PUBLICATIONS
Dynamic chromatin regulatory landscape of human CAR T cell exhaustion
Gennert D, Lynn RC, Granja JM, Weber EW, Mumbach MR, Zhao Y, Duren Z, Sotillo E, Greenleaf WJ, Wong WH, Satpathy AT, Mackall CL, Chang HY.
Proc. Nat. Acad. Sci. 118, 30 (2021). https://doi.org/10.1073/pnas.2104758118
c-Jun overexpression in CAR T cells induces exhaustion resistance
Lynn RC, Weber EW, Sotillo E, Gennert D, Xu P, Good Z, Anbunathan H, Lattin J, Jones R, Tieu V, Nagaraja S, Granja J, de Bourcy CFA, Majzner R, Satpathy AT, Quake SR, Monje M, Chang HY, Mackall CL.
Nature 576, 293-300 (2019). https://doi.org/10.1038/s41586-019-1805-z
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.
Nature Methods 16, 489-492 (2019). https://doi.org/10.1038/s41592-019-0407-x
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 24, 580-590 (2018). https://doi.org/10.1038/s41591-018-0008-8
Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma
Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, Neftel C, Desai N, Nyman J, Izar B, Luo CC, Francis JM, Patel AA, Onozato ML, Riggi N, Livak KJ, Gennert D, Satija R, Nahed BV, Curry WT, Martuza RL, Mylvaganam R, Iafrate AJ, Frosch MP, Golub TR, Rivera MN, Getz G, Rozenblatt-Rosen O, Cahill DP, Monje M, Bernstein BE, Louis DN, Regev A, Suvà ML.
Nature 539, 309-313 (2016). https://doi.org/10.1038/nature20123
A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells
Singer M, Wang C, Cong L, Marjanovic ND, Kowalczyk MS, Zhang H, Nyman J, Sakuishi K, Kurtulus S, Gennert D, Xia J, Kwon JYH, Nevin J, Herbst RH, Yanai I, Rozenblatt-Rosen O, Kuchroo VK, Regev A, Anderson AC.
Cell 166(6):1500-1511. 8 Sept 2016. https://doi.org/10.1016/j.cell.2016.08.052
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O, Dor Y, Regev A, Yanai I.
Genome Biol 17, 77 (2016). https://doi.org/10.1186/s13059-016-0938-8
Spatial reconstruction of single-cell gene expression data
Satija R, Farrell JA, Gennert D, Schier AF, Regev A.
Nat Biotechnol 33, 495-502 (2015). https://doi.org/10.1038/nbt.3192
Dynamic profiling of the protein life cycle in response to pathogens
Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A.
Science. 347:6226. 06 Mar 2015. https://doi.org/10.1126/science.1259038
Deconstructing transcriptional heterogeneity in pluripotent stem cells
Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser A, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ.
Nature 516, 56-61 (2014). https://doi.org/10.1038/nature13920
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing
Trombetta JJ, Gennert D, Lu D, Satija R, Shalek AK, Regev A.
Current Protocols in Molecular Biology, 107: 4.22.1-4.22.17. https://doi.org/10.1002/0471142727.mb0422s107
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A.
Nature 510, 363-369 (2014). https://doi.org/10.1038/nature13437
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
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.
Nature 498, 236-240 (2013). https://doi.org/10.1038/nature12172
Dynamic regulatory network controlling TH17 cell differentiation
Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, Shakya A, Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M, Tantin D, Park H, Kuchroo VK, Regev A.
Nature 496, 461-468 (2013). https://doi.org/10.1038/nature11981