User:Chefmikesf/sandbox/Dana Pe'er
Dana Pe'er | |
|---|---|
 Dana Pe'er speaking at ISMB 2014. | |
| Born | 1971 (age 52–53)[2] |
| Alma mater | Hebrew University of Jerusalem[3] |
| Spouse | Itsik Pe'er[4] |
| Children | Inbar, Carmel[5][6] |
| Awards |
|
| Scientific career | |
| Fields | Biology Computational biology Systems biology |
| Institutions | Harvard Medical School Columbia University Memorial Sloan Kettering Cancer Center |
| Thesis | From Gene Expression to Molecular Pathways (2003) |
| Doctoral advisor | Nir Friedman |
| Other academic advisors | George M. Church |
Dana Pe'er is currently the Chair and Professor in Computational and Systems Biology Program at Sloan Kettering Institute, and regarded as one of the leading researchers in computational systems biology.[4][7] She was selected as a Howard Hughes Medical Institute (HHMI) Investigator in September, 2021.[8] Previously, she was a professor at Columbia Department of Biological Sciences. Pe'er's research focuses on understanding the organization, function and evolution of molecular networks, particularly how genetic variations alter the regulatory network and how these genetic variations can cause cancer.[9][10][11][12][13][14]
Education
[edit]Pe'er received a bachelor's degree in mathematics in 1995, as well as master's in 1999 and PhD degrees in computer science in 2003, from the Hebrew University of Jerusalem. She earned her master’s degree under Dr. Avi Widgerson, and carried out her PhD research in the lab of Dr. Nir Friedman. She subsequently performed postdoctoral work with Dr. George Church at Harvard University.[15][16][17]
Career
[edit]In 2006, Pe'er established a research group in the Department of Biological Sciences and Systems Biology at Columbia University. Pe'er's group at Columbia University developed computational methods that combine diverse sources of high throughput genomics data, with the aim of developing a holistic view of the cell at a systems level.[18]
In 2016, Pe’er joined the Sloan Kettering Institute at Memorial Sloan Kettering Cancer Center in New York City.[19]
She was selected as a Howard Hughes Medical Institute (HHMI) Investigator in September, 2021.[20]
Pe’er is involved in the Human Cell Atlas as a member of the organizing committee, co-chair of the Analysis Working Group, and member of the Human Lung Cell Atlas initiative, and serves on the scientific advisory board of scverse.[21]
Research
[edit]In her PhD work, Pe’er demonstrated that Bayesian networks can describe interactions between thousands of genes, enabling the analysis of data from newly available DNA microarrays, which generate thousands of noisy measurements of gene expression.[22] The approach has been widely applied to genome-scale sequencing data. In her postdoctoral work, she used this framework to study protein signaling networks in multivariate flow cytometry data.[23]
At Columbia, Pe’er applied Bayesian networks to integrate different data types for the study of gene regulatory networks, determining how DNA sequence variation alters the regulation of gene expression, with a view towards personalized medicine.[24]
The Pe’er research group has developed a series of methods for high-throughput single-cell data analysis, initially to address a new high-dimensional data type derived from mass cytometry, which quantifies a few dozen proteins per cell for millions of cells at a time. They introduced the application of non-linear dimensionality reduction by t-distributed stochastic neighbor embedding (t-SNE) to visualize high-dimensional single-cell RNA sequencing data,[25] and the use of a nearest neighbors graph to represent the data manifold of RNA-defined cell states.[26] The Pe’er group used this formalization to identify discrete cell types or cell states by applying the Louvain community detection method to cluster data,[27] and demonstrated that cells can be ordered along differentiation trajectories from individual samples, due to the asynchrony of cells found in tissue samples.[28] By modeling trajectories as a Markov process, they showed that cells can be assigned probabilities for reaching any given terminal fate along a trajectory.[29] In 2020, the Pe’er and Fabian Theis groups presented CellRank, an algorithm that uncovers cellular dynamics by combining trajectories based on cell-cell similarity with local RNA velocity information, which identifies nascent transcriptional states by the proportion of spliced-to-unspliced RNA transcripts.[30]
Pe’er applies these methods to model biological questions around cellular plasticity and single-cell phenotypic variation in cancer, developmental biology [Nowotschin et al. 2020], and immunology, including tumor microenvironments,[31] metastasis[32] and responses to treatments such as immunotherapy. “We are beginning to understand that plasticity is a key hallmark of cancer,” said Dr. Pe’er. “It is the cancer cell’s plasticity that allows it to make such a switch to survive.”
Upon accepting the International Society for Computational Biology’s Overton Prize in 2014, Pe’er said, “Math is rigorous, and biology is messy, so the trick is to find the pattern in the mess, and machine learning provides a powerful toolbox.”[33]
Significant publications
[edit]- Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data. J Comput Biol. 2000;7(3-4):601-20. doi: 10.1089/106652700750050961. PMID: 11108481.
- Sachs K*, Perez O*, Pe'er D*, Lauffenburger DA, Nolan GP. Causal protein-signaling networks derived from multiparameter single-cell data. Science. 2005 Apr 22;308(5721):523-9. doi:10.1126/science.1105809. PMID: 15845847.
- 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. 2014 Apr 24;157(3):714-25. doi: 10.1016/j.cell.2014.04.005. PMID: 24766814; PMCID: PMC4045247.
- 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†. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell. 2015 Jul 2;162(1):184-97. doi: 10.1016/j.cell.2015.05.047. Epub 2015 Jun 18. PMID: 26095251; PMCID: PMC4508757.
- 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. 2018 Aug 23;174(5):1293-1308.e36. doi: 10.1016/j.cell.2018.05.060. Epub 2018 Jun 28. PMID: 29961579; PMCID: PMC6348010.
- 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. 2019 May;569(7756):361-367. doi:10.1038/s41586-019-1127-1. Epub 2019 Apr 8. PMID: 30959515; PMCID: PMC6724221.
- 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†. Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Nat Med. 2020 Feb;26(2):259-269. doi: 10.1038/s41591-019-0750-6. Epub 2020 Feb 10. PMID: 32042191; PMCID: PMC7021003.
Memberships
[edit]- Editorial and Advisory Board of Cell[34]
- Human Cell Atlas Organizing Committee and co-chair of Analysis Working Group[35]
- EMBL Scientific Advisory Committee[36]
- ISREC - EPFL Scientific Advisory Board[37]
- The Pew Charitable Trusts National Advisory Committee, Pew Biomedical Scholars Program[38]
- Fellow of the International Society for Computational Biology[39]
- Howard Hughes Medical Institute (HHMI) Investigator[8]
Awards
[edit]- 2019 Crain’s Notable Women in Healthcare[40]
- 2019 Ernst W. Bertner Memorial Award[41]
- 2014 NIH Director’s Pioneer Award[42]
- 2014 ISCB Overton Prize[43]
- 2012 RECOMB Test of Time Award[44]
- 2011 Stand Up To Cancer Innovative Research Grant[45]
- 2009 Packard Fellowship in Science and Engineering[46]
- 2007 NIH Director's New Innovator Award[4]
- 2005 Career Award at the Interface of Science, Burroughs Wellcome Fund[47]
Personal life
[edit]Her husband, Itsik Pe'er, is a computational biologist at Columbia University. Together, they have raised two daughters.[4]
References
[edit]- ^ Fogg, Christiana N.; Kovats, Diane E. (2014). "International Society for Computational Biology Honors Dana Pe'er with Top Bioinformatics/Computational Biology Award for 2014". PLOS Computational Biology. 10 (6): e1003682. Bibcode:2014PLSCB..10E3682F. doi:10.1371/journal.pcbi.1003682. PMC 4063598. PMID 24945496.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ "98109969".
- ^ "Dana Pe'er - HomePage". Archived from the original on 29 June 2010. Retrieved 8 February 2014.
- ^ a b c d "Columbia News ::: Dana Pe'er: Decoding Genetic Variations and Regulatory Networks". www.columbia.edu. Retrieved 8 February 2014.
- ^ "TEDxYouth@TheSchool - The Spark! - TEDx - TED.com". www.ted.com. Retrieved 8 February 2014.
- ^ "Dana Pe'er - Genealogy". www.geni.com. Retrieved 19 July 2014.
- ^ "GET :: Genomes Environments Traits". www.getconference.org. Retrieved 8 February 2014.
- ^ a b "HHMI Invests $300 Million in 33 New Investigators". HHMI. Retrieved 2021-09-23.
- ^ "Dana Pe'er - Columbia University Department of Systems Biology". Retrieved 9 February 2014.
- ^ Chefmikesf/sandbox/Dana Pe'er's publications indexed by the Scopus bibliographic database. (subscription required)
- ^ Friedman, N.; Linial, M.; Nachman, I.; Pe'er, D. (2000). "Using Bayesian Networks to Analyze Expression Data". Journal of Computational Biology. 7 (3–4): 601–620. CiteSeerX 10.1.1.191.139. doi:10.1089/106652700750050961. PMID 11108481.
- ^ Segal, E.; Shapira, M.; Regev, A.; Pe'er, D.; Botstein, D.; Koller, D.; Friedman, N. (2003). "Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data". Nature Genetics. 34 (2): 166–176. doi:10.1038/ng1165. PMID 12740579. S2CID 6146032.
- ^ Sachs, K.; Perez, O; Pe'Er, D; Lauffenburger, D. A.; Nolan, G. P. (2005). "Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data". Science. 308 (5721): 523–9. Bibcode:2005Sci...308..523S. doi:10.1126/science.1105809. PMID 15845847. S2CID 8160280.
- ^ Bendall, S. C.; Simonds, E. F.; Qiu, P.; Amir, E. -A. D.; Krutzik, P. O.; Finck, R.; Bruggner, R. V.; Melamed, R.; Trejo, A.; Ornatsky, O. I.; Balderas, R. S.; Plevritis, S. K.; Sachs, K.; Pe'Er, D.; Tanner, S. D.; Nolan, G. P. (2011). "Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum". Science. 332 (6030): 687–696. Bibcode:2011Sci...332..687B. doi:10.1126/science.1198704. PMC 3273988. PMID 21551058.
- ^ "2011 Innovative Research Grants Investigator Biographies". www.aacr.org. Archived from the original on 22 February 2014. Retrieved 9 February 2014.
- ^ "Dana Pe'er - Dissertation". Archived from the original on 28 October 2014. Retrieved 9 February 2014.
- ^ Lee, S. I.; Pe'Er, D; Dudley, A. M.; Church, G. M.; Koller, D (2006). "Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification". Proceedings of the National Academy of Sciences. 103 (38): 14062–7. Bibcode:2006PNAS..10314062L. doi:10.1073/pnas.0601852103. PMC 1599912. PMID 16968785.
- ^ "Center for Computational Biology and Bioinformatics (C2B2) | Columbia University Department of Systems Biology". systemsbiology.columbia.edu. Retrieved 2023-02-14.
- ^ "Notable Women in Healthcare - Dana Pe'er". Crain's New York Business. 2019-08-02. Retrieved 2023-02-14.
- ^ "HHMI Invests $300 Million in 33 New Investigators". HHMI. Retrieved 2023-02-14.
- ^ "Hello world". scverse.org. 2022-05-17. Retrieved 2023-02-14.
- ^ Friedman, N.; Linial, M.; Nachman, I.; Pe'er, D. (2000). "Using Bayesian networks to analyze expression data". Journal of Computational Biology: A Journal of Computational Molecular Cell Biology. 7 (3–4): 601–620. doi:10.1089/106652700750050961. ISSN 1066-5277. PMID 11108481.
- ^ Sachs, Karen; Perez, Omar; Pe'er, Dana; Lauffenburger, Douglas A.; Nolan, Garry P. (2005-04-22). "Causal protein-signaling networks derived from multiparameter single-cell data". Science (New York, N.Y.). 308 (5721): 523–529. doi:10.1126/science.1105809. ISSN 1095-9203. PMID 15845847.
- ^ Sanchez-Garcia, Félix; Villagrasa, Patricia; Matsui, Junji; Kotliar, Dylan; Castro, Verónica; Akavia, Uri-David; Chen, Bo-Juen; Saucedo-Cuevas, Laura; Rodriguez Barrueco, Ruth; Llobet-Navas, David; Silva, Jose M.; Pe'er, Dana (2014-12-04). "Integration of genomic data enables selective discovery of breast cancer drivers". Cell. 159 (6): 1461–1475. doi:10.1016/j.cell.2014.10.048. ISSN 1097-4172. PMC 4258423. PMID 25433701.
- ^ Amir, El-ad David; Davis, Kara L.; Tadmor, Michelle D.; Simonds, Erin F.; Levine, Jacob H.; Bendall, Sean C.; Shenfeld, Daniel K.; Krishnaswamy, Smita; Nolan, Garry P.; Pe'er, Dana (2013-06). "viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia". Nature Biotechnology. 31 (6): 545–552. doi:10.1038/nbt.2594. ISSN 1546-1696.
{{cite journal}}: Check date values in:|date=(help) - ^ Bendall, Sean C.; Davis, Kara L.; Amir, El-Ad David; Tadmor, Michelle D.; Simonds, Erin F.; Chen, Tiffany J.; Shenfeld, Daniel K.; Nolan, Garry P.; Pe'er, Dana (2014-04-24). "Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development". Cell. 157 (3): 714–725. doi:10.1016/j.cell.2014.04.005. ISSN 1097-4172. PMC 4045247. PMID 24766814.
- ^ Levine, Jacob H.; Simonds, Erin F.; Bendall, Sean C.; Davis, Kara L.; Amir, El-ad D.; Tadmor, Michelle D.; Litvin, Oren; Fienberg, Harris G.; Jager, Astraea; Zunder, Eli R.; Finck, Rachel; Gedman, Amanda L.; Radtke, Ina; Downing, James R.; Pe'er, Dana (2015-07-02). "Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis". Cell. 162 (1): 184–197. doi:10.1016/j.cell.2015.05.047. ISSN 1097-4172. PMC 4508757. PMID 26095251.
- ^ Bendall, Sean C.; Davis, Kara L.; Amir, El-Ad David; Tadmor, Michelle D.; Simonds, Erin F.; Chen, Tiffany J.; Shenfeld, Daniel K.; Nolan, Garry P.; Pe'er, Dana (2014-04-24). "Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development". Cell. 157 (3): 714–725. doi:10.1016/j.cell.2014.04.005. ISSN 1097-4172. PMC 4045247. PMID 24766814.
- ^ Setty, Manu; Kiseliovas, Vaidotas; Levine, Jacob; Gayoso, Adam; Mazutis, Linas; Pe'er, Dana (2019-04). "Characterization of cell fate probabilities in single-cell data with Palantir". Nature Biotechnology. 37 (4): 451–460. doi:10.1038/s41587-019-0068-4. ISSN 1546-1696. PMC 7549125. PMID 30899105.
{{cite journal}}: Check date values in:|date=(help) - ^ Lange, Marius; Bergen, Volker; Klein, Michal; Setty, Manu; Reuter, Bernhard; Bakhti, Mostafa; Lickert, Heiko; Ansari, Meshal; Schniering, Janine; Schiller, Herbert B.; Pe'er, Dana; Theis, Fabian J. (2022-02). "CellRank for directed single-cell fate mapping". Nature Methods. 19 (2): 159–170. doi:10.1038/s41592-021-01346-6. ISSN 1548-7105. PMC 8828480. PMID 35027767.
{{cite journal}}: Check date values in:|date=(help) - ^ Nowotschin, Sonja; Setty, Manu; Kuo, Ying-Yi; Liu, Vincent; Garg, Vidur; Sharma, Roshan; Simon, Claire S.; Saiz, Nestor; Gardner, Rui; Boutet, Stéphane C.; Church, Deanna M.; Hoodless, Pamela A.; Hadjantonakis, Anna-Katerina; Pe'er, Dana (2019-05). "The emergent landscape of the mouse gut endoderm at single-cell resolution". Nature. 569 (7756): 361–367. doi:10.1038/s41586-019-1127-1. ISSN 1476-4687. PMC 6724221. PMID 30959515.
{{cite journal}}: Check date values in:|date=(help) - ^ Nowotschin, Sonja; Setty, Manu; Kuo, Ying-Yi; Liu, Vincent; Garg, Vidur; Sharma, Roshan; Simon, Claire S.; Saiz, Nestor; Gardner, Rui; Boutet, Stéphane C.; Church, Deanna M.; Hoodless, Pamela A.; Hadjantonakis, Anna-Katerina; Pe'er, Dana (2019-05). "The emergent landscape of the mouse gut endoderm at single-cell resolution". Nature. 569 (7756): 361–367. doi:10.1038/s41586-019-1127-1. ISSN 1476-4687. PMC 6724221. PMID 30959515.
{{cite journal}}: Check date values in:|date=(help) - ^ "2011 Innovative Research Grants Investigator Biographies". www.aacr.org. Archived from the original on 22 February 2014. Retrieved 9 February 2014.
- ^ "Editorial board: Cell". www.cell.com. Retrieved 18 January 2022.
- ^ "Governance". www.humancellatlas.org. Retrieved 2022-12-05.
- ^ "Scientific Advisory Committee – EMBL Council". Retrieved 2022-12-05.
- ^ "About Us". EPFL. Retrieved 2022-12-05.
- ^ "Program Details". pew.org. Retrieved 2022-12-05.
- ^ "March 02, 2021: ISCB Congratulates and Introduces the 2021 Class of Fellows!". www.iscb.org. Retrieved 17 June 2022.
- ^ "Notable Women in Healthcare 2019". Crain's New York Business. 2019-07-23. Retrieved 2022-12-05.
- ^ "Sloan Kettering Institute's Dana Pe'er Named Howard Hughes Medical Institute Investigator | Memorial Sloan Kettering Cancer Center". www.mskcc.org. Retrieved 2022-12-05.
- ^ "NIH Director's Pioneer Award Program - 2014 Award Recipients". commonfund.nih.gov. 2018-09-18. Retrieved 2022-12-05.
- ^ "Jan 24, 2014: Gene Myers and Dana Pe'er Named 2014 ISCB Award Winners". www.iscb.org. ISCB. Retrieved 8 February 2014.
- ^ "RECOMB Awards". RECOMB Conference Series. Retrieved 2022-12-05.
- ^ "Stand Up To Cancer awards next round of Innovative Research Grants - Dana-Farber Cancer Institute | Boston, MA". www.dana-farber.org. Retrieved 2022-12-05.
- ^ "Dana Pe'er - Packard Foundation". www.packard.org. Retrieved 8 February 2014.
- ^ "Sloan Kettering Institute's Dana Pe'er named Howard Hughes Medical Institute Investigator". EurekAlert!. Retrieved 2022-12-05.