Computational Biology and Bioinformatics

A cutting-edge effort in bioinformatics and computational biology exists within our group. Computational techniques are used to analyze and classify large biological datasets from single cells to humans. We have a particular interest in the investigation of the RNA cargo secreted into extracellular vesicles.  

Selected Papers

Lerchenmuller C, Rabolli CP, Yeri AS, Kitchen R, Salvador AM, Liu LX, Ziegler O, Danielson KM, Platt C, Shah R, Damilano F, Kundu P, Riechert E, Katus HA, Saffitz JE, Keshishian H, Carr S, Bezzerides VJ, Das S and Rosenzweig A. CITED4 Protects Against Adverse Remodeling in Response to Physiological and Pathological Stress. Circ Res. 2020.

Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O’Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S and Group NTLW. Deep-coverage whole genome sequences and blood lipids among 16,324 individuals. Nat Commun. 2018;9:3391.

Lino Cardenas CL, Kessinger CW, Cheng Y, MacDonald C, MacGillivray T, Ghoshhajra B, Huleihel L, Nuri S, Yeri AS, Jaffer FA, Kaminski N, Ellinor P, Weintraub NL, Malhotra R, Isselbacher EM and Lindsay ME. An HDAC9-MALAT1-BRG1 complex mediates smooth muscle dysfunction in thoracic aortic aneurysm. Nat Commun. 2018;9:1009.

Shah R, Yeri A, Das A, Courtright-Lim A, Ziegler O, Gervino E, Ocel J, Quintero-Pinzon P, Wooster L, Bailey CS, Tanriverdi K, Beaulieu LM, Freedman JE, Ghiran I, Lewis GD, Van Keuren-Jensen K and Das S. Small RNA-seq during acute maximal exercise reveal RNAs involved in vascular inflammation and cardiometabolic health: brief report. Am J Physiol Heart Circ Physiol. 2017;313:H1162-H1167.

Kitchen RR, Sabine VS, Simen AA, Dixon JM, Bartlett JM and Sims AH. Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments. BMC Genomics. 2011;12:589.