.
     PLoS Comput Biol. 2021;17:e1008839.
     PubMed     Abstract available
     
     
     
103. DECRULLE AL, Frenoy A, Meiller-Legrand TA, Bernheim A, et al
     Engineering gene overlaps to sustain genetic constructs in vivo.
     PLoS Comput Biol. 2021;17:e1009475.
     PubMed     Abstract available
     
     
     September 2021
104. CAMPBELL EM, Boyles A, Shankar A, Kim J, et al
     MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
     PLoS Comput Biol. 2021;17:e1009300.
     PubMed     Abstract available
     
     
     
105. TOGNON M, Bonnici V, Garrison E, Giugno R, et al
     GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
     PLoS Comput Biol. 2021;17:e1009444.
     PubMed     Abstract available
     
     
     
106. VIGNOLLE GA, Schaffer D, Zehetner L, Mach RL, et al
     FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution.
     PLoS Comput Biol. 2021;17:e1009372.
     PubMed     Abstract available
     
     
     
107. DE TOMA I, Sierra C, Dierssen M
     Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome.
     PLoS Comput Biol. 2021;17:e1009317.
     PubMed     Abstract available
     
     
     
108. TANAKA H, Kreisberg JF, Ideker T
     Genetic dissection of complex traits using hierarchical biological knowledge.
     PLoS Comput Biol. 2021;17:e1009373.
     PubMed     Abstract available
     
     
     
109. DAS ROY R, Hallikas O, Christensen MM, Renvoise E, et al
     Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
     PLoS Comput Biol. 2021;17:e1008947.
     PubMed     Abstract available
     
     
     August 2021
110. SHAO Z, Wang T, Zhang M, Jiang Z, et al
     IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA.
     PLoS Comput Biol. 2021;17:e1009250.
     PubMed     Abstract available
     
     
     
111. DUAN R, Gao L, Gao Y, Hu Y, et al
     Evaluation and comparison of multi-omics data integration methods for cancer subtyping.
     PLoS Comput Biol. 2021;17:e1009224.
     PubMed     Abstract available
     
     
     
112. ZHANG JY, Roberts H, Flores DSC, Cutler AJ, et al
     Using de novo assembly to identify structural variation of eight complex immune system gene regions.
     PLoS Comput Biol. 2021;17:e1009254.
     PubMed     Abstract available
     
     
     
113. DOVROLIS N, Kassela K, Konstantinidis K, Kouvela A, et al
     ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
     PLoS Comput Biol. 2021;17:e1009304.
     PubMed     Abstract available
     
     
     
114. MARIN WM, Dandekar R, Augusto DG, Yusufali T, et al
     High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING.
     PLoS Comput Biol. 2021;17:e1008904.
     PubMed     Abstract available
     
     
     July 2021
115. LIU Y, Li J
     Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression.
     PLoS Comput Biol. 2021;17:e1009229.
     PubMed     Abstract available
     
     
     
116. THORNTON AM, Fang L, Lo A, McSharry M, et al
     eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants.
     PLoS Comput Biol. 2021;17:e1009132.
     PubMed     Abstract available
     
     
     
117. CASTELLANO-ESCUDER P, Gonzalez-Dominguez R, Carmona-Pontaque F, Andres-Lacueva C, et al
     POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis.
     PLoS Comput Biol. 2021;17:e1009148.
     PubMed     Abstract available
     
     
     June 2021
118. HUERTAS J, Scholer HR, Cojocaru V
     Histone tails cooperate to control the breathing of genomic nucleosomes.
     PLoS Comput Biol. 2021;17:e1009013.
     PubMed     Abstract available
     
     
     
119. AMBROS S, Gomez-Munoz N, Gimenez-Santamarina S, Sanchez-Vicente J, et al
     Molecular signatures of silencing suppression degeneracy from a complex RNA virus.
     PLoS Comput Biol. 2021;17:e1009166.
     PubMed     Abstract available
     
     
     
120. PROST V, Gazut S, Bruls T
     A zero inflated log-normal model for inference of sparse microbial association networks.
     PLoS Comput Biol. 2021;17:e1009089.
     PubMed     Abstract available
     
     
     
121. ZENG P, Lin Z
     coupleCoC+: An information-theoretic co-clustering-based transfer learning framework for the integrative analysis of single-cell genomic data.
     PLoS Comput Biol. 2021;17:e1009064.
     PubMed     Abstract available
     
     
     May 2021
122. SUKUMARAN J, Holder MT, Knowles LL
     Incorporating the speciation process into species delimitation.
     PLoS Comput Biol. 2021;17:e1008924.
     PubMed     Abstract available
     
     
     
123. BAHMANI A, Ferriter K, Krishnan V, Alavi A, et al
     Swarm: A federated cloud framework for large-scale variant analysis.
     PLoS Comput Biol. 2021;17:e1008977.
     PubMed     Abstract available
     
     
     
124. LUI LM, Nielsen TN, Arkin AP
     A method for achieving complete microbial genomes and improving bins from metagenomics data.
     PLoS Comput Biol. 2021;17:e1008972.
     PubMed     Abstract available
     
     
     
125. HJORLEIFSSON ELDJARN G, Ramsay A, van der Hooft JJJ, Duncan KR, et al
     Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.
     PLoS Comput Biol. 2021;17:e1008920.
     PubMed     Abstract available
     
     
     
126. KOO PK, Majdandzic A, Ploenzke M, Anand P, et al
     Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks.
     PLoS Comput Biol. 2021;17:e1008925.
     PubMed     Abstract available
     
     
     April 2021
127. MENICHELLI C, Guitard V, Martins RM, Lebre S, et al
     Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.
     PLoS Comput Biol. 2021;17:e1008909.
     PubMed     Abstract available
     
     
     
128. UZUNANGELOV V, Wong CK, Stuart JM
     Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.
     PLoS Comput Biol. 2021;17:e1008878.
     PubMed     Abstract available
     
     
     March 2021
129. MARCON Y, Bishop T, Avraam D, Escriba-Montagut X, et al
     Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD.
     PLoS Comput Biol. 2021;17:e1008880.
     PubMed     Abstract available
     
     
     
130. PAVLOVA YS, Paez-Espino D, Morozov AY, Belalov IS, et al
     Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.
     PLoS Comput Biol. 2021;17:e1008841.
     PubMed     Abstract available
     
     
     
131. SUN R, Nikolakopoulos AN
     Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors.
     PLoS Comput Biol. 2021;17:e1008838.
     PubMed     Abstract available
     
     
     
132. BAK JH, Kim MH, Liu L, Hyeon C, et al
     A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C.
     PLoS Comput Biol. 2021;17:e1008834.
     PubMed     Abstract available
     
     
     
133. SACHDEVA V, Mora T, Walczak AM, Palmer SE, et al
     Optimal prediction with resource constraints using the information bottleneck.
     PLoS Comput Biol. 2021;17:e1008743.
     PubMed     Abstract available
     
     
     
134. LAM SD, Babu MM, Lees J, Orengo CA, et al
     Biological impact of mutually exclusive exon switching.
     PLoS Comput Biol. 2021;17:e1008708.
     PubMed     Abstract available
     
     
     
135. CHELOSHKINA K, Poptsova M
     Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements.
     PLoS Comput Biol. 2021;17:e1008749.
     PubMed     Abstract available
     
     
     
136. MERLIN B, Castro Alves JT, de Sa PHCG, de Oliveira MS, et al
     CODON-Software to manual curation of prokaryotic genomes.
     PLoS Comput Biol. 2021;17:e1008797.
     PubMed     Abstract available
     
     
     
137. RICHMOND PA, Kaye AM, Kounkou GJ, Av-Shalom TV, et al
     Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper.
     PLoS Comput Biol. 2021;17:e1008815.
     PubMed     Abstract available
     
     
     February 2021
138. RATNIKOV BI, Cieplak P, Remacle AG, Nguyen E, et al
     Quantitative profiling of protease specificity.
     PLoS Comput Biol. 2021;17:e1008101.
     PubMed     Abstract available
     
     
     
139. VEGA YON GG, Thomas DC, Morrison J, Mi H, et al
     Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.
     PLoS Comput Biol. 2021;17:e1007948.
     PubMed     Abstract available
     
     
     
140. SOMMER MJ, Salzberg SL
     Balrog: A universal protein model for prokaryotic gene prediction.
     PLoS Comput Biol. 2021;17:e1008727.
     PubMed     Abstract available
     
     
     
141. LLOYD JP, Soellner MB, Merajver SD, Li JZ, et al
     Impact of between-tissue differences on pan-cancer predictions of drug sensitivity.
     PLoS Comput Biol. 2021;17:e1008720.
     PubMed     Abstract available
     
     
     
142. JACKSON M, Kavoussanakis K, Wallace EWJ
     Using prototyping to choose a bioinformatics workflow management system.
     PLoS Comput Biol. 2021;17:e1008622.
     PubMed     Abstract available
     
     
     
143. TUNG HR, Durrett R
     Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective.
     PLoS Comput Biol. 2021;17:e1008701.
     PubMed     Abstract available
     
     
     
144. GARRIDO-RODRIGUEZ M, Lopez-Lopez D, Ortuno FM, Pena-Chilet M, et al
     A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.
     PLoS Comput Biol. 2021;17:e1008748.
     PubMed     Abstract available
     
     
     
145. VAN DAMME R, Holzer M, Viehweger A, Muller B, et al
     Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN).
     PLoS Comput Biol. 2021;17:e1008716.
     PubMed     Abstract available
     
     
     
146. YU L, Wang M, Yang Y, Xu F, et al
     Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways.
     PLoS Comput Biol. 2021;17:e1008696.
     PubMed     Abstract available
     
     
     
147. XUE B, Jordan B, Rizvi S, Naegle KM, et al
     KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions.
     PLoS Comput Biol. 2021;17:e1008681.
     PubMed     Abstract available
     
     
     January 2021
148. VALIENTE-MULLOR C, Beamud B, Ansari I, Frances-Cuesta C, et al
     One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
     PLoS Comput Biol. 2021;17:e1008678.
     PubMed     Abstract available
     
     
     
149. AVRAM O, Kigel A, Vaisman-Mentesh A, Kligsberg S, et al
     PASA: Proteomic analysis of serum antibodies web server.
     PLoS Comput Biol. 2021;17:e1008607.
     PubMed     Abstract available
     
     
     
150. MARTINEZ-GARCIA PM, Garcia-Torres M, Divina F, Terron-Bautista J, et al
     Genome-wide prediction of topoisomerase IIbeta binding by architectural factors and chromatin accessibility.
     PLoS Comput Biol. 2021;17:e1007814.
     PubMed     Abstract available
     
     
     
151. KHARERIN H, Bai L
     Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.
     PLoS Comput Biol. 2021;17:e1008560.
     PubMed     Abstract available
     
     
     
152. TJARNBERG A, Mahmood O, Jackson CA, Saldi GA, et al
     Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data.
     PLoS Comput Biol. 2021;17:e1008569.
     PubMed     Abstract available
     
     
     
153. KALKAUSKAS A, Perron U, Sun Y, Goldman N, et al
     Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.
     PLoS Comput Biol. 2021;17:e1008561.
     PubMed     Abstract available
     
     
     
154. KOUKOULI E, Wang D, Dondelinger F, Park J, et al
     A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response.
     PLoS Comput Biol. 2021;17:e1008066.
     PubMed     Abstract available
     
     
     
155. SCELSI MA, Napolioni V, Greicius MD, Altmann A, et al
     Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities.
     PLoS Comput Biol. 2021;17:e1008517.
     PubMed     Abstract available
     
     
     
156. PATUMCHAROENPOL P, Nakphaichit M, Panagiotou G, Senavonge A, et al
     MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome.
     PLoS Comput Biol. 2021;17:e1008487.
     PubMed     Abstract available
     
     
     December 2020
157. LIN D, Yalamanchili HB, Zhang X, Lewis NE, et al
     CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.
     PLoS Comput Biol. 2020;16:e1008498.
     PubMed     Abstract available
     
     
     November 2020
158. TOWNES FW, Carr K, Miller JW
     Identifying longevity associated genes by integrating gene expression and curated annotations.
     PLoS Comput Biol. 2020;16:e1008429.
     PubMed     Abstract available
     
     
     
159. THESSEN AE, Walls RL, Vogt L, Singer J, et al
     Transforming the study of organisms: Phenomic data models and knowledge bases.
     PLoS Comput Biol. 2020;16:e1008376.
     PubMed     Abstract available
     
     
     
160. SETHI R, Becker J, Graaf J, Lower M, et al
     Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.
     PLoS Comput Biol. 2020;16:e1008397.
     PubMed     Abstract available
     
     
     
161. KULMANOV M, Hoehndorf R
     DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier.
     PLoS Comput Biol. 2020;16:e1008453.
     PubMed     Abstract available
     
     
     
162. JUNG H, Ventura T, Chung JS, Kim WJ, et al
     Twelve quick steps for genome assembly and annotation in the classroom.
     PLoS Comput Biol. 2020;16:e1008325.
     PubMed     Abstract available
     
     
     
163. YANG H, Wei Q, Li D, Wang Z, et al
     Cancer classification based on chromatin accessibility profiles with deep adversarial learning model.
     PLoS Comput Biol. 2020;16:e1008405.
     PubMed     Abstract available
     
     
     
164. CROOK OM, Geladaki A, Nightingale DJH, Vennard OL, et al
     A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection.
     PLoS Comput Biol. 2020;16:e1008288.
     PubMed     Abstract available
     
     
     
165. KAVEH K, McAvoy A, Chatterjee K, Nowak MA, et al
     The Moran process on 2-chromatic graphs.
     PLoS Comput Biol. 2020;16:e1008402.
     PubMed     Abstract available
     
     
     October 2020
166. RATHI KS, Arif S, Koptyra M, Naqvi AS, et al
     A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.
     PLoS Comput Biol. 2020;16:e1008263.
     PubMed     Abstract available
     
     
     
167. CLIFF OM, McLean N, Sintchenko V, Fair KM, et al
     Inferring evolutionary pathways and directed genotype networks of foodborne pathogens.
     PLoS Comput Biol. 2020;16:e1008401.
     PubMed     Abstract available
     
     
     
168. PEREIRA-SANTANA A, Gamboa-Tuz SD, Zhao T, Schranz ME, et al
     Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin.
     PLoS Comput Biol. 2020;16:e1008318.
     PubMed     Abstract available
     
     
     
169. NGUYEN M, Olson R, Shukla M, VanOeffelen M, et al
     Predicting antimicrobial resistance using conserved genes.
     PLoS Comput Biol. 2020;16:e1008319.
     PubMed     Abstract available
     
     
     
170. STEVENS I, Mukarram AK, Hortenhuber M, Meehan TF, et al
     Ten simple rules for annotating sequencing experiments.
     PLoS Comput Biol. 2020;16:e1008260.
     PubMed    
     
     
     
171. RODRIGUEZ JM, Pozo F, di Domenico T, Vazquez J, et al
     An analysis of tissue-specific alternative splicing at the protein level.
     PLoS Comput Biol. 2020;16:e1008287.
     PubMed     Abstract available
     
     
     
172. LAM TJ, Stamboulian M, Han W, Ye Y, et al
     Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species.
     PLoS Comput Biol. 2020;16:e1007951.
     PubMed     Abstract available
     
     
     
173. MCCARTER C, Howrylak J, Kim S
     Learning gene networks underlying clinical phenotypes using SNP perturbation.
     PLoS Comput Biol. 2020;16:e1007940.
     PubMed     Abstract available
     
     
     
174. KARCHER MD, Carvalho LM, Suchard MA, Dudas G, et al
     Estimating effective population size changes from preferentially sampled genetic sequences.
     PLoS Comput Biol. 2020;16:e1007774.
     PubMed     Abstract available
     
     
     
175. MANOLOV A, Konanov D, Fedorov D, Osmolovsky I, et al
     Genome Complexity Browser: Visualization and quantification of genome variability.
     PLoS Comput Biol. 2020;16:e1008222.
     PubMed     Abstract available
     
     
     
176. KOJIMA K, Tadaka S, Katsuoka F, Tamiya G, et al
     A genotype imputation method for de-identified haplotype reference information by using recurrent neural network.
     PLoS Comput Biol. 2020;16:e1008207.
     PubMed     Abstract available
     
     
     
177. M A BASHER AR, McLaughlin RJ, Hallam SJ
     Metabolic pathway inference using multi-label classification with rich pathway features.
     PLoS Comput Biol. 2020;16:e1008174.
     PubMed     Abstract available
     
     
     September 2020
178. ZHAO Z, Sokhansanj BA, Malhotra C, Zheng K, et al
     Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization.
     PLoS Comput Biol. 2020;16:e1008269.
     PubMed     Abstract available
     
     
     
179. FIAUX PC, Chen HV, Chen PB, Chen AR, et al
     Discovering functional sequences with RELICS, an analysis method for CRISPR screens.
     PLoS Comput Biol. 2020;16:e1008194.
     PubMed     Abstract available
     
     
     
180. RAPPOPORT N, Safra R, Shamir R
     MONET: Multi-omic module discovery by omic selection.
     PLoS Comput Biol. 2020;16:e1008182.
     PubMed     Abstract available
     
     
     
181. POLITANO G, Benso A
     IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis.
     PLoS Comput Biol. 2020;16:e1008238.
     PubMed     Abstract available
     
     
     August 2020
182. YAO E, Buels R, Stein L, Sen TZ, et al
     JBrowse Connect: A server API to connect JBrowse instances and users.
     PLoS Comput Biol. 2020;16:e1007261.
     PubMed     Abstract available
     
     
     
183. CASEY JR, Follows MJ
     A steady-state model of microbial acclimation to substrate limitation.
     PLoS Comput Biol. 2020;16:e1008140.
     PubMed     Abstract available
     
     

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