Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice.

Chen J, Richardson PR, Kirby C, Eddy SR, Hoekstra HE.

Elife, 2025

doi:10.7554/elife.103109.

Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice

Chen J, Richardson PR, Kirby C, Eddy SR, Hoekstra H.

2024

doi:10.1101/2024.08.22.608850.

Evolution of gene expression across brain regions in behaviorally divergent deer mice

Kautt AF, Chen J, Lewarch CL, Hu C, Turner K, Lassance J, Baier F, Bedford NL, Bendesky A, Hoekstra HE.

2023

doi:10.1101/2023.09.28.559844.

A quantitative framework for characterizing the evolutionary history of mammalian gene expression.

Chen J, Swofford R, Johnson J, Cummings BB, Rogel N, Lindblad-Toh K, Haerty W, Palma FD, Regev A.

Genome Res, 2018

doi:10.1101/gr.237636.118.

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A.

Cell, 2016

doi:10.1016/j.cell.2016.11.038.

Local regulation of gene expression by lncRNA promoters, transcription and splicing.

Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, McDonel PE, Guttman M, Lander ES.

Nature, 2016

doi:10.1038/nature20149.

Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

Chen J, Shishkin AA, Zhu X, Kadri S, Maza I, Hanna JH, Regev A, Garber M.

2015

doi:10.1101/031385.

Simultaneous generation of many RNA-seq libraries in a single reaction.

Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J.

Nat Methods, 2015

doi:10.1038/nmeth.3313.

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver.

Bochkis IM, Przybylski D, Chen J, Regev A.

Cell Rep, 2014

doi:10.1016/j.celrep.2014.09.048.

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.

Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF.

Genome Res, 2014

doi:10.1101/gr.165845.113.

Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data.

Tuteja G, Moreira KB, Chung T, Chen J, Wenger AM, Bejerano G.

PLoS Comput Biol, 2014

doi:10.1371/journal.pcbi.1003449.

PRISM offers a comprehensive genomic approach to transcription factor function prediction.

Wenger AM, Clarke SL, Guturu H, Chen J, Schaar BT, McLean CY, Bejerano G.

Genome Res, 2013

doi:10.1101/gr.139071.112.