Onco-proteogenomics: cancer proteomics joins forces with genomics

Lloyd M Smith, Neil L Kelleher, Michal Linial, David Goodlett, Pat Langridge-Smith, Young Ah Goo, George Safford, Leo Bonilla, George Kruppa, Roman Zubarev, Jon Rontree, Julia Chamot-Rooke, John Garavelli, Albert Heck, Joseph Loo, Deborah Penque, Martin Hornshaw, Christopher Hendrickson, Ljiljana Pasa-Tolic, Christoph Borchers, Dominic Chan, Nicholas Young, Jeffrey Agar, Christophe Masselon, Michael Gross, Fred McLafferty, Yury Tsybin, Ying Ge, Ian Sanders, James Langridge, Julian Whitelegge, Alan Marshall, Proteoform: a single term describing protein complexity Nature Methods. ,vol. 10, pp. 186- 187 ,(2013) , 10.1038/NMETH.2369

Paul C Boutros, Adam D Ewing, Kyle Ellrott, Thea C Norman, Kristen K Dang, Yin Hu, Michael R Kellen, Christine Suver, J Christopher Bare, Lincoln D Stein, Paul T Spellman, Gustavo Stolovitzky, Stephen H Friend, Adam A Margolin, Joshua M Stuart, Global optimization of somatic variant identification in cancer genomes with a global community challenge Nature Genetics. ,vol. 46, pp. 318- 319 ,(2014) , 10.1038/NG.2932

Z. Khan, M. J. Ford, D. A. Cusanovich, A. Mitrano, J. K. Pritchard, Y. Gilad, Primate transcript and protein expression levels evolve under compensatory selection pressures. Science. ,vol. 342, pp. 1100- 1104 ,(2013) , 10.1126/SCIENCE.1242379

Mingyao Li, Isabel X Wang, Yun Li, Alan Bruzel, Allison L Richards, Jonathan M Toung, Vivian G Cheung, None, Widespread RNA and DNA sequence differences in the human transcriptome. Science. ,vol. 333, pp. 53- 58 ,(2011) , 10.1126/SCIENCE.1207018

Brian A. Risk, Wendy J. Spitzer, Morgan C. Giddings, Peppy: Proteogenomic Search Software Journal of Proteome Research. ,vol. 12, pp. 3019- 3025 ,(2013) , 10.1021/PR400208W

Ruedi Aebersold, Gary D. Bader, Aled M. Edwards, Jennifer E. van Eyk, Martin Kussmann, Jun Qin, Gilbert S. Omenn, The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community Journal of Proteome Research. ,vol. 12, pp. 23- 27 ,(2013) , 10.1021/PR301151M

S. A. Forbes, N. Bindal, S. Bamford, C. Cole, C. Y. Kok, D. Beare, M. Jia, R. Shepherd, K. Leung, A. Menzies, J. W. Teague, P. J. Campbell, M. R. Stratton, P. A. Futreal, COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Research. ,vol. 39, pp. 945- 950 ,(2011) , 10.1093/NAR/GKQ929

Amin Moghaddas Gholami, Hannes Hahne, Zhixiang Wu, Florian Johann Auer, Chen Meng, Mathias Wilhelm, Bernhard Kuster, Global Proteome Analysis of the NCI-60 Cell Line Panel Cell Reports. ,vol. 4, pp. 609- 620 ,(2013) , 10.1016/J.CELREP.2013.07.018

Hongbin Liu, Rovshan G. Sadygov, John R. Yates, A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics Analytical Chemistry. ,vol. 76, pp. 4193- 4201 ,(2004) , 10.1021/AC0498563

Ryan D Morin, Maria Mendez-Lago, Andrew J Mungall, Rodrigo Goya, Karen L Mungall, Richard D Corbett, Nathalie A Johnson, Tesa M Severson, Readman Chiu, Matthew Field, Shaun Jackman, Martin Krzywinski, David W Scott, Diane L Trinh, Jessica Tamura-Wells, Sa Li, Marlo R Firme, Sanja Rogic, Malachi Griffith, Susanna Chan, Oleksandr Yakovenko, Irmtraud M Meyer, Eric Y Zhao, Duane Smailus, Michelle Moksa, Suganthi Chittaranjan, Lisa Rimsza, Angela Brooks-Wilson, John J Spinelli, Susana Ben-Neriah, Barbara Meissner, Bruce Woolcock, Merrill Boyle, Helen McDonald, Angela Tam, Yongjun Zhao, Allen Delaney, Thomas Zeng, Kane Tse, Yaron Butterfield, Inanç Birol, Rob Holt, Jacqueline Schein, Douglas E Horsman, Richard Moore, Steven JM Jones, Joseph M Connors, Martin Hirst, Randy D Gascoyne, Marco A Marra, None, Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma Nature. ,vol. 476, pp. 298- 303 ,(2011) , 10.1038/NATURE10351