Sushmita Roy
Sushmita Roy
Associate Professor of Biostatistics and medical informatics, University of Wisconsin-Madison
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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
modENCODE Consortium, S Roy, J Ernst, PV Kharchenko, P Kheradpour, ...
Science 330 (6012), 1787-1797, 2010
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
A Stark, MF Lin, P Kheradpour, JS Pedersen, L Parts, JW Carlson, ...
Nature 450 (7167), 219, 2007
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome
AS Hebert, KE Dittenhafer-Reed, W Yu, DJ Bailey, ES Selen, ...
Molecular cell 49 (1), 186-199, 2013
Comparative functional genomics of the fission yeasts
N Rhind, Z Chen, M Yassour, DA Thompson, BJ Haas, N Habib, ...
Science 332 (6032), 930-936, 2011
Reliable prediction of regulator targets using 12 Drosophila genomes
P Kheradpour, A Stark, S Roy, M Kellis
Genome research 17 (12), 1919-1931, 2007
Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-phase cultures
AD Aragon, AL Rodriguez, O Meirelles, S Roy, GS Davidson, PH Tapia, ...
Molecular biology of the cell 19 (3), 1271-1280, 2008
SIRT3 mediates multi-tissue coupling for metabolic fuel switching
KE Dittenhafer-Reed, AL Richards, J Fan, MJ Smallegan, AF Siahpirani, ...
Cell metabolism 21 (4), 637-646, 2015
Comparative analysis of gene regulatory networks: from network reconstruction to evolution
D Thompson, A Regev, S Roy
Annu Rev Cell Dev Biol 31 (1), 399-428, 2015
Deep sequencing of the Medicago truncatula root transcriptome reveals a massive and early interaction between nodulation factor and ethylene signals
E Larrainzar, BK Riely, SC Kim, N Carrasquilla-Garcia, HJ Yu, HJ Hwang, ...
Plant Physiology 169 (1), 233-265, 2015
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
D Marbach, S Roy, F Ay, PE Meyer, R Candeias, T Kahveci, CA Bristow, ...
Genome research 22 (7), 1334-1349, 2012
A predictive modeling approach for cell line-specific long-range regulatory interactions
S Roy, AF Siahpirani, D Chasman, S Knaack, F Ay, R Stewart, M Wilson, ...
Nucleic acids research 43 (18), 8694-8712, 2015
A predictive modeling approach for cell line-specific long-range regulatory interactions
S Roy, AF Siahpirani, D Chasman, S Knaack, F Ay, R Stewart, M Wilson, ...
Nucleic acids research 43 (18), 8694-8712, 2015
Multivariate curve resolution of time course microarray data
PD Wentzell, TK Karakach, S Roy, MJ Martinez, CP Allen, ...
BMC bioinformatics 7 (1), 1-19, 2006
The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures
GS Davidson, RM Joe, S Roy, O Meirelles, CP Allen, MR Wilson, ...
Molecular biology of the cell 22 (7), 988-998, 2011
A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti
H Marx, CE Minogue, D Jayaraman, AL Richards, NW Kwiecien, ...
Nature biotechnology 34 (11), 1198-1205, 2016
Evolutionary principles of modular gene regulation in yeasts
DA Thompson, S Roy, M Chan, MP Styczynsky, J Pfiffner, C French, ...
Elife 2, e00603, 2013
Exploiting amino acid composition for predicting protein-protein interactions
S Roy, D Martinez, H Platero, T Lane, M Werner-Washburne
PloS one 4 (11), e7813, 2009
Network-based approaches for analysis of complex biological systems
D Chasman, AF Siahpirani, S Roy
Current opinion in biotechnology 39, 157-166, 2016
Integrated module and gene-specific regulatory inference implicates upstream signaling networks
S Roy, S Lagree, Z Hou, JA Thomson, R Stewart, AP Gasch
PLoS computational biology 9 (10), e1003252, 2013
Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress
AD Aragon, GA Quiñones, EV Thomas, S Roy, M Werner-Washburne
Genome biology 7 (2), 1-13, 2006
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