Amrita Basu, PhD

Title(s)Assistant Professor, Surgery
SchoolSchool of Medicine
Address550 16th. Street
San Francisco CA 94158
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    Collapse Biography 
    Collapse Education and Training
    Broad Institute of Harvard and MIT, Cambridge, MAPostdoctoral FellowComputational Chemical Biology
    Rockefeller University, Tri-Institutional Computational Biology Program, New York, New YorkPh.D.Computational Biology
    Cornell University, Ithaca. NY B.S.Electrical Engineering
    Collapse Awards and Honors
    2021  - 2026Burroughs Wellcome Fund Innovation in Regulatory Science Award
    2019  - 2020Interstellar Award (New York Academy of Sciences/Japan Center for Medical Research and Development)
    2016  - 2017White House Presidential Innovation Fellow
    2013Sage Bionetworks Young Investigator Award

    Collapse Overview 
    Collapse 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.

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) 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. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress. Nat Commun. 2021 06 23; 12(1):3887. Teng YC, Sundaresan A, O'Hara R, Gant VU, Li M, Martire S, Warshaw JN, Basu A, Banaszynski LA. PMID: 34162889.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial. JAMIA Open. 2021 Apr; 4(2):ooab038. Hanna RF, Ward TJ, Chow DS, Lagana SM, Moreira RK, Emond JC, Weintraub JL, Prince MR, O'Grady N, Gibbs DL, Abdilleh K, Asare A, Asare S, Venters S, Brown-Swigart L, Hirst GL, Wolf D, Yau C, van 't Veer LJ, Esserman L, Basu A. PMID: 34095775; PMCID: PMC8172495.
      View in: PubMed   Mentions:
    3. Incorporation of Patient-Reported Outcomes Measurement Information System to assess quality of life among patients with breast cancer initiating care at an academic center. Cancer. 2021 Jul 01; 127(13):2342-2349. Matthys MB, Dempsey AM, Melisko ME, Dreher N, Che ML, Van't Veer LJ, Esserman LJ, Basu A. PMID: 33957704.
      View in: PubMed   Mentions:    Fields:    
    4. The quality of life index: a pilot study integrating treatment efficacy and quality of life in oncology. NPJ Breast Cancer. 2020; 6:52. Basu A, Philip EJ, Dewitt B, Hanmer J, Chattopadhyay A, Yau C, Melisko ME, Esserman LJ. PMID: 33083531.
      View in: PubMed   Mentions:
    5. 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:    Translation:Humans
    6. 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: 2     Fields:    Translation:Humans
    7. 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: 4     Fields:    Translation:HumansCells
    8. 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: 205     Fields:    Translation:HumansCells
    9. 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: 17     Fields:    Translation:AnimalsCells
    10. 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
    11. 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: 60     Fields:    Translation:HumansAnimalsCells
    12. 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: 76     Fields:    Translation:AnimalsCells
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