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2049 Chinese

The 20K Word Road to Mandarin Proficiency

By B. S. Kamps et al.


  Genetics

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Articles published in PLoS Comput Biol

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Single Articles


    February 2024
  1. 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


  2. 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
  3. 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


  4. 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


  5. PFLUG FG, Bhat D, Pigolotti S
    Genome replication in asynchronously growing microbial populations.
    PLoS Comput Biol. 2024;20:e1011753.
    PubMed     Abstract available


  6. 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


  7. 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


  8. 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
  9. 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
  10. 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


  11. 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


  12. 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


  13. 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


  14. 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


  15. 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
  16. 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


  17. KOSINSKI JG, Zywicki M
    AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals.
    PLoS Comput Biol. 2023;19:e1011527.
    PubMed     Abstract available


  18. 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
  19. 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


  20. 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


  21. 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


  22. 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
  23. CHARI T, Pachter L
    The specious art of single-cell genomics.
    PLoS Comput Biol. 2023;19:e1011288.
    PubMed     Abstract available


  24. 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


  25. 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
  26. 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


  27. 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
  28. 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
  29. 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
  30. 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


  31. 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


  32. 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
  33. 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


  34. 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


  35. 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


  36. 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


  37. 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
  38. 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


  39. 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
  40. 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
  41. 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    


  42. 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


  43. 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
  44. 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    


  45. 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
  46. 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


  47. 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


  48. 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
  49. 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


  50. UPADHYA G, Steinrucken M
    Robust inference of population size histories from genomic sequencing data.
    PLoS Comput Biol. 2022;18:e1010419.
    PubMed     Abstract available


  51. 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
  52. 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


  53. 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


  54. 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


  55. 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


  56. 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
  57. 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
  58. 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


  59. 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
  60. NGUYEN QP, Hoen AG, Frost HR
    CBEA: Competitive balances for taxonomic enrichment analysis.
    PLoS Comput Biol. 2022;18:e1010091.
    PubMed     Abstract available


  61. 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


  62. 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
  63. 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


  64. DEFFNER D, Kandler A, Fogarty L
    Effective population size for culturally evolving traits.
    PLoS Comput Biol. 2022;18:e1009430.
    PubMed     Abstract available


  65. 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


  66. 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


  67. 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
  68. 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


  69. 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


  70. 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


  71. 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


  72. 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


  73. 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
  74. 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


  75. 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


  76. 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


  77. 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


  78. 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
  79. WICK RR, Holt KE
    Polypolish: Short-read polishing of long-read bacterial genome assemblies.
    PLoS Comput Biol. 2022;18:e1009802.
    PubMed     Abstract available


  80. 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


  81. 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
  82. 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    


  83. LIU L, Zhang B, Hyeon C
    Extracting multi-way chromatin contacts from Hi-C data.
    PLoS Comput Biol. 2021;17:e1009669.
    PubMed     Abstract available


  84. 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


  85. 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
  86. 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


  87. 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


  88. 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


  89. 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


  90. 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
  91. 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


  92. 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


  93. 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


  94. 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


  95. 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


  96. 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


  97. 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


  98. DEMAERE MZ, Darling AE
    qc3C: Reference-free quality control for Hi-C sequencing data.
    PLoS Comput Biol. 2021;17:e1008839.
    PubMed     Abstract available


  99. 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
  100. 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


  101. 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


  102. 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


  103. 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


  104. TANAKA H, Kreisberg JF, Ideker T
    Genetic dissection of complex traits using hierarchical biological knowledge.
    PLoS Comput Biol. 2021;17:e1009373.
    PubMed     Abstract available


  105. 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
  106. 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


  107. 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


  108. 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


  109. 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


  110. 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
  111. 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


  112. 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


  113. 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.
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    June 2021
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    Histone tails cooperate to control the breathing of genomic nucleosomes.
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  115. AMBROS S, Gomez-Munoz N, Gimenez-Santamarina S, Sanchez-Vicente J, et al
    Molecular signatures of silencing suppression degeneracy from a complex RNA virus.
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  116. PROST V, Gazut S, Bruls T
    A zero inflated log-normal model for inference of sparse microbial association networks.
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  117. ZENG P, Lin Z
    coupleCoC+: An information-theoretic co-clustering-based transfer learning framework for the integrative analysis of single-cell genomic data.
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    May 2021
  118. SUKUMARAN J, Holder MT, Knowles LL
    Incorporating the speciation process into species delimitation.
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  119. BAHMANI A, Ferriter K, Krishnan V, Alavi A, et al
    Swarm: A federated cloud framework for large-scale variant analysis.
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  120. LUI LM, Nielsen TN, Arkin AP
    A method for achieving complete microbial genomes and improving bins from metagenomics data.
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  121. HJORLEIFSSON ELDJARN G, Ramsay A, van der Hooft JJJ, Duncan KR, et al
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    April 2021
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    Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.
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  124. UZUNANGELOV V, Wong CK, Stuart JM
    Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.
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    March 2021
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  127. SUN R, Nikolakopoulos AN
    Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors.
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    Biological impact of mutually exclusive exon switching.
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  131. CHELOSHKINA K, Poptsova M
    Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements.
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    February 2021
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  138. JACKSON M, Kavoussanakis K, Wallace EWJ
    Using prototyping to choose a bioinformatics workflow management system.
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  139. TUNG HR, Durrett R
    Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective.
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    Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways.
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    KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions.
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    January 2021
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  147. KHARERIN H, Bai L
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    December 2020
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    November 2020
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    Identifying longevity associated genes by integrating gene expression and curated annotations.
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    October 2020
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    Metabolic pathway inference using multi-label classification with rich pathway features.
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    September 2020
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    Discovering functional sequences with RELICS, an analysis method for CRISPR screens.
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  177. POLITANO G, Benso A
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    August 2020
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    A steady-state model of microbial acclimation to substrate limitation.
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