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Items: 1 to 50 of 56

1.

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. Epub 2018 Jun 28.

PMID:
29961579
2.

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. Epub 2018 Jun 28.

PMID:
29961576
3.

Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells.

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.

Immunity. 2018 May 15;48(5):1029-1045.e5. doi: 10.1016/j.immuni.2018.04.026.

PMID:
29768164
4.

Chromosomal instability drives metastasis through a cytosolic DNA response.

Bakhoum SF, Ngo B, Laughney AM, Cavallo JA, Murphy CJ, Ly P, Shah P, Sriram RK, Watkins TBK, Taunk NK, Duran M, Pauli C, Shaw C, Chadalavada K, Rajasekhar VK, Genovese G, Venkatesan S, Birkbak NJ, McGranahan N, Lundquist M, LaPlant Q, Healey JH, Elemento O, Chung CH, Lee NY, Imielenski M, Nanjangud G, Pe'er D, Cleveland DW, Powell SN, Lammerding J, Swanton C, Cantley LC.

Nature. 2018 Jan 25;553(7689):467-472. doi: 10.1038/nature25432. Epub 2018 Jan 17.

5.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

6.

PhenoGraph and viSNE facilitate the identification of abnormal T-cell populations in routine clinical flow cytometric data.

DiGiuseppe JA, Cardinali JL, Rezuke WN, Pe'er D.

Cytometry B Clin Cytom. 2018 Sep;94(5):588-601. doi: 10.1002/cyto.b.21588. Epub 2017 Sep 26.

PMID:
28865188
7.

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. Epub 2017 Aug 10.

8.

Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses.

Lavin Y, Kobayashi S, Leader A, Amir ED, Elefant N, Bigenwald C, Remark R, Sweeney R, Becker CD, Levine JH, Meinhof K, Chow A, Kim-Shulze S, Wolf A, Medaglia C, Li H, Rytlewski JA, Emerson RO, Solovyov A, Greenbaum BD, Sanders C, Vignali M, Beasley MB, Flores R, Gnjatic S, Pe'er D, Rahman A, Amit I, Merad M.

Cell. 2017 May 4;169(4):750-765.e17. doi: 10.1016/j.cell.2017.04.014.

9.

An Immune Atlas of Clear Cell Renal Cell Carcinoma.

Chevrier S, Levine JH, Zanotelli VRT, Silina K, Schulz D, Bacac M, Ries CH, Ailles L, Jewett MAS, Moch H, van den Broek M, Beisel C, Stadler MB, Gedye C, Reis B, Pe'er D, Bodenmiller B.

Cell. 2017 May 4;169(4):736-749.e18. doi: 10.1016/j.cell.2017.04.016.

10.

Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation.

Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW.

Cell Syst. 2017 Apr 26;4(4):458-469.e5. doi: 10.1016/j.cels.2017.03.010. Epub 2017 Apr 5.

11.

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. Epub 2016 May 2.

12.

PD-1 Blockade Expands Intratumoral Memory T Cells.

Ribas A, Shin DS, Zaretsky J, Frederiksen J, Cornish A, Avramis E, Seja E, Kivork C, Siebert J, Kaplan-Lefko P, Wang X, Chmielowski B, Glaspy JA, Tumeh PC, Chodon T, Pe'er D, Comin-Anduix B.

Cancer Immunol Res. 2016 Mar;4(3):194-203. doi: 10.1158/2326-6066.CIR-15-0210. Epub 2016 Jan 19.

13.

Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance.

Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, Reimand J, Haider M, Virtanen C, Bradner JE, Bader GD, Mills GB, Pe'er D, Moffat J, Neel BG.

Cell. 2016 Jan 14;164(1-2):293-309. doi: 10.1016/j.cell.2015.11.062.

14.

Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data.

Prabhakaran S, Azizi E, Carr A, Pe'er D.

JMLR Workshop Conf Proc. 2016;48:1070-1079.

15.

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. doi: 10.1038/nmeth.3545. Epub 2015 Aug 24.

16.

Context Sensitive Modeling of Cancer Drug Sensitivity.

Chen BJ, Litvin O, Ungar L, Pe'er D.

PLoS One. 2015 Aug 14;10(8):e0133850. doi: 10.1371/journal.pone.0133850. eCollection 2015.

17.

Toward understanding and exploiting tumor heterogeneity.

Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CW, Siu L, Snyder A, Stower H, Swanton C, Verhaak RG, Zenklusen JC, Zuber J, Zucman-Rossi J.

Nat Med. 2015 Aug;21(8):846-53. doi: 10.1038/nm.3915.

18.

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. Epub 2015 Jun 18.

19.

Scalable microfluidics for single-cell RNA printing and sequencing.

Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA.

Genome Biol. 2015 Jun 6;16:120. doi: 10.1186/s13059-015-0684-3.

20.

Detection of minimal residual disease in B lymphoblastic leukemia using viSNE.

DiGiuseppe JA, Tadmor MD, Pe'er D.

Cytometry B Clin Cytom. 2015 Sep-Oct;88(5):294-304. doi: 10.1002/cyto.b.21252. Epub 2015 Jun 2.

21.

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. Epub 2015 Feb 12.

22.

Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands.

Lu Y, Xue Q, Eisele MR, Sulistijo ES, Brower K, Han L, Amir el-AD, Pe'er D, Miller-Jensen K, Fan R.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):E607-15. doi: 10.1073/pnas.1416756112. Epub 2015 Feb 2.

23.

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.

Zunder ER, Finck R, Behbehani GK, Amir el-AD, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe'er D, Nolan GP.

Nat Protoc. 2015 Feb;10(2):316-33. doi: 10.1038/nprot.2015.020. Epub 2015 Jan 22.

24.

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. Epub 2014 Nov 26.

25.

Single-cell mass cytometry of TCR signaling: amplification of small initial differences results in low ERK activation in NOD mice.

Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16466-71. doi: 10.1073/pnas.1419337111. Epub 2014 Oct 31.

26.

Systems biology. 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.

Science. 2014 Nov 28;346(6213):1250689. doi: 10.1126/science.1250689. Epub 2014 Oct 23.

27.

Broadening horizons: holistic viewpoints from the Biology of Genomes.

Carr A, Pe'er D.

Genome Biol. 2014 Jul 25;15(7):416. doi: 10.1186/s13059-014-0416-0.

28.

The onset of p53 loss of heterozygosity is differentially induced in various stem cell types and may involve the loss of either allele.

Shetzer Y, Kagan S, Koifman G, Sarig R, Kogan-Sakin I, Charni M, Kaufman T, Zapatka M, Molchadsky A, Rivlin N, Dinowitz N, Levin S, Landan G, Goldstein I, Goldfinger N, Pe'er D, Radlwimmer B, Lichter P, Rotter V, Aloni-Grinstein R.

Cell Death Differ. 2014 Sep;21(9):1419-31. doi: 10.1038/cdd.2014.57. Epub 2014 May 16.

29.

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.

30.

The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.

Llobet-Navas D, Rodríguez-Barrueco R, Castro V, Ugalde AP, Sumazin P, Jacob-Sendler D, Demircan B, Castillo-Martín M, Putcha P, Marshall N, Villagrasa P, Chan J, Sanchez-Garcia F, Pe'er D, Rabadán R, Iavarone A, Cordón-Cardó C, Califano A, López-Otín C, Ezhkova E, Silva JM.

Genes Dev. 2014 Apr 1;28(7):765-82. doi: 10.1101/gad.237404.114. Epub 2014 Mar 17.

31.

NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals.

Becker-Weimann S, Xiong G, Furuta S, Han J, Kuhn I, Akavia UD, Pe'er D, Bissell MJ, Xu R.

Oncotarget. 2013 Nov;4(11):2010-20.

32.

Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.

Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM.

PLoS Genet. 2013;9(9):e1003803. doi: 10.1371/journal.pgen.1003803. Epub 2013 Sep 19.

33.

Environmental stresses disrupt telomere length homeostasis.

Romano GH, Harari Y, Yehuda T, Podhorzer A, Rubinstein L, Shamir R, Gottlieb A, Silberberg Y, Pe'er D, Ruppin E, Sharan R, Kupiec M.

PLoS Genet. 2013;9(9):e1003721. doi: 10.1371/journal.pgen.1003721. Epub 2013 Sep 5.

34.

Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates.

Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, Rimer J, Putheti P, Pe'er D, Friedman N.

PLoS Biol. 2013 Jul;11(7):e1001616. doi: 10.1371/journal.pbio.1001616. Epub 2013 Jul 30.

35.

RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation.

Danussi C, Akavia UD, Niola F, Jovic A, Lasorella A, Pe'er D, Iavarone A.

Cancer Res. 2013 Aug 15;73(16):5140-50. doi: 10.1158/0008-5472.CAN-13-1168-T. Epub 2013 Jun 17.

36.

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. doi: 10.1038/nbt.2594. Epub 2013 May 19.

37.

Normalization of mass cytometry data with bead standards.

Finck R, Simonds EF, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe'er D, Nolan GP, Bendall SC.

Cytometry A. 2013 May;83(5):483-94. doi: 10.1002/cyto.a.22271. Epub 2013 Mar 19.

38.

Inference of modules associated to eQTLs.

Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I.

Nucleic Acids Res. 2012 Jul;40(13):e98. doi: 10.1093/nar/gks269. Epub 2012 Mar 24.

39.

Using systems and structure biology tools to dissect cellular phenotypes.

Floratos A, Honig B, Pe'er D, Califano A.

J Am Med Inform Assoc. 2012 Mar-Apr;19(2):171-5. doi: 10.1136/amiajnl-2011-000490. Epub 2011 Nov 10.

40.

Modulatory profiling identifies mechanisms of small molecule-induced cell death.

Wolpaw AJ, Shimada K, Skouta R, Welsch ME, Akavia UD, Pe'er D, Shaik F, Bulinski JC, Stockwell BR.

Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):E771-80. doi: 10.1073/pnas.1106149108. Epub 2011 Sep 6.

41.

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.

Bendall SC, Simonds EF, Qiu P, Amir el-AD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP.

Science. 2011 May 6;332(6030):687-96. doi: 10.1126/science.1198704.

42.

Principles and strategies for developing network models in cancer.

Pe'er D, Hacohen N.

Cell. 2011 Mar 18;144(6):864-73. doi: 10.1016/j.cell.2011.03.001.

43.

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. doi: 10.1016/j.cell.2010.11.013. Epub 2010 Dec 2.

44.

JISTIC: identification of significant targets in cancer.

Sanchez-Garcia F, Akavia UD, Mozes E, Pe'er D.

BMC Bioinformatics. 2010 Apr 14;11:189. doi: 10.1186/1471-2105-11-189.

45.

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.

Patwardhan RP, Lee C, Litvin O, Young DL, Pe'er D, Shendure J.

Nat Biotechnol. 2009 Dec;27(12):1173-5. doi: 10.1038/nbt.1589.

46.

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. doi: 10.1038/msb.2009.69. Epub 2009 Oct 13.

47.

Modularity and interactions in the genetics of gene expression.

Litvin O, Causton HC, Chen BJ, Pe'er D.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6441-6. doi: 10.1073/pnas.0810208106. Epub 2009 Feb 17.

48.

Learning signaling network structures with sparsely distributed data.

Sachs K, Itani S, Carlisle J, Nolan GP, Pe'er D, Lauffenburger DA.

J Comput Biol. 2009 Feb;16(2):201-12. doi: 10.1089/cmb.2008.07TT.

49.

Learning a prior on regulatory potential from eQTL data.

Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D.

PLoS Genet. 2009 Jan;5(1):e1000358. doi: 10.1371/journal.pgen.1000358. Epub 2009 Jan 30.

50.

Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification.

Lee SI, Pe'er D, Dudley AM, Church GM, Koller D.

Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14062-7. Epub 2006 Sep 12.

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