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Items: 27

1.

Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency.

Mor N, Rais Y, Sheban D, Peles S, Aguilera-Castrejon A, Zviran A, Elinger D, Viukov S, Geula S, Krupalnik V, Zerbib M, Chomsky E, Lasman L, Shani T, Bayerl J, Gafni O, Hanna S, Buenrostro JD, Hagai T, Masika H, Vainorius G, Bergman Y, Greenleaf WJ, Esteban MA, Elling U, Levin Y, Massarwa R, Merbl Y, Novershtern N, Hanna JH.

Cell Stem Cell. 2018 Sep 6;23(3):412-425.e10. doi: 10.1016/j.stem.2018.07.004. Epub 2018 Aug 16.

PMID:
30122475
2.

Induction and transcriptional regulation of the co-inhibitory gene module in T cells.

Chihara N, Madi A, Kondo T, Zhang H, Acharya N, Singer M, Nyman J, Marjanovic ND, Kowalczyk MS, Wang C, Kurtulus S, Law T, Etminan Y, Nevin J, Buckley CD, Burkett PR, Buenrostro JD, Rozenblatt-Rosen O, Anderson AC, Regev A, Kuchroo VK.

Nature. 2018 Jun;558(7710):454-459. doi: 10.1038/s41586-018-0206-z. Epub 2018 Jun 13.

PMID:
29899446
3.

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ.

Cell. 2018 May 31;173(6):1535-1548.e16. doi: 10.1016/j.cell.2018.03.074. Epub 2018 Apr 26.

PMID:
29706549
4.

Transcript-indexed ATAC-seq for precision immune profiling.

Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, Corces MR, Khodadoust MS, Kim YH, Khavari PA, Greenleaf WJ, Davis MM, Chang HY.

Nat Med. 2018 May;24(5):580-590. doi: 10.1038/s41591-018-0008-8. Epub 2018 Apr 23.

5.

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types.

Finucane HK, Reshef YA, Anttila V, Slowikowski K, Gusev A, Byrnes A, Gazal S, Loh PR, Lareau C, Shoresh N, Genovese G, Saunders A, Macosko E, Pollack S; Brainstorm Consortium, Perry JRB, Buenrostro JD, Bernstein BE, Raychaudhuri S, McCarroll S, Neale BM, Price AL.

Nat Genet. 2018 Apr;50(4):621-629. doi: 10.1038/s41588-018-0081-4. Epub 2018 Apr 9.

6.

Rapid chromatin repression by Aire provides precise control of immune tolerance.

Koh AS, Miller EL, Buenrostro JD, Moskowitz DM, Wang J, Greenleaf WJ, Chang HY, Crabtree GR.

Nat Immunol. 2018 Feb;19(2):162-172. doi: 10.1038/s41590-017-0032-8. Epub 2018 Jan 15.

7.

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans.

Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A.

Genome Res. 2017 Dec;27(12):2096-2107. doi: 10.1101/gr.226233.117. Epub 2017 Nov 15.

8.

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

Schep AN, Wu B, Buenrostro JD, Greenleaf WJ.

Nat Methods. 2017 Oct;14(10):975-978. doi: 10.1038/nmeth.4401. Epub 2017 Aug 21.

9.

PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes.

Soto-Feliciano YM, Bartlebaugh JME, Liu Y, Sánchez-Rivera FJ, Bhutkar A, Weintraub AS, Buenrostro JD, Cheng CS, Regev A, Jacks TE, Young RA, Hemann MT.

Genes Dev. 2017 May 15;31(10):973-989. doi: 10.1101/gad.295857.117. Epub 2017 Jun 12.

10.

Epigenomics of human CD8 T cell differentiation and aging.

Moskowitz DM, Zhang DW, Hu B, Le Saux S, Yanes RE, Ye Z, Buenrostro JD, Weyand CM, Greenleaf WJ, Goronzy JJ.

Sci Immunol. 2017 Feb;2(8). pii: eaag0192. doi: 10.1126/sciimmunol.aag0192. Epub 2017 Feb 17.

11.

Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome.

She R, Chakravarty AK, Layton CJ, Chircus LM, Andreasson JO, Damaraju N, McMahon PL, Buenrostro JD, Jarosz DF, Greenleaf WJ.

Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3619-3624. doi: 10.1073/pnas.1618370114. Epub 2017 Mar 21.

12.

TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin.

Miller EL, Hargreaves DC, Kadoch C, Chang CY, Calarco JP, Hodges C, Buenrostro JD, Cui K, Greenleaf WJ, Zhao K, Crabtree GR.

Nat Struct Mol Biol. 2017 Apr;24(4):344-352. doi: 10.1038/nsmb.3384. Epub 2017 Feb 27.

13.

Single-cell epigenomic variability reveals functional cancer heterogeneity.

Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, Chang HY.

Genome Biol. 2017 Jan 24;18(1):15. doi: 10.1186/s13059-016-1133-7.

14.

Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms.

Guo MH, Nandakumar SK, Ulirsch JC, Zekavat SM, Buenrostro JD, Natarajan P, Salem RM, Chiarle R, Mitt M, Kals M, Pärn K, Fischer K, Milani L, Mägi R, Palta P, Gabriel SB, Metspalu A, Lander ES, Kathiresan S, Hirschhorn JN, Esko T, Sankaran VG.

Proc Natl Acad Sci U S A. 2017 Jan 17;114(3):E327-E336. doi: 10.1073/pnas.1619052114. Epub 2016 Dec 28.

15.

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY.

Nat Methods. 2016 Dec;13(12):1013-1020. doi: 10.1038/nmeth.4031. Epub 2016 Oct 17.

16.

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.

Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY.

Nat Genet. 2016 Oct;48(10):1193-203. doi: 10.1038/ng.3646. Epub 2016 Aug 15.

17.

Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation.

Mazumdar C, Shen Y, Xavy S, Zhao F, Reinisch A, Li R, Corces MR, Flynn RA, Buenrostro JD, Chan SM, Thomas D, Koenig JL, Hong WJ, Chang HY, Majeti R.

Cell Stem Cell. 2015 Dec 3;17(6):675-688. doi: 10.1016/j.stem.2015.09.017. Epub 2015 Oct 22.

18.

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.

Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ.

Genome Res. 2015 Nov;25(11):1757-70. doi: 10.1101/gr.192294.115. Epub 2015 Aug 27.

19.

Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors.

Maza I, Caspi I, Zviran A, Chomsky E, Rais Y, Viukov S, Geula S, Buenrostro JD, Weinberger L, Krupalnik V, Hanna S, Zerbib M, Dutton JR, Greenleaf WJ, Massarwa R, Novershtern N, Hanna JH.

Nat Biotechnol. 2015 Jul;33(7):769-74. doi: 10.1038/nbt.3270. Epub 2015 Jun 22.

20.

Single-cell chromatin accessibility reveals principles of regulatory variation.

Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ.

Nature. 2015 Jul 23;523(7561):486-90. doi: 10.1038/nature14590. Epub 2015 Jun 17.

21.

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.

Buenrostro JD, Wu B, Chang HY, Greenleaf WJ.

Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9. doi: 10.1002/0471142727.mb2129s109.

22.

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.

Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ.

Nat Biotechnol. 2014 Jun;32(6):562-8. doi: 10.1038/nbt.2880. Epub 2014 Apr 13.

23.

Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy.

Couthouis J, Raphael AR, Siskind C, Findlay AR, Buenrostro JD, Greenleaf WJ, Vogel H, Day JW, Flanigan KM, Gitler AD.

Neuromuscul Disord. 2014 May;24(5):431-5. doi: 10.1016/j.nmd.2014.01.014. Epub 2014 Feb 10.

24.

Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries.

Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, Rasmussen M, Gravel S, Guillén S, Nekhrizov G, Leshtakov K, Dimitrova D, Theodossiev N, Pettener D, Luiselli D, Sandoval K, Moreno-Estrada A, Li Y, Wang J, Gilbert MT, Willerslev E, Greenleaf WJ, Bustamante CD.

Am J Hum Genet. 2013 Nov 7;93(5):852-64. doi: 10.1016/j.ajhg.2013.10.002. Epub 2013 Oct 25.

25.

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ.

Nat Methods. 2013 Dec;10(12):1213-8. doi: 10.1038/nmeth.2688. Epub 2013 Oct 6.

26.

Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing.

Myllykangas S, Buenrostro JD, Natsoulis G, Bell JM, Ji HP.

Nat Biotechnol. 2011 Oct 23;29(11):1024-7. doi: 10.1038/nbt.1996.

27.

A flexible approach for highly multiplexed candidate gene targeted resequencing.

Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, Ji HP.

PLoS One. 2011;6(6):e21088. doi: 10.1371/journal.pone.0021088. Epub 2011 Jun 30.

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