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Articles published in PLoS Comput Biol

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

  2. 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

  3. 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
  4. 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

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

  6. 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

  7. 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

  8. 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
  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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
  15. 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

  16. 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

  17. 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

  18. 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

  19. 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
  20. WICK RR, Holt KE
    Polypolish: Short-read polishing of long-read bacterial genome assemblies.
    PLoS Comput Biol. 2022;18:e1009802.
    PubMed     Abstract available

  21. 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

  22. 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
  23. 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.

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

  25. 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

  26. 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
  27. 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

  28. 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

  29. 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

  30. 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

  31. 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
  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

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

  40. 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
  41. 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

  42. 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

  43. 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

  44. 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

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

  46. 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
  47. 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

  48. 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

  49. 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

  50. 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

  51. 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
  52. 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

  53. 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

  54. 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
  55. 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

  56. 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

  57. 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

  58. 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
  59. SUKUMARAN J, Holder MT, Knowles LL
    Incorporating the speciation process into species delimitation.
    PLoS Comput Biol. 2021;17:e1008924.
    PubMed     Abstract available

  60. 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

  61. 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

  62. 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

  63. 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
  64. 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

  65. 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
  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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
  75. RATNIKOV BI, Cieplak P, Remacle AG, Nguyen E, et al
    Quantitative profiling of protease specificity.
    PLoS Comput Biol. 2021;17:e1008101.
    PubMed     Abstract available

  76. 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

  77. SOMMER MJ, Salzberg SL
    Balrog: A universal protein model for prokaryotic gene prediction.
    PLoS Comput Biol. 2021;17:e1008727.
    PubMed     Abstract available

  78. 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

  79. JACKSON M, Kavoussanakis K, Wallace EWJ
    Using prototyping to choose a bioinformatics workflow management system.
    PLoS Comput Biol. 2021;17:e1008622.
    PubMed     Abstract available

  80. TUNG HR, Durrett R
    Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective.
    PLoS Comput Biol. 2021;17:e1008701.
    PubMed     Abstract available

  81. 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

  82. 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

  83. 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

  84. 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
  85. 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

  86. 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

  87. 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

  88. KHARERIN H, Bai L
    Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.
    PLoS Comput Biol. 2021;17:e1008560.
    PubMed     Abstract available

  89. 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

  90. 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

  91. 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

  92. 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

  93. 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
  94. 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
  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. 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
  103. 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

  104. 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

  105. 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

  106. 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

  107. STEVENS I, Mukarram AK, Hortenhuber M, Meehan TF, et al
    Ten simple rules for annotating sequencing experiments.
    PLoS Comput Biol. 2020;16:e1008260.

  108. 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

  109. 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

  110. MCCARTER C, Howrylak J, Kim S
    Learning gene networks underlying clinical phenotypes using SNP perturbation.
    PLoS Comput Biol. 2020;16:e1007940.
    PubMed     Abstract available

  111. 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

  112. 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

  113. 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

  114. 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
  115. 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.
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    Discovering functional sequences with RELICS, an analysis method for CRISPR screens.
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  117. RAPPOPORT N, Safra R, Shamir R
    MONET: Multi-omic module discovery by omic selection.
    PLoS Comput Biol. 2020;16:e1008182.
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  118. POLITANO G, Benso A
    IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis.
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    August 2020
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    Inferring the ancestry of parents and grandparents from genetic data.
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    JBrowse Connect: A server API to connect JBrowse instances and users.
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  121. CASEY JR, Follows MJ
    A steady-state model of microbial acclimation to substrate limitation.
    PLoS Comput Biol. 2020;16:e1008140.
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    July 2020
  122. KELLEY DR
    Cross-species regulatory sequence activity prediction.
    PLoS Comput Biol. 2020;16:e1008050.
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    Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections.
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    June 2020
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    A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data.
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    G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation.
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    May 2020
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    Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis.
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    Predicting host taxonomic information from viral genomes: A comparison of feature representations.
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  128. LE GOALLEC A, Tierney BT, Luber JM, Cofer EM, et al
    A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type.
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    April 2020
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    High-dimensional mediation analysis in survival models.
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    DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data.
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    Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation.
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    Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks.
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    Multiview learning for understanding functional multiomics.
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    March 2020
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    Comparative study of population genomic approaches for mapping colony-level traits.
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    PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
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    SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures.
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    ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis.
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    February 2020
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    Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.
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    Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6,700 cancer genomes.
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    Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
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    CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer.
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    January 2020
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    Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome.
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    ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.
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    December 2019
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    Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.
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    Representation learning of genomic sequence motifs with convolutional neural networks.
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    November 2019
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    A novel network control model for identifying personalized driver genes in cancer.
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    Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity.
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    Clustering-independent analysis of genomic data using spectral simplicial theory.
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    Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps.
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    Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
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    Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.
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    Direct prediction of regulatory elements from partial data without imputation.
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    Bayesian inference of metabolic kinetics from genome-scale multiomics data.
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    Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.
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    October 2019
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    Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers.
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    EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions.
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    Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise.
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    TAPES: A tool for assessment and prioritisation in exome studies.
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    September 2019
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    Unified feature association networks through integration of transcriptomic and proteomic data.
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    August 2019
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    Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
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    Motion, fixation probability and the choice of an evolutionary process.
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    CNEr: A toolkit for exploring extreme noncoding conservation.
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    Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration.
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    July 2019
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    Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.
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    June 2019
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    Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology.
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    Modern technologies and algorithms for scaffolding assembled genomes.
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    May 2019
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    Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification.
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    Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features.
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    Efficient algorithms to discover alterations with complementary functional association in cancer.
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    BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
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