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 136 articles:
HTML format



Single Articles


    November 2022
  1. 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    


  2. 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
  3. 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


  4. 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


  5. 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
  6. 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


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


  8. 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
  9. 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


  10. 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


  11. 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


  12. 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


  13. 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
  14. 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
  15. 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


  16. 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
  17. NGUYEN QP, Hoen AG, Frost HR
    CBEA: Competitive balances for taxonomic enrichment analysis.
    PLoS Comput Biol. 2022;18:e1010091.
    PubMed     Abstract available


  18. 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


  19. 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
  20. 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


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


  22. 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


  23. 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


  24. 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
  25. 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


  26. 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


  27. 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


  28. 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


  29. 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


  30. 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
  31. 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


  32. 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


  33. 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


  34. 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


  35. 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
  36. WICK RR, Holt KE
    Polypolish: Short-read polishing of long-read bacterial genome assemblies.
    PLoS Comput Biol. 2022;18:e1009802.
    PubMed     Abstract available


  37. 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


  38. 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
  39. 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    


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


  41. 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


  42. 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
  43. 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


  44. 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


  45. 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


  46. 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


  47. 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
  48. 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


  49. 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


  50. 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


  51. 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


  52. 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


  53. 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


  54. 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


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


  56. 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
  57. 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


  58. 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


  59. 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


  60. 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


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


  62. 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
  63. 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


  64. 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


  65. 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


  66. 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


  67. 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
  68. 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


  69. 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


  70. 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
  71. 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


  72. 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


  73. 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


  74. 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
  75. SUKUMARAN J, Holder MT, Knowles LL
    Incorporating the speciation process into species delimitation.
    PLoS Comput Biol. 2021;17:e1008924.
    PubMed     Abstract available


  76. 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


  77. 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


  78. 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


  79. 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
  80. 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


  81. 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
  82. 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


  83. 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


  84. 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


  85. 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


  86. 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


  87. 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


  88. 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


  89. 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


  90. 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
  91. RATNIKOV BI, Cieplak P, Remacle AG, Nguyen E, et al
    Quantitative profiling of protease specificity.
    PLoS Comput Biol. 2021;17:e1008101.
    PubMed     Abstract available


  92. 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


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


  94. 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


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


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


  97. 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


  98. 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


  99. 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


  100. 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
  101. 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


  102. 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


  103. 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


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


  105. 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


  106. 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


  107. 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


  108. 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


  109. 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
  110. 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
  111. 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


  112. 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


  113. 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


  114. 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


  115. 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


  116. 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


  117. 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


  118. 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
  119. 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


  120. 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


  121. 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


  122. 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


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


  124. 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


  125. 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


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


  127. 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


  128. 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


  129. 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


  130. 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
  131. 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


  132. 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


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


  134. 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
  135. 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


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