Li Lab

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

Accepted

 

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