J
Jonathan E. Katz
Researcher at University of Southern California
Publications - 40
Citations - 4731
Jonathan E. Katz is an academic researcher from University of Southern California. The author has contributed to research in topics: Cancer & Citrate synthase. The author has an hindex of 22, co-authored 40 publications receiving 3800 citations. Previous affiliations of Jonathan E. Katz include Cedars-Sinai Medical Center & University of California, Los Angeles.
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Journal ArticleDOI
A cross-platform toolkit for mass spectrometry and proteomics
Matthew C. Chambers,Brendan MacLean,Robert Burke,Dario Amodei,Daniel Ruderman,Steffen Neumann,Laurent Gatto,Bernd Fischer,Brian S. Pratt,Jarrett D. Egertson,Katherine Hoff,Darren Kessner,Natalie Tasman,Nicholas J. Shulman,Barbara Frewen,Tahmina A Baker,Mi-Youn Brusniak,Christopher Paulse,David M. Creasy,Lisa Flashner,Kian Kani,Chris Moulding,Sean L. Seymour,Lydia M. Nuwaysir,Brent Lefebvre,Frank E. Kuhlmann,Joe Roark,Paape Rainer,Suckau Detlev,Tina Hemenway,Andreas Huhmer,James I. Langridge,Brian Connolly,Trey Chadick,Krisztina Holly,Josh Eckels,Eric W. Deutsch,Robert L. Moritz,Jonathan E. Katz,David B. Agus,Michael J. MacCoss,David L. Tabb,Parag Mallick,Parag Mallick +43 more
TL;DR: The ProteoWizard Toolkit is developed, a robust set of open-source, software libraries and applications designed to facilitate proteomics research that implements the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats.
Journal ArticleDOI
A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas
Terry Farrah,Eric W. Deutsch,Gilbert S. Omenn,Gilbert S. Omenn,David S. Campbell,Zhi Sun,Julie A. Bletz,Parag Mallick,Jonathan E. Katz,Johan Malmström,Reto Ossola,Julian D. Watts,Biaoyang Lin,Hui Zhang,Robert L. Moritz,Ruedi Aebersold +15 more
TL;DR: This work has identified 20,433 distinct peptides, from which it inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%, and compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high- confidence sets.
Journal ArticleDOI
Automated Identification of Putative Methyltransferases from Genomic Open Reading Frames
TL;DR: It is found that simple pattern matching based on the motif sequence is of limited utility and that a new method of “sensitized matrices for scoring methyltransferases” (SM2) produced with modified versions of the MEME and MAST tools gives greatly improved results for the Saccharomyces cerevisiae yeast genome.
Journal ArticleDOI
The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.
John Klimek,James S. Eddes,Laura Hohmann,Jennifer Jackson,Amelia Peterson,Simon Letarte,Philip R. Gafken,Jonathan E. Katz,Parag Mallick,Hookeun Lee,Alexander Schmidt,Reto Ossola,Jimmy K. Eng,Ruedi Aebersold,Daniel Martin +14 more
TL;DR: This work sought to generate a data set of reference data covering multiple instrumentation platforms to facilitate both the refinement of existing computational approaches and the development of novel software tools.
Journal ArticleDOI
A physical sciences network characterization of non-tumorigenic and metastatic cells
David B. Agus,Jenolyn F. Alexander,Wadih Arap,S.P. Ashili,Joseph E. Aslan,Robert H. Austin,Vadim Backman,Kelly Bethel,Richard Bonneau,Wei Chiang Chen,Chira Chen-Tanyolac,Nathan C. Choi,Steven A. Curley,Matthew R. Dallas,Dhwanil Damania,Paul Davies,Paolo Decuzzi,Laura E. Dickinson,Luis Estévez-Salmerón,Veronica Estrella,Mauro Ferrari,Claudia Fischbach,Jasmine Foo,Stephanie I. Fraley,Christian Frantz,Alexander Fuhrmann,Philippe Gascard,Robert A. Gatenby,Yue Geng,Sharon Gerecht,Robert J. Gillies,Biana Godin,William M. Grady,William M. Grady,Alex Greenfield,Courtney Hemphill,Barbara L. Hempstead,Abigail Hielscher,W. Daniel Hillis,Eric C. Holland,Arig Ibrahim-Hashim,Tyler Jacks,Roger H. Johnson,Ahyoung Joo,Jonathan E. Katz,Laimonas Kelbauskas,Carl Kesselman,Michael R. King,Konstantinos Konstantopoulos,Casey M. Kraning-Rush,Peter Kuhn,Kevin S. Kung,Brian J. Kwee,Johnathon N. Lakins,Guillaume Lambert,David Liao,Jonathan D. Licht,Jan Liphardt,Jan Liphardt,Liyu Liu,Mark C. Lloyd,Anna Lyubimova,Parag Mallick,Parag Mallick,John F. Marko,Owen J. T. McCarty,Deirdre R. Meldrum,Franziska Michor,Shannon M. Mumenthaler,Vivek Nandakumar,Thomas V. O'Halloran,Steve Oh,Renata Pasqualini,Matthew J. Paszek,Kevin G. Philips,Christopher S. Poultney,Kuldeepsinh Rana,Cynthia A. Reinhart-King,Robert Ros,Gregg L. Semenza,Patti Senechal,Michael L. Shuler,Srimeenakshi Srinivasan,Jack R. Staunton,Yolanda Stypula,Hariharan Subramanian,Thea D. Tlsty,Garth W. Tormoen,Yiider Tseng,Yiider Tseng,Alexander van Oudenaarden,Scott S. Verbridge,Scott S. Verbridge,Jenny C. Wan,Valerie M. Weaver,Jonathan Widom,Christine Will,Denis Wirtz,Jonathan W. Wojtkowiak,Pei Hsun Wu +99 more
TL;DR: Comparisons of the non-tumorigenic MCF-10A and metastatic MDA-MB-231 breast epithelial cell lines, commonly used as models of cancer metastasis, reveal dramatic differences in their mechanics, migration, adhesion, oxygen response, and proteomic profiles.