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Articles published in PLoS Comput Biol

Retrieve available abstracts of 51 articles:
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Single Articles


    June 2017
  1. 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


  2. 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


    May 2017
  3. 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


  4. 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


  5. 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
  6. 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
  7. 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
  8. 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


  9. 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


  10. 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


  11. 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
  12. 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
  13. 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


  14. 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


  15. 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


  16. 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
  17. 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


  18. 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
  19. VOGEL C
    Systems Approaches to the Eukaryotic Stress Response.
    PLoS Comput Biol. 2016;12:e1004757.
    PubMed     Text format    


  20. 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


  21. 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


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


    February 2016
  23. 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


  24. 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


  25. 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
  26. 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
  27. PERCHA B, Altman RB
    Learning the Structure of Biomedical Relationships from Unstructured Text.
    PLoS Comput Biol. 2015;11:e1004216.
    PubMed     Text format     Abstract available


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


  29. 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
  30. 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


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


  32. 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
  33. 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


  34. 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


  35. 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


  36. 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


  37. 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


  38. 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
  39. 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


  40. 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


  41. 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


  42. 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
  43. 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


  44. 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


  45. 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
  46. 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


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


  48. 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


  49. 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
  50. 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
  51. 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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