Article thumbnail

Inferring functional modules of protein families with probabilistic topic models

By Sebastian GA Konietzny, Laura Dietz and Alice C McHardy
Topics: Methodology Article
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:3098182
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles

Citations

  1. (2010). a pathway and network discovery approach based on common biological evidence. Bioinformatics
  2. (2009). A: FIGfams: yet another set of protein families.
  3. (2007). al: The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol
  4. (2008). An invitation to the marriage of metagenomics and metabolomics. Cell
  5. (2007). Aravind L: Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment.
  6. (2005). Arkin AP: A latent variable model for chemogenomic profiling. Bioinformatics
  7. (2006). Automated protein function prediction - the genomic challenge. Brief Bioinform
  8. (1999). AW: From molecular to modular cell biology. Nature
  9. (2008). Beissbarth T: Predicting pathway membership via domain signatures. Bioinformatics
  10. (2006). Blei DM: Hierarchical Dirichlet processes. JA m Stat Assoc
  11. (2000). Church GM: Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res
  12. (2004). Claverie JM: FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res
  13. (2000). Cohen FE: Co-evolution of proteins with their interaction partners.
  14. (2010). Community detection in graphs. Phys Rep
  15. (2004). Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol
  16. (2004). Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Brief Bioinform
  17. (2011). Critical Assessment of Function Annotations.
  18. (1999). D: A combined algorithm for genome-wide prediction of protein function.
  19. (2006). Evaluation of clustering algorithms for proteinprotein interaction networks.
  20. Finding scientific topics.
  21. (2011). From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-D357. doi:10.1186/1471-2105-12-141 Cite this article as: Konietzny et al.: Inferring functional modules of protein families with probabilistic topic models.
  22. (2001). Genome annotation: from sequence to biology. Nat Rev Genet
  23. (2003). Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci USA
  24. (2008). Genomics of cellulosic biofuels.
  25. (2006). Griffiths T: Latent semantic analysis: a road to meaning.Edited by: Landauer
  26. (2000). Guilt by association: contextual information in genome analysis. Genome Res
  27. (2003). Huynen MA: Predicting gene function by conserved co-expression. Trends Genet
  28. (2006). Identifying biological concepts from a protein-related corpus with a probabilistic topic model.
  29. (2002). Latent Class Cluster Analysis
  30. (2003). Latent Dirichlet Allocation.
  31. (1999). Maltsev N: The use of gene clusters to infer functional coupling.
  32. (2010). Moreno-Hagelsieb G: Network-based function prediction and interactomics: The case for metabolic enzymes. Metab Eng
  33. (2008). Morett E, Vallejo EE: Inferring modules of functionally interacting proteins using the Bond Energy Algorithm.
  34. (1996). Non-orthologous gene displacement. Trends Genet
  35. (2009). Orengo CA: Protein function prediction - the power of multiplicity. Trends Biotechnol
  36. (2004). Ouzounis CA: Detection of functional modules from protein interaction networks. Proteins
  37. (1999). Ouzounis CA: Protein interaction maps for complete genomes based on gene fusion events. Nature
  38. (2003). Overbeek R: Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol
  39. (2010). P: eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res
  40. (2007). P: Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci USA
  41. (2006). Palsson BO: Towards multidimensional genome annotation. Nat Rev Genet
  42. (2010). PD: Machine learning methods for metabolic pathway prediction.
  43. (2008). Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.
  44. (2009). Predicting homologous signaling pathways using machine learning. Bioinformatics
  45. (2009). Predicting protein-protein relationships from literature using latent topics. Genome Inform
  46. (2005). Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics
  47. (2009). Revealing biological modules via graph summarization.
  48. (2002). Sonnhammer ELL: The Pfam protein families database. Nucleic Acids Res
  49. (1999). Spiegelhalter DJ: Markov Chain Monte Carlo In
  50. (2005). STRING: known and predicted proteinprotein associations, integrated and transferred across organisms. Nucleic Acids Res
  51. (2003). Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol
  52. (2000). The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res
  53. (2010). The nested Chinese restaurant process and Bayesian nonparametric inference of topic hierarchies.
  54. (1999). TO: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.
  55. (2007). Uetz P: The protein network of bacterial motility. Mol Syst Biol
  56. (2001). White O: TIGRFAMs: a protein family resource for the functional identification of proteins.