JinLab

 

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

 

 

 

2019

 

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

 

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.

Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti- Rodríguez P, Won H, de Leeuw CA, Pardiñas AF; BrainSpan Consortium; PsychENCODE Consortium; PsychENCODE Developmental Subgroup, Hu M, Jin F, Li Y, Owen MJ, O'Donovan MC, Walters JTR, Posthuma D, Reimers MA, Levitt P, Weinberger DR, Hyde TM, Kleinman JE, Geschwind DH, Hawrylycz MJ, State MW, Sanders SJ, Sullivan PF, Gerstein MB, Lein ES, Knowles JA, Sestan N.

Science 2018 

PMID: 30545854

 

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

 

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mill J, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O'Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Pettersson E, Peyrot WJ, Pistis G, Posthuma D, Purcell SM, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Saeed Mirza S, Saxena R, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GBC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Stockmeier CA, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Tian C, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS, Yang J, Zhang F; eQTLGen; 23andMe, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus ECJ, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Hinds DA, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PFA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O'Donovan MC, Paciga SA, Pedersen NL, Penninx BWJH, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Winslow AR, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF; Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium.

Nature Genetics 2018

PMID: 29700475

 

 

 

2016

 

HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants.

Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F, Li Y, Hu M.

BMC Res Notes 2016

PMID: 26969411

 

 

 

2015

 

A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data.

Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin Z, Hu M, Li Y.

Bioinformatics 2016

PMID: 26543175

 

 

 

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

 

5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.

Hon GC, Song CX, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao SQ, Wang BA, Kuan S, Edsall LE, Zhao BS, Xu GL, He C, Ren B.

Molecular Cell 2014

PMID: 25263596

 

Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark.

Dai L, Peng C, Montellier E, Lu Z, Chen Y, Ishii H, Debernardi A, Buchou T, Rousseaux S, Jin F, Sabari BR, Deng Z, Allis CD, Ren B, Khochbin S, Zhao Y.

Nature Chemical Biololgy 2014

PMID: 24681537.

 

 

 

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

 

 

 

2012

 

Combined gene expression and DNA occupancy profiling identifies potential therapeutic targets of t(8;21) AML.

Lo MC, Peterson LF, Yan M, Cong X, Jin F, Shia WJ, Matsuura S, Ahn EY, Komeno Y, Ly M, Ommen HB, Chen IM, Hokland P, Willman CL, Ren B, Zhang DE.

Blood 2012

PMID: 22740448

 

CBX3 regulates efficient RNA processing genome-wide.

Smallwood A, Hon GC, Jin F, Henry RE, Espinosa JM, Ren B.

Genome Research 2012

PMID: 22684280

 

 

 

2011

 

Enhancers: multi-dimensional signal integrators.

Jin F, Li Y, Ren B, Natarajan R.

Transcription 2011

PMID: 22231119

 

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.

Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y.

Cell 2011

PMID: 21925322

 

PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers.

Jin F*, Li Y*, Ren B, Natarajan R.

Proc Natl Acad Sci U S A 2011

PMID: 21402921

 

 

 

2007

 

A yeast two-hybrid smart-pool-array system for protein-interaction mapping.

Jin F, Avramova L, Huang J, Hazbun T.

Nature Methods 2007

PMID: 17450148

 

 

 

2006

 

A pooling-deconvolution strategy for biological network elucidation.

Jin F, Hazbun T, Michaud GA, Salcius M, Predki PF, Fields S, Huang J.

Nature Methods 2006

PMID: 16489335

 

 

 

2005

 

Insights into TOR function and rapamycin response: chemical genomic profiling by using a high-density cell array method.

Xie MW, Jin F, Hwang H, Hwang S, Anand V, Duncan MC, Huang J.

Proc Natl Acad Sci U S A 2005

PMID: 15883373

 

 

 

2004

 

Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips.

Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL.

Proc Natl Acad Sci U S A 2004

PMID: 15539461