Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

[1]  P. Zimmermann,et al.  Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics , 2008, Science.

[2]  B. Searle,et al.  Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. , 2008, Journal of proteome research.

[3]  Richard D. Smith,et al.  Proteogenomics: needs and roles to be filled by proteomics in genome annotation. , 2008, Briefings in functional genomics & proteomics.

[4]  Hyungwon Choi,et al.  False discovery rates and related statistical concepts in mass spectrometry-based proteomics. , 2008, Journal of proteome research.

[5]  William Stafford Noble,et al.  Posterior error probabilities and false discovery rates: two sides of the same coin. , 2008, Journal of proteome research.

[6]  Kevin Struhl,et al.  Differential analysis for high density tiling microarray data , 2007, BMC Bioinformatics.

[7]  Mark R Marten,et al.  Proteomics of filamentous fungi. , 2007, Trends in biotechnology.

[8]  Fangli Lu,et al.  cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome , 2007, BMC Genomics.

[9]  Hanno Langen,et al.  From the genome sequence to the proteome and back: Evaluation of E. coli genome annotation with a 2‐D gel‐based proteomics approach , 2007, Proteomics.

[10]  R. Guigó,et al.  Improving gene annotation using peptide mass spectrometry. , 2007, Genome research.

[11]  S. C. Rison,et al.  Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis , 2007, Microbiology.

[12]  J. A. Roubos,et al.  Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 , 2007, Nature Biotechnology.

[13]  K. Resing,et al.  Achieving in-depth proteomics profiling by mass spectrometry. , 2007, ACS chemical biology.

[14]  R. Beynon,et al.  Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization , 2006, Nature Protocols.

[15]  S. Baker Aspergillus niger genomics: past, present and into the future. , 2006, Medical mycology.

[16]  C. Bessant,et al.  GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra. , 2006, Journal of proteome research.

[17]  Daniel Figeys,et al.  Proteomics technology in systems biology. , 2006, Molecular bioSystems.

[18]  F. McCarthy,et al.  Modeling a whole organ using proteomics: The avian bursa of Fabricius , 2006, Proteomics.

[19]  Damian Fermin,et al.  Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics , 2006, Genome Biology.

[20]  R. Aebersold,et al.  Mass Spectrometry and Protein Analysis , 2006, Science.

[21]  Eric W. Deutsch,et al.  The PeptideAtlas project , 2005, Nucleic Acids Res..

[22]  de Winde,et al.  University of Groningen Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 Pel, , 2006 .

[23]  R. Storms,et al.  Generation, annotation, and analysis of an extensive Aspergillus niger EST collection , 2006, BMC Microbiology.

[24]  C. Bessant,et al.  Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds. , 2005, Rapid communications in mass spectrometry : RCM.

[25]  Andrew Emili,et al.  Multidimensional protein identification technology: current status and future prospects , 2005, Expert review of proteomics.

[26]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[27]  Nichole L. King,et al.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry , 2004, Genome Biology.

[28]  T. Veenstra,et al.  What to do with “one‐hit wonders”? , 2004, Electrophoresis.

[29]  S. Searle,et al.  The Ensembl analysis pipeline. , 2004, Genome research.

[30]  Patrick G Buckley,et al.  Genomic microarrays in the spotlight. , 2004, Trends in genetics : TIG.

[31]  Jacob D. Jaffe,et al.  Proteogenomic mapping as a complementary method to perform genome annotation , 2004, Proteomics.

[32]  A. Shevchenko,et al.  Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications , 2003, Proteomics.

[33]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[34]  P. Mortensen,et al.  Mass spectrometry allows direct identification of proteins in large genomes , 2001, Proteomics.

[35]  R. Durbin,et al.  Using GeneWise in the Drosophila annotation experiment. , 2000, Genome research.

[36]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[37]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[38]  M. Bittner,et al.  Expression profiling using cDNA microarrays , 1999, Nature Genetics.

[39]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.