Publications

Magis AT, Earls J.C, Ko Y.H, Eddy JA, Price ND.  2011.  Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. Bioinformatics. 27:872-3.

Lam H, Deutsch EW, Aebersold R.  2010.  Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. J Proteome Res. 9:605-10.

Chandrasekaran S, Price ND.  2010.  Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. 107:17845-50.

Nykter M, Lahdesmaki H, Rust A, Thorsson V, Shmulevich I.  2009.  A data integration framework for prediction of transcription factor targets. Ann N Y Acad Sci. 1158:205-14.

Wollscheid B, Bausch-Fluck D, Henderson C, O'Brien R, Bibel M, Schiess R, Aebersold R, Watts J.  2009.  Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol. 27:378-86.

Carter GW, Galas DJ, Galitski T.  2009.  Maximal extraction of biological information from genetic interaction data. PLoS Comput Biol. 5:e1000347.

Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R.  2007.  BioNetBuilder: automatic integration of biological networks. Bioinformatics. 23:392-3.

Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T et al..  2007.  Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 25:125-31.

Niemisto A, Korpelainen T, Saleem R, Yli-Harja O, Aitchison JD, Shmulevich I.  2007.  A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy. Conf Proc IEEE Eng Med Biol Soc. 2007:5559-62.

Vencio RZ, Shmulevich I.  2007.  ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinformatics. 8:383.

Ahdesmaki M, Lahdesmaki H, Gracey A, Shmulevich I, Yli-Harja O.  2007.  Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics. 8:233.

Vencio RZ, Varuzza L, de PBCA, Brentani H, Shmulevich I.  2007.  Simcluster: clustering enumeration gene expression data on the simplex space. BMC Bioinformatics. 8:246.

Niemisto A, Selinummi J, Saleem R, Shmulevich I, Aitchison JD, Yli-Harja O.  2006.  Extraction of the number of peroxisomes in yeast cells by automated image analysis. Conf Proc IEEE Eng Med Biol Soc. 1:2353-6.

Barrett C.L, Price ND, Palsson BO.  2006.  Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC bioinformatics. 7:132.

Ramsey S, Orrell D, Bolouri H.  2005.  Dizzy: stochastic simulation of large-scale genetic regulatory networks (supplementary material). J Bioinform Comput Biol. 3:437-54.

Carter GW.  2005.  Inferring network interactions within a cell. Brief Bioinform. 6:380-9.

Orrell D, Ramsey S, de Atauri P, Bolouri H.  2005.  A method for estimating stochastic noise in large genetic regulatory networks. Bioinformatics. 21:208-17.

Zhang N, Li XJ, Ye M, Pan S, Schwikowski B, Aebersold R.  2005.  ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics. 5:4096-106.

Papin JA, Stelling J., Price ND, Klamt S., Schuster S., Palsson BO.  2004.  Comparison of network-based pathway analysis methods. Trends in biotechnology. 22:400-5.

Reiss DJ, Schwikowski B.  2004.  Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics. 20 Suppl 1:i274-82.

Price ND, Reed J.L, Papin JA, Famili I., Palsson BO.  2003.  Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophysical journal. 84:794-804.

Hubley RM, Zitzler E, Roach J.  2003.  Evolutionary algorithms for the selection of single nucleotide polymorphisms. BMC Bioinformatics. 4:30.

Zhang N, Aebersold R, Schwikowski B.  2002.  ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics. 2:1406-12.