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Articles published in PLoS Comput Biol

Retrieve available abstracts of 66 articles:
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Single Articles


    September 2017
  1. MURRAY KD, Webers C, Ong CS, Borevitz J, et al
    kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.
    PLoS Comput Biol. 2017;13:e1005727.
    PubMed     Text format     Abstract available


  2. KIM M, Eetemadi A, Tagkopoulos I
    DeepPep: Deep proteome inference from peptide profiles.
    PLoS Comput Biol. 2017;13:e1005661.
    PubMed     Text format     Abstract available


  3. DUMEAUX V, Fjukstad B, Fjosne HE, Frantzen JO, et al
    Interactions between the tumor and the blood systemic response of breast cancer patients.
    PLoS Comput Biol. 2017;13:e1005680.
    PubMed     Text format     Abstract available


  4. LABHSETWAR P, Melo MCR, Cole JA, Luthey-Schulten Z, et al
    Population FBA predicts metabolic phenotypes in yeast.
    PLoS Comput Biol. 2017;13:e1005728.
    PubMed     Text format     Abstract available


    August 2017
  5. MONTI R, Barozzi I, Osterwalder M, Lee E, et al
    Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.
    PLoS Comput Biol. 2017;13:e1005720.
    PubMed     Text format     Abstract available


  6. AMAR D, Shamir R, Yekutieli D
    Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.
    PLoS Comput Biol. 2017;13:e1005700.
    PubMed     Text format     Abstract available


  7. FUKUYAMA J, Rumker L, Sankaran K, Jeganathan P, et al
    Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
    PLoS Comput Biol. 2017;13:e1005706.
    PubMed     Text format     Abstract available


  8. BASSANI-STERNBERG M, Chong C, Guillaume P, Solleder M, et al
    Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity.
    PLoS Comput Biol. 2017;13:e1005725.
    PubMed     Text format     Abstract available


    July 2017
  9. SHAO B, Yuan H, Zhang R, Wang X, et al
    Reconstructing the regulatory circuit of cell fate determination in yeast mating response.
    PLoS Comput Biol. 2017;13:e1005671.
    PubMed     Text format     Abstract available


  10. ATAMAN M, Hatzimanikatis V
    lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites.
    PLoS Comput Biol. 2017;13:e1005513.
    PubMed     Text format     Abstract available


  11. LI Y, Jourdain AA, Calvo SE, Liu JS, et al
    CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets.
    PLoS Comput Biol. 2017;13:e1005653.
    PubMed     Text format     Abstract available


  12. GURSOY G, Xu Y, Liang J
    Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model.
    PLoS Comput Biol. 2017;13:e1005658.
    PubMed     Text format     Abstract available


  13. GILPIN W, Feldman MW
    A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape.
    PLoS Comput Biol. 2017;13:e1005644.
    PubMed     Text format     Abstract available


    June 2017
  14. G C C L CARDENAS R, D Linhares N, L Ferreira R, Pena SDJ, et al
    Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders.
    PLoS Comput Biol. 2017;13:e1005520.
    PubMed     Text format     Abstract available


  15. JONGENEEL CV, Achinike-Oduaran O, Adebiyi E, Adebiyi M, et al
    Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.
    PLoS Comput Biol. 2017;13:e1005419.
    PubMed     Text format     Abstract available


  16. LAI EY, Chen YH, Wu KP
    A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data.
    PLoS Comput Biol. 2017;13:e1005601.
    PubMed     Text format     Abstract available


  17. HU Y, Lu Q, Powles R, Yao X, et al
    Leveraging functional annotations in genetic risk prediction for human complex diseases.
    PLoS Comput Biol. 2017;13:e1005589.
    PubMed     Text format     Abstract available


    May 2017
  18. SUOMI T, Seyednasrollah F, Jaakkola MK, Faux T, et al
    ROTS: An R package for reproducibility-optimized statistical testing.
    PLoS Comput Biol. 2017;13:e1005562.
    PubMed     Text format     Abstract available


  19. CHAN SHJ, Simons MN, Maranas CD
    SteadyCom: Predicting microbial abundances while ensuring community stability.
    PLoS Comput Biol. 2017;13:e1005539.
    PubMed     Text format     Abstract available


  20. LI Y, Zhou X, Zhai Z, Li T, et al
    Co-occurring protein phosphorylation are functionally associated.
    PLoS Comput Biol. 2017;13:e1005502.
    PubMed     Text format     Abstract available


    March 2017
  21. BASILE W, Sachenkova O, Light S, Elofsson A, et al
    High GC content causes orphan proteins to be intrinsically disordered.
    PLoS Comput Biol. 2017;13:e1005375.
    PubMed     Text format     Abstract available


    February 2017
  22. MAGEE D, Suchard MA, Scotch M
    Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.
    PLoS Comput Biol. 2017;13:e1005389.
    PubMed     Text format     Abstract available


    January 2017
  23. WU T, Wang L, Fu F
    Coevolutionary dynamics of phenotypic diversity and contingent cooperation.
    PLoS Comput Biol. 2017;13:e1005363.
    PubMed     Text format     Abstract available


  24. HWANG HY, Wang J
    Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans.
    PLoS Comput Biol. 2017;13:e1005369.
    PubMed     Text format     Abstract available


  25. SAEEDGHALATI M, Farahpour F, Budeus B, Lange A, et al
    Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes.
    PLoS Comput Biol. 2017;13:e1005362.
    PubMed     Text format     Abstract available


  26. PRIGENT S, Frioux C, Dittami SM, Thiele S, et al
    Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.
    PLoS Comput Biol. 2017;13:e1005276.
    PubMed     Text format     Abstract available


    June 2016
  27. BRANKOVICS B, Zhang H, van Diepeningen AD, van der Lee TA, et al
    GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.
    PLoS Comput Biol. 2016;12:e1004753.
    PubMed     Text format     Abstract available


    May 2016
  28. BENDL J, Musil M, Stourac J, Zendulka J, et al
    PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
    PLoS Comput Biol. 2016;12:e1004962.
    PubMed     Text format     Abstract available


  29. BOHLER A, Wu G, Kutmon M, Pradhana LA, et al
    Reactome from a WikiPathways Perspective.
    PLoS Comput Biol. 2016;12:e1004941.
    PubMed     Text format     Abstract available


  30. BRECKELS LM, Holden SB, Wojnar D, Mulvey CM, et al
    Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.
    PLoS Comput Biol. 2016;12:e1004920.
    PubMed     Text format     Abstract available


  31. KELLEHER J, Etheridge AM, McVean G
    Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.
    PLoS Comput Biol. 2016;12:e1004842.
    PubMed     Text format     Abstract available


    April 2016
  32. BORNIGEN D, Tyekucheva S, Wang X, Rider JR, et al
    Computational Reconstruction of NFkappaB Pathway Interaction Mechanisms during Prostate Cancer.
    PLoS Comput Biol. 2016;12:e1004820.
    PubMed     Text format     Abstract available


  33. KENAH E, Britton T, Halloran ME, Longini IM Jr, et al
    Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees.
    PLoS Comput Biol. 2016;12:e1004869.
    PubMed     Text format     Abstract available


    March 2016
  34. VOGEL C
    Systems Approaches to the Eukaryotic Stress Response.
    PLoS Comput Biol. 2016;12:e1004757.
    PubMed     Text format    


  35. KARCHER MD, Palacios JA, Bedford T, Suchard MA, et al
    Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.
    PLoS Comput Biol. 2016;12:e1004789.
    PubMed     Text format     Abstract available


  36. GREENBURY SF, Schaper S, Ahnert SE, Louis AA, et al
    Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability.
    PLoS Comput Biol. 2016;12:e1004773.
    PubMed     Text format     Abstract available


  37. SHEEHAN S, Song YS
    Deep Learning for Population Genetic Inference.
    PLoS Comput Biol. 2016;12:e1004845.
    PubMed     Text format     Abstract available


    February 2016
  38. ORTEGA DR, Zhulin IB
    Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex.
    PLoS Comput Biol. 2016;12:e1004723.
    PubMed     Text format     Abstract available


  39. GUTURU H, Chinchali S, Clarke SL, Bejerano G, et al
    Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories.
    PLoS Comput Biol. 2016;12:e1004711.
    PubMed     Text format     Abstract available


  40. SENBABAOGLU Y, Sumer SO, Sanchez-Vega F, Bemis D, et al
    A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.
    PLoS Comput Biol. 2016;12:e1004765.
    PubMed     Text format     Abstract available


    January 2016
  41. LAMPARTER D, Marbach D, Rueedi R, Kutalik Z, et al
    Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.
    PLoS Comput Biol. 2016;12:e1004714.
    PubMed     Text format     Abstract available


    July 2015
  42. PERCHA B, Altman RB
    Learning the Structure of Biomedical Relationships from Unstructured Text.
    PLoS Comput Biol. 2015;11:e1004216.
    PubMed     Text format     Abstract available


  43. DEARLOVE BL, Frost SD
    Measuring Asymmetry in Time-Stamped Phylogenies.
    PLoS Comput Biol. 2015;11:e1004312.
    PubMed     Text format     Abstract available


  44. NUSSINOV R, Bonhoeffer S, Papin JA, Sporns O, et al
    From "What Is?" to "What Isn't?" Computational Biology.
    PLoS Comput Biol. 2015;11:e1004318.
    PubMed     Text format    


    May 2015
  45. ENGELMANN JC, Amann T, Ott-Rotzer B, Nutzel M, et al
    Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFkappaB Signaling in Hepatocellular Carcinoma.
    PLoS Comput Biol. 2015;11:e1004293.
    PubMed     Text format     Abstract available


  46. DIAMENT A, Tuller T
    Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints.
    PLoS Comput Biol. 2015;11:e1004298.
    PubMed     Text format     Abstract available


  47. KURTZ ZD, Muller CL, Miraldi ER, Littman DR, et al
    Sparse and compositionally robust inference of microbial ecological networks.
    PLoS Comput Biol. 2015;11:e1004226.
    PubMed     Text format     Abstract available


    March 2015
  48. ALBANESE D, De Filippo C, Cavalieri D, Donati C, et al
    Explaining diversity in metagenomic datasets by phylogenetic-based feature weighting.
    PLoS Comput Biol. 2015;11:e1004186.
    PubMed     Text format     Abstract available


  49. VISSER MD, McMahon SM, Merow C, Dixon PM, et al
    Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists.
    PLoS Comput Biol. 2015;11:e1004140.
    PubMed     Text format     Abstract available


  50. LIVNE OE, Han L, Alkorta-Aranburu G, Wentworth-Sheilds W, et al
    PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population.
    PLoS Comput Biol. 2015;11:e1004139.
    PubMed     Text format     Abstract available


  51. FORTNEY K, Griesman J, Kotlyar M, Pastrello C, et al
    Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data.
    PLoS Comput Biol. 2015;11:e1004068.
    PubMed     Text format     Abstract available


  52. WEIGHILL DA, Jacobson DA
    3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics.
    PLoS Comput Biol. 2015;11:e1004079.
    PubMed     Text format     Abstract available


  53. HUTCHISON AL, Maienschein-Cline M, Chiang AH, Tabei SM, et al
    Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data.
    PLoS Comput Biol. 2015;11:e1004094.
    PubMed     Text format     Abstract available


    February 2015
  54. CAUFIELD JH, Abreu M, Wimble C, Uetz P, et al
    Protein complexes in bacteria.
    PLoS Comput Biol. 2015;11:e1004107.
    PubMed     Text format     Abstract available


  55. ALLEN B, Sample C, Dementieva Y, Medeiros RC, et al
    The molecular clock of neutral evolution can be accelerated or slowed by asymmetric spatial structure.
    PLoS Comput Biol. 2015;11:e1004108.
    PubMed     Text format     Abstract available


  56. DUAN G, Walther D
    The roles of post-translational modifications in the context of protein interaction networks.
    PLoS Comput Biol. 2015;11:e1004049.
    PubMed     Text format     Abstract available


  57. DIDELOT X, Wilson DJ
    ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
    PLoS Comput Biol. 2015;11:e1004041.
    PubMed     Text format     Abstract available


    January 2015
  58. KASSAMBARA A, Reme T, Jourdan M, Fest T, et al
    GenomicScape: an easy-to-use web tool for gene expression data analysis. Application to investigate the molecular events in the differentiation of B cells into plasma cells.
    PLoS Comput Biol. 2015;11:e1004077.
    PubMed     Text format     Abstract available


  59. WILKE A, Bischof J, Harrison T, Brettin T, et al
    A RESTful API for accessing microbial community data for MG-RAST.
    PLoS Comput Biol. 2015;11:e1004008.
    PubMed     Text format     Abstract available


  60. PORTA PARDO E, Godzik A
    Analysis of individual protein regions provides novel insights on cancer pharmacogenomics.
    PLoS Comput Biol. 2015;11:e1004024.
    PubMed     Text format     Abstract available


    May 2014
  61. PAPAIX J, Burdon JJ, Lannou C, Thrall PH, et al
    Evolution of pathogen specialisation in a host metapopulation: joint effects of host and pathogen dispersal.
    PLoS Comput Biol. 2014;10:e1003633.
    PubMed     Text format     Abstract available


  62. FOGG CN, Kovats DE
    2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers.
    PLoS Comput Biol. 2014;10:e1003621.
    PubMed     Text format    


  63. GREENE D, Crona K
    The changing geometry of a fitness landscape along an adaptive walk.
    PLoS Comput Biol. 2014;10:e1003520.
    PubMed     Text format     Abstract available


  64. XIE L, Ge X, Tan H, Xie L, et al
    Towards structural systems pharmacology to study complex diseases and personalized medicine.
    PLoS Comput Biol. 2014;10:e1003554.
    PubMed     Text format     Abstract available


    February 2014
  65. LAO O, Liu F, Wollstein A, Kayser M, et al
    GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans.
    PLoS Comput Biol. 2014;10:e1003480.
    PubMed     Text format     Abstract available


    January 2014
  66. HUANG S, Yee C, Ching T, Yu H, et al
    A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer.
    PLoS Comput Biol. 2014;10:e1003851.
    PubMed     Text format     Abstract available


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