 Amrita Basu, PhD
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| Title(s) | Assistant Professor, Surgery |
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| School | School of Medicine |
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| Address | 1600 Divisadero
San Francisco CA 94115
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| Phone | -- |
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| vCard | Download vCard |
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 Biography | Broad Institute of Harvard and MIT, Cambridge, MA | Postdoctoral Fellow | | Computational Chemical Biology | | Rockefeller University, Tri-Institutional Computational Biology Program, New York, New York | Ph.D. | | Computational Biology | | Cornell University, Ithaca. NY | B.S. | | Electrical Engineering |
| 2019
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| 2020 | Interstellar Award (New York Academy of Sciences/Japan Center for Medical Research and Development) | | 2016
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| 2017 | White House Presidential Innovation Fellow | | 2013 | | Sage Bionetworks Young Investigator Award |
Overview Development of computational models for early detection of cancer lesions and progression to metastatic disease can help discriminate between high and low cancer risk profiles. Therefore, we seek to exploit diverse, high-throughput genomic and clinical data to understand the molecular networks underlying fundamental cellular processes that can eventually stratify patients by non-traditional underpinnings, including transcriptional regulation, epigenetic signaling, and chemosensitivity. Our algorithmic methods draw on machine learning, a computational field concerned with learning accurate, predictive models from noisy and high-dimensional data.
Another area of research includes developing standardized methods and measures to integrate drug toxicity, quality of life, and efficacy measures for breast cancer patients. We are building infrastructure and tools to support patient-reported outcomes collection and downstream analysis and visualization.
Research ORNG Applications Bibliographic
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Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication.
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Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes. JCO Clin Cancer Inform. 2020 02; 4:108-116.
Barnholtz-Sloan JS, Rollison DE, Basu A, Borowsky AD, Bui A, DiGiovanna J, Garcia-Closas M, Genkinger JM, Gerke T, Induni M, Lacey JV, Mirel L, Permuth JB, Saltz J, Shenkman EA, Ulrich CM, Zheng WJ, Nadaf S, Kibbe WA. PMID: 32078367.
View in: PubMed Mentions: Fields:
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Call for Data Standardization: Lessons Learned and Recommendations in an Imaging Study. JCO Clin Cancer Inform. 2019 11; 3:1-11.
Basu A, Warzel D, Eftekhari A, Kirby JS, Freymann J, Knable J, Sharma A, Jacobs P. PMID: 31834820.
View in: PubMed Mentions: 1 Fields: Translation: Humans
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RWEN: response-weighted elastic net for prediction of chemosensitivity of cancer cell lines. Bioinformatics. 2018 10 01; 34(19):3332-3339.
Basu A, Mitra R, Liu H, Schreiber SL, Clemons PA. PMID: 29688307.
View in: PubMed Mentions: 1 Fields: Translation: HumansCells
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An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell. 2013 Aug 29; 154(5):1151-1161.
Basu A, Bodycombe NE, Cheah JH, Price EV, Liu K, Schaefer GI, Ebright RY, Stewart ML, Ito D, Wang S, Bracha AL, Liefeld T, Wawer M, Gilbert JC, Wilson AJ, Stransky N, Kryukov GV, Dancik V, Barretina J, Garraway LA, Hon CS, Munoz B, Bittker JA, Stockwell BR, Khabele D, Stern AM, Clemons PA, Shamji AF, Schreiber SL. PMID: 23993102.
View in: PubMed Mentions: 133 Fields: Translation: HumansCells
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mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases. Proc Natl Acad Sci U S A. 2013 Apr 23; 110(17):E1641-50.
Mitchell L, Huard S, Cotrut M, Pourhanifeh-Lemeri R, Steunou AL, Hamza A, Lambert JP, Zhou H, Ning Z, Basu A, Côté J, Figeys DA, Baetz K. PMID: 23572591.
View in: PubMed Mentions: 16 Fields: Translation: AnimalsCells
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Computational prediction of lysine acetylation proteome-wide. Methods Mol Biol. 2013; 981:127-36.
Basu A. PMID: 23381858.
View in: PubMed Mentions: Fields: Translation: HumansCells
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Proteome-wide prediction of acetylation substrates. Proc Natl Acad Sci U S A. 2009 Aug 18; 106(33):13785-90.
Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, Garcia BA, Chait B, Zhao Y, Hunt DF, Segal E, Allis CD, Hake SB. PMID: 19666589.
View in: PubMed Mentions: 57 Fields: Translation: HumansAnimalsCells
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Polycomb Group proteins: an evolutionary perspective. Trends Genet. 2007 Oct; 23(10):494-502.
Whitcomb SJ, Basu A, Allis CD, Bernstein E. PMID: 17825942.
View in: PubMed Mentions: 66 Fields: Translation: AnimalsCells
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| Year | Publications |
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| 2007 | 1 | | 2009 | 1 | | 2013 | 3 | | 2018 | 1 | | 2019 | 1 | | 2020 | 1 |
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This graph shows the number and percent of publications by field.
Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications.
Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
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