Computational Biology at MSR New England

Optimized sgRNA design to maximize activity and minimize off-target effects for genetic screens with CRISPR-Cas9
JG Doench*, N Fusi*, M Sullender*, M Hegde*, EW Vaimberg*, KF Donovan, I Smith, Z Tothova, C Wilen , R Orchard , HW Virgin, J Listgarten*, DE Root, Nature Biotechnology (2016)

Warped linear mixed models for the genetic analysis of transformed phenotypes
Fusi F., Lippert C., Lawrence N., Stegle O, Nature Communications (2014)

Epigenome-wide association studies without the need for cell-type composition
Zou J, Lippert C, Heckerman D, Aryee, M, Listgarten J Nature Methods, 309–311 (2014)

FaST-LMM-Select for addressing confounding from spatial structure and rare variants
Listgarten* J, Lippert* C, Heckerman* D (*equal contributions) Nature Genetics, 45, 470-471 (2013)

Improved linear mixed models for genome-wide association studies
Listgarten J*, Lippert* C, Kadie C, Davidson B, Eskin E, Heckerman* D *(equal contributions)
Nature Methods, 2012

FaST Linear Mixed Models for Genome-Wide Association Studies
Lippert* C, Listgarten* J., Liu Y, Kadie C, Davidson R, Heckerman* D. (*equal contributions) Nature Methods, Aug. 2011

Correction for Hidden Confounders in the Genetic Analysis of Gene Expression
Listgarten J, Kadie C, Schadt E, Heckerman D
Proceedings of the National Academy of Sciences, September 1, 2010

Statistical resolution of ambiguous HLA typing data
Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, Carrington M, Goulder P, Heckerman D, PLoS Computational Biology (2008)

Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry Listgarten J and Emili A, Molecular and Cellular Proteomics (2005)

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting Steiner forest problem (N. Tuncbag, A. Braunstein, A. Pagnani, S.S. Huang, J. Chayes, C. Borgs, R. Zecchina, and E. Fraenkel) Journal of Computational Biology 20 (2013) 124 – 136.

Finding undetected protein associations in cell signaling by belief propagation (with M. Bailly-Bechet, C. Borgs, A. Braunstein, J. Chayes, A. Dagkessamanskaia, J. Francois, and R. Zecchina). Proceedings of the National Academy of Sciences (PNAS) 108 (2011) 882 – 887.

Statistical mechanics of Steiner trees (M. Bayati, C. Borgs, A. Braunstein, A. Ramezanpour, and R. Zecchina, Physical Review Letters 101, 037208 (2008), reprinted in Virtual Journal of Biological Physics Research 16, August 1 (2008)