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2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011

Setty Lab members in bold.

* Authors contributed equally, + Joint corresponding authors.

2024

Kousa AI, Jahn L, Zhao K, Flores AE, Acenas D 2nd, Lederer E, Argyropoulos KV, Lemarquis AL, Granadier D, Cooper K, D'Andrea M, Sheridan JM, Tsai J, Sikkema L, Lazrak A, Nichols K, Lee N, Ghale R, Malard F, Andrlova H, Velardi E, Youssef S, Burgos da Silva M, Docampo M, Sharma R, Mazutis L, Wimmer VC, Rogers KL, DeWolf S, Gipson B, Gomes ALC, Setty M, Pe'er D, Hale L, Manley NR, Gray DHD, van den Brink MRM, Dudakov JA. Age-related epithelial defects limit thymic function and regeneration. Nature Immunology (2024). 

Otto D, Jordan C, Dury B, Dien C, Setty M. Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon. Nature Methods (2024). PDF. Software.

AJ Konecny, Y Huang, M Setty, M Prlic. Signals that control MAIT cell function in healthy and inflamed human tissues. Immunological Reviews (2024). 

2023

Smith AA, Nip Y, Bennett SR, Hamm DC, Lemmers RJLF, van der Vliet PJ, Setty M, van der Maarel SM, Tapscott SJ. DUX4 expression in cancer induces a metastable early embryonic totipotent program. Cell Reports (2023).

Garg V, Yang Y, Nowotschin S, Setty M, Kuo YY, Sharma R, Polyzos A, Salataj E, Murphy D, Jang A, Pe’er D, Apostolou E, Hadjantonakis AK. Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities. bioRxiv (2023).

Purice MD, Quitevis EJA, Manning SR, Severs LZ, Tran NT, Sorrentino V, Setty M⁺, Singhvi A⁺. Molecular heterogeneity of C. elegans glia across sexes. bioRxiv (2023).

Persad S, Choo Z-N, Dien C, Sohail N, Masilionis I, Chaligne R, Nawy T, Brown CC, Sharma R, Pe’er I, Setty M⁺, Pe’er D⁺. SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data. Nature Biotechnology (2023). PDF. Software.

2022

Germanos AA, Arora S, Zheng Y, Goddard ET, Coleman IM, Ku AT, Wilkinson S, Amezquita RA, Zager M, Long A, Yang YC, Bielas JH, Gottardo R, Ghajar CM, Nelson PS, Sowalsky AG, Setty M, Hsieh AC. Defining cellular population dynamics at single cell resolution during prostate cancer progression. eLife (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). PDF. Software.

Chan J, Zaidi S, Love JR, Zhao JL, Setty M, Wadowsky KM, Gopalan A, Choo ZN, Persad S, Choi J, LaClair J, Lawrence KE, Chaudhary O, Xu T, Masilionis I, Linkov I, Wang S, Lee C, Barlas A, Morris MJ, Mazutis M, Chaligne R, Chen Y, Goorich CW, Karthaus WR, Pe’er D, Sawyers C. "Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling." Science (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" Nature Methods (2022)

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." Nature Neuroscience,24,(3):343-354 (2021)

2020

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)

2019

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). PDF. Software.

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). PDF. Software.

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)

2018

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)

2016

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). PDF. Software.

2015

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). PDF. 

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

2014

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)

2013

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)

2012

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). PDF.  Software.

2011

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). PDF.