Professor / Director
Lester and Sue Smith Breast Center - Administrative
Oncology/Medicine and MCB
Baylor College of Medicine
Houston, TX, US
McNair Scholar
Baylor College of Medicine
Houston, Texas, United States
Associate Director of Precision Medicine
Dan L Duncan Comprehensive Cancer Center
Baylor College of Medicine
Houston, Texas, United States


MD from University of Cambridge
MB., BChir.
PhD from University of London
Molecular Biology
Fellowship at Georgetown University Hospital
Medical Oncology
Residency at Royal College of Physicians
BSc from University of London

Honors & Awards

CPRIT Scholar in Cancer Research
C. Kent Osborne Endowed Chair
Gianni Bonadonna Breast Cancer Award
Elected Member

Professional Interests

  • Breast Cancer Oncology
  • Breast Cancer Genomics
  • Metastatic Breast Cancer
  • Clinical Trials

Professional Statement

Dr. Matthew James Ellis is a native of the United Kingdom. He completed his medical degree at Queens’ College & School of Clinical Medicine at the University of Cambridge in England, postgraduate clinical training at the Royal College of Physicians in London and gained a Ph.D. at the Royal Postgraduate Medical School and Imperial Cancer Research Fund at the University of London. After a medical oncology fellowship at the Lombardi Cancer Center, Georgetown University, Washington DC, he was an Assistant Professor there until moving to Duke University in 2000 and subsequently to Washington University in St Louis where he served as professor of medicine and section head of breast oncology until 2014. Ellis was recently recruited to Baylor College of Medicine to serve as the Director of the Lester and Sue Smith Breast Center and to hold the C. Kent Osborne Chair of Breast Oncology. Both the McNair Foundation and the Cancer Prevention Research Institute of Texas recently awarded him scholarships. He has been instrumental in developing a Genome Atlas and Therapeutic Road Map for estrogen receptor positive breast cancer by applying genomic techniques to samples accrued through a series of neoadjuvant endocrine therapy trials. Most recently, he has found that metastatic breast tumors harbor mutations and translocations in the estrogen receptor gene that render the tumor resistant to therapies used to block estrogen receptor function. He also pioneered research into the clinical relevance of activating mutations in HER2 and in the deployment of patient-derived xenografts for the pharmacological annotation of breast cancer genomes. He is currently Co-Chair of the translational medicine committee for the NRG cooperative group, co-leader for The Cancer Genome Atlas (TCGA) Breast Project and also serves as a Co-PI for the Clinical Proteomic Tumor Analysis Consortium that endeavors to translate TCGA genomic discoveries into protein-based biomarkers with clinical utility. Dr. Ellis has a successful track record in international clinical and translational research, with recent trainees from Brazil, Chile, Poland and Turkey.

Selected Publications

  • "Activating HER2 mutations in HER2 gene amplification negative breast cancer." Cancer discovery. 2013;3(2):224-37. 2013
  • "Whole-genome analysis informs breast cancer response to aromatase inhibition." Nature. 2012;486(7403):353-60.. 2012
  • "Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium." Cancer discovery. 2013;3(10):1108-12. 2012
  • "The genomic landscape of breast cancer as a therapeutic roadmap." Cancer discovery. 2013;3(1):27-34. 2013
  • "New concepts in breast cancer genomics and genetics.." Breast cancer research : BCR. 2014;16(5):460.. 2014
  • "Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts." Cell reports. 2013;4(6):1116-30. 2013
  • "Incorporating genomics into breast cancer clinical trials and care." Clinical cancer research: an official journal. 2013
  • Li Ding, Amanda G Paulovich, David Fenyö, Matthew J Ellis, Steven A Carr,. "Proteogenomics connects somatic mutations to signalling in breast cancer." 2016 June 2;534(7605):55-62. Pubmed PMID: 27251275
  • Sherri R Davies, Kelly Hunt, Vera J Suman, Jacqueline Snider, Thomas Walsh, Graham A Colditz, Katherine DeSchryver, Richard K Wilson, Elaine R Mardis, Matthew J Ellis. "Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers." 2016 August 9;7 Pubmed PMID: 27502118


Genomic, Clinical, and Behavioral Signatures of Long-term Breast Cancer Survival
Grant funding from NIH
Mechanisms of Endocrine Resistance in Estrogen Receptor Positive Breast Cancer
Grant funding from Komen Leadership Grant
Investigation of the Genomics and Biology of Metastasis Using Patient-Derived-Xenograft
Breast Cancer Research Foundation Founder’s Fund
Cell Death Activation to Prevent Late Relapse in Breast Cancer
Grant funding from Komen Promise Grant
Investigation of the Genomics and Biology of Metastasis Using Patient-Derived-Xenografts
BCRF Founders Fund
Metastatic Research
Gift funding from Theresa's Research Foundation
Funding is used to support metastatic research projects within the breast center