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Items: 25

1.

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis.

Nandakumar SK, McFarland SK, Mateyka LM, Lareau CA, Ulirsch JC, Ludwig LS, Agarwal G, Engreitz JM, Przychodzen B, McConkey M, Cowley GS, Doench JG, Maciejewski JP, Ebert BL, Root DE, Sankaran VG.

Elife. 2019 May 9;8. pii: e44080. doi: 10.7554/eLife.44080.

2.

Discovering metabolic disease gene interactions by correlated effects on cellular morphology.

Jiao Y, Ahmed U, Sim MFM, Bejar A, Zhang X, Talukder MMU, Rice R, Flannick J, Podgornaia AI, Reilly DF, Engreitz JM, Kost-Alimova M, Hartland K, Mercader JM, Georges S, Wagh V, Tadin-Strapps M, Doench JG, Edwardson JM, Rochford JJ, Rosen ED, Majithia AR.

Mol Metab. 2019 Jun;24:108-119. doi: 10.1016/j.molmet.2019.03.001. Epub 2019 Mar 13.

3.

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.

Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L.

Nat Methods. 2018 Dec;15(12):992-993. doi: 10.1038/s41592-018-0225-6. No abstract available.

PMID:
30504875
4.

Publisher Correction: The NORAD lncRNA assembles a topoisomerase complex critical for genome stability.

Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES.

Nature. 2018 Nov;563(7733):E32. doi: 10.1038/s41586-018-0584-2.

PMID:
30279576
5.

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability.

Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES.

Nature. 2018 Sep;561(7721):132-136. doi: 10.1038/s41586-018-0453-z. Epub 2018 Aug 27. Erratum in: Nature. 2018 Oct 2;:.

PMID:
30150775
6.

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.

Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S; NHLBI TOPMed Lipids Working Group.

Nat Commun. 2018 Aug 23;9(1):3391. doi: 10.1038/s41467-018-05747-8.

7.

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis.

Khajuria RK, Munschauer M, Ulirsch JC, Fiorini C, Ludwig LS, McFarland SK, Abdulhay NJ, Specht H, Keshishian H, Mani DR, Jovanovic M, Ellis SR, Fulco CP, Engreitz JM, Schütz S, Lian J, Gripp KW, Weinberg OK, Pinkus GS, Gehrke L, Regev A, Lander ES, Gazda HT, Lee WY, Panse VG, Carr SA, Sankaran VG.

Cell. 2018 Mar 22;173(1):90-103.e19. doi: 10.1016/j.cell.2018.02.036. Epub 2018 Mar 15.

8.

Cohesin Loss Eliminates All Loop Domains.

Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL.

Cell. 2017 Oct 5;171(2):305-320.e24. doi: 10.1016/j.cell.2017.09.026.

9.

Erratum: Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood.

Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, Zhang F.

Nature. 2017 Sep 20;549(7672):418. doi: 10.1038/nature24009.

PMID:
28933431
10.

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood.

Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, Zhang F.

Nature. 2017 Aug 17;548(7667):343-346. doi: 10.1038/nature23451. Epub 2017 Aug 11. Erratum in: Nature. 2017 Sep 20;549(7672):418.

11.

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression.

Gupta RM, Hadaya J, Trehan A, Zekavat SM, Roselli C, Klarin D, Emdin CA, Hilvering CRE, Bianchi V, Mueller C, Khera AV, Ryan RJH, Engreitz JM, Issner R, Shoresh N, Epstein CB, de Laat W, Brown JD, Schnabel RB, Bernstein BE, Kathiresan S.

Cell. 2017 Jul 27;170(3):522-533.e15. doi: 10.1016/j.cell.2017.06.049.

12.

Recurrent and functional regulatory mutations in breast cancer.

Rheinbay E, Parasuraman P, Grimsby J, Tiao G, Engreitz JM, Kim J, Lawrence MS, Taylor-Weiner A, Rodriguez-Cuevas S, Rosenberg M, Hess J, Stewart C, Maruvka YE, Stojanov P, Cortes ML, Seepo S, Cibulskis C, Tracy A, Pugh TJ, Lee J, Zheng Z, Ellisen LW, Iafrate AJ, Boehm JS, Gabriel SB, Meyerson M, Golub TR, Baselga J, Hidalgo-Miranda A, Shioda T, Bernards A, Lander ES, Getz G.

Nature. 2017 Jul 6;547(7661):55-60. doi: 10.1038/nature22992. Epub 2017 Jun 28.

13.

Local regulation of gene expression by lncRNA promoters, transcription and splicing.

Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, McDonel PE, Guttman M, Lander ES.

Nature. 2016 Nov 17;539(7629):452-455. doi: 10.1038/nature20149. Epub 2016 Oct 26.

PMID:
27783602
14.

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression.

Engreitz JM, Ollikainen N, Guttman M.

Nat Rev Mol Cell Biol. 2016 Dec;17(12):756-770. doi: 10.1038/nrm.2016.126. Epub 2016 Oct 26. Review.

PMID:
27780979
15.

Eradication of large established tumors in mice by combination immunotherapy that engages innate and adaptive immune responses.

Moynihan KD, Opel CF, Szeto GL, Tzeng A, Zhu EF, Engreitz JM, Williams RT, Rakhra K, Zhang MH, Rothschilds AM, Kumari S, Kelly RL, Kwan BH, Abraham W, Hu K, Mehta NK, Kauke MJ, Suh H, Cochran JR, Lauffenburger DA, Wittrup KD, Irvine DJ.

Nat Med. 2016 Dec;22(12):1402-1410. doi: 10.1038/nm.4200. Epub 2016 Oct 24.

16.

Systematic mapping of functional enhancer-promoter connections with CRISPR interference.

Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM.

Science. 2016 Nov 11;354(6313):769-773. Epub 2016 Sep 29.

17.

RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites.

Engreitz JM, Sirokman K, McDonel P, Shishkin AA, Surka C, Russell P, Grossman SR, Chow AY, Guttman M, Lander ES.

Cell. 2014 Sep 25;159(1):188-199. doi: 10.1016/j.cell.2014.08.018.

18.

Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A.

Cell. 2014 Sep 25;159(1):148-162. doi: 10.1016/j.cell.2014.08.028. Epub 2014 Sep 11.

19.

Neuregulin autocrine signaling promotes self-renewal of breast tumor-initiating cells by triggering HER2/HER3 activation.

Lee CY, Lin Y, Bratman SV, Feng W, Kuo AH, Scheeren FA, Engreitz JM, Varma S, West RB, Diehn M.

Cancer Res. 2014 Jan 1;74(1):341-52. doi: 10.1158/0008-5472.CAN-13-1055. Epub 2013 Oct 31.

20.

The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome.

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.

Science. 2013 Aug 16;341(6147):1237973. doi: 10.1126/science.1237973. Epub 2013 Jul 4.

21.

Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease.

Engreitz JM, Agarwala V, Mirny LA.

PLoS One. 2012;7(9):e44196. doi: 10.1371/journal.pone.0044196. Epub 2012 Sep 28.

22.

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.

Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ.

Bioinformatics. 2011 Dec 1;27(23):3317-8. doi: 10.1093/bioinformatics/btr548. Epub 2011 Oct 3.

23.

The Lin28/let-7 axis regulates glucose metabolism.

Zhu H, Shyh-Chang N, Segrè AV, Shinoda G, Shah SP, Einhorn WS, Takeuchi A, Engreitz JM, Hagan JP, Kharas MG, Urbach A, Thornton JE, Triboulet R, Gregory RI; DIAGRAM Consortium; MAGIC Investigators, Altshuler D, Daley GQ.

Cell. 2011 Sep 30;147(1):81-94. doi: 10.1016/j.cell.2011.08.033.

24.

Content-based microarray search using differential expression profiles.

Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ.

BMC Bioinformatics. 2010 Dec 21;11:603. doi: 10.1186/1471-2105-11-603.

25.

Independent component analysis: mining microarray data for fundamental human gene expression modules.

Engreitz JM, Daigle BJ Jr, Marshall JJ, Altman RB.

J Biomed Inform. 2010 Dec;43(6):932-44. doi: 10.1016/j.jbi.2010.07.001. Epub 2010 Jul 7.

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