Anne E. Carpenter

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Anne E. Carpenter
Cell Biology, microscopy, computational biology, artificial intelligence, drug discovery
InstitutionsBroad Institute
Academic advisorsDavid M. Sabatini
Websitebroadinstitute.org

Anne E. Carpenter is an American scientist in the field of image analysis for cell biology and artificial intelligence for drug discovery. She is the co-creator of CellProfiler, open-source software for high-throughput biological image analysis, and a co-inventor of the Cell Painting assay, a method for image-based profiling. She is an Institute Scientist and Senior Director of the Imaging Platform at the Broad Institute.[1]

Education & early career

Undergraduate training

Carpenter received her B.Sc. in Biological Sciences in 1997 from

enhancers in Drosophila neural development as a research assistant in the laboratory of Chris Q. Doe, then at the University of Illinois Urbana-Champaign
.

Graduate training

Carpenter carried out research for her Ph.D. in the laboratory of Andrew S. Belmont at the

fluorescence microscopy. This work laid the foundation for studies of engineered regions of the genome, the movement of genes within the nucleus upon gene activation, and chromatin-related high-throughput screens. She received her PhD in cell biology in May 2003.[3][4][5]

Post-doctoral training and creation of CellProfiler software

Carpenter trained in the laboratory of

microarrays to reveal gene function. This required new image analysis methods, so Carpenter and collaborator Thouis Jones designed and in 2005 released the first open-source high-throughput cell image analysis software, CellProfiler, which was first published in 2006.[6] Using this new tool, she led a team of 5 researchers to develop advanced data mining
methods to systematically examine the necessity of proteins for a variety of biological processes.

Research and impact

In January 2007, Carpenter founded her laboratory at the

NIH R01 grant was awarded in 2010, at the age of 33. In 2017, she became a Broad Institute Scientist.[7]

The Carpenter group develops novel strategies and tools to analyse biological images, particularly microscopy images from high-throughput experiments. Her

C. elegans
, 3D cell cultures, and time-lapse video of growing cells.

The focus of the Carpenter lab turned towards machine learning by 2009, and later deep learning, to identify biological structures of interest and to identify patterns resulting from chemical or genetic perturbations to identify cures for diseases. She was an early pioneer of the new field of image-based profiling,[9] which is related to gene expression profiling but uses microscopy images as the data source. Together with Stuart Schreiber, the Carpenter laboratory invented the Cell Painting assay, [10][11] which is the most widely used for this purpose. Carpenter's CellProfiler software and Cell Painting assay formed the initial scientific platform for Recursion Pharmaceuticals.[12] Dr. Carpenter is a member of the Scientific and Technical Advisory Board for Recursion Pharmaceuticals,[13] in addition to that of Bio-Rad Laboratories.[14]

Carpenter has given more than 200 invited lectures and has chaired several

postdoctoral to high-school level and is known for her informal mentoring as well.[5][17]

In 2021, Dr. Shantanu Singh became co-leader of Carpenter's laboratory, now called the Carpenter–Singh lab.[18]

Awards & honors

  • 2021 Honorary Fellow of the Royal Microscopical Society [19]
  • 2019 Named in Top 100 AI Leaders in Drug Discovery and Advanced Healthcare [20]
  • 2019 Merkin Institute Fellow[21]
  • 2018 Outstanding Young Alumni Award from University of Illinois Urbana-Champaign[22]
  • 2017 Maximizing Investigators' Research Award (MIRA), NIH NIGMS[23]
  • 2017 Elected Fellow,
    SLAS (Society for Laboratory Automation and Screening)[24]
  • 2014 Broad Institute Next Generation Award[25]
  • 2012 Awarded NSF CAREER grant[26]
  • 2011 Named Young Leader of the French-American Foundation[27]
  • 2008 Elected fellow of the Massachusetts Academy of Sciences[28]
  • 2008 Featured in PBS special, “Bold Visions: Women in Science & Technology”[29]
  • 2007 Named a “Rising Young Investigator” by Genome Technology magazine[27]

References

  1. ^ "Broad Institute Imaging Platform". Broad Institute. 2016-01-08. Retrieved 2019-02-02.
  2. ^ "Anne Carpenter • iBiology". iBiology. Retrieved 2019-10-08.
  3. ^ "Computational Drug Discovery: An Interview with Dr. Anne Carpenter". Iridescent. 2018-02-09. Retrieved 2019-10-08.
  4. ^ "Profile: Anne Carpenter | The School of Molecular and Cellular Biology | University of Illinois Urbana-Champaign". mcb.illinois.edu. Retrieved 2019-10-08.
  5. ^ a b "Carpenter Reddit AMA". Reddit. 2018-02-15. Retrieved 2019-02-21.
  6. PMID 17076895
    .
  7. ^ "Broad Institute Scientists". Broad Institute. 21 June 2017. Retrieved 2019-02-21.
  8. ^ "Mining cellular images". Research.gov. Retrieved 2019-02-21.
  9. PMID 27199393
    . Retrieved 2019-02-02.
  10. PMID 24312513
    .
  11. PMID 27560178
    .
  12. ^ Ray, Tiernan. "The subtle art of really big data: Recursion Pharma maps the body". ZDNet. Retrieved 2019-10-08.
  13. ^ "Anne Carpenter". Recursion Pharmaceuticals. Retrieved 2019-10-08.
  14. ^ "Recursion Pharmaceuticals Announces Formation of its Scientific and Technical Advisory Board". Recursion Pharmaceuticals. Retrieved 2019-10-08.
  15. ^ "Anne Carpenter Google Scholar profile". Google Scholar. Retrieved 2022-09-11.
  16. ^ "2018 Data Science Bowl". Kaggle. Retrieved 2019-02-21.
  17. ^ "Carpenter Twitter feed". Twitter. Retrieved 2019-02-21.
  18. PMID 36063089
    .
  19. ^ "Quartet of world-leading scientists to receive RMS Honorary Fellowships". Royal Microscopical Society. Retrieved 10 November 2020.
  20. ^ "Top 100 AI Leaders in Drug Discovery and Advanced Healthcare". Deep Knowledge Analytics. Retrieved 2019-02-02.
  21. ^ "Anne Carpenter, PhD". New Frontiers in 3D. Retrieved 2019-10-08.
  22. ^ "UIUC LAS Outstanding Young Alumni Award". University of Illinois. Retrieved 2019-02-21.
  23. ^ "NIH Reporter project page". NIH. Retrieved 2019-02-21.
  24. ^ "The SLAS Fellow Member Program". SLAS. Retrieved 2019-02-21.
  25. ^ "Meet our new award recipients…and watch a video of our science fair!". myemail.constantcontact.com. Retrieved 2019-10-08.
  26. ^ "CAREER: Image information extraction from heterogeneous populations of co-cultured cells". National Science Foundation. Retrieved 2019-02-21.
  27. ^ a b "Anne Carpenter". French-American Foundation. 2012-08-15. Retrieved 2019-02-21.
  28. ^ "List of Fellows". Massachusetts Academy of Sciences. Retrieved 2019-02-21.
  29. OCLC 213362306
    .

External links

L, Esther; huis (2021-11-02). "Her Machine Learning Tools Pull Insights From Cell Images". Quanta Magazine.

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