University of California San Francisco

Publications

  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
    J Am Med Inform Assoc. 2025 Jan 01; 32(1):172-180.; 
    PubMed
  2. The "PRO"mise and "PRO"gress of PROs in cancer clinical trials.
    Basu A, Hershman DL
    J Natl Cancer Inst. 2024 Oct 01; 116(10):1544-1546.; 
    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
    NPJ Breast Cancer. 2024 Aug 04; 10(1):71.; 
    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
    Cancer Med. 2023 11; 12(22):20906-20917.; 
    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
    Breast Cancer Res. 2023 10 04; 25(1):117.; 
    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
    Front Oncol. 2023; 13:1192208.; 
    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
    Breast Cancer Res Treat. 2023 Apr; 198(2):383-390.; 
    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
    Cancer Res Commun. 2022 12; 2(12):1579-1589.; 
    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
    Cancer Cell. 2022 06 13; 40(6):609-623.e6.; 
    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
    Ann Oncol. 2022 08; 33(8):814-823.; 
    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
    Nat Commun. 2021 06 23; 12(1):3887.; 
    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
    JAMIA Open. 2021 Apr; 4(2):ooab038.; 
    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
    Cancer. 2021 07 01; 127(13):2342-2349.; 
    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
    NPJ Breast Cancer. 2020; 6:52.; 
    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
    JCO Clin Cancer Inform. 2020 02; 4:108-116.; 
    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
    JCO Clin Cancer Inform. 2019 11; 3:1-11.; 
    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
    Bioinformatics. 2018 10 01; 34(19):3332-3339.; 
    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
    Cell. 2013 Aug 29; 154(5):1151-1161.; 
    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
    Proc Natl Acad Sci U S A. 2013 Apr 23; 110(17):E1641-50.; 
    PubMed
  20. Computational prediction of lysine acetylation proteome-wide.
    Basu A
    Methods Mol Biol. 2013; 981:127-36.; 
    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
    Proc Natl Acad Sci U S A. 2009 Aug 18; 106(33):13785-90.; 
    PubMed
  22. Polycomb Group proteins: an evolutionary perspective.
    Whitcomb SJ, Basu A, Allis CD, Bernstein E
    Trends Genet. 2007 Oct; 23(10):494-502.; 
    PubMed