Nicholas Navin, Ph.D.

Department of Systems Biology, Division of Discovery Science

About Dr. Nicholas Navin

Dr. Navin is a Professor at MD Anderson Cancer Center, with a joint appointment in the Department of Bioinformatics. He is a faculty member at The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences. He is also the Director of the CPRIT Single Cell Genomic Center (Single Core) and the Co-Director of the Advanced Technology Genomics Core (ATGC) at MD Anderson.

He conducted his graduate training and postdoctoral training at the Cold Spring Harbor laboratory under the mentorship of Dr. Michael Wigler. During this time, he invented the first single cell DNA sequencing method (Single-Nucleus-Sequencing) for sequencing the genome of a mammalian cell (Navin et al. 2011, Nature.). This work played a pivotal role in establishing the field of single cell genomics. The Navin laboratory continues to be at the forefront of the single cell cancer genomics field, where they have discovered a punctuated model of copy number evolution in triple-negative breast cancer (Gao et al. 2016, Nature Genetics) and elucidated the role mutator phentoypes and subclonal mutations in breast cancer evolution (Wang et al. 2014, Nature).

Dr. Navin’s group continues to pioneer the developing novel technologies for performing single cell DNA and RNA sequencing, in addition to innovative computational and statistical methods for analyzing the resulting large-scale datasets. These methods are being applied to study cancer evolution in the context of invasion, metastasis and therapy resistance. His laboratory works closely with leading oncologists and pathologist at MD Anderson to translate these technologies into the clinic, where they are poised to make a major impact on reducing the morbidity in human patients.

Dr. Navin has been the recipient of many prestigious awards in recognition of his work, including the Damon-Runyon Innovator Award, AAAS Wachtel Award, ACS Research Scholar Award, Wilson Stone Award, the Randall Innovator Award and the MD Anderson President’s Award for Research Excellence.

Visit Dr. Navin's lab website.
View a complete list of Dr. Navin's publications.
Dr. Navin - Google Scholar

Meet Nicholas Navin, Ph.D.

In the News

Healthy women have cells that resemble breast cancer, study finds

Researcher uses art to share science with a broad audience

Largest-ever atlas of normal breast cells brings unprecedented insights into mammary biology

Immunofluorescent image of a breast duct filled with DCIS tumor cells (cyan). Cell nuclei are shown in blue. Image courtesy of Fei Yang, M.D., Ph.D.

Genetic study offers new insights into DCIS biology, progression

Present Title & Affiliation

Dual/Joint/Adjunct Appointment

Chair, Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas

Professor, Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas

Professor, Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas

Professor, Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas

Faculty Member, Graduate School of Biological Sciences, University of Texas, Houston, Texas

Research Interests

I am the chair of the department of Systems Biology and the Grady Saunders Distinguished Professor at the M.D. Anderson Cancer Center. I am also the director of the CPRIT Single Cell Genomics Core and the director of the CPRIT Advanced Spatial Genomics Core facility at MD Anderson that is funded by a 3M grant (RP240497). During my career, I invented the first single cell DNA sequencing method (Single-Nucleus-Sequencing) for sequencing the genome of a mammalian cell (Navin et al. 2011, Nature), which played a pivotal role in establishing the field of single cell genomics. Over the past 15 years, my lab has been at the forefront of developed single cell DNA, RNA, epigenetic and spatial technologies. My laboratory focuses on understanding the role of clonal evolution and intratumor heterogeneity in the context of invasion, metastasis and therapy resistance in human cancers, with a major focus on breast cancer. I am also the leader of the Human Breast Cell Atlas (HBCA) project that aims to identify all cell types and cell states in normal breast tissues and their variation across women (Kumar et al. 2023, Nature). I am currently leading an RO1 focused on multi-organ metastasis in TNBC patients using post-mortem tissue samples (RO1CA299696). I am also passionate about mentoring and have mentored 31 graduate students and 17 postdoctoral fellows over the last 15 years, many of whom have gone on to postdoctoral positions, faculty positions or senior positions in the biotech industry.

Visit Dr. Navin's Lab Website.

View a complete list of Dr. Navin's publications.

Dr. Navin - Google Scholar

https://mdanderson.elsevierpure.com/en/persons/nicholas-navin

Education & Training

Degree-Granting Education

2010	Cold Spring Harbor Laboratory and Stony Brook University, Cold Spring Harbor, New York, US, Ph.D. in Molecular Genetics

Postgraduate Training

2010-2011

Postdoctoral Fellow, Cancer Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

Experience & Service

Faculty Academic Appointments

Associate Professor, Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2016 - 2020

Associate Professor, Bioinformatics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2016 - 2020

Assistant Professor, Bioinformatics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2011 - 2016

Assistant Professor, Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2011 - 2016

Administrative Appointments/Responsibilities

Director, Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2025 - Present

Director, Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2024 - Present

Co-Chair, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2019 - 2024

Director, Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2018 - Present

Co-Director, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2016 - Present

Other Professional Positions

Postdoctoral Fellow, Advisors: James Hicks, Michael Wigler, Cold Spring Harbor Laboratory, Cold Springs, New York, 2010 - 2011

Computational Biologist, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2005

Bioinformatics Scientist, Informax, Oxford, England, 2004

Research Coordinator, Mt. Sinai School of Medicine, New York City, New York, 2003

Intramural Institutional Committee Activities

Committee Member, Cancer Breakthroughs Advisory Committee, The University of Texas MD Anderson Cancer Center, 2022 - 2024

Extramural Institutional Committee Activities

Committee Member, VP of Research, The University of Texas MD Anderson Cancer Center, 2021 - Present

Committee Member, COVID-19 Research Response, The University of Texas MD Anderson Cancer Center, 2020 - Present

Committee Member, TMC3 Research Planning Committee, The University of Texas MD Anderson Cancer Center, 2020 - Present

Committee Member, Mid-Career Faculty Committee, The University of Texas MD Anderson Cancer Center, 2020 - Present

Co-Chair, MD Anderson Cancer Symposium, The University of Texas MD Anderson Cancer Center, 2019 - Present

Committee Member, Technology Review Task Force, The University of Texas MD Anderson Cancer Center, 2019 - 2020

Committee Member, Institutional Tissue Bank, The University of Texas MD Anderson Cancer Center, 2018 - Present

Faculty Search Committee, Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, 2018 - Present

Organizer, Texas Single Cell Seminar (TXSC) Series, The University of Texas MD Anderson Cancer Center, 2018 - 2021

Committee Member, Symptoms Research Chair, The University of Texas MD Anderson Cancer Center, 2017 - Present

Co-Organizer, Single Cell Journal Club, The University of Texas MD Anderson Cancer Center, 2017 - 2020

Committee Member, Future of Science Postdoc Symposium, The University of Texas MD Anderson Cancer Center, 2016 - Present

Chair, Faculty Search Committee - Genetics, The University of Texas MD Anderson Cancer Center, 2016 - 2018

Committee Member, Cancer Biology Symposium, The University of Texas MD Anderson Cancer Center, 2015 - Present

Committee Member, Faculty Search Committee - Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2014 - Present

Committee Member, Faculty Search Committee - Genetics, The University of Texas MD Anderson Cancer Center, 2014 - Present

Interviewer, Faculty Search Committee - Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 2014 - Present

Organizer/Host, Future of Science Postdoc Symposium, The University of Texas MD Anderson Cancer Center, 2014 - Present

Committee Member, Institutional Website Oversight Committee, The University of Texas MD Anderson Cancer Center, 2013 - Present

Committee Member, Faculty Search Committee - Genetics, The University of Texas MD Anderson Cancer Center, 2013 - Present

Interviewer, Faculty Search Committee - Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 2013 - 2015

Chair, John H. Blaffer Lecture Series, The University of Texas MD Anderson Cancer Center, 2012 - 2018

Co-Organizer, Single Cell Genomics Seminar, The University of Texas MD Anderson Cancer Center, 2012 - 2013

Editorial Activities

Editorial Board, Cell Genomics, 2020 - Present

Editorial Board, Science, 2019 - 2021

Editorial Board, Genome Research, 2019 - 2020

Editorial Board Member, Genome Biology, 2015 - Present

Editorial Board, Genome Biology, 2015 - 2020

Editorial Board, Nature Precision Oncology, 2015 - 2020

Editorial Board, Genes, Chromosomes, Cancer, 2015 - 2020

Editorial Review, Nature Precision Medicine, 2013 - Present

Honors & Awards

2025 - Present	Susan Komen Rising Star Research Award, San Antonio Breast Cancer Conference AACR
2024 - Present	Nobel Forum, Spatial Genomics Symposium Lecture, Stockholm, Sweden
2023 - Present	Princess Takamatsu Symposium Lecture, Tokyo, Japan
2021	AAAS Fellow Award, AAAS
2021	Robert M. Chamberlain Distinguished Mentorship Award, University of Texas M.D. Anderson Cancer Center
2021	AACR Award for Outstanding Achievement in Basic Cancer Research, America Association for Cancer Research
2019	President's Award for Research Excellence, University of Texas M.D. Anderson Cancer Center
2019	Blavatnik Award in Life Sciences, National Finalist
2018	The Dallas/Fort Worth Living Legend Faculty Achievement Award in Basic Research, University of Texas M.D. Anderson Cancer Center
2017	40 under 40 Award, Stoney Brook University
2017	Jack and Beverly Randall Prize for Excellence in Cancer Treatment, Randall Family Foundation
2017	Challenge Award, Prostate Cancer Foundation
2016	Sabin Fellowship, Andrew Sabin Family Foundation
2016	Faculty Scholar Award, University of Texas M.D. Anderson Cancer Center
2016	ACS Research Scholar, American Cancer Society (ACS)
2016	President's Scholar Award, University of Texas M.D. Anderson Cancer Center
2016	President's Recognition for Faculty Excellence, University of Texas M.D. Anderson Cancer Center
2015	AAAS Martin & Rose Wachtel Award, American Association for the Advancement of Science
2014	Faculty Educator Award, University of Texas M.D. Anderson Cancer Center
2013	Damon-Runyon Innovator Award, Damon-Runyon Rachleff Foundation
2013	Wilson S. Stone Memorial Award
2013	T.C. Hsu Award, Young Investigator Award
2010	Young Investigator Award, Genome Technology Magazine
2009	T32 NCI Fellowship, National Cancer Institute
2009	Abraham's Award, Stony Brook University
2008	King and Miller Fellowship, Stony Brook University
2005	Lindsey-Goldberg Fellowship, Cold Spring Harbor Laboratory

Professional Memberships

New York Academy of Sciences (NYAS)

2019 - 2020

American Society of Cell Biology (ASCB)

2014 - 2015

American Association of Cancer Research (AACR)

2013 - Present

American Association for the Advancement of Science (AAAS)

2013 - Present

American Society for Human Genetics (ASHG)

2013 - 2020

European Society for Human Genetics (ESHG)

2013 - 2018

American Society of Investigative Pathology (ASIP)

2012 - 2020

Selected Presentations & Talks

Local Presentations

2022. GCC/CPRIT Single Cell Omics Data Science Workshop. Invited. Houston, Texas, US.
2020. Gulf Coast Consortium: Single Cell Omics Annual Symposium (Online). Invited. Houston, Texas, US.
2020. Gulf Coast Consortium: Single Cell Omics Annual Symposium (Online). Invited. Houston, Texas, US.
2020. Keck Seminar (Online). Invited. Houston, Texas, US.
2018. PACMEN Symposium. Conference. PACMEN Symposium. Houston, TX, US.
2018. Breast Cancer Program. Conference. Breast Cancer Program. Houston, TX, US.
2018. Breast Medical Oncology Symposium. Conference. Breast Medical Oncology Symposium. Houston, TX, US.
2017. Department of Biochemistry. Conference. Department of Biochemistry. Houston, TX, US.
2017. Human and Molecular Genetics. Conference. Human and Molecular Genetics. Houston, TX, US.
2017. SBMI Center. Conference. SBMI Center. Houston, TX, US.
2016. Invited Speaker. Conference. Invited Speaker. Houston, TX, US.
2016. Invited Speaker. Conference. Invited Speaker. Houston, TX, US.
2016. Keynote. Conference. Keynote. Houston, TX, US.
2015. Advances in Molecular Diagnostics. Conference. Advances in Molecular Diagnostics. Houston, TX, US.
2014. Baylor College of Medicine Seminar. Conference. Baylor College of Medicine Seminar. Houston, TX, US.
2014. Pathology. Conference. Pathology. Houston, TX, US.
2014. MD Anderson, Dept. of Cancer Biology. Conference. MD Anderson, Dept. of Cancer Biology. Houston, TX, US.
2014. Keck Lecture. Conference. Keck Lecture. Houston, TX, US.
2013. Cancer Biology Seminar. Conference. Cancer Biology Seminar. Houston, TX, US.
2013. Nanotechnology Symposium. Conference. Nanotechnology Symposium. Houston, TX, US.
2013. UT Health, Dept. of Biochemistry and Molecular Biology. Conference. UT Health, Dept. of Biochemistry and Molecular Biology. Houston, TX, US.
2013. MD Anderson Postdoc Symposium. Conference. MD Anderson Postdoc Symposium. Houston, TX, US.
2013. MD Anderson Dept. Systems Biology. Conference. MD Anderson Dept. Systems Biology. Houston, TX, US.
2013. Microfluidics Symposium. Conference. Microfluidics Symposium. Houston, TX, US.
2013. Stone Award, Honorary Lecture. Conference. Stone Award, Honorary Lecture. Houston, TX, US.
2012. Department of Molecular Biology. Conference. Department of Molecular Biology. Houston, TX, US.
2012. School of Public Health. Conference. School of Public Health. Houston, TX, US.

Regional Presentations

2019. Keynote Speaker. Conference. Keynote Speaker. Austin, TX, US.
2019. Breast Cancer Evolution - Insights from Single Cell Genomics. Conference. Breast Cancer Evolution - Insights from Single Cell Genomics. Dallas, TX, US.
2019. Reeve's International Breast Cancer Symposium, "Breast Cancer Evolution: Insights from Single Cell Genomics". Conference. Reeve's International Breast Cancer Symposium, "Breast Cancer Evolution: Insights from Single Cell Genomics". Dallas, TX, US.
2016. Keynote for UT San Antonio Single Cell Genomics. Conference. Keynote for UT San Antonio Single Cell Genomics. San Antonio, TX, US.
2016. Invited Speaker. Conference. Invited Speaker, US.
2015. Invited Speaker. Conference. Invited Speaker. Galveston, TX, US.
2015. UTSW Seminar. Conference. UTSW Seminar. Dallas, TX, US.

National Presentations

2026. Advanced in Genome Biology Technologies (AGBT). Invited. Orlando, FL, US.
2026. AACR Annual Conference, Major Session: Single Cell Multiomics in Cancer. Invited. San Diego, CA, US.
2025. AACR Annual Conference: Innovative Approaches in TME Biology Session. Invited. AACR Annual Conference: Innovative Approaches in TME Biology Session. Chicago, IL, US.
2025. Cold Spring Harbor Laboratory: Biology of Genomes. Invited. Cold Spring Harbor, NY, US.
2025. Cornell-Weill University, Department of Pharmacology Seminar. Invited. New York, NY, US.
2022. SLAS2022 Annual Conference. Conference. SLAS2022 Annual Conference. Boston, MA, US.
2022. ATTIS Symposium (Online). Invited. Tuscaloosa, AL, US.
2022. NIH/NCI Bioinformatics Training and Education Program (BTEP) Seminar Series Online. Invited, US.
2022. 10X Genomics Symposium. Conference. 10X Genomics Symposium. Houston, TX, US.
2022. Baylor Advanced Breast Cancer Symposium. Conference. Baylor Advanced Breast Cancer Symposium. Houston, TX, US.
2022. AACR Annual 2022 Meeting, Symposium Seminar. Conference. AACR Annual 2022 Meeting, Symposium Seminar. New Orleans, LA, US.
2022. AACR Evolutionary Dynamics in Carcinogenesis Conference. Conference. AACR Evolutionary Dynamics in Carcinogenesis Conference. Tampa, FL, US.
2022. Seminars in Oncology. Invited. Boston, MA, US.
2022. Chan-Zuckerberg Initiative -Human Cell Atlas Symposium. Invited. San Francisco, CA, US.
2022. Department of Biochemistry & Molecular Genetics Seminar. Invited. Chicago, IL, US.
2021. McArdle Lecture (Online & Hybrid). Invited. Madison, WI, US.
2021. 10X Genomics Symposium: Human Breast Cell Atlas (On-line). Invited. San Francisco, CA, US.
2021. Chan-Zuckberg Initiative Human Cell Atlas Symposium (Online). Conference. Chan-Zuckberg Initiative Human Cell Atlas Symposium (Online). San Francisco, CA, US.
2021. 8th Annual Metastatic Breast Cancer Symposium at Baylor (Online & Hybrid). Invited. Salt Lake City, UT, US.
2021. Gulf Coast Consortium 2nd Annual Single Cell Omics Symposium (Online). Conference. Gulf Coast Consortium 2nd Annual Single Cell Omics Symposium (Online). Houston, TX, US.
2020. TRIST Cancer Symposium. Invited. Chicago, Illinois, US.
2020. Chan-Zuckerberg Initiative Seed Network Meeting (Online). Invited. San Francisco, CA, US.
2020. Fred Hutch Cancer Research Center Seminar. Invited. Seattle, WA, US.
2020. From Single Cells to Clinical Applications (Online). Invited. AACR Tumor Heterogeneity Conference:. Pennsylvania, PA, US.
2020. Connect Science Seminar Series (Online). Invited. Boston, MA, US.
2020. 10X Genomics Symposium (Online). San Francisco, CA, US.
2019. Blavatnik Science Symposium, "Chromosomal Instability and Inflammation - Mediated Metastasis in Cancer Cells". Conference. Blavatnik Science Symposium, "Chromosomal Instability and Inflammation - Mediated Metastasis in Cancer Cells". New York, NY, US.
2019. The H Foundation Basic Science Symposium, "Delineating Breast Cancer Evolution with Single Cell Genomics". Conference. The H Foundation Basic Science Symposium, "Delineating Breast Cancer Evolution with Single Cell Genomics". Chicago, IL, US.
2019. Janelia Farm's Cell Lineages Conference. Conference. Janelia Farm's Cell Lineages Conference. Washington, DC, US.
2019. Mission Biosciences. Invited. San Francisco, US.
2019. Great Lakes Breast Medical Oncology Symposium. Conference. Great Lakes Breast Medical Oncology Symposium. Columbus, OH, US.
2019. AACR Annual Meeting, "Delineating Human Breast Tissue Architecture with Single Cell Genomics". Conference. AACR Annual Meeting, "Delineating Human Breast Tissue Architecture with Single Cell Genomics". Atlanta, GA, US.
2019. 28th Annual Short Course on Experimental Models of Human Cancer. Invited. Bar Harbor, ME, US.
2018. Physical-Oncology Sciences Program Seminar. Invited. Philadelphia, PA, US.
2018. Cancer Evolution Symposium. Conference. Cancer Evolution Symposium. Salt Lake City, UT, US.
2018. Cell Circuits Seminar. Invited. Boston, MA, US.
2018. Zuckerberg BioHub Seminar. Invited. San Francisco, CA, US.
2018. Molecular Oncology. Invited. Tampa, FL, US.
2018. Dartmouth College Seminar. Invited. Dartmouth, MA, US.
2018. Single Cell Analysis Symposium. Conference. Single Cell Analysis Symposium. Bethesda, MD, US.
2018. Pre-Malignancies Session. Conference. Pre-Malignancies Session. Chicago, IL, US.
2018. ACMG Annual Clinical Genetics Meeting. Conference. ACMG Annual Clinical Genetics Meeting. Charlotte, NC, US.
2018. Advances in Genome Biology and Technology. Conference. Advances in Genome Biology and Technology. Orlando, FL, US.
2018. Delineating Breast Cancer Evolution with Single Cell Genomics. Invited. Boston, MA, US.
2017. Salk Institute Seminar. Invited. San Diego, CA, US.
2017. Stanford Cell Atlas Meeting. Conference. Stanford Cell Atlas Meeting. Stanford, CA, US.
2017. PS-OC. Conference. PS-OC. Bethesda, MD, US.
2017. Advances in Cancer Evolution. Conference. Advances in Cancer Evolution. Washington, DC, US.
2017. Frontiers in Single Cell Biology Symposium. Conference. Frontiers in Single Cell Biology Symposium. San Diego, CA, US.
2017. 29th Annual Usha Mahajani Symposium. Conference. 29th Annual Usha Mahajani Symposium. San Diego, CA, US.
2017. Kansas University Medical Center Seminar. Invited. Kansas City, MO, US.
2017. Cancer Biology and Evolution Center. Invited. Tampa, FL, US.
2017. Takara Biosciences Seminar Series. Invited. Ann Arbor, MI, US.
2017. Pre-TCGA. Conference. Pre-TCGA. Bethesda, MD, US.
2017. Jackson Laboratory Workshop. Invited. Bar Harbor, ME, US.
2017. Children's Hospital of Pennsylvania Seminar. Invited. Philadelphia, PA, US.
2017. Biology of Cancer Meeting. Conference. Biology of Cancer Meeting. Cold Spring Harbor, NY, US.
2017. Cellular and Molecular Biology. Invited. Ann Arbor, MI, US.
2017. University of Notre Dame Seminar. Invited. Notre Dame, IN, US.
2017. JIMB Metrology Seminar. Invited. Stanford, CA, US.
2017. New York University Seminar. Invited. New York, NY, US.
2016. New York Genome Center Seminar. Invited. New York, NY, US.
2016. Jackson Laboratory Seminar. Invited. Maine, ME, US.
2016. Harvard Dana-Farber Cancer Institute Seminar. Invited. Boston, MA, US.
2016. Invited Speaker for AACR Education Session. Conference. Invited Speaker for AACR Education Session. New Orleans, LA, US.
2016. Internal seminar for the 'Icahn School of Medicine. Invited. New York, New York, US.
2016. Illumina Experts Panel. Invited. Boston, MA, US.
2016. Van Andel Research Institute Seminar. Invited. Grand Rapids, MI, US.
2016. University of Pennsylvania Seminar. Invited. Philadelphia, PA, US.
2015. AACR. Conference. AACR. Philadelphia, PA, US.
2015. CNV and tumor heterogeneity talk. Invited. San Francisco, CA, US.
2015. Jackson Laboratories Seminar. Invited. Bar Harbor, ME, US.
2015. Advances in Genome Biology and Technology. Conference. Advances in Genome Biology and Technology. Marco Island, FL, US.
2015. Gordon Conference: Cell Proliferation. Conference. Gordon Conference: Cell Proliferation. Mt. Snow, VT, US.
2015. Harvard Medical School Seminar. Invited. Boston, MA, US.
2015. 24th Ann Arbor Mouse Seminar. Invited. Ann Arbor, MI, US.
2015. Harvard PQG Conference. Invited. Boston, MA, US.
2015. AAAS. Conference. AAAS. Washington, DC, US.
2015. AACR 2015 Annual Meeting. Conference. AACR 2015 Annual Meeting. Philadelphia, PA, US.
2015. 27th Graduate Student Symposium. Invited. Boulder, CO, US.
2014. UPENN Lecture. Invited. Philadelphia, PA, US.
2014. Cell-to-Cell Communication Cancer Symposium. Conference. Cell-to-Cell Communication Cancer Symposium. New York, NY, US.
2014. Biology of Genomics Seminar. Invited. Cold Spring Harbor, NY, US.
2014. New England Biolabs Seminar. Invited. Ipswich, MA, US.
2014. Univ. of Virginia Seminar. Invited. Charlottesville, VA, US.
2014. Genentech Damon-Runyon Cancer Symposium. Invited. San Francisco, CA, US.
2014. New England Biolabs. Conference. New England Biolabs. Boston, MA, US.
2014. The Biology of Genomes. Conference. The Biology of Genomes. Cold Spring Harbor, NY, US.
2014. Beyond the Genome. Conference. Beyond the Genome. San Francisco, CO, US.
2014. American Society of Investigative Therapeutics Symposium. Conference. American Society of Investigative Therapeutics Symposium. San Diego, CA, US.
2014. Illumina Discovery Symposium. Conference. Illumina Discovery Symposium. San Diego, CA, US.
2014. Memorial Sloan-Kettering Cancer Symposium. Conference. Memorial Sloan-Kettering Cancer Symposium. New York, NY, US.
2014. Single Cell Analysis Workshop. Conference. Single Cell Analysis Workshop. Bethesda, MD, US.
2014. CE Beyond the Genome Conference. Conference. CE Beyond the Genome Conference. Boston, MA, US.
2014. AACR, Education Session. Conference. AACR, Education Session. San Diego, CA, US.
2014. Investigative Therapeutics. Conference. Investigative Therapeutics. Orlando, FL, US.
2014. AACR Illumina Symposium. Conference. AACR Illumina Symposium. San Diego, CA, US.
2014. Genome Sciences Seminar. Invited. Charlottesville, VA, US.
2013. NIH Single Cell Analysis Workshop. Invited. Bethesda, MD, US.
2013. Damon Runyon Symposium. Invited. New York, NY, US.
2013. Experts Panel. Panelist. Seattle, WA, US.
2013. Cell Biology. Conference. Cell Biology. New Orleans, LA, US.
2013. Stanford Department of Genetics Seminar. Invited. Stanford, CA, US.
2013. IMPAKT Breast Cancer Symposium. Conference. IMPAKT Breast Cancer Symposium. Belgium, US.
2013. ZS Genetics. Conference. ZS Genetics. Boston, MA, US.
2013. Beyond the Genome 2013. Conference. Beyond the Genome 2013. San Francisco, CA, US.
2012. Nanotechnology Center. Invited. Los Alamos, NM, US.
2012. Frontiers in Biological Research Seminar. Invited. Palo Alto, CA, US.
2012. Keynote Presentation - Single Cell Analysis Summit. Conference. Keynote Presentation - Single Cell Analysis Summit. San Francisco, CA, US.
2012. Keynote Speaker - Single Cell Analysis Europe. Conference. Keynote Speaker - Single Cell Analysis Europe. Edinburgh.
2012. Ilumina Experts Panel. Conference. Ilumina Experts Panel. Alexandria, NC, US.
2012. Breast Cancer Symposium. Conference. Breast Cancer Symposium. San Antonio, TX, US.
2012. Biology of Genomes (Platform Presentation). Conference. Biology of Genomes (Platform Presentation). Cold Spring Harbor, NY, US.
2012. Frontiers of Biology Lecture. Invited. Stanford, CA, US.
2010. Biology of Genomes Platform Presentation. Conference. Biology of Genomes Platform Presentation. Cold Spring Harbor, NY, US.
2010. Washington University Seminar. Invited. St. Louis, MO, US.
2010. Dana-Farber. Invited. Boston, MA, US.
2010. UCSF. Invited. San Francisco, CA, US.
2009. Cancer Center. Invited. Cold Spring Harbor, NY, US.
2009. President's Provost Lecture. Invited. Cold Spring Harbor, NY, US.

International Presentations

2026. Breast Cancer Think Tank Symposium. Invited. Nassau, BS.
2025. The Third International Conference on Single-cell and Spatial Omics (TICSSO-3). Invited. Shanghai, CN.
2024. Nobel Forum, Karolinska Institute. Invited. Stockholm, SE.
2024. EMBO The Spatial Biology of Cancer Symposium. Invited. London, GB.
2023. Princess Takamatsu Symposium, Royal Palace. Invited. Tokyo, JP.
2022. JCA Annual Symposium (online). Conference. JCA Annual Symposium (online). Yokohama, JP.
2021. DSR Sarma Lectureship. Conference. DSR Sarma Lectureship. Toronto, CA.
2021. Westlake University & Cell Press Symposium: Single Cell Omics in Biomedicine (Online). Conference. Westlake University & Cell Press Symposium: Single Cell Omics in Biomedicine (Online). Hongzhou, CN.
2021. Cancer UK Grand Challenge Symposium (Online). Conference. Cancer UK Grand Challenge Symposium (Online). England, GB.
2020. CRUK Grand Challenge Cancer UK Symposium. Conference. CRUK Grand Challenge Cancer UK Symposium. Windsor, GB.
2020. Cancer Research UK Grand Challenge Symposium. Conference. Cancer Research UK Grand Challenge Symposium. Windsor, GB.
2020. Garvin Cancer Institute Lecture. Conference. Garvin Cancer Institute Lecture. Sydney, AU.
2020. Lorne Cancer Symposium. Conference. Lorne Cancer Symposium. Lorne, AU.
2019. NKI Graduate Student Symposium. Conference. NKI Graduate Student Symposium. Amsterdam, NL.
2019. Cancer UK DCIS Symposium. Conference. Cancer UK DCIS Symposium. Amsterdam, NL.
2019. Seed Networks for the Human Cell Atlas Conference. Conference. Seed Networks for the Human Cell Atlas Conference. Toronto, CA.
2018. Gordon Research Conference: Mammary Gland. Conference. Gordon Research Conference: Mammary Gland. Tuscany, IT.
2017. ETH Zurich Single Cell Statistics Conference. Conference. ETH Zurich Single Cell Statistics Conference. Ascona, CH.
2016. Cancer Genomics Keystone Conference. Conference. Cancer Genomics Keystone Conference. Alberta, CA.
2016. Keystone Symposium on Cancer Genomics. Conference. Keystone Symposium on Cancer Genomics. Banff, CA.
2016. Frontiers in Single Cell Genomics. Conference. Frontiers in Single Cell Genomics. Suzhou, CN.
2015. Radium Hospital Seminar. Conference. Radium Hospital Seminar. Oslo, NO.
2015. Nature Medicine Herrenhouse Symposium. Conference. Nature Medicine Herrenhouse Symposium. Hannover, DE.
2015. Nobel Forum at Karolinska Univ. Conference. Nobel Forum at Karolinska Univ. Stockholm, SE.
2015. Cancer Crosslinks Symposium, Keynote. Conference. Cancer Crosslinks Symposium, Keynote. Olso, NO.
2015. Breast Cancer Evolution and Precursors Conference. Conference. Breast Cancer Evolution and Precursors Conference. Bridgetown, BB.
2015. Mildred Scheel Cancer Conference. Conference. Mildred Scheel Cancer Conference. Bonn, DE.
2015. Innovation in Breast Cancer Symposium. Conference. Innovation in Breast Cancer Symposium. Madrid, ES.
2014. Single Cell Genomics Meeting. Conference. Single Cell Genomics Meeting. Stockholm, SE.
2014. Single Cell Genomics Conference. Conference. Single Cell Genomics Conference. Stockholm, SE.
2014. 2nd Individualized Management of Breast Cancer Conference. Conference. 2nd Individualized Management of Breast Cancer Conference. Beijing, CN.
2014. BIOPIC Conference. Conference. BIOPIC Conference. Beijing, CN.
2014. COMBS Breast Cancer Symposium. Conference. COMBS Breast Cancer Symposium. Beijing, CN.
2013. McGill Univ. Genome Center. Conference. McGill Univ. Genome Center. Montreal, CA.
2013. WIN Cancer Symposium. Conference. WIN Cancer Symposium. Paris, FR.
2013. Cell Epigenomics Symposium. Conference. Cell Epigenomics Symposium. Barcelona, ES.
2012. Princess Takamatsu Cancer Symposium. Conference. Princess Takamatsu Cancer Symposium. Tokyo, JP.
2012. National Cancer Center of Japan. Conference. National Cancer Center of Japan. Tokyo, JP.
2012. European Society Human Genetics Conference. Conference. European Society Human Genetics Conference. Nurnberg, DE.
2010. James Watson Cancer Symposium. Conference. James Watson Cancer Symposium. Suzhou, CN.

Less

Grant & Contract Support

Date:	2025 - 2029
Title:	Decoding the co-evolution of cancer subclones and their ecosystem in TNBC multi-organ metastasis
Funding Source:	NIH/NCI
Role:	PI
ID:	CA299696

Date:	2024 - 2029
Title:	Integrated Single Cell Genomics Core Facility
Funding Source:	CPRIT
Role:	PI

Date:	2022 - 2027
Title:	Acquired Resistance to Therapy and Iron (ARTI) Center – Project 3
Funding Source:	NIH/NCI
Role:	Collaborator
ID:	FP0015284

Date:	2022 - 2027
Title:	Novel Approaches Targeting B7-H3 in Castration-resistant Prostate Cancer
Funding Source:	NIH/NCI
Role:	Collaborator
ID:	R01CA275990

Date:	2022 - 2024
Title:	Multimodal single-cell data integration through bi-order canonical correlational analysis (bi-CCA) and extensions
Funding Source:	Chan Zuckerberg Initiative
Role:	Co-PI
ID:	DI-0000000119

Date:	2022 - 2026
Title:	Mechanics, Mechanisms and Consequences of Metastatic Cancer Cell Invasion into Bone
Funding Source:	NIH/NCI
Role:	CO-I
ID:	CA254869

Date:	2022 - 2027
Title:	Cancer Immune-Interception for Lynch Syndrome
Funding Source:	NIH/NCI
Role:	CO-I
ID:	R01CA257375

Date:	2022 - 2027
Title:	Developing a novel combination immunotherapy for triple-negative breast cancer
Funding Source:	NIH
Role:	CO-I
ID:	FP00012186

Date:	2022 - 2027
Title:	Epigenomic Reprogramming in DCIS Malignancy: Mechanism and Therapeutics
Funding Source:	NIH/NCI
Role:	CO-I

Date:	2022 - 2027
Title:	The evolution of intra-tumor heterogeneity of lung cancers with or without immunotherapy and its impact on patient survival
Funding Source:	NIH/NCI
Role:	CO-I

Date:	2022 - 2027
Title:	Defining drivers of the metastatic niche in pancreatic cancer
Funding Source:	NIH/NCI
Role:	Collaborator

Date:	2022 - 2025
Title:	Targeting metastatic niches in pancreatic cancer
Funding Source:	Cancer Prevention & Research Institute of Texas (CPRIT)
Role:	Collaborator

Date:	2021 - 2024
Title:	The Human Breast Cell Atlas (HBCA) Ancestry Network
Funding Source:	Chan Zuckerberg Initiative-Subk w/ UCI
Role:	Co-PI

Date:	2021 - 2024
Title:	Epigenomic Reprogramming in DCIS Malignancy: Mechanism and Therapeutics
Funding Source:	Department of Defense (DOD)
Role:	CO-I

Date:	2021 - 2026
Title:	Statistical methods for genomic analysis of heterogeneous tumors
Funding Source:	NIH/NCI
Role:	Collaborator
ID:	CA183793

Date:	2021 - 2026
Title:	Disabling genetic drivers in pancreatic cancer
Funding Source:	NIH/NCI
Role:	Collaborator
ID:	CA266089

Date:	2021 - 2026
Title:	The Gut Microbiome as a Biomarker and Mediator of Treatment Response and Toxicity in Locally Advanced Anal Cancer
Funding Source:	NIH/NCI
Role:	CO-I
ID:	CA266561

Date:	2021 - 2026
Title:	Deciphering the gene regulatory networks and biophysical cues that sustain high-grade osteosarcoma
Funding Source:	NIH/NCI
Role:	CO-I

Date:	2021 - 2024
Title:	Tumor cell transcriptome ploidy: a novel classifier for high risk prostate cancer
Funding Source:	Department of Defense (DOD)
Role:	CO-I
ID:	FP00012055

Date:	2021 - 2026
Title:	Uncovering Mutant TP53 Dependencies in Spontaneously-Arising Triple Negative Breast Cancer
Funding Source:	NIH/NCI
Role:	CO-I
ID:	CA257375

Date:	2021 - 2021
Title:	Single Cell Genomic Analysis of Metastatic Dissemination in Breast and Colorectal Cancers
Funding Source:	Vivian L. Smith Foundation
Role:	PI
ID:	N/A

Date:	2020 - 2025
Title:	Barrett’s Esophagus Pre-Cancer Atlas
Funding Source:	NIH/NCI
Role:	CO-I
ID:	FP00009026

Date:	2020 - 2023
Title:	Single-cell evaluation to identify tumor-stroma niches driving the transition from in situ to invasive breast cancer
Funding Source:	Cancer Prevention & Research Institute of Texas (CPRIT)
Role:	Collaborator
ID:	RP200120

Date:	2019 - 2024
Title:	Delineating the Evolution and Ecology of Chemoresistance in Breast Cancer with Single Cell Genomics
Funding Source:	NIH/NCI
Role:	PI
ID:	R01CA236864

Date:	2019 - 2021
Title:	PAN-CANCER SINGLE CELL ANALYSIS OF COPY NUMBER SUBSTRUCTURE AND MUTATIONAL DIVERSITY IN HUMAN TUMORS
Funding Source:	NIH/NCI
Role:	PI
ID:	R01CA236864 (Supplement)

Date:	2019 - 2021
Title:	AML/MDS Moon Shot Flagship 3: Targeting Minimal Residual Disease and Stem-like Cells in High-Risk AML
Funding Source:	UTMDACC Moon Shot Program
Role:	CO-I

Date:	2019 - 2021
Title:	Breast Cancer Moon Shot
Funding Source:	UTMDACC Moon Shot Program
Role:	CO-I

Date:	2019 - 2021
Title:	Prostate Cancer Moon Shot
Funding Source:	UTMDACC Moon Shot Program
Role:	CO-I

Date:	2019 - 2024
Title:	Investigating Tumor Initiation and Invasion in Premalignant Breast Cancer with Spatial Single Cell Genomics
Funding Source:	NIH/NCI
Role:	PI
ID:	R01CA240526

Date:	2019 - 2022
Title:	Human Breast Cell Atlas Seed Network
Funding Source:	Chan Zuckerberg Initiative
Role:	PI
ID:	FP00008028

Date:	2019 - 2021
Title:	Delineating the evolution of resistance to HER2-targeted therapy in breast cancer using single-cell genomics
Funding Source:	Sister Institution Network Fund, UTMDACC
Role:	PI
ID:	00057160

Date:	2019 - 2024
Title:	Translating Intestinal Radioprotection by EGLN Inhibition to Improve Clinical Outcomes in Unresectable Pancreatic Cancer
Funding Source:	NIH/NCI
Role:	CO-I
ID:	R01CA227517

Date:	2019 - 2022
Title:	Investigating DCIS and matched recurrence invasive tumors using single cell DNA sequencing technologies
Funding Source:	Cancer UK Grand Challenge PRECISION
Role:	CO-I

Date:	2018 - 2021
Title:	Delineating the Evolution of Multi-Organ Metastasis in Breast Cancer with Single Cell Genomics
Funding Source:	Emerson Collective Cancer Research Fund
Role:	PI

Date:	2018 - 2023
Title:	Omic and Multidimensional Spatial Atlas of Metastatic Breast and Prostate Cancers (OMS Atlas)
Funding Source:	NIH/NCI
Role:	CO-I
ID:	U2CCA233280

Date:	2018 - 2022
Title:	Prostate Cancer Moon Shot Priority Project 2: Delineating Longitudinal Therapeutic Resistance and Metastatic Progression in Lethal Prostate Cancer Using Single Cell and Plasma Genome Sequencing Approaches
Funding Source:	UTMDACC Moon Shot Program
Role:	CO-I

Date:	2018 - 2020
Title:	Delineating the Evolution of Multi-Organ Metastasis in Breast Cancer with Single Cell Genomics
Funding Source:	Emerson Collective Cancer Research Fund
Role:	PI

Date:	2018 - 2019
Title:	Flagship 1: 'Longitudinal CSF Monitoring
Funding Source:	UTMDACC Moon Shot Program, GBM Moon Shot
Role:	Collaborator

Date:	2018 - 2023
Title:	Integrated Single Cell Genomics Core Facility
Funding Source:	Cancer Prevention & Research Institute of Texas (CPRIT)
Role:	PI
ID:	RP180684

Date:	2018 - 2020
Title:	LC170171 Tumor heterogeneity and therapeutic resistance in small cell lung cancer (SCLC)
Funding Source:	Department of Defense (DOD)
Role:	CO-I
ID:	Grant12489127-LC170171

Date:	2018 - 2022
Title:	Characterizing cancer genome instability and translational impact using new sequencing technologies
Funding Source:	Cancer Prevention & Research Institute of Texas (CPRIT)
Role:	CO-I
ID:	RP180248

Date:	2018 - 2018
Title:	Genomic Profiling of Therapy Resistance in Triple-Negative Breast Cancer Patients Using Longitudinal Liquid Biopsies
Funding Source:	UTMDACC, Institutional Research Grant
Role:	PI

Date:	2018 - 2023
Title:	Spatial-omic Analysis of Therapeutic Resistance in Metastatic Breast Cancer patients
Funding Source:	NIH/NCI
Role:	CO-I

Date:	2017 - 2022
Title:	Flagship 3: Targeting Minimal Residual Disease and Stem-like Cells in High-Risk AML
Funding Source:	UTMDACC Moon Shot Program, AML/MDS Moon Shot
Role:	CO-I

Date:	2017 - 2019
Title:	Flagship 1: Longitudinal analysis of patient samples at single cell resolution
Funding Source:	UTMDACC Moon Shot Program, Prostate Cancer Moon Shot
Role:	Collaborator

Date:	2017 - 2019
Title:	Linking the Effect of Local Therapy to Molecularly Defined 'Androgen-Responsive' and 'Androgen-Indifferent' Prostate Cancer Subsets in Men with de novo Metastatic Disease
Funding Source:	Prostate Cancer Research Foundation
Role:	Co-PI
ID:	17CHAL01

Date:	2017 - 2018
Title:	Human Breast Cell Atlas Project
Funding Source:	Chan-Zuckerberg Initiative Foundation
Role:	PI
ID:	2017-173955

Date:	2017 - 2018
Title:	Flagship 1: Targeting the Undruggable Genome
Funding Source:	UTMDACC Moon Shot Program, Pancreatic Moon Shot
Role:	CO-I

Date:	2017 - 2018
Title:	Flagship 2: Clinical Applications of Consensus Molecular Subtypes: Variations in Tumor Heterogeneity
Funding Source:	UTMDACC Moon Shot Program, CRC Moon Shot
Role:	CO-I

Date:	2017 - 2022
Title:	Prevent Ductal Carcinoma in Situ Invasive Overtreatment Now – PRECISION
Funding Source:	Cancer Research UK
Role:	CO-I
ID:	FP00001035

Date:	2017 - 2019
Title:	Pan-omics single-cell data integration for joint cell-type identification
Funding Source:	Silicon Valley Community Foundation/Chan Zuckerberg Initiative
Role:	CO-I
ID:	2018-182735

Date:	2017 - 2019
Title:	Human Breast Cell Atlas Project
Funding Source:	Chan-Zuckerberg Initiative
Role:	PI

Date:	2016 - 2020
Title:	Investigating Mutational Evolution and Intratumor Heterogeneity in TNBC
Funding Source:	American Cancer Society (ACS)
Role:	PI
ID:	129098-RSG-16-092-01-TBG

Date:	2016 - 2018
Title:	Investigating Chemotherapy Resistance Application in TNBC by Single-Cell Sequencing
Funding Source:	Sabin Fellows Award
Role:	PI

Date:	2016 - 2018
Title:	Investigating chemoresistance evolution in triple-negative breast cancer with single cell sequencing
Funding Source:	Sabin Fellowship
Role:	PI

Date:	2015 - 2016
Title:	Single Cell Sequencing of Circulating Tumor Cells in Metastatic Breast Cancer Patients
Funding Source:	Angle Inc. - Sponsored Research Grant
Role:	PI

Date:	2015 - 2016
Title:	Investigating Chemoresistance Evolution in TNBC Breast Cancer Patients with Single Cell Sequencing
Funding Source:	Lefkofsky Foundation
Role:	PI

Date:	2015 - 2015
Title:	Investigating Clonal Evolution in Triple-Negative Breast Cancers with Single-Cell Sequencing
Funding Source:	Agilent University Relations Grant
Role:	PI

Date:	2014 - 2016
Title:	Integrated Single-Cell Technologies to Advance Personalized Oncology (SINCELONC)
Funding Source:	UTMDACC Sister Institution Network Fund (SINF)
Role:	Co-PI

Date:	2014 - 2015
Title:	Investigating Metastasis and Non-Invasive Monitoring in TNBC by Single-Cell Sequencing
Funding Source:	Moonshot Knowledge Gap Award
Role:	PI

Date:	2014 - 2019
Title:	Statistical methods for genomic analysis of heterogeneous tumors
Funding Source:	NIH/NCI
Role:	Co-PI
ID:	5R01CA183793-04

Date:	2014 - 2017
Title:	Non-Invasive monitoring of Breast Cancer Mutations Using Circulating Free DNA
Funding Source:	T.C. Hsu Award - UTMDACC
Role:	PI

Date:	2014 - 2015
Title:	Developing single cell sequencing methods for epigenetic profiling of human cells
Funding Source:	Center for Epigenetics Award
Role:	PI

Date:	2013 - 2019
Title:	Cancer Center Support Grant, Sequencing and Microarray Facility (SMF)
Funding Source:	NIH/NCI
Role:	CO-I
ID:	P30CA016672

Date:	2013 - 2018
Title:	Cancer Center Support Grant, Sequencing and Microarray Facility (SMF)
Funding Source:	NIH/NCI
Role:	Co-Director
ID:	P30 CA016672

Date:	2013 - 2016
Title:	Developing Single Cell Sequencing Methods to Investigate Metastatic Seeding
Funding Source:	Damon-Runyon Rachleff Innovation Award
Role:	PI

Date:	2012 - 2014
Title:	Developing a Whole-Genome Sequencing Method for Single Human Cells
Funding Source:	NIH/NIMH
Role:	PI
ID:	R21-CA-174397-01

Date:	2012 - 2018
Title:	Single-Cell Sequencing of Breast Tumors to Investigate Genome Evolution
Funding Source:	NIH/NCI
Role:	PI
ID:	R01 CA 169244-01

Date:	2011 - 2012
Title:	Investigating the Evolution of Somatic Mutations in Breast Cancer by Single-Cell Sequencing
Funding Source:	Center for Genetics and Genomics, UTMDACC
Role:	Principal Investigator-MDACC

Date:	2011 - 2014
Title:	Next-Generation Sequencing Grant
Funding Source:	Kleberg Foundation
Role:	PI

Date:	2011 - 2012
Title:	Research for Computational and Statistical Modeling of Genotype Data
Funding Source:	Center for Genomics Award
Role:	PI

Date:	1996 - 2024
Title:	Cancer Center Support Grant, Sequencing and Microarray Facility (SMF)
Funding Source:	NIH/NCI
Role:	Co-Director
ID:	P30 CA016672

Selected Publications

Peer-Reviewed Articles

Wang, J, Minussi, DC, Davis, A, Wei, R, Ye, H, Sei, E, Schalck, A, Yan, Y, Wu, HJ, Bai, S, Peng, C, Hu, M, Casasent, A, Contreras, A, Chen, H, Hui, D, Damodaran, S, Edgerton, ME, Kopetz, S, Lim, B, Navin, N. Delineating the copy-number substructure of metastatic tumors with CopyKit. Molecular cell 86(2):407-422.e6, 2026. e-Pub 2026. PMID: 41534520.
Sobral-Leite, M, Castillo, SP, Vonk, S, Messal, HA, Melillo, X, Lam, N, de Bruijn, B, Hagos, YB, van den Bos, M, Sanders, J, Almekinders, MM, Visser, LL, Groen, EJ, Kristel, P, Ercan, C, Azarang, L, Van Rheenen, J, Hwang, ES, Yuan, Y, van Oirsouw, M, Verschuur, E, Pinto, D, Collyar, D, Stobart, H, Bhattacharjee, P, Rea, D, Wessels, LF, Schmidt, MK, Behbod, F, Jonkers, J, Navin, N, Futreal, A, Davies, H, Sawyer, EJ, Nik-Zainal, S, Thompson, A, Menezes, R, Lips, EH, Wesseling, J. A morphometric signature to identify ductal carcinoma in situ with a low risk of progression. npj Precision Oncology 9(1), 2025. e-Pub 2025. PMID: 39875514.
Stur, E, Peng, F, Teng, PN, Bayraktar, E, Hu, M, Corvigno, S, Brown, DJ, Lee, S, Moore, KN, Bateman, NW, Darcy, KM, Maxwell, GL, P. Conrads, T, Sahni, N, Vázquez-García, I, Shah, S, Celestino, J, D. Fleming, N, Navin, N, Wang, L, Sood, AK. The dynamic immune behavior of primary and metastatic ovarian carcinoma. npj Precision Oncology 9(1), 2025. e-Pub 2025. PMID: 40281242.
Hou R, Grimm LJ, Marks JR, King LM, Lynch T, Rogers K, Lyburn ID, Stone N, Wallis M, Mann RM, Lips EH, Alaeikhanehshir S, van Leeuwen MM, Teuwen J, Wesseling J, Lo JY, Hwang E, PRECISION consortium GC. Cross-National Radiomics Validation Using Mammography to Predict Occult Invasion in Ductal Carcinoma in Situ. Radiology 317(2), 2025. e-Pub 2025. PMID: 41251557.
Wang K, Ye R, Bai S, Xiao Z, Yang L, Li J, Tang C, Sei E, Peng J, Casasent AK, Lin SH, Nagi C, Thompson AM, Krishnamurthy S, Navin NE. Coalescing single- cell genomes and transcriptomes to decode breast cancer progression. Cell 188(22):6355-6369.e16, 2025. e-Pub 2025. PMID: 40912251.
Aminu M, Zhu B, Vokes N, Chen H, Hong L, Li J, Fujimoto J, Chaib M, Yang Y, Wang B, Poteete A, Nilsson MB, Le X, Cascone T, Jaffray D, Navin N, Wang T, Byers LA, Gibbons DL, Heymach J, Chen K, Cheng C, Zhang J, Wu J. CoCo-ST detects global and local biological structures in spatial transcriptomics datasets. Nat Cell Biol 27:2019–2031, 2025. e-Pub 2025. PMID: 41083603.
Gray GK, Carlson EG, Lev T, Marshall B, Reed AD, Sánchez-Covarrubias AP, Twigger AJ, Puig-Barbe A, Thennavan A, Omotoso A, Murrow LM, Chatterjee D, He S, Pensa S, Aevermann B, Tavares NK, Chen N, Hilton JA, Blake K, Liu Y, Phong K, Gartner ZJ, Lawson DA, Swarbrick A, Dos Santos CO, George SHL, Brugge JS, LaBarge MA, Nakshatri H, Navin N, Kessenbrock K, Khaled WT. Defining breast epithelial cell types in the single-cell era. Dev Cell 60(17):2218-2236, 2025. e-Pub 2025. PMID: 40925326.
Lei, G, Sun, M, Cheng, J, Ye, R, Lu, Z, Horbath, A, Huo, D, Wu, S, Alapati, A, Aggarwal, S, Xu, Z, Mao, C, Yan, Y, Yao, J, Li, Q, Chen, X, Lee, H, Zhuang, L, Jiang, D, Pataer, A, Roth, JA, Navin, N, Koong, AC, You, MJ, Lin, SH, Gan, B. Radiotherapy promotes cuproptosis and synergizes with cuproptosis inducers to overcome tumor radioresistance. Cancer cell 43(6):1076-1092.e5, 2025. e-Pub 2025. PMID: 40215978.
Zhu, B, Chen, P, Aminu, M, Li, J, Fujimoto, J, Tian, Y, Hong, L, Chen, H, Hu, X, Li, C, Vokes, N, Moreira, AL, Gibbons, DL, Solis Soto, LM, Parra Cuentas, ER, Shi, O, Diao, S, Ye, J, Rojas, FR, Vilar Sanchez, E, Maitra, A, Chen, K, Navin, N, Nilsson, M, Huang, B, Heeke, S, Zhang, J, Haymaker, CL, Velcheti, V, Sterman, DH, Kochat, V, Padron, WI, Alexandrov, LB, Wei, Z, Le, X, Wang, L, Fukuoka, J, Lee, JJ, Wistuba, II, Pass, HI, Davis, MM, Hanash, S, Cheng, C, Dubinett, SM, Spira, A, Rai, K, Lippman, SM, Futreal, A, Heymach, JV, Reuben, A, Wu, J, Zhang, J. Spatial and multiomics analysis of human and mouse lung adenocarcinoma precursors reveals TIM-3 as a putative target for precancer interception. Cancer cell 43(6):1125-1140.e10, 2025. e-Pub 2025. PMID: 40345189.
Bernard V, Ku LT, Wang T, Acevedo-Diaz A, Rajapakshe KI, Jacobson G, Tovar D, Min J, Pei G, Tat C, Suresh A, Tzeng CD, Katz MH, Bhutani MS, Wang H, Wolff RA, Haymaker C, Ludmir EB, Huang H, Chen X, Li L, Koong AC, Wang L, Navin NE, Jiang D, Li Z, Maitra A, Koay EJ. A spatial atlas of chemoradiation therapy in pancreatic cancer identifies cellular and microenvironmental determinants of persister populations. bioRxiv. e-Pub 2025. PMID: 40667350.
Doyle S, Lips EH, Marcus E, Mulder L, Liu YH, Canton FD, Kootstra T, van Seijen MM, Bouybayoune I, Sawyer EJ, Thompson AM, Pinder SE, Sánchez CI, Teuwen J, Wesseling J, PRECISION Consortium GC. Deep learning for predicting invasive recurrence of ductal carcinoma in situ: leveraging histopathology images and clinical features. EBioMedicine 116. e-Pub 2025. PMID: 40440915.
Schalck, A, Tran, TM, Li, J, Sei, E, Bai, S, Hu, M, Lin, J, Bright, SJ, Reddick, S, Yang, F, Batra, H, Contreras, A, Raso, G, Stauder, MC, Hoffman, K, Reddy, JP, Nead, KT, Smith, B, Sawakuchi, GO, Woodward, W, Watowich, SS, Litton, J, Bedrosian, I, Mittendorf, EA, Le-Petross, H, Navin, N, Shaitelman, SF. The impact of breast radiotherapy on the tumor genome and immune ecosystem. Cell Reports 44(5), 2025. e-Pub 2025. PMID: 40378044.
Zhao, Y, Ramesh, N, Xu, P, Sei, E, Hu, M, Bai, S, Troncoso, P, Aparicio, A, Logothetis, CJ, Corn, P, Navin, N, Zurita-Saavedra, A. Longitudinal Profiling of Circulating Tumor DNA Reveals the Evolutionary Dynamics of Metastatic Prostate Cancer during Serial Therapy. Cancer Research 85(9):1680-1695, 2025. e-Pub 2025. PMID: 39992716.
Bhattacharjee P, Lips EH, Sawyer EJ, Hwang ES, Thompson AM, Wesseling J, PRECISION Consortium CGC. Conquering Overtreatment of DCIS: Lessons from PRECISION. Cancer Discov 15(1):28–33, 2025. e-Pub 2025. PMID: 39801240.
Gupta, P, Dang, M, Oberai, S, Migliozzi, S, Trivedi, R, Kumar, G, Peshoff, MM, Milam, N, Ahmed, A, Bojja, K, Tran, TM, Gumin, J, Kamiya Matsuoka, C, Huse, J, Cox, K, Li, J, Shehwana, H, Sheth, SA, Saxon, R, Baohua, S, Parker Kerrigan, BC, Maheshwari, A, Parra Cuentas, ER, Navin, N, Heimberger, AB, Lang Jr, FF, Iavarone, A, Dwyer, KC, Wang, L, Bhat, KP. Immune landscape of isocitrate dehydrogenase-stratified primary and recurrent human gliomas. Neuro-oncology 26(12):2239-2255, 2024. e-Pub 2024. PMID: 39126294.
Lin Y, Wang J, Wang K, Bai S, Thennavan A, Wei R, Yan Y, Li J, Elgamal H, Sei E, Casasent A, Rao M, Tang C, Multani AS, Ma J, Montalvan J, Nagi C, Winocour S, Lim B, Thompson A, Navin N. Normal breast tissues harbour rare populations of aneuploid epithelial cells. Nature 636:663–670, 2024. e-Pub 2024. PMID: 39567687.
Engelhardt, EG, Schmitz, RS, Gerritsma, MA, Sondermeijer, CM, Verschuur, E, Houtzager, JH, Griffioen, R, Bijker, N, Mann, RM, Retèl, V, van Duijnhoven, FH, Wesseling, J, Bleiker, E, Thompson, A, Nik-Zainal, S, Sawyer, EJ, Davies, H, Futreal, A, Navin, N, Hwang, ES, Jonkers, J, Van Rheenen, J, Behbod, F, Lips, EH, Schmidt, MK, Wessels, LF, Rea, D, Bhattacharjee, P, Stobart, H, Collyar, D, Pinto, D, van Oirsouw, M, Alaeikhanehshir, S, Elshof, L. DCIS knowledge of women choosing between active surveillance and surgery for low-risk DCIS. Breast 77, 2024. e-Pub 2024. PMID: 38970983.
Ciwinska, M, Messal, HA, Hristova, HR, Lutz, C, Bornes, L, Chalkiadakis, T, Harkes, R, Langedijk, NS, Hutten, SJ, Menezes, R, Jonkers, J, Prekovic, S, van Oirsouw, M, Verschuur, E, Pinto, D, Collyar, D, Stobart, H, Bhattacharjee, P, Rea, D, Wessels, LF, Schmidt, MK, Lips, EH, Behbod, F, Van Rheenen, J, Jonkers, J, Hwang, ES, Navin, N, Futreal, A, Davies, H, Sawyer, EJ, Nik-Zainal, S, Thompson, A, Wesseling, J, Simons, BD, Scheele, CL, Van Rheenen, J. Mechanisms that clear mutations drive field cancerization in mammary tissue. Nature 633(8028):198-206, 2024. e-Pub 2024. PMID: 39232148.
Wang K, Yan Y, Elgamal H, Li J, Tang C, Bai S, Xiao Z, Sei E, Lin Y, Wang J, Montalvan J, Nagi C, Thompson AM, Navin N. Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer. bioRxiv. e-Pub 2024. PMID: 39314325.
Hutten SJ, Messal HA, Lips EH, Sheinman M, Ciwinska M, Braams E, van der Borden C, Kristel P, Stoffers S, Wessels LF, PRECISION Consortium GC, Jonkers J, van Rheenen J, Wesseling J, Scheele CL. Ductal carcinoma in situ develops within clonal fields of mutant cells in morphologically normal ducts. J Pathol 263(3):360-371, 2024. e-Pub 2024. PMID: 38779852.
Dou, J, Tan, Y, Kock, KH, Wang, J, Cheng, X, Tan, LM, Han, KY, Hon, CC, Park, WY, Shin, JW, Jin, H, Wang, Y, Chen, H, Ding, L, Prabhakar, S, Navin, N, Chen, R, Chen, K. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nature Biotechnology 42(5):803-812, 2024. e-Pub 2024. PMID: 37592035.
Alaeikhanehshir S, Voets MM, van Duijnhoven FH, Lips EH, Groen EJ, van Oirsouw MCJ, Hwang SE, Lo JY, Wesseling J, Mann RM, Teuwen J, Steering Group GCPC. Application of deep learning on mammographies to discriminate between low and high-risk DCIS for patient participation in active surveillance trials. Cancer Imaging 24(48), 2024. e-Pub 2024. PMID: 38576031.
Truong, DD, Lamhamedi-Cherradi, SE, Porter, RW, Krishnan, S, Swaminathan, J, Gibson, A, Lazar, A, Livingston, JA, Gopalakrishnan, V, Gordon, N, Daw Bitar, N, Navin, N, Gorlick, R, Ludwig, JA. Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing. BMC cancer 23(1):488, 2023. e-Pub 2023. PMID: 37254069.
Gosling, SB, Arnold, EL, Davies, SK, Cross, H, Bouybayoune, I, Calabrese, D, Nallala, J, Pinder, S, Fu, L, Lips, EH, King, LM, Marks, JR, Hall, AH, Grimm, LJ, Lynch, T, Pinto, D, Stobart, H, Hwang, ES, Wesseling, J, Geraki, K, Stone, N, Lyburn, ID, Greenwood, C, Rogers, K, Thompson, A, Nik-Zainal, S, Sawyer, EJ, Davies, H, Futreal, A, Navin, N, Jonkers, J, Van Rheenen, J, Behbod, F, Schmidt, MK, Wessels, LF, Rea, D, Bhattacharjee, P, Collyar, D, Verschuur, E, van Oirsouw, M. Microcalcification crystallography as a potential marker of DCIS recurrence. Scientific reports 13(1), 2023. e-Pub 2023. PMID: 37291276.
RSJM S, van den Belt-Dusebout AW, Clements K, Ren Y, Cresta C, Timbres J, Liu YH, Byng D, Lynch T, Menegaz BA, Collyar D, Hyslop T, Thomas S, Love JK, Schaapveld M, Bhattacharjee P, Ryser MD, Sawyer E, Hwang ES, Thompson A, Wesseling J, Lips EH, Schmidt MK, PRECISION consortium GC. Association of DCIS size and margin status with risk of developing breast cancer post-treatment: multinational, pooled cohort study. BMJ, 2023. e-Pub 2023. PMID: 37903527.
Wang, K, Kumar, T, Wang, J, Minussi, DC, Sei, E, Li, J, Tran, TM, Thennavan, A, Hu, M, Casasent, A, Xiao, Z, Bai, S, Yang, L, King, LM, Shah, V, Kristel, P, van der Borden, CL, Marks, JR, Zhao, Y, Zurita-Saavedra, A, Aparicio, A, Chapin, BF, Ye, J, Zhang, J, Gibbons, DL, Sawyer, EJ, Thompson, A, Futreal, A, Hwang, ES, Wesseling, J, Lips, EH, Navin, N. Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell 186(18):3968-3982.e15, 2023. e-Pub 2023. PMID: 37586362.
Kumar, T, Nee, K, Wei, R, He, S, Nguyen, QH, Bai, S, Blake, K, Pein, M, Gong, Y, Sei, E, Hu, M, Casasent, A, Thennavan, A, Li, J, Tran, TM, Chen, K, Nilges, B, Kashikar, N, Braubach, O, Ben Cheikh, B, Nikulina, N, Chen, H, Teshome, M, Menegaz, BA, Javaid, H, Nagi, C, Montalvan, J, Lev, T, Mallya, S, Tifrea, DF, Edwards, RA, Lin, E, Parajuli, R, Hanson, SE, Winocour, SJ, Thompson, A, Lim, B, Lawson, DA, Kessenbrock, K, Navin, N. A spatially resolved single-cell genomic atlas of the adult human breast. Nature 620(7972):181-191, 2023. e-Pub 2023. PMID: 37380767.
Lu, L, Wang, RJ, Henderson, Y, Bai, S, Yang, J, Hu, M, Shiau, CK, Pan, T, Yan, Y, Tran, TM, Li, J, Kieser, R, Zhao, X, Wang, J, Nurieva, R, Williams, MD, Cabanillas, ME, Dadu, R, Busaidy, NL, Zafereo, M, Navin, N, Lai, SY, Gao, R. Anaplastic transformation in thyroid cancer revealed by single-cell transcriptomics. Journal of Clinical Investigation 133(11), 2023. e-Pub 2023. PMID: 37053016.
Gencel-Augusto, J, Su, X, Qi, Y, Whitley, EM, Pant, V, Xiong, S, Shah, VV, Lin, J, Perez, E, Fiorotto, M, Mahmud, I, Jain, A, Lorenzi, PL, Navin, N, Richie, ER, Lozano, G. Dimeric p53 Mutant Elicits Unique Tumor-Suppressive Activities through an Altered Metabolic Program. Cancer discovery 13(5):1230-1249, 2023. e-Pub 2023. PMID: 37067911.
Leighton, J, Hu, M, Sei, E, Meric-Bernstam, F, Navin, N. Reconstructing mutational lineages in breast cancer by multi-patient-targeted single-cell DNA sequencing. Cell Genomics 3(1), 2023. e-Pub 2023. PMID: 36777188.
Leighton, J, Hu, M, Sei, E, Meric-Bernstam, F, Navin, N. Reconstructing mutational lineages in breast cancer by multi-patient-targeted single-cell DNA sequencing. Cell Genomics 3(1), 2023. e-Pub 2023. PMID: 36777188.
Gulhati, P, Schalck, A, Jiang, S, Shang, X, Wu, C, Hou, P, Hernandez, S, Solis Soto, LM, Parra Cuentas, ER, Ying, H, Han, J, Dey, P, Li, J, Deng, P, Sei, E, Maeda, DY, Zebala, JA, Spring, DJ, Kim, M, Wang, H, Maitra, A, Moore, DF, Dwyer, KC, Wang, YA, Navin, N, DePinho, RA. Targeting T cell checkpoints 41BB and LAG3 and myeloid cell CXCR1/CXCR2 results in antitumor immunity and durable response in pancreatic cancer. Nature Cancer 4(1):62-80, 2023. e-Pub 2023. PMID: 36585453.
Wang, X, Semba, T, Manyam, GC, Wang, J, Shao, SH, Bertucci, F, Finetti, P, Krishnamurthy, S, Phi, LH, Pearson, T, Van Laere, S, Burks, JK, Cohen, E, Reuben, JM, Yang, F, Min, H, Navin, N, Trinh, VA, Iwase, T, Batra, H, Shen, Y, Zhang, X, Tripathy, D, Ueno, NT. EGFR is a master switch between immunosuppressive and immunoactive tumor microenvironment in inflammatory breast cancer. Science Advances 8(50), 2022. e-Pub 2022. PMID: 36525493.
Kaufmann TL, Petkovic M, Watkins TBK, Colliver EC, Laskina S, Thapa N, Minussi DC, Navin N, Swanton C, Van Loo P, Haase K, Tarabichi M, Schwarz RF. MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biol 23(1):241, 2022. e-Pub 2022. PMID: 36376909.
Schalck A, Sakellariou-Thompson D, Forget MA, Sei E, Hughes TG, Reuben A, Bai S, Hu M, Kumar T, Hurd MW, Katz MHG, Tzeng CD, Pant S, Javle M, Fogelman DR, Maitra A, Haymaker CL, Kim MP, Navin NE, Bernatchez C. Single-Cell Sequencing Reveals Trajectory of Tumor-Infiltrating Lymphocyte States in Pancreatic Cancer. Cancer Discov 12(10):2330-2349, 2022. e-Pub 2022. PMID: 35849783.
Mathew MT, Antoniou A, Ramesh N, Hu M, Gaither J, Mouhlas D, Hashimoto S, Humphrey M, Matthews T, Hunter JM, Reshmi S, Schultz M, Lee K, Pfau R, Cottrell C, McBride KL, Navin NE, Chaudhari BP, Leung ML. A Decade's Experience in Pediatric Chromosomal Microarray Reveals Distinct Characteristics Across Ordering Specialties. J Mol Diagn 24(9):1031-1040, 2022. e-Pub 2022. PMID: 35718094.
Wu, HJ, Temko, D, Maliga, Z, Moreira, AL, Sei, E, Minussi, DC, Dean, J, Lee, C, Xu, Q, Hochart, G, Jacobson, CA, Yapp, C, Schapiro, D, Sorger, PK, Seeley, EH, Navin, N, Downey, RJ, Michor, F. Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. Cell Genomics 2(8), 2022. e-Pub 2022. PMID: 36419822.
Wei R, He S, Bai S, Sei E, Hu M, Thompson A, Chen K, Krishnamurthy S, Navin NE. Spatial charting of single-cell transcriptomes in tissues. Nat Biotechnol 40(8):1190-1199, 2022. e-Pub 2022. PMID: 35314812.
Lips EH, Kumar T, Megalios A, Visser LL, Sheinman M, Fortunato A, Shah V, Hoogstraat M, Sei E, Mallo D, Roman-Escorza M, Ahmed AA, Xu M, van den Belt-Dusebout AW, Brugman W, Casasent AK, Clements K, Davies HR, Fu L, Grigoriadis A, Hardman TM, King LM, Krete M, Kristel P, de Maaker M, Maley CC, Marks JR, Menegaz BA, Mulder L, Nieboer F, Nowinski S, Pinder S, Quist J, Salinas-Souza C, Schaapveld M, Schmidt MK, Shaaban AM, Shami R, Sridharan M, Zhang J, Stobart H, Collyar D, Nik-Zainal S, Wessels LFA, Hwang ES, Navin NE, Futreal PA, PRECISION consortium GC, Thompson AM, Wesseling J, Sawyer EJ. Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer. Nat Genet 54(6):850-860, 2022. e-Pub 2022. PMID: 35681052.
Han H, Wang Y, Curto J, Gurrapu S, Laudato S, Rumandla A, Chakraborty G, Wang X, Chen H, Jiang Y, Kumar D, Caggiano EG, Capogiri M, Zhang B, Ji Y, Maity SN, Hu M, Bai S, Aparicio AM, Efstathiou E, Logothetis CJ, Navin N, Navone NM, Chen Y, Giancotti FG. Mesenchymal and stem-like prostate cancer linked to therapy-induced lineage plasticity and metastasis. Cell Rep 39(1):110595, 2022. e-Pub 2022. PMID: 35385726.
Johnson KC, Anderson KJ, Courtois ET, Gujar AD, Barthel FP, Varn FS, Luo D, Seignon M, Yi E, Kim H, Estecio MRH, Zhao D, Tang M, Navin NE, Maurya R, Ngan CY, Verburg N, de Witt Hamer PC, Bulsara K, Samuels ML, Das S, Robson P, Verhaak RGW. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet 53(10):1456-1468, 2021. e-Pub 2021. PMID: 34594038.
Wang K, Xiao Z, Yan Y, Ye R, Hu M, Bai S, Sei E, Qiao Y, Chen H, Lim B, Lin SH, Navin NE. Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility. Mol Cell 81(20):4319-4332, 2021. e-Pub 2021. PMID: 34686316.
Gao R, Bai S, Henderson YC, Lin Y, Schalck A, Yan Y, Kumar T, Hu M, Sei E, Davis A, Wang F, Shaitelman SF, Wang JR, Chen K, Moulder S, Lai SY, Navin NE. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat Biotechnol 39(5):599-608, 2021. e-Pub 2021. PMID: 33462507.
Minussi DC, Nicholson MD, Ye H, Davis A, Wang K, Baker T, Tarabichi M, Sei E, Du H, Rabbani M, Peng C, Hu M, Bai S, Lin YW, Schalck A, Multani A, Ma J, McDonald TO, Casasent A, Barrera A, Chen H, Lim B, Arun B, Meric-Bernstam F, Van Loo P, Michor F, Navin NE. Breast tumours maintain a reservoir of subclonal diversity during expansion. Nature 592(7853):302-308, 2021. e-Pub 2021. PMID: 33762732.
Wang F, Wang O, Mohanty V, Liang S, Dou J, Han J, Minussi DC, Gao R, Ding L, Navin N, Chen K. MEDALT: single-cell copy number lineage tracing enabling gene discovery. Genome Biol 70(22(1)):doi: 10.1186/s13059-021-02291-5, 2021. e-Pub 2021. PMID: 33622385.
Naffar-Abu Amara S, Kuiken HJ, Selfors LM, Butler T, Leung ML, Leung CT, Kuhn EP, Kolarova T, Hage C, Ganesh K, Panayiotou R, Foster R, Rueda BR, Aktipis A, Spellman P, Ince TA, Xiu J, Oberley M, Gatalica Z, Navin N, Mills GB, Bronson RT, Brugge JS. Transient commensal clonal interactions can drive tumor metastasis. Nat Commun 11(1):5799, 2020. e-Pub 2020. PMID: 33199705.
Morita K, Wang F, Jahn K, Hu T, Tanaka T, Sasaki Y, Kuipers J, Loghavi S, Wang SA, Yan Y, Furudate K, Matthews J, Little L, Gumbs C, Zhang J, Song X, Thompson E, Patel KP, Bueso-Ramos CE, DiNardo CD, Ravandi F, Jabbour E, Andreeff M, Cortes J, Bhalla K, Garcia-Manero G, Kantarjian H, Konopleva M, Nakada D, Navin N, Beerenwinkel N, Futreal PA, Takahashi K. Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics. Nat Commun 11(1):5327, 2020. e-Pub 2020. PMID: 33087716.
Malihi PD, Graf RP, Rodriguez A, Ramesh N, Lee J, Sutton R, Jiles R, Velasco CR, Sei E, Kolatkar A, Logothetis C, Navin NE, Corn P, Aparicio AM, Dittamore R, Hicks J, Kuhn P, Zurita AJ. Single-Cell Circulating Tumor Cell Analysis Reveals Genomic Instability as a Distinctive Feature of Aggressive Prostate Cancer. Clin Cancer Res 1(26(15)):4143-4153, 2020. e-Pub 2020. PMID: 32341031.
Manzo T, Prentice BM, Anderson KG, Raman A, Schalck A, Codreanu GS, Nava Lauson CB, Tiberti S, Raimondi A, Jones MA, Reyzer M, Bates BM, Spraggins JM, Patterson NH, McLean JA, Rai K, Tacchetti C, Tucci S, Wargo JA, Rodighiero S, Clise-Dwyer K, Sherrod SD, Kim M, Navin NE, Caprioli RM, Greenberg PD, Draetta G, Nezi L. Accumulation of long-chain fatty acids in the tumor microenvironment drives dysfunction in intrapancreatic CD8+ T cells. J Exp Med 217(8):e20191920, 2020. e-Pub 2020. PMID: 32491160.
Mallory XF, Edrisi M, Navin N, Nakhleh L. Methods for copy number aberration detection from single-cell DNA-sequencing data. Genome Biol 17(21(1)):208, 2020. e-Pub 2020. PMID: 32807205.
Ramesh N, Sei E, Tsai PC, Bai S, Zhao Y, Troncoso P, Corn PG, Logothetis C, Zurita AJ, Navin NE. Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing. Genome Biol 21(1):162, 2020. e-Pub 2020. PMID: 32631448.
Mallory XF, Edrisi M, Navin N, Nakhleh L. Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data. PLoS Comput Biol 16(7):e1008012, 2020. e-Pub 2020. PMID: 32658894.
Malihi PD, Graf RP, Rodriguez A, Ramesh N, Lee J, Sutton R, Jiles R, Ruiz Velasco C, Sei E, Kolatkar A, Logothetis C, Navin NE, Corn P, Aparicio AM, Dittamore R, Hicks J, Kuhn P, Zurita AJ. Single-cell circulating tumor cell analysis reveals genomic instability as a distinctive feature of aggressive prostate cancer. Clin Cancer Res. e-Pub 2020. PMID: 32341031.
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell 181(2):236-249, 2020. e-Pub 2020. PMID: 32302568.
Mitra A, Andrews MC, Roh W, De Macedo MP, Hudgens CW, Carapeto F, Singh S, Reuben A, Wang F, Mao X, Song X, Wani K, Tippen S, Ng KS, Schalck A, Sakellariou-Thompson DA, Chen E, Reddy SM, Spencer CN, Wiesnoski D, Little LD, Gumbs C, Cooper ZA, Burton EM, Hwu P, Davies MA, Zhang J, Bernatchez C, Navin N, Sharma P, Allison JP, Wargo JA, Yee C, Tetzlaff MT, Hwu WJ, Lazar AJ, Futreal PA. Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma. Nat Commun 11(1):1839, 2020. e-Pub 2020. PMID: 32296058.
Davis A, Gao R, Navin N. SCOPIT: sample size calculations for single-cell sequencing experiments. BMC Bioinformatics 20(1):566, 2019. e-Pub 2019. PMID: 31718533.
Zafar H, Navin N, Chen K, Nakhleh L. SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data. Genome Res(11):1847-1859, 2019. e-Pub 2019. PMID: 31628257.
Wang F, Liang S, Kumar T, Navin N, Chen K. SCMarker: Ab initio marker selection for single cell transcriptome profiling. PLoS Comput Biol 15(10):e1007445, 2019. e-Pub 2019. PMID: 31658262.
Corn PG, Heath EI, Zurita A, Ramesh N, Xiao L, Sei E, Li-Ning-Tapia E, Tu SM, Subudhi SK, Wang J, Wang X, Efstathiou E, Thompson TC, Troncoso P, Navin N, Logothetis CJ, Aparicio AM. Cabazitaxel plus carboplatin for the treatment of men with metastatic castration-resistant prostate cancers: a randomised, open-label, phase 1-2 trial. Lancet Oncol 20(10):1432-1443, 2019. e-Pub 2019. PMID: 31515154.
Zhang Y, Xiong S, Liu B, Pant V, Celii F, Chau G, Elizondo-Fraire AC, Yang P, You MJ, El-Naggar AK, Navin NE, Lozano G. Somatic Trp53 mutations differentially drive breast cancer and evolution of metastases. Nat Commun 9(1):3953, 2018. e-Pub 2018. PMID: 30262850.
Kim C & Gao R, Sei E, Brandt R, Hartman J, Hatshek T, Crosetto N, Foukakis T and Navin N. Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single Cell Sequencing. Cell 173(4):879-893, 2018. e-Pub 2018. PMID: 29681456.
Casasent AK, Schalck A, Gao R, Sei E, Long A, Pangburn W, Casasent T, Meric-Bernstam F, Edgerton ME, Navin NE. Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing. Cell 172(1-2):205-217, 2018. e-Pub 2018. PMID: 29307488.
Gausachs M, Borras E, Chang K, Gonzalez S, Azuara D, Delgado Amador A, Lopez-Doriga A, San Lucas FA, Sanjuan X, Paules MJ, Taggart MW, Davies GE, Ehli EA, Fowler J, Moreno V, Pineda M, You YN, Lynch PM, Lazaro C, Navin NE, Scheet PA, Hawk ET, Capella G, Vilar E. Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis. Clin Cancer Res 23(19):5936-5947, 2017. e-Pub 2017. PMID: 28645942.
Zafar H, Tzen A, Navin N, Chen K, Nakhleh L. SiFit: Inferring tumor trees from single-cell sequencing data under finite-sites models. Genome Bio 18(1):178, 2017. e-Pub 2017. PMID: 28927434.
Leung ML, Davis A, Gao R, Casasent A, Wang Y, Sei E, Vilar E, Maru D, Kopetz, Navin, N. Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer. Genome Res 27(8):1287-1299, 2017. e-Pub 2017. PMID: 28546418.
Gao R, Kim C, Sei E, Chan L, Srinivasan M, Zhang A, Meric-Bernstam F and Navin N. Nanogrid Single Nucleus RNA Sequencing Reveals Phenotypic Diversity in Breast Cancer. Nature Commun 8(1):228, 2017. e-Pub 2017. PMID: 28794488.
Casasent A, Edgerton M, Navin N. Genome evolution in ductal carcinoma in situ: invasion of the clones. J of Pathology 241(2):208-218, 2017. e-Pub 2017. PMID: 27861897.
Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV, Teichman SA. Single-Cell Analysis at the Threshold. Nature Biotech 34(11):1111-18, 2016. e-Pub 2016. PMID: 27824834.
Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat Genet 48(10):1119-30, 2016. e-Pub 2016. PMID: 27526321.
Mann KM, Newberg JY, Black MA, Jones DJ, Amaya-Manzanares F, Guzman-Rojas L, Kodama T, Ward JM, Rust AG, van der Weyden L, Yew CC, Waters JL, Leung ML, Rogers K, Rogers SM, McNoe LA, Selvanesan L, Navin N, Jenkins NA, Copeland NG, Mann MB. Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq. Nature Biotech 34(9):962-72, 2016. e-Pub 2016. PMID: 27479497.
Navin N, Chen K. Genotyping Tumor Clones from Single-Cell Data. Nature Methods 13(7):555-6, 2016. e-Pub 2016. PMID: 27355792.
Davis A, Navin N. Computing tumor trees from single cells. Genome Biology 17(1):113, 2016. e-Pub 2016. PMID: 27230879.
Zafar H, Wang Y, Nakhlem L, Navin N, Chen K. Monovar: Single Nucleotide Variant Detection in Single Cells. Nature Methods, 2016. e-Pub 2016. PMID: 27088313.
Leung ML, Wang Y, Kim C, Gao R, Jiang J, Sei E, Navin NE. Highly multiplexed targeted DNA sequencing from single nuclei. Nat Protoc 11(2):214-35, 2016. e-Pub 2016. PMID: 26741407.
Alizadeth A, Aranda V, Bardelli A, Blanpain C, Bocl C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel J, Lichter P, Mason C, Navin N, Pe'er D, Polyak K, Roberts C, Sio L, Snyder A, Stower H, Swanton C, Verhaak R, Zenklusen J, Zuber J, Zucman-Rossi J. Toward Understanding and Exploiting Tumor Heterogeneity. Nature Med 21(8):846-53, 2015. e-Pub 2015. PMID: 26248267.
Leung M, Wang Y, Waters J, Navin N. SNES: Single Nuclei Exome Sequencing. Genome Biol 25(16):55, 2015. e-Pub 2015. PMID: 25853327.
Molhatra A, Wang Y, Waters J, Hall I, Navin N. Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations. Genomic Med 7(1):6, 2015. e-Pub 2015. PMID: 25729435.
Wang Y, Waters J, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512(7513):155-60, 2014. e-Pub 2014. PMID: 25079324.
Chen K, Navin N, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, Mardis ER, Ley TJ, Perou CM, Wilson RK, Ding L. BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol 14(8):87, 2013. e-Pub 2013. PMID: 23972288.
Baslan T, Kendall J, Troge J, Stepansky A, Wigler M, Navin N, Hicks J. Genome-wide Copy Number Analysis of Single Cells. Nature Protocols 7(6):1024-41, 2012. e-Pub 2012. PMID: 22555242.
Russnes GH, Navin N, Hicks J, Borresen-Dale AL. Insight into the Heterogeneity of Breast Cancer through Next-Generation Sequencing. J Clin Invest 121(10):3810-8, 2011. e-Pub 2011. PMID: 21965338.
Chen M, Pratt CP, Zeeman ME, Schultz N, Taylor BS, O'Neill A, Castillo-Martin M, Nowak DG, Naguib A, Grace DM, Murn J, Navin N, Atwal GS, Sander C, Gerald WL, Cordon-Cardo C, Newton AC, Carver BS, Trotman LC. Identification of PHLPP1 as a Tumor Suppressor Reveals the Role of Feedback Activation in PTEN-Mutant Prostate Cancer Progression. Cancer Cell 20(2):173-86, 2011. e-Pub 2011. PMID: 21840483.
Navin N, Kendall J, Troge J, Rodgers L, Cook K, Stepansky A, Levy D, Lee Y, Esposito D, Muthuswamy L, Hicks J, Wigler M. Tumor Evolution Inferred by Single Cell Sequencing. Nature 7(472):90-4, 2011. e-Pub 2011. PMID: 21399628.
Navin N, Hicks, J. Tracing the Tumor Lineage. Mol Onc 4(3):267-283, 2010. e-Pub 2010. PMID: 20537601.
Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M. Inferring Tumor Progression from Genomic Heterogeneity. Genome Research(1):68-80, 2010. e-Pub 2010. PMID: 19903760.
Grubor V, Krasnitz A, Troge JE, Meth JL, Lakshmi B, Kendall JT, Yamrom B, Alex G, Pai D, Navin N, Hufnagel LA, Lee YH, Cook K, Allen SL, Rai KR, Damle RN, Calissano C, Chiorazzi N, Wigler M, Esposito D. Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood 113(6):1294-303, 2009. e-Pub 2009. PMID: 18922857.
Pelham RJ, Rodgers L, Hall I, Lucito R, Nguyen KC, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D. Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci U S A 103(52):19848-53, 2006. e-Pub 2006. PMID: 17167050.
Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Børresen-Dale AL, Naume B, Schlicting E, Norton L, Hägerström T, Skoog L, Auer G, Månér S, Lundin P, Zetterberg A. Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 16(12):1465-79, 2006. e-Pub 2006. PMID: 17142309.
Navin N, Grubor V, Hicks J, Leibu E, Thomas E, Troge J, Riggs M, Lundin P, Månér S, Sebat J, Zetterberg A, Wigler M. PROBER: oligonucleotide FISH probe design software. Bioinformatics 22(19):2437-8, 2006. e-Pub 2006. PMID: 16740623.
Hicks J, Muthuswamy L, Krasnitz A, Navin N, Riggs M, Grubor V, Esposito D, Alexander J, Troge J, Wigler M, Maner S, Lundin P, Zetterberg A. High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. Cold Spring Harb Symp Quant Biol 70:51-63, 2005. e-Pub 2005. PMID: 16869738.
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Månér S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. Large-scale copy number polymorphism in the human genome. Science 305(5683):525-8, 2004. e-Pub 2004. PMID: 15273396.
Thomas EE, Srebro N, Sebat J, Navin N, Healy J, Mishra B, Wigler M. Distribution of short paired duplications in mammalian genomes. Proc Natl Acad Sci U S A 101(28):10349-54, 2004. e-Pub 2004. PMID: 15240876.
Espanel X, Navin N, Kato Y, Tanokura M, Sudol M. Probing WW Domains to Uncover and Refine Determinants of Specificity in Ligand Recognition. Cytotechnology 43(1-3):105-11, 2003. e-Pub 2003. PMID: 19003214.
Komuro A, Nagai M, Navin NE, Sudol M. WW domain-containing protein YAP associates with ErbB-4 and acts as a co-transcriptional activator for the carboxyl-terminal fragment of ErbB-4 that translocates to the nucleus. J Biol Chem 278(35):33334-41, 2003. e-Pub 2003. PMID: 12807903.

Invited Articles

Schalck A, Bernatchez C, Navin N. Resident Breast T Cells: The Troops Are Already There. Trends Mol Med 10:821-822, 2018. e-Pub 2018. PMID: 30077643.
Davis A, Gao R, Navin N. Tumor evolution: Linear, branched, punctuated or neutral?. BBA Cancer(2):151-161, 2017. e-Pub 2017. PMID: 28110020.
Navin N. The first five years of single-cell cancer genomics and beyond. Genome Res 25(10):1499-507, 2015. e-Pub 2015. PMID: 26430160.
Navin N. Delineating cancer evolution with single-cell sequencing. Science Trans Med 15(7):296, 2015. e-Pub 2015. PMID: 26180099.
Wang Y, Navin N. Advances and Applications of Single-Cell Sequencing Technologies. Molecular Cell 58(4):598-609, 2015. e-Pub 2015. PMID: 26000845.
Navin N. Tumor evolution in response to chemotherapy: phenotype versus genotype. Cell Reports 6(3):417-9, 2015. e-Pub 2015. PMID: 24529750.
Navin N. Cancer Genomics: One Cell at a Time. Genome Biol 15(452), 2014. e-Pub 2014. PMID: 25222669.
Blake PM, Decker DA, Glennon TM, Liang YM, Losko S, Navin N, Suh KS. Toward an integrated knowledge environment to support modern oncology. Cancer J 17(4):257-63, 2011. e-Pub 2011. PMID: 21799334.
Navin N, Hicks J. Future Medical Applications of Single-Cell Sequencing in Cancer. Genome Medicine 3(5):31, 2011. e-Pub 2011. PMID: 21631906.

Review Articles

Casasent AK, Almekinders MM, Mulder C, Bhattacharjee P, Collyar D, Thompson AM, Jonkers J, Lips EH, van Rheenen J, Hwang ES, Nik-Zainal S, Navin NE, Wesseling J, PRECISION Consortium GC. Learning to distinguish progressive and non-progressive ductal carcinoma in situ. Nat Rev Cancer 22(12):663-678, 2022. e-Pub 2022. PMID: 36261705.
Lim B, Lin Y, Navin N. Advancing Cancer Research and Medicine with Single Cell Genomics. Cancer Cell 37(4):456-470, 2020. e-Pub 2020. PMID: 32289270.

Patents

Varietal Counting of Nucleic Acids for Obtaining Genomic Copy Number Information. Patent Number: US20140065609A1.
Methods and applications for cell barcoding. Patent Number: UTSC.P1153US.P1.

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CV information above last modified July 22, 2026

Nicholas Navin, Ph.D.

About Dr. Nicholas Navin

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