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Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
Damian Fermin, Baxter B Allen, Thomas W Blackwell, Rajasree Menon, Marcin Adamski, Yin Xu, Peter Ulintz, Gilbert S Omenn, David J States
Genome Biol. 2006; 7(4): R35. Published online 2006 April 28. doi: 10.1186/gb-2006-7-4-r35
PMCID:
PMC1557991
Abstract Full Text PDF–278K Supplementary Material

Is Cited by the Following 28 Articles in this Archive:

Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments
Brandi L. Cantarel, Alison R. Erickson, Nathan C. VerBerkmoes, Brian K. Erickson, Patricia A. Carey, Chongle Pan, Manesh Shah, Emmanuel F. Mongodin, Janet K. Jansson, Claire M. Fraser-Liggett, Robert L. Hettich
PLoS One. 2011; 6(11): e27173. Published online 2011 November 23. doi: 10.1371/journal.pone.0027173
PMCID:
PMC3223167
Abstract Full Text PDF–398K Supplementary Material
A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF
Lina Zhao, Liguo Liu, Wenchuan Leng, Candong Wei, Qi Jin
BMC Genomics. 2011; 12: 528. Published online 2011 October 28. doi: 10.1186/1471-2164-12-528
PMCID:
PMC3219829
Abstract Full Text PDF–446K Supplementary Material
OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics
Mohamed Helmy, Masaru Tomita, Yasushi Ishihama
BMC Plant Biol. 2011; 11: 63. Published online 2011 April 12. doi: 10.1186/1471-2229-11-63
PMCID:
PMC3094275
Abstract Full Text PDF–743K Supplementary Material
Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability
Danny A. Bitton, Valerie Wood, Paul J. Scutt, Agnes Grallert, Tim Yates, Duncan L. Smith, Iain M. Hagan, Crispin J. Miller
Genetics. 2011 April; 187(4): 1207–1217. doi: 10.1534/genetics.110.123497
PMCID:
PMC3070528
Abstract Full Text PDF–4.9M
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment
Kang Ning, Alexey I Nesvizhskii
BMC Bioinformatics. 2010; 11(Suppl 11): S14. Published online 2010 December 14. doi: 10.1186/1471-2105-11-S11-S14
PMCID:
PMC3024872
Abstract Full Text PDF–342K
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
Alexey I. Nesvizhskii
J Proteomics. Author manuscript; available in PMC 2011 October 10.
Published in final edited form as: J Proteomics. 2010 October 10; 73(11): 2092–2123. Published online 2010 September 8. doi: 10.1016/j.jprot.2010.08.009
PMCID:
PMC2956504
Abstract Full Text PDF–3.5M
Oral lichen planus is a unique disease model for studying chronic inflammation and oral cancer
Yi Liu, Diana Messadi, Hongkun Wu, Shen Hu
Med Hypotheses. Author manuscript; available in PMC 2011 December 1.
Published in final edited form as: Med Hypotheses. 2010 December; 75(6): 492–494. Published online 2010 July 31. doi: 10.1016/j.mehy.2010.07.002
PMCID:
PMC3181218
Abstract Full Text PDF–293K
Proteogenomics to discover the full coding content of genomes: a computational perspective
Natalie Castellana, Vineet Bafna
J Proteomics. Author manuscript; available in PMC 2011 October 10.
Published in final edited form as: J Proteomics. 2010 October 10; 73(11): 2124–2135. Published online 2010 July 8. doi: 10.1016/j.jprot.2010.06.007
PMCID:
PMC2949459
Abstract Full Text PDF–587K
Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models
Nadine Borchert, Christoph Dieterich, Karsten Krug, Wolfgang Schütz, Stephan Jung, Alfred Nordheim, Ralf J. Sommer, Boris Macek
Genome Res. 2010 June; 20(6): 837–846. doi: 10.1101/gr.103119.109
PMCID:
PMC2877580
Abstract Full Text PDF–899K
Proteomic Characterization of Novel Alternative Splice Variant Proteins in HER2/neu-induced Breast Cancers
Rajasree Menon, Gilbert S. Omenn
Cancer Res. Author manuscript; available in PMC 2011 May 1.
Published in final edited form as: Cancer Res. 2010 May 1; 70(9): 3440–3449. Published online 2010 April 13. doi: 10.1158/0008-5472.CAN-09-2631
PMCID:
PMC2866518
Abstract Full Text PDF–740K Supplementary Material
Template Proteogenomics: Sequencing Whole Proteins Using an Imperfect Database
Natalie E. Castellana, Victoria Pham, David Arnott, Jennie R. Lill, Vineet Bafna
Mol Cell Proteomics. 2010 June; 9(6): 1260–1270. Published online 2010 February 17. doi: 10.1074/mcp.M900504-MCP200
PMCID:
PMC2877985
Abstract Full Text
An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome
Danny A. Bitton, Duncan L. Smith, Yvonne Connolly, Paul J. Scutt, Crispin J. Miller
PLoS One. 2010; 5(1): e8949. Published online 2010 January 28. doi: 10.1371/journal.pone.0008949
PMCID:
PMC2812506
Abstract Full Text PDF–378K Supplementary Material
A Ranking-Based Scoring Function For Peptide-Spectrum Matches
Ari M. Frank
J Proteome Res. Author manuscript; available in PMC 2010 May 1.
Published in final edited form as: J Proteome Res. 2009 May; 8(5): 2241–2252. doi: 10.1021/pr800678b
PMCID:
PMC2692183
Abstract Full Text PDF–896K Supplementary Material
LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia
Thomas Fröhlich, Georg J Arnold, Rainer Fritsch, Tobias Mayr, Christian Laforsch
BMC Genomics. 2009; 10: 171. Published online 2009 April 21. doi: 10.1186/1471-2164-10-171
PMCID:
PMC2674882
Abstract Full Text PDF–1.2M Supplementary Material
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation
Sandra N Loevenich, Erich Brunner, Nichole L King, Eric W Deutsch, Stephen E Stein, The FlyBase Consortium, Ruedi Aebersold, Ernst Hafen
BMC Bioinformatics. 2009; 10: 59. Published online 2009 February 11. doi: 10.1186/1471-2105-10-59
PMCID:
PMC2648944
Abstract Full Text PDF–665K Supplementary Material
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger
James C Wright, Deana Sugden, Sue Francis-McIntyre, Isabel Riba-Garcia, Simon J Gaskell, Igor V Grigoriev, Scott E Baker, Robert J Beynon, Simon J Hubbard
BMC Genomics. 2009; 10: 61. Published online 2009 February 4. doi: 10.1186/1471-2164-10-61
PMCID:
PMC2644712
Abstract Full Text PDF–1.8M Supplementary Material
Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
Sébastien Gallien, Emmanuel Perrodou, Christine Carapito, Caroline Deshayes, Jean-Marc Reyrat, Alain Van Dorsselaer, Olivier Poch, Christine Schaeffer, Odile Lecompte
Genome Res. 2009 January; 19(1): 128–135. doi: 10.1101/gr.081901.108
PMCID:
PMC2612966
Abstract Full Text PDF–382K
Identification of Novel Alternative Splice Isoforms of Circulating Proteins in a Mouse Model of Human Pancreatic Cancer
Rajasree Menon, Qing Zhang, Yan Zhang, Damian Fermin, Nabeel Bardeesy, Ronald A. DePinho, Chunxia Lu, Samir M. Hanash, Gilbert S. Omenn, David J. States
Cancer Res. Author manuscript; available in PMC 2010 January 1.
Published in final edited form as: Cancer Res. 2009 January 1; 69(1): 300–309. doi: 10.1158/0008-5472.CAN-08-2145
PMCID:
PMC2613545
Abstract Full Text PDF–402K Supplementary Material
Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra
Sangtae Kim, Nitin Gupta, Nuno Bandeira, Pavel A. Pevzner
Mol Cell Proteomics. 2009 January; 8(1): 53–69. doi: 10.1074/mcp.M800103-MCP200
PMCID:
PMC2621003
Abstract Full Text Supplementary Material
Discovery and revision of Arabidopsis genes by proteogenomics
Natalie E. Castellana, Samuel H. Payne, Zhouxin Shen, Mario Stanke, Vineet Bafna, Steven P. Briggs
Proc Natl Acad Sci U S A. 2008 December 30; 105(52): 21034–21038. Published online 2008 December 19. doi: 10.1073/pnas.0811066106
PMCID:
PMC2605632
Abstract Full Text PDF–870K Supplementary Material
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
Fan Mo, Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbert S Omenn, Biaoyang Lin
BMC Bioinformatics. 2008; 9: 537. Published online 2008 December 16. doi: 10.1186/1471-2105-9-537
PMCID:
PMC2636810
Abstract Full Text PDF–763K Supplementary Material
Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach
Manuel J Rodríguez-Ortega, Inmaculada Luque, Carmen Tarradas, José A Bárcena
BMC Genomics. 2008; 9: 588. Published online 2008 December 5. doi: 10.1186/1471-2164-9-588
PMCID:
PMC2613929
Abstract Full Text PDF–362K Supplementary Material
The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation
Dong Xia, Sanya J Sanderson, Andrew R Jones, Judith H Prieto, John R Yates, Elizabeth Bromley, Fiona M Tomley, Kalpana Lal, Robert E Sinden, Brian P Brunk, David S Roos, Jonathan M Wastling
Genome Biol. 2008; 9(7): R116. Published online 2008 July 21. doi: 10.1186/gb-2008-9-7-r116
PMCID:
PMC2530874
Abstract Full Text PDF–2.7M Supplementary Material
Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
Nitin Gupta, Jamal Benhamida, Vipul Bhargava, Daniel Goodman, Elisabeth Kain, Ian Kerman, Ngan Nguyen, Noah Ollikainen, Jesse Rodriguez, Jian Wang, Mary S. Lipton, Margaret Romine, Vineet Bafna, Richard D. Smith, Pavel A. Pevzner
Genome Res. 2008 July; 18(7): 1133–1142. doi: 10.1101/gr.074344.107
PMCID:
PMC2493402
Abstract Full Text PDF–573K
A mouse plasma peptide atlas as a resource for disease proteomics
Qing Zhang, Rajasree Menon, Eric W Deutsch, Sharon J Pitteri, Vitor M Faca, Hong Wang, Lisa F Newcomb, Ronald A DePinho, Nabeel Bardeesy, Daniela Dinulescu, Kenneth E Hung, Raju Kucherlapati, Tyler Jacks, Katerina Politi, Ruedi Aebersold, Gilbert S Omenn, David J States, Samir M Hanash
Genome Biol. 2008; 9(6): R93. Published online 2008 June 3. doi: 10.1186/gb-2008-9-6-r93
PMCID:
PMC2481425
Abstract Full Text PDF–364K
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
Nitin Gupta, Stephen Tanner, Navdeep Jaitly, Joshua N. Adkins, Mary Lipton, Robert Edwards, Margaret Romine, Andrei Osterman, Vineet Bafna, Richard D. Smith, Pavel A. Pevzner
Genome Res. 2007 September; 17(9): 1362–1377. doi: 10.1101/gr.6427907
PMCID:
PMC1950905
Abstract Full Text PDF–1.1M
Novel peptide identification from tandem mass spectra using ESTs and sequence database compression
Nathan J Edwards
Mol Syst Biol. 2007; 3: 102. Published online 2007 April 17. doi: 10.1038/msb4100142
PMCID:
PMC1865584
Abstract Full Text PDF–217K Supplementary Material
Improving gene annotation using peptide mass spectrometry
Stephen Tanner, Zhouxin Shen, Julio Ng, Liliana Florea, Roderic Guigó, Steven P. Briggs, Vineet Bafna
Genome Res. 2007 February; 17(2): 231–239. doi: 10.1101/gr.5646507
PMCID:
PMC1781355
Abstract Full Text PDF–441K
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