University of California San Francisco

Amrita Basu large
Amrita Basu, PhD

Associate Professor of Surgery
Division of Surgical Oncology

Address

550 16th Street, #6351
San Francisco, CA 94158
United States

Email: [email protected]

Education

Institution Degree Dept or School End Date
Broad Institute of Harvard and MIT Postdoctoral Fellow Computational Chemical Biology
Cornell University B.S. Electrical Engineering
Rockefeller University, Tri-Institutional Computational Biology Program Ph.D. Computational Biology

Awards & Honors

Award Conferred By Date
Burroughs Wellcome Fund Innovation in Regulatory Science Award 2021/2026
Interstellar Award (New York Academy of Sciences/Japan Center for Medical Research and Development) 2019/2020
White House Presidential Innovation Fellow 2016/2017
Sage Bionetworks Young Investigator Award 2013

Grants and Funding

  • Analyzing Patient-level Data in a Breast Cancer Clinical Trial | NCI | 2023-07-19 - 2028-07-19 | Role: Principal Investigator
  • Developing a Toxicity Framework using Patient-Reported Outcome | The Burroughs Wellcome Fund | 2021-09-01 - 2026-09-17 | Role: Principal Investigator
  • Predicting the Likelihood of Immune-related Adverse Events in Breast Cancer Patients | NIH | 2021-09-15 - 2023-08-31 | Role: Principal Investigator
  • | NIH | 2017-09-08 - 2022-08-31 | Role: Co-Investigator

Publications

MOST RECENT PUBLICATIONS FROM A TOTAL OF 22
  1. ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress.
    Teng YC, Sundaresan A, O'Hara R, Gant VU, Li M, Martire S, Warshaw JN, Basu A, Banaszynski LA| | PubMed
  2. PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial.
    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| | PubMed
  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.
    Matthys MB, Dempsey AM, Melisko ME, Dreher N, Che ML, Van't Veer LJ, Esserman LJ, Basu A| | PubMed
  4. The quality of life index: a pilot study integrating treatment efficacy and quality of life in oncology.
    Basu A, Philip EJ, Dewitt B, Hanmer J, Chattopadhyay A, Yau C, Melisko ME, Esserman LJ| | PubMed
  5. Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.
    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| | PubMed
  6. Call for Data Standardization: Lessons Learned and Recommendations in an Imaging Study.
    Basu A, Warzel D, Eftekhari A, Kirby JS, Freymann J, Knable J, Sharma A, Jacobs P| | PubMed
  7. RWEN: response-weighted elastic net for prediction of chemosensitivity of cancer cell lines.
    Basu A, Mitra R, Liu H, Schreiber SL, Clemons PA| | PubMed
  8. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules.
    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| | PubMed
  9. mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases.
    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| | PubMed
  10. Computational prediction of lysine acetylation proteome-wide.
    Basu A| | PubMed
22
View all 22 Publications
MOST RECENT PUBLICATIONS FROM A TOTAL OF 22
  1. Implementation and impact of an electronic patient reported outcomes system in a phase II multi-site adaptive platform clinical trial for early-stage breast cancer.
    Northrop A, Christofferson A, Umashankar S, Melisko M, Castillo P, Brown T, Heditsian D, Brain S, Simmons C, Hieken T, Ruddy KJ, Mainor C, Afghahi A, Tevis S, Blaes A, Kang I, Asare A, Esserman L, Hershman DL, Basu A| | PubMed
  2. The "PRO"mise and "PRO"gress of PROs in cancer clinical trials.
    Basu A, Hershman DL| | PubMed
  3. Magnetic resonance imaging insights from active surveillance of women with ductal carcinoma in situ.
    Greenwood HI, Maldonado Rodas CK, Freimanis RI, Glencer AC, Miller PN, Mukhtar RA, Brabham C, Yau C, Rosenbluth JM, Hirst GL, Campbell MJ, Borowsky A, Hylton N, Esserman LJ, Basu A| | PubMed
  4. Concordance between patient-reported and physician-documented comorbidities and symptoms among Stage 4 breast cancer patients.
    Umashankar S, Basu A, Esserman L, Van't Veer L, Melisko ME| | PubMed
  5. B-cells and regulatory T-cells in the microenvironment of HER2+ breast cancer are associated with decreased survival: a real-world analysis of women with HER2+ metastatic breast cancer.
    Steenbruggen TG, Wolf DM, Campbell MJ, Sanders J, Cornelissen S, Thijssen B, Salgado RA, Yau C, O-Grady N, Basu A, Bhaskaran R, Mittempergher L, Hirst GL, Coppe JP, Kok M, Sonke GS, van 't Veer LJ, Horlings HM| | PubMed
  6. Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes.
    Yu K, Basu A, Yau C, Wolf DM, Goodarzi H, Bandyopadhyay S, Korkola JE, Hirst GL, Asare S, DeMichele A, Hylton N, Yee D, Esserman L, van 't Veer L, Sirota M| | PubMed
  7. Outcomes and clinicopathologic characteristics associated with disseminated tumor cells in bone marrow after neoadjuvant chemotherapy in high-risk early stage breast cancer: the I-SPY SURMOUNT study.
    Magbanua MJM, van 't Veer L, Clark AS, Chien AJ, Boughey JC, Han HS, Wallace A, Beckwith H, Liu MC, Yau C, Wileyto EP, Ordonez A, Solanki TI, Hsiao F, Lee JC, Basu A, Brown Swigart L, Perlmutter J, Delson AL, Bayne L, Deluca S, Yee SS, Carpenter EL, Esserman LJ, Park JW, Chodosh LA, DeMichele A| | PubMed
  8. Identifying Good Candidates for Active Surveillance of Ductal Carcinoma In Situ: Insights from a Large Neoadjuvant Endocrine Therapy Cohort.
    Glencer AC, Miller PN, Greenwood H, Maldonado Rodas CK, Freimanis R, Basu A, Mukhtar RA, Brabham C, Kim P, Hwang ES, Rosenbluth JM, Hirst GL, Campbell MJ, Borowsky AD, Esserman LJ| | PubMed
  9. Redefining breast cancer subtypes to guide treatment prioritization and maximize response: Predictive biomarkers across 10 cancer therapies.
    Wolf DM, Yau C, Wulfkuhle J, Brown-Swigart L, Gallagher RI, Lee PRE, Zhu Z, Magbanua MJ, Sayaman R, O'Grady N, Basu A, Delson A, Coppé JP, Lu R, Braun J, I-SPY2 Investigators, Asare SM, Sit L, Matthews JB, Perlmutter J, Hylton N, Liu MC, Pohlmann P, Symmans WF, Rugo HS, Isaacs C, DeMichele AM, Yee D, Berry DA, Pusztai L, Petricoin EF, Hirst GL, Esserman LJ, van 't Veer LJ| | PubMed
  10. Treatment Efficacy Score-continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between randomized trial arms in breast cancer trials.
    Marczyk M, Mrukwa A, Yau C, Wolf D, Chen YY, Balassanian R, Nanda R, Parker BA, Krings G, Sattar H, Zeck JC, Albain KS, Boughey JC, Liu MC, Elias AD, Clark AS, Venters SJ, Shad S, Basu A, Asare SM, Buxton M, Asare AL, Rugo HS, Perlmutter J, DeMichele AM, Yee D, Berry DA, Veer LV, Symmans WF, Esserman L, Pusztai L, I-SPY Consortium| | PubMed
  11. ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress.
    Teng YC, Sundaresan A, O'Hara R, Gant VU, Li M, Martire S, Warshaw JN, Basu A, Banaszynski LA| | PubMed
  12. PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial.
    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| | PubMed
  13. Incorporation of Patient-Reported Outcomes Measurement Information System to assess quality of life among patients with breast cancer initiating care at an academic center.
    Matthys MB, Dempsey AM, Melisko ME, Dreher N, Che ML, Van't Veer LJ, Esserman LJ, Basu A| | PubMed
  14. The quality of life index: a pilot study integrating treatment efficacy and quality of life in oncology.
    Basu A, Philip EJ, Dewitt B, Hanmer J, Chattopadhyay A, Yau C, Melisko ME, Esserman LJ| | PubMed
  15. Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.
    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| | PubMed
  16. Call for Data Standardization: Lessons Learned and Recommendations in an Imaging Study.
    Basu A, Warzel D, Eftekhari A, Kirby JS, Freymann J, Knable J, Sharma A, Jacobs P| | PubMed
  17. RWEN: response-weighted elastic net for prediction of chemosensitivity of cancer cell lines.
    Basu A, Mitra R, Liu H, Schreiber SL, Clemons PA| | PubMed
  18. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules.
    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| | PubMed
  19. mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases.
    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| | PubMed
  20. Computational prediction of lysine acetylation proteome-wide.
    Basu A| | PubMed
  21. Proteome-wide prediction of acetylation substrates.
    Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, Garcia BA, Chait B, Zhao Y, Hunt DF, Segal E, Allis CD, Hake SB| | PubMed
  22. Polycomb Group proteins: an evolutionary perspective.
    Whitcomb SJ, Basu A, Allis CD, Bernstein E| | PubMed