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Eugene Kolker

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Genes & Molecular Sequences

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Publications

TOP 3
Winston A Haynes; Roger Higdon; Dwayne Collins; Larissa Stanberry; Eugene Kolker
Differential expression analysis for pathways.
Roger Higdon; Ruedi Aebersold; Andrew T Bauman; Gregory Hather; Winston Haynes; Natali Kolker; Paola Picotti; Lukas Reiter; Alexander Schmidt; Elizabeth Stewart; Gerald van Belle; Eugene Kolker
IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
Eugene Kolker; Andrew Bauman; William Broomall; Winston Haynes; Roger Higdon; Elizabeth Stewart; Dean Welch; Phil Morgan; Margaret Sedensky; Natali Kolker
SPIRE: Systematic protein investigative research environment.

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All Publications

2013: Winston A Haynes; Roger Higdon; Dwayne Collins; Larissa Stanberry; Eugene Kolker
Differential expression analysis for pathways.
PLoS computational biology 2013;9(3):e1002967.
2011: Roger Higdon; Ruedi Aebersold; Andrew T Bauman; Gregory Hather; Winston Haynes; Natali Kolker; Paola Picotti; Lukas Reiter; Alexander Schmidt; Elizabeth Stewart; Gerald van Belle; Eugene Kolker
IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
Journal of proteomics 2011;75(1):116-21.
2011: Eugene Kolker; Andrew Bauman; William Broomall; Winston Haynes; Roger Higdon; Elizabeth Stewart; Dean Welch; Phil Morgan; Margaret Sedensky; Natali Kolker
SPIRE: Systematic protein investigative research environment.
Journal of proteomics 2011;75(1):122-6.
2011: Jürgen Cox; Peter James; Jesús V Jorrin-Novo; Eugene Kolker; Fredrik Levander; Ron M A Heeren; György Marko-Varga; Nicholas Morrice; Sinead O'Donovan; Serena O'Neil; Paola Picotti; Jozsef Prechl; Pier Giorgio Righetti; Jean-Charles Sánchez; Tânia Simões; Christoph W Turck; Wolfram Weckwerth; Roman Zubarev; Bruno M Alexandre; Fernando J Corrales; Deborah Penque
Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010.
Journal of proteomics 2011;75(1):4-17.
2011: Natali Kolker; Wei Lu; Larissa Stanberry; Dean Welch; Roger Barga; William Broomall; Winston Haynes; Roger Higdon; Eugene Kolker
Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins.
Omics : a journal of integrative biology 2011;15(7-8):513-21.
2010: Gregory Hather; Roger Higdon; Andrew Bauman; Priska D von Haller; Eugene Kolker
Estimating false discovery rates for peptide and protein identification using randomized databases.
Proteomics 2010;10(12):2369-76.
2010: Gregory J Hather; Winston Haynes; Roger Higdon; Natali Kolker; Elizabeth A Stewart; Peter Arzberger; Patrick Chain; Dawn Field; B Robert Franza; Lin Biao; Folker Meyer; Vural Ozdemir; Charles V Smith; Gerald van Belle; John Wooley; Eugene Kolker
The United States of America and scientific research.
PloS one 2010;5(8):e12203.
2008: Christy L Ventura; Roger Higdon; Eugene Kolker; Shawn J Skerrett; Craig E Rubens
Host airway proteins interact with Staphylococcus aureus during early pneumonia.
Infection and immunity 2008;76(3):888-98.
2007: Eugene Kolker; Jason M Hogan; Roger Higdon; Natali Kolker; Elizabeth Landorf; Alexander F Yakunin; Frank R Collart; Gerald van Belle
Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression.
Proteomics 2007;7(20):3693-8.
2007: Roger Higdon; Eugene Kolker
A predictive model for identifying proteins by a single peptide match.
Bioinformatics (Oxford, England) 2007;23(3):277-80.
2007: Roger Higdon; Jason M Hogan; Natali Kolker; Gerald van Belle; Eugene Kolker
Experiment-specific estimation of peptide identification probabilities using a randomized database.
Omics : a journal of integrative biology 2007;11(4):351-65.
2006: Eugene Kolker; Roger Higdon; Jason M Hogan
Protein identification and expression analysis using mass spectrometry.
Trends in microbiology 2006;14(5):229-35.
2006: Jason M Hogan; Roger Higdon; Eugene Kolker
Experimental standards for high-throughput proteomics.
Omics : a journal of integrative biology 2006;10(2):152-7.
2005: Brenton Louie; Peter Mork; R Shaker; Natali Kolker; Eugene Kolker; Peter Tarczy-Hornoch
Integration of data for gene annotation using the BioMediator system.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2005;():1036.
2005: Roger Higdon; Jason M Hogan; Gerald van Belle; Eugene Kolker
Randomized sequence databases for tandem mass spectrometry peptide and protein identification.
Omics : a journal of integrative biology 2005;9(4):364-79.
2005: Jason M Hogan; Roger Higdon; Natali Kolker; Eugene Kolker
Charge state estimation for tandem mass spectrometry proteomics.
Omics : a journal of integrative biology 2005;9(3):233-50.
2004: Ted Holzman; Eugene Kolker
Statistical analysis of global gene expression data: some practical considerations.
Current opinion in biotechnology 2004;15(1):52-7.
2004: Roger Higdon; Natali Kolker; Alex F Picone; Gerald van Belle; Eugene Kolker
LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression.
Omics : a journal of integrative biology 2004;8(4):357-69.
2004: Samuel O Purvine; Natali Kolker; Eugene Kolker
Spectral quality assessment for high-throughput tandem mass spectrometry proteomics.
Omics : a journal of integrative biology 2004;8(3):255-65.
2004: Eugene Kolker; Kira S Makarova; Svetlana A Shabalina; Alex F Picone; Samuel O Purvine; Ted Holzman; Tim Cherny; David Armbruster; Robert munson; Grigory Kolesov; Dmitrij Frishman; Michael Galperin
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.
Nucleic acids research 2004;32(8):2353-61.
2004: Samuel O Purvine; Alex F Picone; Eugene Kolker
Standard mixtures for proteome studies.
Omics : a journal of integrative biology 2004;8(1):79-92.
2004: Anu Raghunathan; Nathan Price; Michael Galperin; Kira S Makarova; Samuel O Purvine; Alex F Picone; Tim Cherny; Tao Xie; Thomas J Reilly; Robert munson; Ryan E Tyler; Brian Akerley; Arnold L. Smith; Bernhard Ø Palsson; Eugene Kolker
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
Omics : a journal of integrative biology 2004;8(1):25-41.
2003: Alexey I Nesvizhskii; Andrew Keller; Eugene Kolker; Ruedi Aebersold
A statistical model for identifying proteins by tandem mass spectrometry.
Analytical chemistry 2003;75(17):4646-58.
2003: Eugene Kolker; Samuel O Purvine; Michael Galperin; Sergey Stolyar; David R Goodlett; Alexey I Nesvizhskii; Andrew Keller; Tao Xie; Jimmy K Eng; Eugene Yi; Leroy Hood; Alex F Picone; Tim Cherny; Brian C Tjaden; Andrew F Siegel; Thomas J Reilly; Kira S Makarova; Bernhard Ø Palsson; Arnold L. Smith
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.
Journal of bacteriology 2003;185(15):4593-602.
2002: Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
Analytical chemistry 2002;74(20):5383-92.
2002: Brian Tjaden; Rini Mukherjee Saxena; Sergey Stolyar; David R Haynor; Eugene Kolker; Carsten Rosenow
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays.
Nucleic acids research 2002;30(17):3732-8.
2002: Eugene Kolker; Samuel O Purvine; Alex F Picone; Tim Cherny; Brian Akerley; Robert munson; Bernhard Ø Palsson; Dayle A Daines; Arnold L. Smith
H. influenzae Consortium: integrative study of H. influenzae-human interactions.
Omics : a journal of integrative biology 2002;6(4):341-8.
2002: Brian Tjaden; David R Haynor; Sergey Stolyar; Carsten Rosenow; Eugene Kolker
Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S337-44.
2002: Andrew Keller; Samuel O Purvine; Alexey I Nesvizhskii; Sergey Stolyar; David R Goodlett; Eugene Kolker
Experimental protein mixture for validating tandem mass spectral analysis.
Omics : a journal of integrative biology 2002;6(2):207-12.
2002: Eugene Kolker; Brian C Tjaden; Robert Hubley; Edward N Trifonov; Andrew F Siegel
Spectral analysis of distributions: finding periodic components in eukaryotic enzyme length data.
Omics : a journal of integrative biology 2002;6(1):123-30.
2001: David R Goodlett; Andrew Keller; Julian D Watts; R Newitt; Eugene C Yi; Samuel O Purvine; Jimmy K Eng; Priska D von Haller; Ruedi Aebersold; Eugene Kolker
Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.
Rapid communications in mass spectrometry : RCM 2001;15(14):1214-21.