Home The Word Brain My Amedeo FAQ Privacy About Flying Publisher   


The Angels Initiative

Stroke prevention


  Genetics

  Free Subscription


Articles published in PLoS Comput Biol

Retrieve available abstracts of 170 articles:
HTML format



Single Articles


    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.
    PubMed    


  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.
    PubMed    


  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.
    PLoS Comput Biol. 2020;16:e1008269.
    PubMed     Abstract available


  116. FIAUX PC, Chen HV, Chen PB, Chen AR, et al
    Discovering functional sequences with RELICS, an analysis method for CRISPR screens.
    PLoS Comput Biol. 2020;16:e1008194.
    PubMed     Abstract available


  117. RAPPOPORT N, Safra R, Shamir R
    MONET: Multi-omic module discovery by omic selection.
    PLoS Comput Biol. 2020;16:e1008182.
    PubMed     Abstract available


  118. POLITANO G, Benso A
    IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis.
    PLoS Comput Biol. 2020;16:e1008238.
    PubMed     Abstract available


    August 2020
  119. PEI J, Zhang Y, Nielsen R, Wu Y, et al
    Inferring the ancestry of parents and grandparents from genetic data.
    PLoS Comput Biol. 2020;16:e1008065.
    PubMed     Abstract available


  120. YAO E, Buels R, Stein L, Sen TZ, et al
    JBrowse Connect: A server API to connect JBrowse instances and users.
    PLoS Comput Biol. 2020;16:e1007261.
    PubMed     Abstract available


  121. CASEY JR, Follows MJ
    A steady-state model of microbial acclimation to substrate limitation.
    PLoS Comput Biol. 2020;16:e1008140.
    PubMed     Abstract available


    July 2020
  122. KELLEY DR
    Cross-species regulatory sequence activity prediction.
    PLoS Comput Biol. 2020;16:e1008050.
    PubMed     Abstract available


  123. KRIEGER MS, Denison CE, Anderson TL, Nowak MA, et al
    Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections.
    PLoS Comput Biol. 2020;16:e1008010.
    PubMed     Abstract available


    June 2020
  124. LAMPARTER D, Bhatnagar R, Hebestreit K, Belgard TG, et al
    A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data.
    PLoS Comput Biol. 2020;16:e1007770.
    PubMed     Abstract available


  125. SARGENT L, Liu Y, Leung W, Mortimer NT, et al
    G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation.
    PLoS Comput Biol. 2020;16:e1007863.
    PubMed     Abstract available


    May 2020
  126. BRUCKER A, Lu W, Marceau West R, Yu QY, et al
    Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis.
    PLoS Comput Biol. 2020;16:e1007797.
    PubMed     Abstract available


  127. YOUNG F, Rogers S, Robertson DL
    Predicting host taxonomic information from viral genomes: A comparison of feature representations.
    PLoS Comput Biol. 2020;16:e1007894.
    PubMed     Abstract available


  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.
    PLoS Comput Biol. 2020;16:e1007895.
    PubMed     Abstract available


    April 2020
  129. LUO C, Fa B, Yan Y, Wang Y, et al
    High-dimensional mediation analysis in survival models.
    PLoS Comput Biol. 2020;16:e1007768.
    PubMed     Abstract available


  130. JIANG Y, Giase G, Grennan K, Shieh AW, et al
    DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data.
    PLoS Comput Biol. 2020;16:e1007522.
    PubMed     Abstract available


  131. BUSTO-MONER L, Morival J, Ren H, Fahim A, et al
    Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation.
    PLoS Comput Biol. 2020;16:e1007195.
    PubMed     Abstract available


  132. KLEIN HU, Schafer M, Bennett DA, Schwender H, et al
    Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks.
    PLoS Comput Biol. 2020;16:e1007771.
    PubMed     Abstract available


  133. NGUYEN ND, Wang D
    Multiview learning for understanding functional multiomics.
    PLoS Comput Biol. 2020;16:e1007677.
    PubMed     Abstract available


    March 2020
  134. INBAR S, Cohen P, Yahav T, Privman E, et al
    Comparative study of population genomic approaches for mapping colony-level traits.
    PLoS Comput Biol. 2020;16:e1007653.
    PubMed     Abstract available


  135. GAUTREAU G, Bazin A, Gachet M, Planel R, et al
    PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
    PLoS Comput Biol. 2020;16:e1007732.
    PubMed     Abstract available


  136. KATHURIA K, Ratan A
    SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures.
    PLoS Comput Biol. 2020;16:e1007737.
    PubMed     Abstract available


  137. MOORADIAN AD, van der Post S, Naegle KM, Held JM, et al
    ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis.
    PLoS Comput Biol. 2020;16:e1007741.
    PubMed     Abstract available


    February 2020
  138. REIMERING S, Munoz S, McHardy AC
    Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.
    PLoS Comput Biol. 2020;16:e1007101.
    PubMed     Abstract available


  139. LIU C, Zhao J, Lu W, Dai Y, et al
    Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6,700 cancer genomes.
    PLoS Comput Biol. 2020;16:e1007701.
    PubMed     Abstract available


  140. LOVE MI, Soneson C, Hickey PF, Johnson LK, et al
    Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
    PLoS Comput Biol. 2020;16:e1007664.
    PubMed     Abstract available


  141. DEROUAULT P, Chauzeix J, Rizzo D, Miressi F, et al
    CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer.
    PLoS Comput Biol. 2020;16:e1007503.
    PubMed     Abstract available


    January 2020
  142. CASCARINA SM, Elder MR, Ross ED
    Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome.
    PLoS Comput Biol. 2020;16:e1007487.
    PubMed     Abstract available


  143. LAVENDER CA, Shapiro AJ, Day FS, Fargo DC, et al
    ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.
    PLoS Comput Biol. 2020;16:e1007571.
    PubMed     Abstract available


    December 2019
  144. JANDRASITS C, Kroger S, Haas W, Renard BY, et al
    Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.
    PLoS Comput Biol. 2019;15:e1007527.
    PubMed     Abstract available


  145. KOO PK, Eddy SR
    Representation learning of genomic sequence motifs with convolutional neural networks.
    PLoS Comput Biol. 2019;15:e1007560.
    PubMed     Abstract available


    November 2019
  146. GUO WF, Zhang SW, Zeng T, Li Y, et al
    A novel network control model for identifying personalized driver genes in cancer.
    PLoS Comput Biol. 2019;15:e1007520.
    PubMed     Abstract available


  147. WATTS GS, Thornton JE Jr, Youens-Clark K, Ponsero AJ, et al
    Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity.
    PLoS Comput Biol. 2019;15:e1006863.
    PubMed     Abstract available


  148. GOVEK KW, Yamajala VS, Camara PG
    Clustering-independent analysis of genomic data using spectral simplicial theory.
    PLoS Comput Biol. 2019;15:e1007509.
    PubMed     Abstract available


  149. ZHENG Y, Wiehe T
    Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps.
    PLoS Comput Biol. 2019;15:e1007426.
    PubMed     Abstract available


  150. PLYUSNIN I, Holm L, Toronen P
    Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
    PLoS Comput Biol. 2019;15:e1007419.
    PubMed     Abstract available


  151. JANSEN C, Ramirez RN, El-Ali NC, Gomez-Cabrero D, et al
    Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.
    PLoS Comput Biol. 2019;15:e1006555.
    PubMed     Abstract available


  152. ZHANG Y, Mahony S
    Direct prediction of regulatory elements from partial data without imputation.
    PLoS Comput Biol. 2019;15:e1007399.
    PubMed     Abstract available


  153. ST JOHN PC, Strutz J, Broadbelt LJ, Tyo KEJ, et al
    Bayesian inference of metabolic kinetics from genome-scale multiomics data.
    PLoS Comput Biol. 2019;15:e1007424.
    PubMed     Abstract available


  154. VIJAYABASKAR MS, Goode DK, Obier N, Lichtinger M, et al
    Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.
    PLoS Comput Biol. 2019;15:e1007337.
    PubMed     Abstract available


    October 2019
  155. WOOTEN DJ, Groves SM, Tyson DR, Liu Q, et al
    Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers.
    PLoS Comput Biol. 2019;15:e1007343.
    PubMed     Abstract available


  156. GAO T, Qian J
    EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions.
    PLoS Comput Biol. 2019;15:e1007436.
    PubMed     Abstract available


  157. GOMEZ-SCHIAVON M, Buchler NE
    Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise.
    PLoS Comput Biol. 2019;15:e1007364.
    PubMed     Abstract available


  158. XAVIER A, Scott RJ, Talseth-Palmer BA
    TAPES: A tool for assessment and prioritisation in exome studies.
    PLoS Comput Biol. 2019;15:e1007453.
    PubMed     Abstract available


    September 2019
  159. MCCLURE RS, Wendler JP, Adkins JN, Swanstrom J, et al
    Unified feature association networks through integration of transcriptomic and proteomic data.
    PLoS Comput Biol. 2019;15:e1007241.
    PubMed     Abstract available


    August 2019
  160. GHURYE J, Rhie A, Walenz BP, Schmitt A, et al
    Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
    PLoS Comput Biol. 2019;15:e1007273.
    PubMed     Abstract available


  161. HERRERIAS-AZCUE F, Perez-Munuzuri V, Galla T
    Motion, fixation probability and the choice of an evolutionary process.
    PLoS Comput Biol. 2019;15:e1007238.
    PubMed     Abstract available


  162. TAN G, Polychronopoulos D, Lenhard B
    CNEr: A toolkit for exploring extreme noncoding conservation.
    PLoS Comput Biol. 2019;15:e1006940.
    PubMed     Abstract available


  163. YANG J, Muller NF, Bouckaert R, Xu B, et al
    Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration.
    PLoS Comput Biol. 2019;15:e1007189.
    PubMed     Abstract available


    July 2019
  164. SEILER E, Trappe K, Renard BY
    Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.
    PLoS Comput Biol. 2019;15:e1007208.
    PubMed     Abstract available


    June 2019
  165. LIM H, He D, Qiu Y, Krawczuk P, et al
    Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology.
    PLoS Comput Biol. 2019;15:e1006619.
    PubMed     Abstract available


  166. GHURYE J, Pop M
    Modern technologies and algorithms for scaffolding assembled genomes.
    PLoS Comput Biol. 2019;15:e1006994.
    PubMed     Abstract available


    May 2019
  167. OHAYON S, Girsault A, Nasser M, Shen-Orr S, et al
    Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification.
    PLoS Comput Biol. 2019;15:e1007067.
    PubMed     Abstract available


  168. KNOWLES DA, Bouchard G, Plevritis S
    Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features.
    PLoS Comput Biol. 2019;15:e1006743.
    PubMed     Abstract available


  169. SARTO BASSO R, Hochbaum DS, Vandin F
    Efficient algorithms to discover alterations with complementary functional association in cancer.
    PLoS Comput Biol. 2019;15:e1006802.
    PubMed     Abstract available


    April 2019
  170. LACHANCE JC, Lloyd CJ, Monk JM, Yang L, et al
    BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
    PLoS Comput Biol. 2019;15:e1006971.
    PubMed     Abstract available


Thank you for your interest in scientific medicine.


AMEDEO Genetics is free of charge.
This policy is made possible thanks to a media sponsorship by Boehringer Ingelheim.

Design: