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Genetics

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March 2024
1. 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
   
   
   
2. 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
3. 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
   
   
   
4. 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
5. 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
   
   
   
6. 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
   
   
   
7. PFLUG FG, Bhat D, Pigolotti S
   Genome replication in asynchronously growing microbial populations.
   PLoS Comput Biol. 2024;20:e1011753.
   PubMed     Abstract available
   
   
   
8. 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
   
   
   
9. 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
   
   
   
10. 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
11. 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
12. 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
    
    
    
13. 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
    
    
    
14. 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
    
    
    
15. 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
    
    
    
16. 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
    
    
    
17. 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
18. 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
    
    
    
19. KOSINSKI JG, Zywicki M
    AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals.
    PLoS Comput Biol. 2023;19:e1011527.
    PubMed     Abstract available
    
    
    
20. 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
21. 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
    
    
    
22. 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
    
    
    
23. 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
    
    
    
24. 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
25. CHARI T, Pachter L
    The specious art of single-cell genomics.
    PLoS Comput Biol. 2023;19:e1011288.
    PubMed     Abstract available
    
    
    
26. 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
    
    
    
27. 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
28. 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
    
    
    
29. 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
30. 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
31. 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
32. 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
    
    
    
33. 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
    
    
    
34. 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
35. 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
    
    
    
36. 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
    
    
    
37. 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
    
    
    
38. 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
    
    
    
39. 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
40. 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
    
    
    
41. 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
42. 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
43. 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    
    
    
    
44. 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
    
    
    
45. 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
46. 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    
    
    
    
47. 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
48. 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
    
    
    
49. 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
    
    
    
50. 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
51. 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
    
    
    
52. UPADHYA G, Steinrucken M
    Robust inference of population size histories from genomic sequencing data.
    PLoS Comput Biol. 2022;18:e1010419.
    PubMed     Abstract available
    
    
    
53. 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
54. 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
    
    
    
55. 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
    
    
    
56. 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
    
    
    
57. 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
    
    
    
58. 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
59. 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
60. 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
    
    
    
61. 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
62. NGUYEN QP, Hoen AG, Frost HR
    CBEA: Competitive balances for taxonomic enrichment analysis.
    PLoS Comput Biol. 2022;18:e1010091.
    PubMed     Abstract available
    
    
    
63. 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
    
    
    
64. 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
65. 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
    
    
    
66. DEFFNER D, Kandler A, Fogarty L
    Effective population size for culturally evolving traits.
    PLoS Comput Biol. 2022;18:e1009430.
    PubMed     Abstract available
    
    
    
67. 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
    
    
    
68. 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
    
    
    
69. 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
70. 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
    
    
    
71. 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
    
    
    
72. 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
    
    
    
73. 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
    
    
    
74. 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
    
    
    
75. 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
76. 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
    
    
    
77. 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
    
    
    
78. 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
    
    
    
79. 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
    
    
    
80. 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
81. WICK RR, Holt KE
    Polypolish: Short-read polishing of long-read bacterial genome assemblies.
    PLoS Comput Biol. 2022;18:e1009802.
    PubMed     Abstract available
    
    
    
82. 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
    
    
    
83. 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
84. 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    
    
    
    
85. LIU L, Zhang B, Hyeon C
    Extracting multi-way chromatin contacts from Hi-C data.
    PLoS Comput Biol. 2021;17:e1009669.
    PubMed     Abstract available
    
    
    
86. 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
    
    
    
87. 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
88. 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
    
    
    
89. 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
    
    
    
90. 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
    
    
    
91. 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
    
    
    
92. 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
93. 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
    
    
    
94. 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
    
    
    
95. 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
    
    
    
96. 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
    
    
    
97. 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
    
    
    
98. 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
    
    
    
99. 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
    
    
    
100. DEMAERE MZ, Darling AE
     qc3C: Reference-free quality control for Hi-C sequencing data.
     PLoS Comput Biol. 2021;17:e1008839.
     PubMed     Abstract available
     
     
     
101. 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
102. 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
     
     
     
103. 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
     
     
     
104. 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
     
     
     
105. 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
     
     
     
106. TANAKA H, Kreisberg JF, Ideker T
     Genetic dissection of complex traits using hierarchical biological knowledge.
     PLoS Comput Biol. 2021;17:e1009373.
     PubMed     Abstract available
     
     
     
107. 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
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