Mass spectrometry and the proteome (abstract). - John R. Yates III (RECOMB, 1998)

Automatic Quality Assessment of Peptide Tandem Mass Spectra. - Marshall W. Bern; David Goldberg 001; W. Hayes McDonald; John R. Yates III (ISMB/ECCB (Supplement of Bioinformatics), 2004)

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)

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)

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)

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)

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 (RECOMB, 2011)

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)

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

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)

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)