Opportunities and challenges for the life sciences community.
Omics : a journal of integrative biology
, 2012 Mar: 16(3)138-47
MOPED: Model Organism Protein Expression Database.
Nucleic acids research
, Jan. 2012: 40(Database issue)D1093-9
Statistical Methods in Systems Biology
Encyclopedia of Systems Biology
, 2012
SPIRE: Systematic protein investigative research environment.
Journal of proteomics
, Dec. 2011: 75(1)122-6
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 Dec 10: 75(1)4-17
IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
Journal of proteomics
, 2011 Dec 10: 75(1)116-21
In-silico human genomics with GeneCards.
Human genomics
, 2011 Oct: 5(6)709-17
Vaccines of the 21st century and vaccinomics: data-enabled science meets global health to spark collective action for vaccine innovation.
Omics : a journal of integrative biology
, 2011 Sep: 15(9)523-7
Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins.
Omics : a journal of integrative biology
, 2011 Jul-Aug: 15(7-8)513-21
Special issue on data-intensive science.
Omics : a journal of integrative biology
, 2011 Apr: 15(4)197-8
Bioinformatics and data-intensive scientific discovery in the beginning of the 21st century.
Omics : a journal of integrative biology
, 2011 Apr: 15(4)199-201
Technology and data-intensive science in the beginning of the 21st century.
Omics : a journal of integrative biology
, 2011 Apr: 15(4)203-7
Biology and data-intensive scientific discovery in the beginning of the 21st century.
Omics : a journal of integrative biology
, 2011 Apr: 15(4)209-12
Communication and data-intensive science in the beginning of the 21st century.
Omics : a journal of integrative biology
, 2011 Apr: 15(4)213-5
Education and data-intensive science in the beginning of the 21st century.
Omics : a journal of integrative biology
, 2011 Apr: 15(4)217-9
Policy and data-intensive scientific discovery in the beginning of the 21st century.
Omics : a journal of integrative biology
, 2011 Apr: 15(4)221-5
Design and initial characterization of the SC-200 proteomics standard mixture.
Omics : a journal of integrative biology
, 2011 Jan-Feb: 15(1-2)73-82
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project.
Standards in genomic sciences
, 2010 Dec 25: 3(3)243-8
The necessity of adjusting tests of protein category enrichment in discovery proteomics.
Bioinformatics (Oxford, England)
, 2010 Dec 15: 26(24)3007-11
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.
Standards in genomic sciences
, 2010 Dec 4: 3(3)216-24
The United States of America and scientific research.
PloS one
, 2010 Aug 16: 5(8)e12203
A vision for 21st century U.S. Policy to support sustainable advancement of scientific discovery and technological innovation.
Omics : a journal of integrative biology
, 2010 Aug: 14(4)333-5
Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
Standards in genomic sciences
, 2010 Jun 15: 2(3)357-60
Estimating false discovery rates for peptide and protein identification using randomized databases.
Proteomics
, 2010 Jun: 10(12)2369-76
Editorial: global issues.
Omics : a journal of integrative biology
, 2010 Jun: 14(3)229
Meta-analysis for protein identification: a case study on yeast data.
Omics : a journal of integrative biology
, 2010 Jun: 14(3)309-14
Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.
Molecular bioSystems
, 2010 Apr: 6(4)721-8
Quantifying protein function specificity in the gene ontology.
Standards in genomic sciences
, 2010 Mar 30: 2(2)238-44
OMICS: 2009, 2010, and Beyond.
Omics : a journal of integrative biology
, 2009 Dec: 13(6)451
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions.
PloS one
, 2009 Oct 21: 4(10)e7546
Megascience. 'Omics data sharing.
Science (New York, N.Y.)
, 2009 Oct 9: 326(5950)234-6
Meeting report: the 2009 Westlake International Conference on Personalized Medicine.
Omics : a journal of integrative biology
, 2009 Aug: 13(4)285-9
Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics.
Omics : a journal of integrative biology
, 2009 Feb: 13(1)1-6
Risk assessment and communication tools for genotype associations with multifactorial phenotypes: the concept of "edge effect" and cultivating an ethical bridge between omics innovations and society.
Omics : a journal of integrative biology
, 2009 Feb: 13(1)43-61
Modeling sequence and function similarity between proteins for protein functional annotation
HPDC '10 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing
, 2009: 499-502
Staphylococcus aureus elicits marked alterations in the airway proteome during early pneumonia.
Infection and immunity
, 2008 Dec: 76(12)5862-72
Validating annotations for uncharacterized proteins in Shewanella oneidensis.
Omics : a journal of integrative biology
, 2008 Sep: 12(3)211-5
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Nature biotechnology
, 2008 Aug: 26(8)889-96
Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.
Omics : a journal of integrative biology
, 2008 Jun: 12(2)101-8
Toward a standards-compliant genomic and metagenomic publication record.
Omics : a journal of integrative biology
, 2008 Jun: 12(2)157-60
A note on the false discovery rate and inconsistent comparisons between experiments.
Bioinformatics (Oxford, England)
, 2008 May 15: 24(10)1225-8
The minimum information about a genome sequence (MIGS) specification.
Nature biotechnology
, 2008 May: 26(5)541-7
Host airway proteins interact with Staphylococcus aureus during early pneumonia.
Infection and immunity
, 2008 Mar: 76(3)888-98
Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression.
Proteomics
, 2007 Oct: 7(20)3693-8
A predictive model for identifying proteins by a single peptide match.
Bioinformatics (Oxford, England)
, 2007 Feb 1: 23(3)277-80
Experiment-specific estimation of peptide identification probabilities using a randomized database.
Omics : a journal of integrative biology
, 2007 Winter: 11(4)351-65
New metrics for comparative genomics.
Current opinion in biotechnology
, 2006 Oct: 17(5)440-7
Protein identification and expression analysis using mass spectrometry.
Trends in microbiology
, 2006 May: 14(5)229-35
Experimental standards for high-throughput proteomics.
Omics : a journal of integrative biology
, 2006 Summer: 10(2)152-7
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.
Proceedings of the National Academy of Sciences of the United States of America
, 2005 Feb 8: 102(6)2099-104
Integration of data for gene annotation using the BioMediator system
AMIA Annual Symposium Proceedings
, 2005: 1036
Randomized sequence databases for tandem mass spectrometry peptide and protein identification.
Omics : a journal of integrative biology
, 2005 Winter: 9(4)364-79
Charge state estimation for tandem mass spectrometry proteomics.
Omics : a journal of integrative biology
, 2005 Fall: 9(3)233-50
Statistical analysis of global gene expression data: some practical considerations.
Current opinion in biotechnology
, 2004 Feb: 15(1)52-7
LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression.
Omics : a journal of integrative biology
, 2004 Winter: 8(4)357-69
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
Omics : a journal of integrative biology
, 2004 Spring: 8(1)25-41
Standard mixtures for proteome studies.
Omics : a journal of integrative biology
, 2004 Spring: 8(1)79-92
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.
Nucleic acids research
, 2004: 32(8)2353-61
Spectral quality assessment for high-throughput tandem mass spectrometry proteomics.
Omics : a journal of integrative biology
, 2004 Fall: 8(3)255-65
Statistical analysis of global gene expression data: Some practical considerations
Current Opinion in Biotechnology
, 2003: 15(1)52-57
Annotating and re-annotating genomes
OMICS
, 2003: 7(2)141
Initial proteome analysis of model microorganism Haemophilus influenzae Rd KW20
Journal of Bacteriology
, 2003: 185(15)
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
Analytical Chemistry
, 2002: 74(20)5383-5392
H. influenzae consortium: Integrative study of H. influenzae-Human interactions
OMICS
, 2002: 6(4)341-348
Integrative Microbiology
OMICS
, 2002: 6(4)285
Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
Bioinformatics
, 2002: 18(S1)337-344
Experimental protein mixture for validating tandem mass spectrometry analysis
OMICS
, 2002: 6(2)207-212
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
Nucleic Acids Research
, 2002: 30(17)3737-3738
Spectral analysis of distributions: finding periodic component in eukaryotic enzyme length data
OMICS
, 2002: 6(1)123-130
Differential isotopic labeling of peptides for quantitation and de novo sequence derivation
Rapid Communications in Mass Spectrometry
, 2001: 15(14)1214-1221
Segments, folds and overall protein structure
Biological Structure and Dynamics
, 1996: 257-265
Sequence sizes of eukaryotic enzymes
Pacific Symposium on Biocomputing '96
, 1996: 351-361
Sequence markers of segmented protein structure
Modeling of Biomolecular Structures and Mechanisms
, 1995: 461-471
Periodic recurrence of methionines: Fossil of gene fusion?
Proceedings of the National Academy of Sciences of USA
, 1995: 92(2)557-560
Underlying order in protein sequence organization
Proceedings of the National Academy of Sciences of USA
, 1994: 91(9)4044-4047
MOPED: Model Organism Protein Expression Database
,
SPIRE: Systematic Protein Investigative Research Environment
,
Peptide_Prophet, Protein_Prophet and Proteomics Standards
,