Amrita Basu, PhD
Assistant Professor
Surgery
School of Medicine
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.
Show full bio (100 words) Hide full bio
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.
Awards
Show all (4) Hide
- 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
Education & Training
Show all (3) Hide
- Postdoctoral Fellow Computational Chemical Biology Broad Institute of Harvard and MIT
- B.S. Electrical Engineering Cornell University
- Ph.D. Computational Biology Rockefeller University, Tri-Institutional Computational Biology Program
Grants and Projects
Show all (4) Hide
- Analyzing Patient-level Data in a Breast Cancer Clinical Trial, NCI, 2023-2028
- Developing a Toxicity Framework using Patient-Reported Outcome, The Burroughs Wellcome Fund, 2021-2026
- Predicting the Likelihood of Immune-related Adverse Events in Breast Cancer Patients, NIH, 2021-2023
- , NIH, 2017-2022
Publications (19)
Top publication keywords:
ProteomeLysineNeoplasmsAcetylationComputational BiologyG-QuadruplexesAntineoplastic AgentsHealth Information InteroperabilityX-linked Nuclear ProteinDatabases, PharmaceuticalDrug DiscoveryBreast NeoplasmsQuality of LifeHistonesData Curation
-
Concordance between patient-reported and physician-documented comorbidities and symptoms among Stage 4 breast cancer patients.
Cancer medicine 2023 Umashankar S, Basu A, Esserman L, Van't Veer L, Melisko ME -
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.
Breast cancer research : BCR 2023 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, … -
Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes.
Frontiers in oncology 2023 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 -
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.
Breast cancer research and treatment 2023 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, … -
Identifying Good Candidates for Active Surveillance of Ductal Carcinoma In Situ: Insights from a Large Neoadjuvant Endocrine Therapy Cohort.
Cancer research communications 2022 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
Show all (14 more) Hide
-
Redefining breast cancer subtypes to guide treatment prioritization and maximize response: Predictive biomarkers across 10 cancer therapies.
Cancer cell 2022 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, … -
Treatment Efficacy Score-continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between randomized trial arms in breast cancer trials.
Annals of oncology : official journal of the European Society for Medical Oncology 2022 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, … -
ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress.
Nature communications 2021 Teng YC, Sundaresan A, O'Hara R, Gant VU, Li M, Martire S, Warshaw JN, Basu A, Banaszynski LA -
PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial.
JAMIA open 2021 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 -
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 Matthys MB, Dempsey AM, Melisko ME, Dreher N, Che ML, Van't Veer LJ, Esserman LJ, Basu A -
The quality of life index: a pilot study integrating treatment efficacy and quality of life in oncology.
NPJ breast cancer 2020 Basu A, Philip EJ, Dewitt B, Hanmer J, Chattopadhyay A, Yau C, Melisko ME, Esserman LJ -
Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.
JCO clinical cancer informatics 2020 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, … -
Call for Data Standardization: Lessons Learned and Recommendations in an Imaging Study.
JCO clinical cancer informatics 2019 Basu A, Warzel D, Eftekhari A, Kirby JS, Freymann J, Knable J, Sharma A, Jacobs P -
RWEN: response-weighted elastic net for prediction of chemosensitivity of cancer cell lines.
Bioinformatics (Oxford, England) 2018 Basu A, Mitra R, Liu H, Schreiber SL, Clemons PA -
An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules.
Cell 2013 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… -
mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases.
Proceedings of the National Academy of Sciences of the United States of America 2013 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 -
Computational prediction of lysine acetylation proteome-wide.
Methods in molecular biology (Clifton, N.J.) 2013 Basu A -
Proteome-wide prediction of acetylation substrates.
Proceedings of the National Academy of Sciences of the United States of America 2009 Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, Garcia BA, Chait B, Zhao Y, Hunt DF, Segal E, Allis CD, Hake SB -
Polycomb Group proteins: an evolutionary perspective.
Trends in genetics : TIG 2007 Whitcomb SJ, Basu A, Allis CD, Bernstein E