Computational Biology at MSR New England

Optimized sgRNA design to maximize activity and minimize off-target effects for genetic screens with CRISPR-Cas9 (opens in new tab)
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 (opens in new tab)
Fusi F., Lippert C., Lawrence N., Stegle O, Nature Communications (2014)

Epigenome-wide association studies without the need for cell-type composition (opens in new tab)
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 (opens in new tab)
Listgarten* J, Lippert* C, Heckerman* D (*equal contributions) Nature Genetics, 45, 470-471 (2013)

Improved linear mixed models for genome-wide association studies (opens in new tab)
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 (opens in new tab)
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 (opens in new tab)
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 (opens in new tab) Listgarten J and Emili A, Molecular and Cellular Proteomics (2005)

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting Steiner forest problem (opens in new tab) (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 (opens in new tab) (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)