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Items: 16

1.

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion.

Satpathy AT, Granja JM, Yost KE, Qi Y, Meschi F, McDermott GP, Olsen BN, Mumbach MR, Pierce SE, Corces MR, Shah P, Bell JC, Jhutty D, Nemec CM, Wang J, Wang L, Yin Y, Giresi PG, Chang ALS, Zheng GXY, Greenleaf WJ, Chang HY.

Nat Biotechnol. 2019 Aug;37(8):925-936. doi: 10.1038/s41587-019-0206-z. Epub 2019 Aug 2.

PMID:
31375813
2.

HiChIRP reveals RNA-associated chromosome conformation.

Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY.

Nat Methods. 2019 Jun;16(6):489-492. doi: 10.1038/s41592-019-0407-x. Epub 2019 May 27.

3.

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA.

Xu J, Nuno K, Litzenburger UM, Qi Y, Corces MR, Majeti R, Chang HY.

Elife. 2019 Apr 9;8. pii: e45105. doi: 10.7554/eLife.45105.

4.

The chromatin accessibility landscape of primary human cancers.

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network, Greenleaf WJ, Chang HY.

Science. 2018 Oct 26;362(6413). pii: eaav1898. doi: 10.1126/science.aav1898.

5.

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.

6.

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.

7.

Preleukemic Hematopoietic Stem Cells in Human Acute Myeloid Leukemia.

Corces MR, Chang HY, Majeti R.

Front Oncol. 2017 Nov 6;7:263. doi: 10.3389/fonc.2017.00263. eCollection 2017. Review.

8.

Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons.

Wapinski OL, Lee QY, Chen AC, Li R, Corces MR, Ang CE, Treutlein B, Xiang C, Baubet V, Suchy FP, Sankar V, Sim S, Quake SR, Dahmane N, Wernig M, Chang HY.

Cell Rep. 2017 Sep 26;20(13):3236-3247. doi: 10.1016/j.celrep.2017.09.011.

9.

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY.

Nat Genet. 2017 Nov;49(11):1602-1612. doi: 10.1038/ng.3963. Epub 2017 Sep 25.

10.

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY.

Nat Methods. 2017 Oct;14(10):959-962. doi: 10.1038/nmeth.4396. Epub 2017 Aug 28.

11.

Superenhancer Analysis Defines Novel Epigenomic Subtypes of Non-APL AML, Including an RARα Dependency Targetable by SY-1425, a Potent and Selective RARα Agonist.

McKeown MR, Corces MR, Eaton ML, Fiore C, Lee E, Lopez JT, Chen MW, Smith D, Chan SM, Koenig JL, Austgen K, Guenther MG, Orlando DA, Lovén J, Fritz CC, Majeti R.

Cancer Discov. 2017 Oct;7(10):1136-1153. doi: 10.1158/2159-8290.CD-17-0399. Epub 2017 Jul 20.

12.

Human AML-iPSCs Reacquire Leukemic Properties after Differentiation and Model Clonal Variation of Disease.

Chao MP, Gentles AJ, Chatterjee S, Lan F, Reinisch A, Corces MR, Xavy S, Shen J, Haag D, Chanda S, Sinha R, Morganti RM, Nishimura T, Ameen M, Wu H, Wernig M, Wu JC, Majeti R.

Cell Stem Cell. 2017 Mar 2;20(3):329-344.e7. doi: 10.1016/j.stem.2016.11.018. Epub 2017 Jan 12.

13.

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.

14.

A humanized bone marrow ossicle xenotransplantation model enables improved engraftment of healthy and leukemic human hematopoietic cells.

Reinisch A, Thomas D, Corces MR, Zhang X, Gratzinger D, Hong WJ, Schallmoser K, Strunk D, Majeti R.

Nat Med. 2016 Jul;22(7):812-21. doi: 10.1038/nm.4103. Epub 2016 May 23.

15.

The three-dimensional cancer genome.

Corces MR, Corces VG.

Curr Opin Genet Dev. 2016 Feb;36:1-7. doi: 10.1016/j.gde.2016.01.002. Epub 2016 Feb 6. Review.

16.

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.

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