Selected Publications



Ernlund AE, Schnieder RJ, Ruggles KV. (2018) RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data. BMC Genomics 19:809

Ruggles KV, Wang J, Volkova A, Contreras M, Noya-Alarcon O, Lander O, Caballero H, Dominguez Bello MG. (2018) Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village. mSphere PMID: 30158281

Devlin JC, Battaglia T, Blaser MJ, Ruggles KV. (2018) WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequence data. BMC Genomics. PMID: 29940835

Ruggles KV*, Krug K*, Wang X*, Clauser KR, Wang J, Payne SH, Fenyo D, Zhang B, Mani DR. (2017) Methods, tools and current perspectives in proteogenomics. Molecular and Cellular Proteomics. PMID:28456751

Huang K, Li S, Mertins P, Gunawardena HP, Cao S, Ruggles KV, Mani DR, Xie L, Yoon C, Clauser KR, Qiao JW, Wrobel J, Wyczalkowski M, Erdmann-Gilmore P, Snider JE, Hoog J, Niu B, Sun SQ, Kawaler E, Scott A, Ye K, McLellan MD, Wendl MC, Held JM, Gillette MA, Perou CM, Fenyo D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Ma C, Townsend RR, Chen X, Ellis MJ, Carr SA, Ding L. (2017) Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nature Communications.  PMID: 28348404

Mertins P*, Mani DR*, Ruggles KV*, Gillette MA*, Clauser KR, Wang P, Wang, X, Qiao JW, Cao S, Petralia F, Mundt F, Tu Z, Lei JT, Gatza M, Perou CM, Yellapantula V, Lin C, Ding L, McLellan M, Ping Y, Davies SR, Townsend R, Zhang B, Rodriguez H, Paulovich A, Fenyo D, Ellis M, Carr SA & the NCI CPTAC (2016) Proteogenomic analysis of human breast cancer connects genetic alterations to phosphorylation networks. Nature.  534(7605):55-62  PMID: 27251275 

Ruggles KV*, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLennan M, Clauser K, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Gunawardena HP,  Liu T, Zhou J, Hoadley KA, Perou CM, Chen X, Davies S, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Clinical Proteomic Tumor Analysis Consortium (CPTAC), Payne S, Ellis MJ, & Fenyo D (2015)  An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer. Molecular and Cellular Proteomics.  PMID: 26631509

Ruggles KV*& Rajan S (2014).  Gun possession among American youth: A discovery-based approach to understand gun violence. PLOS ONE. 9(11):e111893 PMID: 25372864

Ruggles KV*, Turkish A., Sturley SL. (2013) Making, Baking and Breaking: The Synthesis, Storage and Hydrolysis of Neutral Lipids. Annual Review of Nutrition. 33:413-51 PMID: 23701589

Ruggles KV*, Garbarino J., Liu Y, Moon J, Schneider K, Henneberry A, Bilheimer J, Millar JS, Marchadier D, Valasek MA, Joblin-Mills A, Gulati S, Munkacsi AB, Repa JJ, Radar D, Sturley SL.  (2013) A functional, genome-wide evaluation of liposensitive yeast identifies the "ARE2 required for viability" (ARV1) gene product as a major component of eukaryotic fatty acid resistance.   Journal of Biol Chem 289(7):4417-31 PMID:24273168