See our lab publication policy.

Publications

2024

Patel LA, Cao Y, Mendenhall EM, Benner C^#, Goren A^#
The Wild West of spike-in normalization (2024) Nat Biotechnol. [link]

2023

Margoliash J, Fuchs S, Li Y, Zhang X, Massarat A, Goren A^# & Melissa Gymrek^#.
Polymorphic short tandem repeats make widespread contributions to blood and serum traits (2023) Cell Genom. [link]; Accompanying perspective [link]

Maksimov MO, Wu C, Ashbrook DG, Villani F, Colonna V, Mousavi N, Ma N, Lu L, Pritchard JK, Goren A, Williams RW, Palmer AA, Gymrek M.
A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice (2023) Genome Res. [link]; Cover Image highlighting this study [link]

2022

Gandhi S, Mitterhoff R, Rapoport R, Farago M, Greenberg A, Hodge L, Eden S, Benner C, Goren A, Simon I.
Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3, and SIRT1. (2022) Life Sci Alliance. [link]

McDaniel S, Komor A^#, Goren A^#.
The use of base editing technology to characterize single nucleotide variants (2022) Comput Struct Biotechnol J. [link]

2021

Gymrek M^#, Goren A^#.
Missing heritability may be hiding in repeats (2021) Science [link]

Zheng A, Lamkin M, Qiu Y, Ren K, Goren A^# & Melissa Gymrek^#.
A flexible simulation toolkit for designing and evaluating ChIP-sequencing experiments (2021) BMC Bioinformatics [link]

2019

Fotsing S, Margoliash J, Wang C, Saini S, Shleizer-Burko S, Goren A^# & Melissa Gymrek^#.
The impact of short tandem repeat variation on gene expression. (2019) Nat Genet. [pubmed]

Ben-Yair R, Butty VL, Busby M, Qiu Y, Levine SS, Goren A^#, Boyer LA^#, Burns CG^# & Burns CE^#.
H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration. (2019) Development. [pubmed]

Etchegaray JP^#, Zhong L, Li C, Henriques T, Ablondi E, Nakadai T, Van Rechem C, Ferrer C, Ross KN, Choi JE, Samarakkody A, Ji F, Chang A, Sadreyev RI, Ramaswamy S, Nechaev S, Whetstine JR, Roeder RG, Adelman K, Goren A^# & Mostoslavsky R^#.
The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing. (2019) Molecular Cell [pubmed]

2018

Greenfield R, Tabib A, Keshet I, Moss J, Sabag O, Goren A & Cedar H.
Role of transcription complexes in the formation of the basal methylation pattern in early development. (2018) PNAS. [pubmed]

Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A^# & Simon I^#.
Study of the mitotic chromatin shows involvement of histone modifications in bookmarking and reveals nucleosome deposition patterns. (2018) Genome Res. [pubmed]

Reizel Y, Sabag O, Skversky Y, Spiro A, Steinberg B, Bernstein D, Wang A, Kieckhaefer J, Li C, Pikarsky E, Levin-Klein R, Goren A, Rajewsky K, Kaestner KH, Cedar H.
Postnatal DNA demethylation and its role in tissue maturation. (2018) Nature Commun. [pubmed]

2017

Vardi O, Shamir I, Javasky E, Goren A, Simon I.
Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences. (2017) PloS one. [pubmed]

2016

Busby M, Xue C, Li C, Farjoun Y, Gienger E, Yofe I, Gladden A, Epstein CB, Cornett EM, Rothbart SB, Nusbaum C & Goren A.
Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq. (2016) Epigenetics & chromatin. [pubmed]

Bandopadhayay P, Ramkissoon LA, Jain P, Bergthold G, Wala J, Zeid R, Schumacher SE, Urbanski L, O'Rourke R, Gibson WJ, Pelton K, Ramkissoon SH, Han HJ, Zhu Y, Choudhari N, Silva A, Boucher K, Henn RE, Kang YJ, Knoff D, Paolella BR, Gladden-Young A, Varlet P, Pages M, Horowitz PM, Federation A, Malkin H, Tracy AA, Seepo S, Ducar M, Van Hummelen P, Santi M, Buccoliero AM, Scagnet M, Bowers DC, Giannini C, Puget S, Hawkins C, Tabori U, Klekner A, Bognar L, Burger PC, Eberhart C, Rodriguez FJ, Hill DA, Mueller S Haas-Kogan DA, Phillips JJ, Santagata S, Stiles CD, Bradner JE, Jabado N, Goren A, Grill J, Ligon AH, Goumnerova L, Waanders AJ, Storm PB, Kieran MW, Ligon KL, Beroukhim R, Resnick AC.
MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. (2016) Nat Genet. [pubmed]

Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D.
Oct1 and OCA-B are selectively required for CD4 memory T cell function. (2015) J Exp Med. [pubmed]

Rotem, A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA and Bernstein BE.
Single-cell chromatin profiles reveal a spectrum of stem cell epigenetic states. (2015) Nature Biotechnol. [pubmed]

2015

Etchegaray JP^#, Chavez L, Huang Y, Ross KN, Choi J, Martinez-Pastor B, Walsh RM, Sommer CA, Lienhard M, Kugel S, Gladden A, Silberman DM, Ramaswamy S, Mostoslavsky G, Hochedlinger G, Goren A^#, Rao A and Mostoslavsky R^#.
The Histone Deacetylase Sirt6 Controls Embryonic Stem Cell Fate Via Tet-Mediated Production of 5-Hydroxymethylcytosine. (2015) Nature Cell Biol. [pubmed]

Shakya A, Callister C, Goren A, Yosef N, Garg N, Khoddami V, Nix D, Regev A, Tantin D.
Pluripotency transcription factor oct4 mediates stepwise nucleosome demethylation and depletion. (2015) Mol Cell Biol. [pubmed]

Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y and Meissner A.
Dissecting neural differentiation regulatory networks through epigenetic footprinting. (2015) Nature [pubmed]

2014

Krebs W, Schmidt SV, Goren A, De Nardo D, Labzin L, Bovier A, Ulas T, Theis H, Kraut M, Latz E, Beyer M, Schultze JL.
Optimization of transcription factor binding map accuracy utilizing knockout mouse models. (2014) Nuc. Acids Research. [pubmed]

2013

Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M.
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. (2013)Science [pubmed]

Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A.
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. (2013) Nature [pubmed]

2012

Sebastian C, Zwaans BM, Silberman DM, Gymrek M, Goren A, Zhong L, Ram O, Truelove J, Guimaraes AR, Toiber D, Cosentino C, Greenson JK, MacDonald AI, McGlynn L, Maxwell F, Edwards J, Giacosa S, Guccione E, Weissleder R, Bernstein BE, Regev A, Shiels PG, Lombard DB, Mostoslavsky R.
The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. (2012) Cell [pubmed]

ENCODE Project Consortium.
An integrated encyclopedia of DNA elements in the human genome. (2012) Nature [pubmed]

Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I.
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. (2012) Mol Cell. [pubmed]

2011

Ram O*, Goren A*, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE.
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. (2011) Cell [pubmed]

Zhou VW*, Goren A*, Bernstein BE.
Charting histone modifications and the functional organization of mammalian genomes. (2011) Nat Rev Genet. [pubmed]

2010

Ozsolak F*, Goren A*, Gymrek M*, Guttman M, Regev A, Bernstein BE, Milos PM.
Digital transcriptome profiling from attomole-level RNA samples. (2010) Genome Res. [pubmed]

Goren A*, Ozsolak F*, Shoresh N*, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE.
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.(2010) Nat Methods [pubmed]

2009

Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A.
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. (2009) Science [pubmed]

2008

Farkash-Amar S, Lipson D, Polten A, Goren A, Helmstetter C, Yakhini Z, Simon I.
Global organization of replication time zones of the mouse genome.(2008) Genome Res. [pubmed]

Goren A, Tabib A, Hecht M, Cedar H.
DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin. (2008) Genes Dev. [pubmed]

2006

Goren A, Simchen G, Fibach E, Szabo PE, Tanimoto K, Chakalova L, Pfeifer GP, Fraser PJ, Engel JD, Cedar H.
Fine tuning of globin gene expression by DNA methylation. (2006) PLoS One. [pubmed]

2004

Lande-Diner L, Zhang J, Hashimshony T, Goren A, Keshet I, Cedar H.
Gene repression paradigms in animal cells. (2004) Cold Spring Harbor Symp Quant Biol. [pubmed]

2003

Goren A, Cedar H.
Replicating by the clock. (2003) Nat Rev Mol Cell Biol. [pubmed]

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*=co-first author; ^#=co-corresponding author