Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers - Shaun S. Sanders; Dale D. O. Martin; Stefanie L. Butland; Mathieu Lavallée-Adam; Diego Calzolari; Chris Kay; John R. Yates III; Michael R. Hayden (PLoS Comput. Biol., 2015)

Census 2: isobaric labeling data analysis - Sung Kyu Robin Park; Aaron Aslanian; Daniel B. McClatchy; Xuemei Han; Harshil Shah; Meha Singh; Navin Rauniyar; James J. Moresco; Antonio F. M. Pinto; Jolene K. Diedrich; Claire Delahunty; John R. Yates III (Bioinform., 2014)

Improving the TFold test for differential shotgun proteomics - Paulo C. Carvalho; John R. Yates III; Valmir Carneiro Barbosa (Bioinform., 2012)

Analyzing marginal cases in differential shotgun proteomics - Paulo C. Carvalho; Juliana S. G. Fischer; Jonas Perales; John R. Yates III; Valmir Carneiro Barbosa; Elias Bareinboim (Bioinform., 2011)

Constrained De Novo Sequencing of Peptides with Application to Conotoxins - Swapnil Bhatia; Yong J. Kil; Beatrix Ueberheide; Brian T. Chait; Lemmuel Lara Tayo; Lourdes J. Cruz; Bingwen Lu; John R. Yates III; Marshall W. Bern (Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings, 2011)

XDIA: improving on the label-free data-independent analysis - Paulo C. Carvalho; Xuemei Han; Tao Xu; Daniel Cociorva; Maria da Gloria Carvalho; Valmir Carneiro Barbosa; John R. Yates III (Bioinform., 2010)

YADA: a tool for taking the most out of high-resolution spectra - Paulo C. Carvalho; Tao Xu; Xuemei Han; Daniel Cociorva; Valmir Carneiro Barbosa; John R. Yates III (Bioinform., 2009)

PatternLab for proteomics: a tool for differential shotgun proteomics - Paulo C. Carvalho; Juliana S. G. Fischer; Emily I. Chen; John R. Yates III; Valmir Carneiro Barbosa (BMC Bioinform., 2008)

CEBS object model for systems biology data, SysBio-OM - Sandhya Xirasagar; Scott F. Gustafson; B. Alex Merrick; Kenneth B. Tomer; Stanley Stasiewicz; Denny D. Chan; Kenneth J. Yost III; John R. Yates III; Susan Sumner; Nianqing Xiao; Michael D. Waters (Bioinform., 2004)

Automatic Quality Assessment of Peptide Tandem Mass Spectra - Marshall W. Bern; David Goldberg; W. Hayes McDonald; John R. Yates III (Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, Glasgow, UK, July 31-August 4, 2004, 2004)

Mass spectrometry and the proteome (abstract) - John R. Yates III (Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, RECOMB 1998, New York, NY, USA, March 22-25, 1998, 1998)