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1.

SIRT6 Suppresses Pancreatic Cancer through Control of Lin28b.

Kugel, Sita; Sebastián, Carlos; Fitamant, Julien; Ross, Kenneth N; Saha, Supriya K; Jain, Esha; Gladden, Adrianne; Arora, Kshitij S; Kato, Yasutaka; Rivera, Miguel N; Ramaswamy, Sridhar; Sadreyev, Ruslan I; Goren, Alon; Deshpande, Vikram; Bardeesy, Nabeel; Mostoslavsky, Raul.

Cell ; 165(6): 1401-1415, 2016 Jun 02.

Article in English | MEDLINE | ID: mdl-27180906

2.

The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism.

Sebastián, Carlos; Zwaans, Bernadette M M; Silberman, Dafne M; Gymrek, Melissa; Goren, Alon; Zhong, Lei; Ram, Oren; Truelove, Jessica; Guimaraes, Alexander R; Toiber, Debra; Cosentino, Claudia; Greenson, Joel K; MacDonald, Alasdair I; McGlynn, Liane; Maxwell, Fraser; Edwards, Joanne; Giacosa, Sofia; Guccione, Ernesto; Weissleder, Ralph; Bernstein, Bradley E; Regev, Aviv; Shiels, Paul G; Lombard, David B; Mostoslavsky, Raul.

Cell ; 151(6): 1185-99, 2012 Dec 07.

Article in English | MEDLINE | ID: mdl-23217706

3.

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing.

Etchegaray, Jean-Pierre; Zhong, Lei; Li, Catherine; Henriques, Telmo; Ablondi, Eileen; Nakadai, Tomoyoshi; Van Rechem, Capucine; Ferrer, Christina; Ross, Kenneth N; Choi, Jee-Eun; Samarakkody, Ann; Ji, Fei; Chang, Andrew; Sadreyev, Ruslan I; Ramaswamy, Sridhar; Nechaev, Sergei; Whetstine, Johnathan R; Roeder, Robert G; Adelman, Karen; Goren, Alon; Mostoslavsky, Raul.

Mol Cell ; 75(4): 683-699.e7, 2019 08 22.

Article in English | MEDLINE | ID: mdl-31399344

4.

A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice.

Maksimov, Mikhail O; Wu, Cynthia; Ashbrook, David G; Villani, Flavia; Colonna, Vincenza; Mousavi, Nima; Ma, Nichole; Lu, Lu; Pritchard, Jonathan K; Goren, Alon; Williams, Robert W; Palmer, Abraham A; Gymrek, Melissa.

Genome Res ; 33(5): 689-702, 2023 May.

Article in English | MEDLINE | ID: mdl-37127331

5.

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.

Ram, Oren; Goren, Alon; Amit, Ido; Shoresh, Noam; Yosef, Nir; Ernst, Jason; Kellis, Manolis; Gymrek, Melissa; Issner, Robbyn; Coyne, Michael; Durham, Timothy; Zhang, Xiaolan; Donaghey, Julie; Epstein, Charles B; Regev, Aviv; Bernstein, Bradley E.

Cell ; 147(7): 1628-39, 2011 Dec 23.

Article in English | MEDLINE | ID: mdl-22196736

6.

H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration.

Ben-Yair, Raz; Butty, Vincent L; Busby, Michele; Qiu, Yutong; Levine, Stuart S; Goren, Alon; Boyer, Laurie A; Burns, C Geoffrey; Burns, Caroline E.

Development ; 146(19)2019 10 09.

Article in English | MEDLINE | ID: mdl-31427288

7.

A flexible ChIP-sequencing simulation toolkit.

Zheng, An; Lamkin, Michael; Qiu, Yutong; Ren, Kevin; Goren, Alon; Gymrek, Melissa.

BMC Bioinformatics ; 22(1): 201, 2021 Apr 20.

Article in English | MEDLINE | ID: mdl-33879052

8.

Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns.

Javasky, Elisheva; Shamir, Inbal; Gandhi, Shashi; Egri, Shawn; Sandler, Oded; Rothbart, Scott B; Kaplan, Noam; Jaffe, Jacob D; Goren, Alon; Simon, Itamar.

Genome Res ; 28(10): 1455-1466, 2018 10.

Article in English | MEDLINE | ID: mdl-30166406

9.

Dissecting neural differentiation regulatory networks through epigenetic footprinting.

Ziller, Michael J; Edri, Reuven; Yaffe, Yakey; Donaghey, Julie; Pop, Ramona; Mallard, William; Issner, Robbyn; Gifford, Casey A; Goren, Alon; Xing, Jeff; Gu, Hongcang; Cachiarelli, Davide; Tsankov, Alexander; Epstein, Chuck; Rinn, John R; Mikkelsen, Tarjei S; Kohlbacher, Oliver; Gnirke, Andreas; Bernstein, Bradley E; Elkabetz, Yechiel; Meissner, Alexander.

Nature ; 518(7539): 355-359, 2015 Feb 19.

Article in English | MEDLINE | ID: mdl-25533951

10.

Role of transcription complexes in the formation of the basal methylation pattern in early development.

Greenfield, Razi; Tabib, Amalia; Keshet, Ilana; Moss, Joshua; Sabag, Ofra; Goren, Alon; Cedar, Howard.

Proc Natl Acad Sci U S A ; 115(41): 10387-10391, 2018 10 09.

Article in English | MEDLINE | ID: mdl-30257947

11.

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.

Garber, Manuel; Yosef, Nir; Goren, Alon; Raychowdhury, Raktima; Thielke, Anne; Guttman, Mitchell; Robinson, James; Minie, Brian; Chevrier, Nicolas; Itzhaki, Zohar; Blecher-Gonen, Ronnie; Bornstein, Chamutal; Amann-Zalcenstein, Daniela; Weiner, Assaf; Friedrich, Dennis; Meldrim, James; Ram, Oren; Cheng, Christine; Gnirke, Andreas; Fisher, Sheila; Friedman, Nir; Wong, Bang; Bernstein, Bradley E; Nusbaum, Chad; Hacohen, Nir; Regev, Aviv; Amit, Ido.

Mol Cell ; 47(5): 810-22, 2012 Sep 14.

Article in English | MEDLINE | ID: mdl-22940246

12.

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

Shalek, Alex K; Satija, Rahul; Adiconis, Xian; Gertner, Rona S; Gaublomme, Jellert T; Raychowdhury, Raktima; Schwartz, Schraga; Yosef, Nir; Malboeuf, Christine; Lu, Diana; Trombetta, John J; Gennert, Dave; Gnirke, Andreas; Goren, Alon; Hacohen, Nir; Levin, Joshua Z; Park, Hongkun; Regev, Aviv.

Nature ; 498(7453): 236-40, 2013 Jun 13.

Article in English | MEDLINE | ID: mdl-23685454

13.

Charting histone modifications and the functional organization of mammalian genomes.

Zhou, Vicky W; Goren, Alon; Bernstein, Bradley E.

Nat Rev Genet ; 12(1): 7-18, 2011 Jan.

Article in English | MEDLINE | ID: mdl-21116306

14.

Optimization of transcription factor binding map accuracy utilizing knockout-mouse models.

Krebs, Wolfgang; Schmidt, Susanne V; Goren, Alon; De Nardo, Dominic; Labzin, Larisa; Bovier, Anton; Ulas, Thomas; Theis, Heidi; Kraut, Michael; Latz, Eicke; Beyer, Marc; Schultze, Joachim L.

Nucleic Acids Res ; 42(21): 13051-60, 2014 Dec 01.

Article in English | MEDLINE | ID: mdl-25378309

15.

Digital transcriptome profiling from attomole-level RNA samples.

Ozsolak, Fatih; Goren, Alon; Gymrek, Melissa; Guttman, Mitchell; Regev, Aviv; Bernstein, Bradley E; Milos, Patrice M.

Genome Res ; 20(4): 519-25, 2010 Apr.

Article in English | MEDLINE | ID: mdl-20133332

16.

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.

Goren, Alon; Ozsolak, Fatih; Shoresh, Noam; Ku, Manching; Adli, Mazhar; Hart, Chris; Gymrek, Melissa; Zuk, Or; Regev, Aviv; Milos, Patrice M; Bernstein, Bradley E.

Nat Methods ; 7(1): 47-9, 2010 Jan.

Article in English | MEDLINE | ID: mdl-19946276

17.

Polymorphic short tandem repeats make widespread contributions to blood and serum traits.

Margoliash, Jonathan; Fuchs, Shai; Li, Yang; Zhang, Xuan; Massarat, Arya; Goren, Alon; Gymrek, Melissa.

Cell Genom ; 3(12): 100458, 2023 Dec 13.

Article in English | MEDLINE | ID: mdl-38116119

18.

The use of base editing technology to characterize single nucleotide variants.

McDaniel, Sophia; Komor, Alexis; Goren, Alon.

Comput Struct Biotechnol J ; 20: 1670-1680, 2022.

Article in English | MEDLINE | ID: mdl-35465164

19.

Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3, and SIRT1.

Gandhi, Shashi; Mitterhoff, Raizy; Rapoport, Rachel; Farago, Marganit; Greenberg, Avraham; Hodge, Lauren; Eden, Sharon; Benner, Christopher; Goren, Alon; Simon, Itamar.

Life Sci Alliance ; 5(10)2022 10.

Article in English | MEDLINE | ID: mdl-35981887

20.

Missing heritability may be hiding in repeats.

Gymrek, Melissa; Goren, Alon.

Science ; 373(6562): 1440-1441, 2021 Sep 24.

Article in English | MEDLINE | ID: mdl-34554784

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