2023
Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A.
Weng C#, Gu A#, Zhang S#, Lu L, Ke L, Gao P, Liu X, Wang Y, Hu P, Plummer D, MacDonald E, Zhang S, Xi J, Lai S, Leskov K, Yuan K, Jin F*, Li Y*.
Nature Communications 2023
PMID: 37669939
Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk.
Celis K, Moreno MDMM, Rajabli F, Whitehead P, Hamilton-Nelson K, Dykxhoorn DM, Nuytemans K, Wang L, Flanagan M, Weintraub S, Geula C, Gearing M, Dalgard CL, Jin F, Bennett DA, Schuck T, Pericak-Vance MA, Griswold AJ, Young JI, Vance JM.
Alzheimer's & Dementia 2023
PMID: 37037656
Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephaly.
Fu C, Ngo J, Zhang S, Lu L, Miron A, Schafer S, Gage FH, Jin F, Schumacher FR, Wynshaw-Boris A.
Human Molecular Genetics 2023
PMID: 36519762
Easy Hi-C: A Low-Input Method for Capturing Genome Organization.
Lu L, Jin F
Methods in Molecular Biology 2023
PMID: 36427146
2022
DeepLoop robustly maps chromatin interactions 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
A locus at 19q13.31 significantly reduces the ApoE ε4 risk for Alzheimer's Disease in African Ancestry.
Rajabli F, Beecham GW, Hendrie HC, Baiyewu O, Ogunniyi A, Gao S, Kushch NA, Lipkin-Vasquez M, Hamilton-Nelson KL, Young JI, Dykxhoorn DM, Nuytemans K, Kunkle BW, Wang L, Jin F, Liu X, Feliciano-Astacio BE; Alzheimer’s Disease Sequencing Project, Alzheimer’s Disease Genetic Consortium, Schellenberg GD, Dalgard CL, Griswold AJ, Byrd GS, Reitz C, Cuccaro ML, Haines JL, Pericak-Vance MA, Vance JM.
PLoS Genetics 2022
PMID: 35788729
53BP1 regulates heterochromatin through liquid phase separation.
Zhang L, Geng X, Wang F, Tang J, Ichida Y, Sharma A, Jin S, Chen M, Tang M, Pozo FM, Wang W, Wang J, Wozniak M, Guo X, Miyagi M, Jin F, Xu Y, Yao X, Zhang Y.
Nature Communications 2022
PMID: 35042897
Identifying differential regulatory control of APOE ɛP on African versus European haplotypes as potential therapeutic targets.
Nuytemans K, Lipkin Vasquez M, Wang L, Van Booven D, Griswold AJ, Rajabli F, Celis K, Oron O, Hofmann N, Rolati S, Garcia-Serje C, Zhang S, Jin F, Argenziano M, Grant SFA, Chesi A, Brown CD, Young JI, Dykxhoorn DM, Pericak-Vance MA, Vance JM.
Alzheimer's & Dementia 2022
PMID: 34978147
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
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