CellRank 2: unified fate mapping in multiview single-cell data. Weiler P*, Lange M*, Klein M, Pe’er D, Theis F. Nat Methods. 2024 Jun 13. PMID: 38871986.

The covariance environment defines cellular niches for spatial inference. Haviv D, Remšík J, Gatie M, Snopkowski C, Takizawa M, Pereira N, Bashki J, Jovanovich S, Nawy T, Chaligne R, Boire A, Hadjantonakis A-K, Pe’er D. Nat Biotechnol. Epub 2024 Apr 02. PMID: 38565973.

Supervised discovery of interpretable gene programs from single-cell data. Kunes RZ*, Walle T*, Land M, Nawy T, Pe’er D. Nat Biotechnol. 2023 Sep 21. Epub ahead of print. PMID: 37735262.

scKINETICS: inference of regulatory velocity with single-cell transcriptomics data. Burdziak C*, Zhao CJ*, Haviv D, Alonso-Curbelo D, Lowe SW, Pe’er D. Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i394- i403. PMID: 37387147.

Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis. Burdziak C*, Alonso-Curbelo D*, Walle T, Reyes J, Barriga FM, Haviv D, Xie Y, Zhao Z, Zhao CJ, Chen HA, Chaudhary O, Masilionis I, Choo ZN, Gao V, Luan W, Wuest A, Ho YJ, Wei Y, Quail DF, Koche R, Mazutis L, Chaligné R, Nawy T, Lowe SW†, Pe’er D†. Science. 2023 May 12;380(6645):eadd5327. PMID: 37167403.

Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies. Glasner A*, Rose SA*, Sharma R*, Gudjonson H, Chu T, Green JA, Rampersaud S, Valdez IK, Andretta ES, Dhillon BS, Schizas M, Dikiy S, Mendoza A, Hu W, Wang ZM, Chaudhary O, Xu T, Mazutis L, Rizzuto G, Quintanal-Villalonga A, Manoj P, de Stanchina E, Rudin CM, Pe’er D†, Rudensky AY†. Nat Immunol. 2023 May 1. PMID: 37127830.

SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data. Persad S, Choo Z-N, Dien C, Sohail N, Masilionis I, Chaligné R, Nawy T, Brown CC, Sharma R, Pe’er I, Setty M†, Pe’er D†. Nat Biotechnol. PMID 36973557.

Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling. Chan JM*, Zaidi S*, Love JR, Zhao JL, Setty M, Wadosky 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 L, Chaligne R, Chen Y, Goodrich DW, Karthaus WR†, Pe’er D†, Sawyers CL†. Science. 2022 Sep 9;377(6611):1180-1191. PMID: 35981096.

Lymphatics act as a signaling hub to regulate intestinal stem cell activity. Niec RE*, Chu T*, Schernthanner M*, Gur-Cohen S*, Hidalgo L, Pasolli HA, Luckett KA, Wang Z, Bhalla SR, Cambuli F, Kataru RP, Ganesh K, Mehrara BJ, Pe’er D†, Fuchs E†. Cell Stem Cell. 2022 Jun 15:S1934-5909(22)00207-7. PMID: 35728595.

CellRank for directed single-cell fate mapping. Lange M, Bergen V, Klein M, Setty M, Reuter B, Bakhti M, Lickert H, Ansari M, Schniering J, Schiller HB, Pe’er D†, Theis FJ†. CellRank for directed single-cell fate mapping. Nat Methods. 2022 Feb;19(2):159-170. PMID: 35027767.

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. 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. PMID: 34653364.

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. 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. PMID: 33536616.

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. PMID: 33125890.

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. PMID: 32675368.

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. PMID: 32042191.

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. PMID: 32656539.

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. 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. 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. 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. 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. 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. 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. 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. PMID: 29961576.

The Human Cell Atlas. Regev A et al. Elife. 2017 Dec 5;6. pii: e27041. 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. 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. PMID: 27136076.

Trajectories of cell-cycle progression from fixed cell populations. Gut G*, Tadmor MD*, Pe’er D†, Pelkmans L†, Liberali P†. Nat Methods. 2015 Oct;12(10):951-4. PMID: 26301842.

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. 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. 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. 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. 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. PMID: 24766814.

RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation. Danussi C*, Akavia UD*, Niola F, Jovic A, Lasorella A, Pe’er D†, Lavarone A†. Cancer Res. 2013 Aug 15;73(16):5140-50. PMID: 23774217.

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Amir el-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe’er D. Nat Biotechnol. 2013 Jun;31(6):545-52. PMID: 23685480.

An integrated approach to uncover drivers of cancer. Akavia UD*, Litvin O*, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe’er D. Cell. 2010 Dec 10;143(6):1005-17. PMID: 21129771.

Harnessing gene expression to identify the genetic basis of drug resistance. Chen BJ, Causton HC, Mancenido D, Goddard NL, Perlstein EO, Pe’er D. Mol Syst Biol. 2009;5:310. PMID: 19888205.