CellRank for directed single-cell fate mapping. Marius Lange, Volker Bergen, Michal Klein, Manu Setty, Bernhard Reuter, Mostafa Bakhti, Heiko Lickert, Meshal Ansari, Janine Schniering, Herbert B. Schiller, Dana Pe’er, Fabian J. Theis. Nat Methods, in press. bioRxiv 20 Oct 2020 doi: 10.1101/2020.10.19.345983

Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Bachireddy P, Azizi E, Burdziak C, Nguyen VN, Ennis CS, Maurer K, Park CY, Choo ZN, Li S, Gohil SH, Ruthen NG, Ge Z, Keskin DB, Cieri N, Livak KJ, Kim HT, Neuberg DS, Soiffer RJ, Ritz J, Alyea EP, Pe’er D, Wu CJ. Cell Rep. 2021 Nov 9;37(6):109992. doi: 10.1016/j.celrep.2021.109992. PMID: 34758319.

Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. Chan JM, Quintanal-Villalonga Á, Gao VR, Xie Y, Allaj V, Chaudhary O, Masilionis I, Egger J, Chow A, Walle T, Mattar M, Yarlagadda DVK, Wang JL, Uddin F, Offin M, Ciampricotti M, Qeriqi B, Bahr A, de Stanchina E, Bhanot UK, Lai WV, Bott MJ, Jones DR, Ruiz A, Baine MK, Li Y, Rekhtman N, Poirier JT, Nawy T, Sen T, Mazutis L, Hollmann TJ, Pe’er D, Rudin CM. Cancer Cell. 2021 Nov 8;39(11):1479-1496.e18. doi: 10.1016/j.ccell.2021.09.008. Epub 2021 Oct 14. PMID: 34653364; PMCID: PMC8628860.

Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease. 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. Nat Neurosci. 2021 Mar;24(3):343-354. doi: 10.1038/s41593-020-00796-z. Epub 2021 Feb 8. PMID: 33558694.

A gene-environment-induced epigenetic program initiates tumorigenesis. Alonso-Curbelo D, Ho YJ, Burdziak C, Maag JLV, Morris JP 4th, Chandwani R, Chen HA, Tsanov KM, Barriga FM, Luan W, Tasdemir N, Livshits G, Azizi E, Chun J, Wilkinson JE, Mazutis L, Leach SD, Koche R, Pe’er D, Lowe SW. Nature. 2021 Feb;590(7847):642-648. doi: 10.1038/s41586-020-03147-x. Epub 2021 Feb 3. PMID: 33536616; PMCID: PMC8482641.

Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages. 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 AK, Hoodless PA. Cell. 2020 Oct 29;183(3):702-716.e14. doi: 10.1016/j.cell.2020.09.012. PMID: 33125890; PMCID: PMC7643810.

Cancer cells deploy lipocalin-2 to collect limiting iron in leptomeningeal metastasis. Chi Y, Remsik J, Kiseliovas V, Derderian C, Sener U, Alghader M, Saadeh F, Nikishina K, Bale T, Iacobuzio-Donahue C, Thomas T, Pe’er D, Mazutis L, Boire A. Science. 2020 Jul 17;369(6501):276-282. doi: 10.1126/science.aaz2193. PMID: 32675368; PMCID: PMC7816199.

Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Laughney AM, Hu J, Campbell NR, Bakhoum SF, Setty M, Lavallée VP, Xie Y, Masilionis I, Carr AJ, Kottapalli S, Allaj V, Mattar M, Rekhtman N, Xavier JB, Mazutis L, Poirier JT, Rudin CM, Pe’er D, Massagué J. Nat Med. 2020 Feb;26(2):259-269. doi: 10.1038/s41591-019-0750-6. Epub 2020 Feb 10. PMID: 32042191; PMCID: PMC7021003.

L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer. Ganesh K, Basnet H, Kaygusuz Y, Laughney AM, He L, Sharma R, O’Rourke KP, Reuter VP, Huang YH, Turkekul M, Emrah E, Masilionis I, Manova-Todorova K, Weiser MR, Saltz LB, Garcia-Aguilar J, Koche R, Lowe SW, Pe’er D, Shia J, Massagué J. Nat Cancer. 2020 Jan;1(1):28-45. doi: 10.1038/s43018-019-0006-x. Epub 2020 Jan 13. PMID: 32656539; PMCID: PMC7351134.

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity. Brown CC, Gudjonson H, Pritykin Y, Deep D, Lavallée VP, Mendoza A, Fromme R, Mazutis L, Ariyan C, Leslie C, Pe’er D, Rudensky AY. Cell. 2019 Oct 31;179(4):846-863.e24. doi: 10.1016/j.cell.2019.09.035. Epub 2019 Oct 24. PMID: 31668803

Combination anti-CTLA-4 plus anti-PD-1 checkpoint blockade utilizes cellular mechanisms partially distinct from monotherapies. Wei SC, Anang NAS, Sharma R, Andrews MC, Reuben A, Levine JH, Cogdill AP, Mancuso JJ, Wargo JA, Pe’er D, Allison JP. Proc Natl Acad Sci U S A. 2019 Nov 5;116(45):22699-22709. doi: 10.1073/pnas.1821218116. Epub 2019 Oct 21. PMID: 31636208

Engineering γδT cells limits tonic signaling associated with chimeric antigen receptors. Fisher J, Sharma R, Don DW, Barisa M, Hurtado MO, Abramowski P, Porter L, Day W, Borea R, Inglott S, Anderson J, Pe’er D. Sci Signal. 2019 Sep 10;12(598). pii: eaax1872. doi: 10.1126/scisignal.aax1872. PMID: 31506382

The emergent landscape of the mouse gut endoderm at single-cell resolution. 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. Nature. 2019 May;569(7756):361-367. doi: 10.1038/s41586-019-1127-1. Epub 2019 Apr 8. PMID: 30959515

Natural genetic variation reveals key features of epigenetic and transcriptional memory in virus-specific CD8 T cells. van der Veeken J, Zhong Y, Sharma R, Mazutis L, Dao P, Pe’er D, Leslie CS, Rudensky AY. Immunity. 2019 May 21;50(5):1202-1217.e7. doi: 10.1016/j.immuni.2019.03.031. PMID: 31027997.

Characterization of cell fate probabilities in single-cell data with Palantir. Setty M, Kiseliovas V, Levine J, Gayoso A, Mazutis L, Pe’er D. Nat Biotechnol. 2019 Apr;37(4):451-460. doi: 10.1038/s41587-019-0068-4. PMID: 30899105.

Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. 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. Cell. 2018 Aug 23;174(5):1293-1308.e36. doi: 10.1016/j.cell.2018.05.060. PMID: 29961579

Recovering gene interactions from single-cell data using data diffusion. van Dijk D, Sharma R, Nainys J, Yim K, Kathail P, Carr AJ, Burdziak C, Moon KR, Chaffer CL, Pattabiraman D, Bierie B, Mazutis L, Wolf G, Krishnaswamy S, Pe’er D. Cell. 2018 Jul 26;174(3):716-729.e27. doi: 10.1016/j.cell.2018.05.061. PMID: 29961576

The Human Cell Atlas. Regev A et al. Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041. PubMed PMID: 29206104

Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade. Wei SC, Levine JH, Cogdill AP, Zhao Y, Anang NAS, Andrews MC, Sharma P, Wang J, Wargo JA, Pe’er D, Allison JP. Cell. 2017 Sep 7;170(6):1120-1133.e17. doi: 10.1016/j.cell.2017.07.024. PMID: 28803728

Wishbone identifies bifurcating developmental trajectories from single-cell data. Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TM, Kathail P, Choi K, Bendall S, Friedman N, Pe’er D. Nat Biotechnol. 2016 Jun;34(6):637-45. doi: 10.1038/nbt.3569. PMID: 27136076

Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Levine JH, Simonds EF, Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe’er D, Nolan GP. Cell. 2015 Jul 2;162(1):184-97. doi: 10.1016/j.cell.2015.05.047. PMID: 26095251

Interferon α/β enhances the cytotoxic response of MEK inhibition in melanoma. Litvin O, Schwartz S, Wan Z, Schild T, Rocco M, Oh NL, Chen BJ, Goddard N, Pratilas C, Pe’er D. Mol Cell. 2015 Mar 5;57(5):784-796. doi: 10.1016/j.molcel.2014.12.030. PMID: 25684207

Integration of genomic data enables selective discovery of breast cancer drivers. Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia UD, Chen BJ, Saucedo-Cuevas L, Rodriguez Barrueco R, Llobet-Navas D, Silva JM, Pe’er D. Cell. 2014 Dec 4;159(6):1461-75. doi: 10.1016/j.cell.2014.10.048. PMID: 25433701

Conditional density-based analysis of T cell signaling in single-cell data. Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe’er D, Nolan GP. Systems biology. Science. 2014 Nov 28;346(6213):1250689. doi: 10.1126/science.1250689. PMID: 25342659

Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe’er D. Cell. 2014 Apr 24;157(3):714-25. doi: 10.1016/j.cell.2014.04.005. PMID: 24766814