Dana Pe'er - Publications

Affiliations: 
Computer Science Columbia University, New York, NY 
Area:
Computational Biology, Machine Learning, Biological Networks, Genomics and Systems Biology

55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Setty M, Kiseliovas V, Levine J, Gayoso A, Mazutis L, Pe'er D. Author Correction: Characterization of cell fate probabilities in single-cell data with Palantir. Nature Biotechnology. PMID 31534198 DOI: 10.1038/s41587-019-0282-0  0.44
2019 Viny AD, Bowman RL, Liu Y, Lavallée VP, Eisman SE, Xiao W, Durham BH, Navitski A, Park J, Braunstein S, Alija B, Karzai A, Csete IS, Witkin M, Azizi E, et al. Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. Cell Stem Cell. PMID 31495782 DOI: 10.1016/j.stem.2019.08.003  0.4
2019 van der Veeken J, Zhong Y, Sharma R, Mazutis L, Dao P, Pe'er D, Leslie CS, Rudensky AY. Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells. Immunity. PMID 31027997 DOI: 10.1016/j.immuni.2019.03.031  0.44
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. PMID 30899105 DOI: 10.1038/s41587-019-0068-4  0.44
2018 Fan X, Moltedo B, Mendoza A, Davydov AN, Faire MB, Mazutis L, Sharma R, Pe'er D, Chudakov DM, Rudensky AY. CD49b defines functionally mature Treg cells that survey skin and vascular tissues. The Journal of Experimental Medicine. PMID 30355617 DOI: 10.1084/jem.20181442  0.44
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, et al. Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. Cell. PMID 29961579 DOI: 10.1016/j.cell.2018.05.060  0.44
2018 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. Recovering Gene Interactions from Single-Cell Data Using Data Diffusion. Cell. PMID 29961576 DOI: 10.1016/j.cell.2018.05.061  0.44
2017 Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW. Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation. Cell Systems. PMID 28396000 DOI: 10.1016/j.cels.2017.03.010  0.4
2016 Prabhakaran S, Azizi E, Carr A, Pe'er D. Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data. Jmlr Workshop and Conference Proceedings. 48: 1070-1079. PMID 29928470  0.44
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. PMID 27136076 DOI: 10.1038/nbt.3569  0.44
2016 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, et al. PD-1 blockade expands intratumoral T memory cells. Cancer Immunology Research. PMID 26787823 DOI: 10.1158/2326-6066.CIR-15-0210  0.52
2016 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. Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance. Cell. 164: 293-309. PMID 26771497 DOI: 10.1016/j.cell.2015.11.062  0.52
2015 Gut G, Tadmor MD, Pe'er D, Pelkmans L, Liberali P. Trajectories of cell-cycle progression from fixed cell populations. Nature Methods. 12: 951-4. PMID 26301842 DOI: 10.1038/nmeth.3545  0.52
2015 Chen BJ, Litvin O, Ungar L, Pe'er D. Context Sensitive Modeling of Cancer Drug Sensitivity. Plos One. 10: e0133850. PMID 26274927 DOI: 10.1371/journal.pone.0133850  0.52
2015 Levine JH, Simonds EF, Bendall SC, Davis KL, Amir ED, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe'er D, et al. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell. PMID 26095251 DOI: 10.1016/j.cell.2015.05.047  0.52
2015 Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA. Scalable microfluidics for single cell RNA printing and sequencing. Genome Biology. 16: 120. PMID 26047807 DOI: 10.1186/s13059-015-0684-3  0.52
2015 DiGiuseppe JA, Tadmor MD, Pe'er D. Detection of minimal residual disease in B lymphoblastic leukemia using viSNE. Cytometry. Part B, Clinical Cytometry. 88: 294-304. PMID 25974871 DOI: 10.1002/cyto.b.21252  0.52
2015 Litvin O, Schwartz S, Wan Z, Schild T, Rocco M, Oh NL, Chen BJ, Goddard N, Pratilas C, Pe'er D. Interferon α/β Enhances the Cytotoxic Response of MEK Inhibition in Melanoma. Molecular Cell. 57: 784-96. PMID 25684207 DOI: 10.1016/j.molcel.2014.12.030  0.52
2015 Lu Y, Xue Q, Eisele MR, Sulistijo ES, Brower K, Han L, Amir el-AD, Pe'er D, Miller-Jensen K, Fan R. Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands. Proceedings of the National Academy of Sciences of the United States of America. 112: E607-15. PMID 25646488 DOI: 10.1073/pnas.1416756112  0.52
2015 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. Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nature Protocols. 10: 316-33. PMID 25612231 DOI: 10.1038/nprot.2015.020  0.52
2015 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, et al. Toward understanding and exploiting tumor heterogeneity Nature Medicine. 21: 846-853. DOI: 10.1038/nm.3915  0.52
2014 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. Integration of genomic data enables selective discovery of breast cancer drivers. Cell. 159: 1461-75. PMID 25433701 DOI: 10.1016/j.cell.2014.10.048  0.52
2014 Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C. Single-cell mass cytometry of TCR signaling: amplification of small initial differences results in low ERK activation in NOD mice. Proceedings of the National Academy of Sciences of the United States of America. 111: 16466-71. PMID 25362052 DOI: 10.1073/pnas.1419337111  0.52
2014 Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'er D, Nolan GP. Systems biology. Conditional density-based analysis of T cell signaling in single-cell data. Science (New York, N.Y.). 346: 1250689. PMID 25342659 DOI: 10.1126/science.1250689  0.36
2014 Carr A, Pe'er D. Broadening horizons: holistic viewpoints from the Biology of Genomes. Genome Biology. 15: 416. PMID 25145924 DOI: 10.1186/s13059-014-0416-0  0.52
2014 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, et al. The onset of p53 loss of heterozygosity is differentially induced in various stem cell types and may involve the loss of either allele. Cell Death and Differentiation. 21: 1419-31. PMID 24832469 DOI: 10.1038/cdd.2014.57  0.52
2014 Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell. 157: 714-25. PMID 24766814 DOI: 10.1016/j.cell.2014.04.005  0.52
2014 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, et al. The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes & Development. 28: 765-82. PMID 24636986 DOI: 10.1101/gad.237404.114  0.52
2014 Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'Er D, Nolan GP. Conditional density-based analysis of T cell signaling in single-cell data Science. 346. DOI: 10.1126/science/1250689  0.52
2013 Becker-Weimann S, Xiong G, Furuta S, Han J, Kuhn I, Akavia UD, Pe'er D, Bissell MJ, Xu R. NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals. Oncotarget. 4: 2010-20. PMID 24243820  0.52
2013 Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM. Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype. Plos Genetics. 9: e1003803. PMID 24068968 DOI: 10.1371/journal.pgen.1003803  0.52
2013 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. Environmental stresses disrupt telomere length homeostasis. Plos Genetics. 9: e1003721. PMID 24039592 DOI: 10.1371/journal.pgen.1003721  0.52
2013 Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, Rimer J, Putheti P, Pe'er D, Friedman N. Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates. Plos Biology. 11: e1001616. PMID 23935451 DOI: 10.1371/journal.pbio.1001616  0.52
2013 Danussi C, Akavia UD, Niola F, Jovic A, Lasorella A, Pe'er D, Iavarone A. RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation. Cancer Research. 73: 5140-50. PMID 23774217 DOI: 10.1158/0008-5472.CAN-13-1168-T  0.52
2013 Amir el-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D. viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nature Biotechnology. 31: 545-52. PMID 23685480 DOI: 10.1038/nbt.2594  0.52
2013 Finck R, Simonds EF, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe'er D, Nolan GP, Bendall SC. Normalization of mass cytometry data with bead standards. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. 83: 483-94. PMID 23512433 DOI: 10.1002/cyto.a.22271  0.52
2013 Krishnaswamy S, Bodenmiller B, Pe'er D. Can CAD cure cancer? Proceedings - Design Automation Conference. DOI: 10.1145/2463209.2488910  0.52
2012 Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I. Inference of modules associated to eQTLs. Nucleic Acids Research. 40: e98. PMID 22447449 DOI: 10.1093/nar/gks269  0.52
2011 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, et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science (New York, N.Y.). 332: 687-96. PMID 21551058 DOI: 10.1126/science.1198704  0.52
2010 Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D. An integrated approach to uncover drivers of cancer. Cell. 143: 1005-17. PMID 21129771 DOI: 10.1016/j.cell.2010.11.013  0.36
2010 Sanchez-Garcia F, Akavia UD, Mozes E, Pe'er D. JISTIC: identification of significant targets in cancer. Bmc Bioinformatics. 11: 189. PMID 20398270 DOI: 10.1186/1471-2105-11-189  0.52
2009 Patwardhan RP, Lee C, Litvin O, Young DL, Pe'Er D, Shendure J. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis Nature Biotechnology. 27: 1173-1175. PMID 19915551 DOI: 10.1038/nbt.1589  0.52
2009 Chen BJ, Causton HC, Mancenido D, Goddard NL, Perlstein EO, Pe'er D. Harnessing gene expression to identify the genetic basis of drug resistance. Molecular Systems Biology. 5: 310. PMID 19888205 DOI: 10.1038/msb.2009.69  0.48
2009 Litvin O, Causton HC, Chen BJ, Pe'er D. Modularity and interactions in the genetics of gene expression. Proceedings of the National Academy of Sciences of the United States of America. 106: 6441-6. PMID 19223586 DOI: 10.1073/pnas.0810208106  0.52
2009 Sachs K, Itani S, Carlisle J, Nolan GP, Pe'er D, Lauffenburger DA. Learning signaling network structures with sparsely distributed data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 201-12. PMID 19193145 DOI: 10.1089/cmb.2008.07TT  0.52
2009 Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D. Learning a prior on regulatory potential from eQTL data. Plos Genetics. 5: e1000358. PMID 19180192 DOI: 10.1371/journal.pgen.1000358  0.52
2006 Lee SI, Pe'er D, Dudley AM, Church GM, Koller D. Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proceedings of the National Academy of Sciences of the United States of America. 103: 14062-7. PMID 16968785 DOI: 10.1073/pnas.0601852103  0.52
2006 Pe'er D, Tanay A, Regev A. MinReg: A scalable algorithm for learning parsimonious regulatory networks in yeast and mammals Journal of Machine Learning Research. 7: 167-189.  0.52
2005 Pe'er D. Bayesian network analysis of signaling networks: a primer. Science's Stke : Signal Transduction Knowledge Environment. 2005: pl4. PMID 15855409 DOI: 10.1126/stke.2812005pl4  0.52
2005 Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP. Causal protein-signaling networks derived from multiparameter single-cell data. Science (New York, N.Y.). 308: 523-9. PMID 15845847 DOI: 10.1126/science.1105809  0.52
2005 Segal E, Pe'er D, Regev A, Koller D, Friedman N. Learning module networks Journal of Machine Learning Research. 6.  0.52
2004 Sachs K, Perez OD, Pe'er D, Nolan GP, Gifford DK, Jaakkola TS, Lauffenburger DA. Analysis of signaling pathways in human T-cells using Bayesian network modeling of single cell data Proceedings - 2004 Ieee Computational Systems Bioinformatics Conference, Csb 2004. 644.  0.52
2003 Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics. 34: 166-76. PMID 12740579 DOI: 10.1038/ng1165  0.52
2001 Pe'er D, Regev A, Elidan G, Friedman N. Inferring subnetworks from perturbed expression profiles Bioinformatics. 17: S215-S224. PMID 11473012  0.52
2000 Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data Journal of Computational Biology. 7: 601-620. PMID 11108481 DOI: 10.1089/106652700750050961  0.52
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