Biography:Barbara Engelhardt
Barbara Engelhardt | |
---|---|
Born | Barbara Elizabeth Engelhardt |
Alma mater | Stanford University (BS, MS) University of California, Berkeley (PhD) |
Awards | Overton Prize (2021) |
Scientific career | |
Fields | Statistical genetics Bayesian statistics Machine learning Statistical inference Genomics[1] |
Institutions | Princeton University Chicago University Jet Propulsion Laboratory |
Thesis | Predicting protein molecular function (2007) |
Doctoral advisor | Michael I. Jordan[2] |
Website | {{{1}}} |
Barbara Elizabeth Engelhardt is an American computer scientist and specialist in bioinformatics. Working as a Professor at Stanford University, her work has focused on latent variable models, exploratory data analysis for genomic data, and QTLs.[1] In 2021, she was awarded the Overton Prize by the International Society for Computational Biology.
Education
Engelhardt received a Bachelor of Science in Symbolic Systems and a Master of Science in Computer Science from Stanford University. She received a PhD in 2008 from the University of California, Berkeley supervised by Michael I. Jordan.[3]
Career and research
Engelhardt worked as a postdoctoral researcher at the University of Chicago in the Department of Human Genetics with Matthew Stephens from 2008 to 2011.[4] She joined Duke University in 2011 as an assistant professor in the Biostatistics and Bioinformatics Department. She joined Princeton University as an assistant professor in 2014 and received a promotion to Associate Professor with tenure in 2017.[5] In August 2022, she moved to California, she now holds the position of Professor at Stanford University and Gladstone Institute of Data Science and Biotechnology. [6][7]
After graduating from Stanford, Engelhardt worked at the Jet Propulsion Laboratory in the Artificial Intelligence group for two years, working on planning and scheduling for autonomous spacecraft.[8] As a graduate student at Berkeley, she developed statistical models for protein function annotation and statistical frameworks for reasoning about ontologies.[9][10] During her postdoctoral research, she developed sparse factor analysis models for population structure[11] and Bayesian models for association testing.[12]
In her faculty position, the bulk of Engelhardt's research focused on developing latent variable models and exploratory data analysis for genomic data,[13] and also on statistical models for association testing in expression QTLs.[14] As a member of the Genotype Tissue Expression (GTEx) Consortium, her group was responsible for the trans-eQTL discovery and analysis in the GTEx v6[15] and v8 data.[16]
Post tenure, Engelhardt's research in these latent variable models has expanded to include single cell sequencing, with a particular focus on spatial transcriptomics.[17] She also has work on Bayesian experimental design using contextual multi-armed bandits, and has adapted this work to the novel species problem in order to inform single cell data collection for atlas building.[18] Her work has also expanded into machine learning for electronic healthcare records.[19][20]
Engelhardt's work has been featured in Quanta Magazine. In 2017, she gave a TEDx talk entitled: 'Not What but Why: Machine Learning for Understanding Genomics.' [21]
Honors and awards
Engelhardt's research has been funded by the National Institutes of Health through two R01 grants and a number of other mechanisms. Engelhardt has been recognized by several awards including an Alfred P. Sloan Fellowship in Computational Biology,[22] a National Science Foundation CAREER Award,[23] two Chan Zuckerberg Initiative grants for the Human Cell Atlas,[24] and a Fast Grant for her recent work on COVID-19.[25] In 2021, she was awarded the Overton Prize by the International Society for Computational Biology.[26]
Engelhardt's postdoctoral work was partly funded through an NIH NHGRI K99 grant,[27] and her PhD was partly funded through an NSF Graduate Research Fellowship and the Google Anita Borg Scholarship in 2005.[28] She received SMBE's Walter M. Fitch Prize in 2004.[29]
Service and leadership
Engelhardt served on the Board of Directors (2014–2017) and the Senior Advisory Council (2017–present) for Women in Machine Learning.[30] She is the Diversity & Inclusion Co-chair at the International Conference on Machine Learning (ICML, 2018–2022).[31] In 2019, she was a member of the NIH Advisory Committee to the Director, Working Group on Artificial Intelligence[32]
References
- ↑ 1.0 1.1 {{Google Scholar id}} template missing ID and not present in Wikidata.
- ↑ Barbara Engelhardt at the Mathematics Genealogy Project
- ↑ "Michael I. Jordan's Home Page". https://people.eecs.berkeley.edu/~jordan/.
- ↑ "Stephens Lab". https://stephenslab.uchicago.edu/people.html.
- ↑ "Eleven Women Faculty Members Who Have Been Assigned New Duties". 2018-03-08. https://www.wiareport.com/2018/03/eleven-women-faculty-members-assigned-new-duties/.
- ↑ "Barbara Elizabeth Engelhardt's Profile | Stanford Profiles". https://profiles.stanford.edu/barbara-engelhardt.
- ↑ "barbara.engelhardt@gladstone.ucsf.edu" (in en). https://gladstone.org/people/barbara-engelhardt.
- ↑ "3cs | AIG" (in en). https://sensorwebs.jpl.nasa.gov/public/projects/3cs/.
- ↑ Engelhardt, Barbara E.; Jordan, Michael I.; Muratore, Kathryn E.; Brenner, Steven E. (2005-10-07). "Protein Molecular Function Prediction by Bayesian Phylogenomics" (in en). PLOS Computational Biology 1 (5): e45. doi:10.1371/journal.pcbi.0010045. ISSN 1553-7358. PMID 16217548. Bibcode: 2005PLSCB...1...45E.
- ↑ Engelhardt, Barbara E.; Jordan, Michael I.; Srouji, John R.; Brenner, Steven E. (2011-11-01). "Genome-scale phylogenetic function annotation of large and diverse protein families" (in en). Genome Research 21 (11): 1969–1980. doi:10.1101/gr.104687.109. ISSN 1088-9051. PMID 21784873. PMC 3205580. http://genome.cshlp.org/content/21/11/1969.
- ↑ Engelhardt, Barbara E.; Stephens, Matthew (2010-09-16). "Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis" (in en). PLOS Genetics 6 (9): e1001117. doi:10.1371/journal.pgen.1001117. ISSN 1553-7404. PMID 20862358.
- ↑ Mangravite, Lara M.; Engelhardt, Barbara E.; Medina, Marisa W.; Smith, Joshua D.; Brown, Christopher D.; Chasman, Daniel I.; Mecham, Brigham H.; Howie, Bryan et al. (October 2013). "A statin-dependent QTL for GATM expression is associated with statin-induced myopathy" (in en). Nature 502 (7471): 377–380. doi:10.1038/nature12508. ISSN 1476-4687. PMID 23995691. Bibcode: 2013Natur.502..377M.
- ↑ Gao, Chuan; McDowell, Ian C.; Zhao, Shiwen; Brown, Christopher D.; Engelhardt, Barbara E. (2016-07-28). Zhou, Xianghong Jasmine. ed. "Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering" (in en). PLOS Computational Biology 12 (7): e1004791. doi:10.1371/journal.pcbi.1004791. ISSN 1553-7358. PMID 27467526. Bibcode: 2016PLSCB..12E4791G.
- ↑ Dumitrascu, Bianca; Darnell, Gregory; Ayroles, Julien; Engelhardt, Barbara E (2019-01-15). Hancock, John. ed. "Statistical tests for detecting variance effects in quantitative trait studies" (in en). Bioinformatics 35 (2): 200–210. doi:10.1093/bioinformatics/bty565. ISSN 1367-4803. PMID 29982387. PMC 6330007. https://academic.oup.com/bioinformatics/article/35/2/200/5050024.
- ↑ Aguet, François; Brown, Andrew A.; Castel, Stephane E.; Davis, Joe R.; He, Yuan; Jo, Brian; Mohammadi, Pejman; Park, YoSon et al. (October 2017). "Genetic effects on gene expression across human tissues" (in en). Nature 550 (7675): 204–213. doi:10.1038/nature24277. ISSN 1476-4687. PMID 29022597. Bibcode: 2017Natur.550..204A.
- ↑ The GTEx Consortium (2020-09-11). "The GTEx Consortium atlas of genetic regulatory effects across human tissues" (in en). Science 369 (6509): 1318–1330. doi:10.1126/science.aaz1776. ISSN 0036-8075. PMID 32913098. Bibcode: 2020Sci...369.1318..
- ↑ Verma, Archit; Engelhardt, Barbara E. (2020-07-21). "A robust nonlinear low-dimensional manifold for single cell RNA-seq data". BMC Bioinformatics 21 (1): 324. doi:10.1186/s12859-020-03625-z. ISSN 1471-2105. PMID 32693778.
- ↑ Camerlenghi, Federico; Dumitrascu, Bianca; Ferrari, Federico; Engelhardt, Barbara E.; Favaro, Stefano (December 2020). "Nonparametric Bayesian multiarmed bandits for single-cell experiment design" (in EN). Annals of Applied Statistics 14 (4): 2003–2019. doi:10.1214/20-AOAS1370. ISSN 1932-6157. https://projecteuclid.org/euclid.aoas/1608346909.
- ↑ Cheng, Li-Fang; Dumitrascu, Bianca; Darnell, Gregory; Chivers, Corey; Draugelis, Michael; Li, Kai; Engelhardt, Barbara E. (2020-07-08). "Sparse multi-output Gaussian processes for online medical time series prediction". BMC Medical Informatics and Decision Making 20 (1): 152. doi:10.1186/s12911-020-1069-4. ISSN 1472-6947. PMID 32641134.
- ↑ Cheng, Li-Fang; Prasad, Niranjani; Engelhardt, Barbara E. (2019). "An Optimal Policy for Patient Laboratory Tests in Intensive Care Units". Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 24: 320–331. ISSN 2335-6936. PMID 30864333.
- ↑ "A Statistical Search for Genomic Truths". 27 February 2018. https://www.quantamagazine.org/barbara-engelhardts-statistical-search-for-genomic-truths-20180227/.
- ↑ "Prof. Barbara Engelhardt recipient of an Alfred P. Sloan Foundation Research Fellowship | Computer Science Department at Princeton University". https://www.cs.princeton.edu/news/prof-barbara-engelhardt-recipient-alfred-p-sloan-foundation-research-fellowship.
- ↑ "Barbara Engelhardt wins CAREER award for research with high-dimensional genomic data | Computer Science Department at Princeton University". https://www.cs.princeton.edu/news/barbara-engelhardt-receives-nsf-career-award.
- ↑ "Grants" (in en-US). https://chanzuckerberg.com/grants-ventures/grants/.
- ↑ "Fast Grants" (in en). https://fastgrants.org/.
- ↑ "Overton Prize". https://www.iscb.org/iscb-awards/overton-prize.
- ↑ "NHGRI supports seven young investigators on research career paths" (in en). https://www.genome.gov/27545993/2012-news-feature-nhgri-supports-seven-young-investigators-on-research-career-paths.
- ↑ "2005 Google Anita Borg Memorial Scholarship Winners Announced – News announcements – News from Google – Google". http://googlepress.blogspot.com/2005/04/2005-google-anita-borg-memorial_08.html.
- ↑ The Society for Molecular Biology & Evolution. "The Walter M. Fitch Award" (in en-US). https://www.smbe.org/smbe/AWARDS/TheWalterMFitchAward.aspx.
- ↑ "Senior Advisory Council" (in en-US). https://wimlworkshop.org/senior-advisory-council/.
- ↑ "2021 Conference". https://icml.cc/.
- ↑ "ACD Working Group on Artificial Intelligence" (in en). https://www.acd.od.nih.gov/working-groups/ai.html.
Original source: https://en.wikipedia.org/wiki/Barbara Engelhardt.
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