Cited by ..

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 27 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

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