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Articles published in PLoS Comput Biol

Retrieve available abstracts of 52 articles:
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Single Articles


    April 2016
  1. 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


  2. 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
  3. VOGEL C
    Systems Approaches to the Eukaryotic Stress Response.
    PLoS Comput Biol. 2016;12:e1004757.
    PubMed     Text format    


  4. 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


  5. 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


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


    February 2016
  7. 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


  8. 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


  9. 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
  10. 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
  11. PERCHA B, Altman RB
    Learning the Structure of Biomedical Relationships from Unstructured Text.
    PLoS Comput Biol. 2015;11:e1004216.
    PubMed     Text format     Abstract available


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


  13. 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
  14. 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


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


  16. 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
  17. 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


  18. 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


  19. 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


  20. 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


  21. 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


  22. 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
  23. 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


  24. 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


  25. 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


  26. 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
  27. 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


  28. 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


  29. 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


    August 2014
  30. VAN TONDER AJ, Mistry S, Bray JE, Hill DM, et al
    Defining the estimated core genome of bacterial populations using a Bayesian decision model.
    PLoS Comput Biol. 2014;10:e1003788.
    PubMed     Text format     Abstract available


  31. YOO S, Huang T, Campbell JD, Lee E, et al
    MODMatcher: multi-omics data matcher for integrative genomic analysis.
    PLoS Comput Biol. 2014;10:e1003790.
    PubMed     Text format     Abstract available


  32. ZHANG Y, Sun Y, Cole JR
    A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.
    PLoS Comput Biol. 2014;10:e1003737.
    PubMed     Text format     Abstract available


  33. LANG AH, Li H, Collins JJ, Mehta P, et al
    Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes.
    PLoS Comput Biol. 2014;10:e1003734.
    PubMed     Text format     Abstract available


    July 2014
  34. GONZALEZ G, Hannigan B, DeGrado WF
    A real-time all-atom structural search engine for proteins.
    PLoS Comput Biol. 2014;10:e1003750.
    PubMed     Text format     Abstract available


  35. LOVING KA, Lin A, Cheng AC
    Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.
    PLoS Comput Biol. 2014;10:e1003741.
    PubMed     Text format     Abstract available


  36. BARRERA A, Alastruey-Izquierdo A, Martin MJ, Cuesta I, et al
    Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.
    PLoS Comput Biol. 2014;10:e1003733.
    PubMed     Text format     Abstract available


  37. ZARECKI R, Oberhardt MA, Reshef L, Gophna U, et al
    A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness.
    PLoS Comput Biol. 2014;10:e1003726.
    PubMed     Text format     Abstract available


  38. KARLSSON FH, Nookaew I, Nielsen J
    Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue.
    PLoS Comput Biol. 2014;10:e1003706.
    PubMed     Text format     Abstract available


    May 2014
  39. 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


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


  41. 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


  42. 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


    April 2014
  43. BRAZAS MD, Lewitter F, Schneider MV, van Gelder CW, et al
    A quick guide to genomics and bioinformatics training for clinical and public audiences.
    PLoS Comput Biol. 2014;10:e1003510.
    PubMed     Text format    


    March 2014
  44. SZCZUREK E, Beerenwinkel N
    Modeling mutual exclusivity of cancer mutations.
    PLoS Comput Biol. 2014;10:e1003503.
    PubMed     Text format     Abstract available


  45. WORBY CJ, Lipsitch M, Hanage WP
    Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data.
    PLoS Comput Biol. 2014;10:e1003549.
    PubMed     Text format     Abstract available


    February 2014
  46. 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
  47. NASIR A, Kim KM, Caetano-Anolles G
    Global patterns of protein domain gain and loss in superkingdoms.
    PLoS Comput Biol. 2014;10:e1003452.
    PubMed     Text format     Abstract available


  48. TUTEJA G, Moreira KB, Chung T, Chen J, et al
    Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data.
    PLoS Comput Biol. 2014;10:e1003449.
    PubMed     Text format     Abstract available


  49. JOMBART T, Cori A, Didelot X, Cauchemez S, et al
    Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data.
    PLoS Comput Biol. 2014;10:e1003457.
    PubMed     Text format     Abstract available


  50. CARNEGIE NB, Wang R, Novitsky V, De Gruttola V, et al
    Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data.
    PLoS Comput Biol. 2014;10:e1003430.
    PubMed     Text format     Abstract available


  51. VON KAMP A, Klamt S
    Enumeration of smallest intervention strategies in genome-scale metabolic networks.
    PLoS Comput Biol. 2014;10:e1003378.
    PubMed     Text format     Abstract available


  52. 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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