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202220212020 | 2019 | 2018 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011


Persad S, Choo ZN, Dien C, Masilionis I, Chaligné R, Nawy T, Brown C, Pe'er I, Setty M, Pe'er D. "SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data" bioRxiv (2022)

Janssens D, Otto D, Meers M, Setty M, Ahmad K, Henikoff S.  "CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells." Genome Biology 23, 81 (2022)


Lange M, Bergen V, Klein M, Setty M, Reuter B, Bakhti M, Lickert H, Ansari M, Schniering J, Schiller H, Pe’er D, Theis F. "CellRank for directed single-cell fate mapping." bioRxiv (2021)

Guttikonda SR, Sikkema L, Tchieu J, Saurat N, Walsh RM, Harschnitz O, Ciceri G, Sneeboer M, Mazutis L, Setty M, Zumbo P, Betel D, de Witte LD, Pe'er D,Studer L."Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer's disease." Nat Neurosci,24,(3):343-354 (2021)


Lotto J, Drissler S, Cullum R, Wei W, Setty M, Bell EM, Boutet SC, Nowotschin S, Kuo YY, Garg V, Pe'er D, Church DM, Hadjantonakis, AKHoodless PA."Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages." Cell,183,(3):702-716 e714 (2020)

Laughney A, Hu J, Campbell N, Bakhoum S, Setty M, Lavallée V-P, Xie Y, Masilionis I, Carr A, Allaj V, Mattar M, Rekhtman N, Xavier J, Mazutis L, Poirier J, Rudin C, Pe’er D, Massague J. "Regenerative lineages and immune-mediated pruning in lung cancer metastasis." Nature Medicine, 26(2):259-269 (2020)


Nowotschin S*, Setty M*, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK*, Pe’er D*. "The emergent landscape of the mouse gut endoderm at single-cell resolution.Nature, 569(7756):361-367 (2019)

Setty M, Kiseliovas V, Levine J, Gayoso A, Mazutis L, Pe’er D. "Characterization of cell fate probabilities in single-cell data with Palantir.Nature Biotechnology, 37(4):451-460 (2019)

Wei SC*, Sharma R*, Anang NAS, Levine JH, Zhao Y, Mancuso JJ, Setty M, Sharma P, Wang J, Pe’er D, Allison JP. "Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States.Immunity, 50(4):1084-1098.e10 (2019)


Azizi E*, Carr AJ*, Plitas G*, Cornish AE*, Konopacki C, Prabhakaran S, Nainys J, Wu K, Kiseliovas V, Setty M, Choi K, Fromme RM, Dao P, McKenney PT, Wasti RC, Kadaveru K, Mazutis L, Rudensky AY, Pe’er D. "Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment.Cell, 174(5):1293-1308.e36 (2018)

Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O’Brien S, Gherardini PF,Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen N, Pe’er D, Albelda SM, Wherry EJ. "Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Ex- hausted CD8 T Cells.Immunity, 48(5):1029-1045.e5 (2018)


Setty M*, Tadmor MD*, Reich-Zeliger S, Angel O, Salame TM, Kathail P, Choi K, Bendall S, Friedman N, Pe’er D. "Wishbone identifies bifurcating developmental trajectories from single-cell data." Nature Biotechnology, 34(6):637-45 (2016)


González AJ*, Setty M*, Leslie CS. "Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation." Nature Genetics, 47(11):1249-59 (2015)

Setty M, Leslie CS. "SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps." PLoS Computational Biology, 11(5):e1004271 (2015)


Furman RR, Cheng S, Lu P, Setty M, Perez AR, Guo A, Racchumi J, Xu G, Wu H, Ma J, Steggerda SM, Coleman M, Leslie C, Wang YL. "Ibrutinib resistance in chronic lymphocytic leukemia." New England Journal of Medicine, 2014370(24):2352-4, (2014)

Schneider C, Setty M, Holmes AB, Maute RL, Leslie CS, Mussolin L, Rosolen A, Dalla- Favera R, Basso K. "MicroRNA 28 controls cell proliferation and is down-regulated in B-cell lymphomas.Proceedings of the National Academy of Sciences USA, 111(22):8185-90 (2014)


Pyonteck SM, Akkari L, Schuhmacher AJ, Bowman RL, Sevenich L, Quail DF, Olson OC, Quick ML, Huse JT, Teijeiro V, Setty M, Leslie CS, Oei Y, Pedraza A, Zhang J, Brennan CW, Sutton JC, Holland EC, Daniel D, Joyce JA. "CSF-1R inhibition alters macrophage polarization and blocks glioma progression." Nature Medicine, 19(10):1264-72 (2013)


Basso K, Schneider C, Shen Q, Holmes AB, Setty M, Leslie C, Dalla-Favera R. "BCL6 positively regulates AID and germinal center gene expression via repression of miR-155." Journal of Experimental Medicine, 209(13):2455-65 (2012)

Setty M, Helmy K, Khan AA, Silber J, Arvey A, Neezen F, Agius P, Huse JT, Holland EC, Leslie CS. "Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma." Nature/EMBO Molecular Systems Biology, 8:605 (2012)


Mavrakis KJ, Van Der Meulen J, Wolfe AL, Liu X, Mets E, Taghon T, Khan AA, Setty M, Rondou P, Vandenberghe P, Delabesse E, Benoit Y, Socci NB, Leslie CS, Van Vlierberghe P, Speleman F, Wendel HG. "A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL)." Nature Genetics, 5;43(7):673-8 (2011)

Papapetrou EP, Lee G, Malani N, Setty M, Riviere I, Tirunagari LM, Kadota K, Roth SL, Giardina P, Viale A, Leslie C, Bushman FD, Studer L, Sadelain M. "Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells." Nature Biotechnology, 29(1):73-8 (2011)

Setty M, Gusev A, Pe’er I. "HLA type inference via haplotypes identical by descent." RE- COMB - Journal of Computational Biology, 18(3):483-93, (2011)

* Authors contributed equally.