Publications

Peer reviewed journals

* co-first; co-corresponding

2021

Large-scale genetic association and single cell accessible chromatin mapping defines cell type-specific mechanisms of type 1 diabetes risk. Chiou J, Geusz RJ, Okino ML, Han JY, Miller M, Melton R, Beebe E, Benaglio P, Huang S, Korgaonkar K, Heller S, Kleger A, Preissl S, Gorkin DU, Sander M, Gaulton KJ. Nature. 2021. May. PMID: 34012112.

Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk. Chiou J*, Zeng C*, Cheng Z, Han JY, Schlichting M, Miller M, Mendez R, Huang S, Wang J, Sui Y, Deogaygay A, Okino ML, Qiu Y, Sun Y, Kudtarkar P, Fang R, Preissl S, Sander M†, Gorkin DU†, Gaulton KJ†. Nature Genetics. 2021 Apr. PMID: 33795864.

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, Ren B. Nat Struct Mol Biol. 2021 Jan 4. PMID: 33398174.

2020

An atlas of dynamic chromatin landscapes in mouse fetal development. Gorkin DU*, Barozzi I*, Zhao Y*, Zhang Y*, Huang H*, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A†, Pennacchio LA†, Ren B†. Nature. 2020 Jul. PMID: 32728240.

Expanded encyclopaedias of DNA elements in the human and mouse genomes. ENCODE Project Consortium, Moore JE*, Purcaro MJ*, Pratt HE*, Epstein CB*, Shoresh N*, Adrian J*, Kawli T*, Davis CA*, Dobin A*, Kaul R, Halow J*, Van Nostrand EL*, Freese P*, Gorkin DU*, Shen Y*, He Y*, Mackiewicz M*, Pauli-Behn F*, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Nature. 2020 Jul. PMID: 32728249.

Spatiotemporal DNA methylome dynamics of the developing mouse fetus. He Y, Hariharan M, Gorkin DU, Dickel DE, Luo C, Castanon RG, Nery JR, Lee AY, Zhao Y, Huang H, Williams BA, Trout D, Amrhein H, Fang R, Chen H, Li B, Visel A, Pennacchio LA, Ren B, Ecker JR. Nature. 2020 Jul. PMID: 32728242.

Before 2020

Common DNA sequence variation influences 3-dimensional conformation of the human genome. Gorkin DU*, Qiu Y*, Hu M*†, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Chiou J, Gaulton KJ, Sebat J, Li Y, Hansen KD, Ren B†. Genome Biol. 2019 Nov 28. PMID: 31779666.

Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. Greenwald WW*, Chiou J*, Yan J*, Qiu Y*, Dai N*, Wang A, Nariai N, Aylward A, Han JY, Kadakia N, Regue L, Okino ML, Drees F, Kramer D, Vinckier N, Minichiello L, Gorkin D, Avruch J, Frazer KA†, Sander M†, Ren B†, Gaulton KJ†. Nat Commun. 2019 May 7. PMID: 31064983.

Multi-platform discovery of haplotype-resolved structural variation in human genomes. Chaisson MJP*, Sanders AD*, Zhao X,* Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO†, Eichler EE†, Lee C†. Nat Commun. 2019 Apr 16. PMID: 30992455.

N6-methyladenine DNA Modification in Glioblastoma. Xie Q*, Wu TP*, Gimple RC*, Li Z, Prager BC, Wu Q, Yu Y, Wang P, Wang Y, Gorkin DU, Zhang C, Dowiak AV, Lin K, Zeng C, Sui Y, Kim LJY, Miller TE, Jiang L, Lee CH, Huang Z, Fang X, Zhai K, Mack SC, Sander M, Bao S, Kerstetter-Fogle AE, Sloan AE, Xiao AZ†, Rich JN†. Cell. 2018 Nov 15. PMID: 30392959.

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Preissl S*, Fang R*, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. Nat Neurosci. 2018 Mar. PMID: 29434377.

Improved regulatory element prediction based on tissue-specific local epigenomic signatures. He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR. Proc Natl Acad Sci U S A. 2017 Feb 28. PMID: 28193886.

Genome-wide compendium and functional assessment of in vivo heart enhancers. Dickel DE†, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama JA, Afzal V, Lee AY, Gorkin DU, Ren B, Rubin EM, Visel A†, Pennacchio LA†. Nat Commun. 2016 Oct 5. PMID: 27703156.

Chromatin Domains: The Unit of Chromosome Organization. Dixon JR, Gorkin DU, Ren B. Mol Cell. 2016 Jun 2. PMID: 27259200. [Review]

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Guo Y*, Xu Q*, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, Ren B, Krainer AR, Maniatis T†, Wu Q†. Cell. 2015 Aug 13. PMID: 26276636.

Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. Fufa TD, Harris ML, Watkins-Chow DE, Levy D, Gorkin DU, Gildea DE, Song L, Safi A, Crawford GE, Sviderskaya EV, Bennett DC, Mccallion AS, Loftus SK, Pavan WJ. Hum Mol Genet. 2015 Oct 1. PMID: 26206884.

A method to predict the impact of regulatory variants from DNA sequence. Lee D*, Gorkin DU*, Baker M, Strober BJ, Asoni AL, McCallion AS†, Beer MA†. Nat Genet. 2015 Aug. PMID: 26075791.

The 3D genome in transcriptional regulation and pluripotency. Gorkin DU, Leung D, Ren B. Cell Stem Cell. 2014 Jun 5. PMID: 24905166. [Review]

Genetics: Closing the distance on obesity culprits. Gorkin DU, Ren B. Nature. 2014 Mar 20. PMID: 24646989. [News & views]

A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway. Praetorius C, Grill C, Stacey SN, Metcalf AM, Gorkin DU, Robinson KC, Van Otterloo E, Kim RS, Bergsteinsdottir K, Ogmundsdottir MH, Magnusdottir E, Mishra PJ, Davis SR, Guo T, Zaidi MR, Helgason AS, Sigurdsson MI, Meltzer PS, Merlino G, Petit V, Larue L, Loftus SK, Adams DR, Sobhiafshar U, Emre NC, Pavan WJ, Cornell R, Smith AG, McCallion AS, Fisher DE, Stefansson K, Sturm RA, Steingrimsson E. Cell. 2013 Nov 21. PMID: 24267888.

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Gorkin DU, Lee D, Reed X, Fletez-Brant C, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS. Genome Res. 2012 Nov. PMID: 23019145.

SOX10 directly modulates ERBB3 transcription via an intronic neural crest enhancer. Prasad MK, Reed X, Gorkin DU, Cronin JC, McAdow AR, Chain K, Hodonsky CJ, Jones EA, Svaren J, Antonellis A, Johnson SL, Loftus SK, Pavan WJ, McCallion AS. BMC Dev Biol. 2011 Jun 14. PMID: 21672228.

Knock in of the AKT1 E17K mutation in human breast epithelial cells does not recapitulate oncogenic PIK3CA mutations. Lauring J*, Cosgrove DP*, Fontana S, Gustin JP, Konishi H, Abukhdeir AM, Garay JP, Mohseni M, Wang GM, Higgins MJ, Gorkin D, Reis M, Vogelstein B, Polyak K, Cowherd M, Buckhaults PJ, Park BH. Oncogene. 2010 Apr 22. PMID: 20101210.

Oligodendroglial and pan-neural crest expression of Cre recombinase directed by Sox10 enhancer. Stine ZE, Huynh JL, Loftus SK, Gorkin DU, Salmasi AH, Novak T, Purves T, Miller RA, Antonellis A, Gearhart JP, Pavan WJ, McCallion AS. Genesis. 2009 Nov. PMID: 19830815.

Preprints

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum. Yang Eric Li*, Sebastian Preissl*, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Rongxin Fang, Yunjiang Qiu, Olivier Poirion, Bin Li, Hanqing Liu, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Samantha Kuan, David Gorkin, Michael Nunn, Eran A. Mukamel, M. Margarita Behrens, Joseph Ecker, Bing Ren. https://doi.org/10.1101/2020.05.10.087585

De Novo Mutation in an Enhancer of EBF3 in simplex autism. Evin M. Padhi, Tristan J. Hayeck, Brandon Mannion, Sumantra Chatterjee, Marta Byrska-Bishop, Rajeeva Musunuri, Giuseppe Narzisi, Avinash Abhyankar, Zhang Cheng, Riana D. Hunter, Jennifer Akiyama, Lauren E. Fries, Jeffrey Ng, Nick Stong, Andrew S. Allen, Diane E. Dickel, Raphael A. Bernier, David U. Gorkin, Len A. Pennacchio, Michael C. Zody, Tychele N. Turner. https://doi.org/10.1101/2020.08.28.270751

Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro. Morten Seirup, Srikumar Sengupta, Scott Swanson, Brian E. McIntosh, Mike Colins, Li-Fang Chu, Zhang Cheng, David U. Gorkin, Bret Duffin, Jennifer M. Bolin, Cara Argus, Ron Stewart, James A. Thomson. https://doi.org/10.1101/2020.09.21.307363

Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq. Paola Benaglio, Jacklyn Newsome, Jee Yun Han, Joshua Chiou, Anthony Aylward, Sierra Corban, Mei-Lin Okino, Jaspreet Kaur, David U Gorkin, Kyle J Gaulton. https://doi.org/10.1101/2020.12.03.387894

Removing unwanted variation between samples in Hi-C experiments. Kipper Fletez-Brant, Yunjiang Qiu, David U. Gorkin, Ming Hu, Kasper D. Hansen
bioRxiv 214361; doi: https://doi.org/10.1101/214361