Burak Alver
Burak H Alver, Ph.D.
Scientific Project Manager, 4D Nucleome DCIC

Burak Alver is the Scientific Project Manager of the 4D Nucleome Data Coordination and Integration Center , led by the Park Lab at DBMI, overseeing the operations of the center.

Before that, he was a Research Fellow in the lab, working on various problems in epigenetic regulation of transcription. His main interests involve enhancer malfunction in cancer and the role of 3D chromatin structure in gene regulation.

And before that, he completed his PhD in experimental high energy physics at MIT. His research involved computational analysis of data collected at the Relativistic Heavy Ion Collider at Brookhaven National Laboratory.

HiGlass: web-based visual exploration and analysis of genome interaction maps.
Authors: Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N.
Genome Biol
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Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation.
Authors: Shetty A, Kallgren SP, Demel C, Maier KC, Spatt D, Alver BH, Cramer P, Park PJ, Winston F.
Mol Cell
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The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers.
Authors: Alver BH, Kim KH, Lu P, Wang X, Manchester HE, Wang W, Haswell JR, Park PJ, Roberts CW.
Nat Commun
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ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice.
Authors: Mathur R, Alver BH, San Roman AK, Wilson BG, Wang X, Agoston AT, Park PJ, Shivdasani RA, Roberts CW.
Nat Genet
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SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation.
Authors: Wang X, Lee RS, Alver BH, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, Bernstein BE, Park PJ, Roberts CW.
Nat Genet
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MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.
Authors: Mieczkowski J, Cook A, Bowman SK, Mueller B, Alver BH, Kundu S, Deaton AM, Urban JA, Larschan E, Park PJ, Kingston RE, Tolstorukov MY.
Nat Commun
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EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.
Authors: Lee S, Seo CH, Alver BH, Lee S, Park PJ.
BMC Bioinformatics
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Comparative analysis of metazoan chromatin organization.
Authors: Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ.
Nature
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Comparative analysis of the transcriptome across distant species.
Authors: Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.
Nature
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Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming.
Authors: West JA, Cook A, Alver BH, Stadtfeld M, Deaton AM, Hochedlinger K, Park PJ, Tolstorukov MY, Kingston RE.
Nat Commun
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