PubMed

Extracting biologically significant patterns from short time series gene expression data.

Tchagang AB, Bui KV, McGinnis T, Benos PV.

BMC Bioinformatics. 2009 Aug 20;10:255.PMID: 19695084 [PubMed - in process]Related articlesFree article

A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations.

Liu L, Koharudin LM, Gronenborn AM, Bahar I.

Proteins. 2009 Dec;77(4):927-39.PMID: 19688820 [PubMed - in process]Related articlesFree article

Heterolytic reduction of fatty acid hydroperoxides by cytochrome c/cardiolipin complexes: antioxidant function in mitochondria.

Belikova NA, Tyurina YY, Borisenko G, Tyurin V, Samhan Arias AK, Yanamala N, Furtmüller PG, Klein-Seetharaman J, Obinger C, Kagan VE.

J Am Chem Soc. 2009 Aug 19;131(32):11288-9.PMID: 19627079 [PubMed - in process]Related articles

Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity.

Yang Z, Bahar I, Widom M.

Biophys J. 2009 Jun 3;96(11):4438-48.PMID: 19486668 [PubMed - indexed for MEDLINE]Related articles

Prediction of interactions between HIV-1 and human proteins by information integration.

Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J.

Pac Symp Biocomput. 2009:516-27.PMID: 19209727 [PubMed - indexed for MEDLINE]Related articlesFree article

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.

Yang LW, Eyal E, Bahar I, Kitao A.

Bioinformatics. 2009 Mar 1;25(5):606-14. Epub 2009 Jan 15.PMID: 19147661 [PubMed - indexed for MEDLINE]Related articles

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.

Genome Biol. 2008;9 Suppl 1:S2. Epub 2008 Jun 27.PMID: 18613946 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein complex identification by supervised graph local clustering.

Qi Y, Balem F, Faloutsos C, Klein-Seetharaman J, Bar-Joseph Z.

Bioinformatics. 2008 Jul 1;24(13):i250-8.PMID: 18586722 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of correlated mutations in HIV-1 protease using spectral clustering.

Liu Y, Eyal E, Bahar I.

Bioinformatics. 2008 May 15;24(10):1243-50. Epub 2008 Mar 28.PMID: 18375964 [PubMed - indexed for MEDLINE]Related articlesFree article

Transmembrane helix prediction using amino acid property features and latent semantic analysis.

Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J.

BMC Bioinformatics. 2008;9 Suppl 1:S4.PMID: 18315857 [PubMed - indexed for MEDLINE]Related articlesFree article

A mixture of feature experts approach for protein-protein interaction prediction.

Qi Y, Klein-Seetharaman J, Bar-Joseph Z.

BMC Bioinformatics. 2007;8 Suppl 10:S6.PMID: 18269700 [PubMed - indexed for MEDLINE]Related articlesFree article

Subfamily specific conservation profiles for proteins based on n-gram patterns.

Vries JK, Liu X.

BMC Bioinformatics. 2008 Jan 30;9:72.PMID: 18234090 [PubMed - indexed for MEDLINE]Related articlesFree article

Web-based identification of evolutionary conserved DNA cis-regulatory elements.

Benos PV, Corcoran DL, Feingold E.

Methods Mol Biol. 2007;395:425-36.PMID: 17993689 [PubMed - indexed for MEDLINE]Related articles

Markov methods for hierarchical coarse-graining of large protein dynamics.

Chennubhotla C, Bahar I.

J Comput Biol. 2007 Jul-Aug;14(6):765-76.PMID: 17691893 [PubMed - indexed for MEDLINE]Related articles

Inferring protein-DNA dependencies using motif alignments and mutual information.

Mahony S, Auron PE, Benos PV.

Bioinformatics. 2007 Jul 1;23(13):i297-304.PMID: 17646310 [PubMed - indexed for MEDLINE]Related articlesFree article

Recruitment of rare 3-grams at functional sites: is this a mechanism for increasing enzyme specificity?

Tobi D, Bahar I.

BMC Bioinformatics. 2007 Jun 28;8:226.PMID: 17598909 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison of stability predictions and simulated unfolding of rhodopsin structures.

Tastan O, Yu E, Ganapathiraju M, Aref A, Rader AJ, Klein-Seetharaman J.

Photochem Photobiol. 2007 Mar-Apr;83(2):351-62.PMID: 17576347 [PubMed - indexed for MEDLINE]Related articles

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I.

Structure. 2007 Jun;15(6):741-9.PMID: 17562320 [PubMed - indexed for MEDLINE]Related articlesFree article

The relationship between n-gram patterns and protein secondary structure.

Vries JK, Liu X, Bahar I.

Proteins. 2007 Sep 1;68(4):830-8.PMID: 17523186 [PubMed - indexed for MEDLINE]Related articles

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome.

Mahony S, Corcoran DL, Feingold E, Benos PV.

Genome Biol. 2007;8(5):R84.PMID: 17506886 [PubMed - indexed for MEDLINE]Related articlesFree article