2022
DeepLoop robustly maps chromatin loops from sparse allele-resolved or single-cell Hi-C data at kilobase resolution.
Zhang S, Plummer D, Lu L, Cui J, Xu W, Wang M, Liu X, Prabhakar N, Shrinet J, Srinivasan D, Fraser P, Li Y*, Li J*, Jin F*.
Nature Genetics 2022
PMID: 35817982
2021
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants
Dong C, Simonett SP, Shin S, Stapleton DS, Schueler KL, Churchill GA, Lu L, Liu X, Jin F, Li Y, Attie AD, Keller MP, Keleş S.
Genome Biology 2021
PMID: 34425882
2020
Single cell lineage analysis reveals extensive multimodal transcriptional control during directed β-cell differentiation.
Weng C, Xi J, Li H, Cui J, Gu A, Lai S, Leskov K, Ke L, Jin F*, Li Y*.
Nature Metabolism 2020
PMID: 33257854
Aberrant Methylation Underlies Insulin Gene Expression in Human Insulinoma.
Karakose E, Wang H, Inabnet W, Thakker RV, Libutti S, Fernandez-Ranvier G, Suh H, Stevenson M, Kinoshita Y, Donovan M, Antipin Y, Li Y, Liu X, Jin F, Wang P, Uzilov A, Argmann C, Schadt EE, Stewart AF, Scott DK, Lambertini L.
Nature Communications 2020
PMID: 33060578
TWO-SIGMA: a novel TWO-component SInGle cell Model-based Association method for single-cell RNA-seq data.
Buren EV, Hu M, Weng C, Jin F, Li Y, Wu D, Li Y.
Genetic Epidemiology 2020
PMID: 32989764
Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases.
Lu L, Liu X, Huang WK, Giusti-Rodríguez P, Cui J, Zhang S, Xu W, Wen Z, Ma S, Rosen JD, Xu Z, Bartels CF, Kawaguchi R, Hu M, Scacheri PC, Rong Z, Li Y, Sullivan PF, Song H, Ming GL*, Li Y*, Jin F*.
Molecular Cell 2020
PMID: 32592681
Myt Transcription Factors Prevent Stress-Response Gene Overactivation to Enable Postnatal Pancreatic β Cell Proliferation, Function, and Survival.
Hu R, Walker E, Huang C, Xu Y, Weng C, Erickson GE, Coldren A, Yang X, Brissova M, Kaverina I, Balamurugan AN, Wright CVE, Li Y, Stein R, Gu G.
Developmental Cell 2020
PMID: 32359405
2019
Exploring the Trans-Cleavage Activity of CRISPR-Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor.
Dai Y, Somoza RA, Wang L, Welter JF, Li Y, Caplan AI, Liu CC.
Angew Chem Int Ed Engl. 2019
PMID: 31568601
Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes.
Fang Z, Weng C, Li H, Tao R, Mai W, Liu X, Lu L, Lai S, Duan Q, Alvarez C, Arvan P, Wynshaw-Boris A, Li Y, Pei Y, Jin F*, Li Y*.
Cell Reports 2019
PMID: 30865899
2018
Chemical Screening Identifies Enhancers of Mutant Oligodendrocyte Survival and Unmasks a Distinct Pathological Phase in Pelizaeus-Merzbacher Disease.
Elitt MS, Shick HE, Madhavan M, Allan KC, Clayton BLL, Weng C, Miller TE, Factor DC, Barbar L, Nawash BS, Nevin ZS, Lager AM, Li Y, Jin F, Adams DJ, Tesar PJ.
Stem Cell Reports 2018
PMID: 30146490
Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling.
Mack SC, Pajtler KW, Chavez L, Okonechnikov K, Bertrand KC, Wang X, Erkek S, Federation A, Song A, Lee C, Wang X, McDonald L, Morrow JJ, Saiakhova A, Sin-Chan P, Wu Q, Michaelraj KA, Miller TE, Hubert CG, Ryzhova M, Garzia L, Donovan L, Dombrowski S, Factor DC, Luu B, Valentim CLL, Gimple RC, Morton A, Kim L, Prager BC, Lee JJY, Wu X, Zuccaro J, Thompson Y, Holgado BL, Reimand J, Ke SQ, Tropper A, Lai S, Vijayarajah S, Doan S, Mahadev V, Miñan AF, Gröbner SN, Lienhard M, Zapatka M, Huang Z, Aldape KD, Carcaboso AM, Houghton PJ, Keir ST, Milde T, Witt H, Li Y, Li CJ, Bian XW, Jones DTW, Scott I, Singh SK, Huang A, Dirks PB, Bouffet E, Bradner JE, Ramaswamy V, Jabado N, Rutka JT, Northcott PA, Lupien M, Lichter P, Korshunov A, Scacheri PC, Pfister SM, Kool M, Taylor MD, Rich JN.
Nature 2018
PMID: 29258295
2015
Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates.
Wang A*, Yue F*, Li Y*, Xie R, Harper T, Patel NA, Muth K, Palmer J, Qiu Y, Wang J, Lam DK, Raum JC, Stoffers DA, Ren B, Sander M.
Cell Stem Cell 2015
PMID: 25842977
Integrative analysis of 111 reference human epigenomes.
Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.
Nature 2015
PMID: 25693563
2014
CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.
Li Y, Rivera CM, Ishii H, Jin F, Selvaraj S, Lee AY, Dixon JR, Ren B.
PLoS One 2014
PMID: 25486255
2013
A high-resolution map of the three-dimensional chromatin interactome in human cells.
Jin F*, Li Y*, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B.
Nature 2013
PMID: 24141950
Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B.
Cell 2013
PMID: 23664764
RFECS: a random-forest based algorithm for enhancer identification from chromatin state.
Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B.
PLoS Computational Biolology 2013
PMID: 23526891
2012
Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.
Nature 2012
PMID: 22495300
2011
Enhancers: multi-dimensional signal integrators.
Jin F, Li Y, Ren B, Natarajan R.
Transcription 2011
PMID: 22231119
PU.1 and C/EBPα synergistically program distinct response to NF-κB activation through establishing monocyte specific enhancers.
Jin F*, Li Y*, Ren B, Natarajan R.
Proc Natl Acad Sci U S A 2011
PMID: 21402921
2008
Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-κB-dependent inflammatory genes.
Li Y, Reddy MA, Miao F, Shanmugam N, Yee JK, Hawkins D, Ren B, Natarajan R.
J Biol Chem. 2008
PMID: 18650421
Proinflammatory effects of advanced lipoxidation end products in monocytes.
Shanmugam N, Figarola JL, Li Y, Swiderski PM, Rahbar S, Natarajan R.
Diabetes 2008
PMID: 18003754