Meet Nicholas Navin, Ph.D.
Nicholas Navin, Ph.D.
Department of Genetics, Division of Basic Sciences
About Dr. Navin
Dr. Navin is an Associate 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
Present Title & Affiliation
Primary Appointment
Associate Professor, Department of Genetics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX
Director, CPRIT Single Cell Genomics Center, Department of Genetics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX
Co-Director, Advanced Technology Genomics Core, Department of Genetics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX
Dual/Joint/Adjunct Appointment
Associate Professor, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Associate Professor, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX
Research Interests
Single Cell Genomics; Cancer Evolution; Liquid Biopsy Genomics; Computational Biology
Our group has pioneered the development of single cell genome sequencing technologies, which we apply to understand complex biological processes in human cancers, including tumor initiation, invasion, metastasis and therapeutic resistance. We study cancer as an evolutionary process in which clones undergo selection and expansion in response to selective pressures. We understand the tumor as a complex ecosystem which is maintained by intricate interactions between the tumor cells and stromal cell types. Our mission is to gain new knowledge of cancer evolution that can be exploited to improve the quality of life and decrease morbidity in cancer patients. At MD Anderson we are uniquely positioned to translate our genomic technologies into the clinic, where they are poised to make a major impact on early detection, diagnostics and therapeutic strategies in cancer patients.
Visit Dr. Navin's Lab Website. View a complete list of Dr. Navin's publications. Dr. Navin - Google Scholar
Education & Training
Degree-Granting Education
| 2010 | Cold Spring Harbor Laboratory and Stony Brook University, Cold Spring Harbor, NY, USA, PHD, Molecular Genetics |
| 2003 | Skidmore College, Saratoga Springs, NY, USA, BS, Cell Biology |
Postgraduate Training
| 2010-2011 | Postdoctoral Fellow, Cancer Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY |
Experience & Service
Academic Appointments
Assistant Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 2011 - 2016
Assistant Professor, Department of Genetics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 2011 - 2016
Assistant Professor, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 2011 - 2016
Honors & Awards
| 2021 | 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 | Faculty Educator Award, University of Texas M.D. Anderson Cancer Center |
| 2018 | The Dallas/Fort Worth Living Legend Faculty Achievement Award in Basic Research, University of Texas M.D. Anderson Cancer Center |
| 2017 | Jack and Beverly Randall Prize for Excellence in Cancer Treatment, Randall Family Foundation |
| 2017 | Challenge Award, Prostate Cancer Foundation |
| 2017 | 40 under 40 Award, Stoney Brook University |
| 2016 | President's Scholar Award, University of Texas M.D. Anderson Cancer Center |
| 2016 | Sabin Fellowship, Andrew Sabin Family Foundation |
| 2016 | ACS Research Scholar, American Cancer Society (ACS) |
| 2016 | President's Recognition for Faculty Excellence, University of Texas M.D. Anderson Cancer Center |
| 2016 | Faculty Scholar Award, 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 | T.C. Hsu Award, Young Investigator Award |
| 2013 | Wilson S. Stone Memorial Award |
| 2013 | Damon-Runyon Innovator Award, Damon-Runyon Rachleff Foundation |
| 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 |
Selected Publications
Peer-Reviewed Articles
- 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. 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. 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. PMID: 33087716.
- 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. 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. PMID: 32807205.
- 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. PMID: 32341031.
- 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. PMID: 32658894.
- Lim B, Lin Y, Navin N. Advancing Cancer Research and Medicine with Single Cell Genomics. Cancer Cell 37(4):456-470, 2020. PMID: 32289270.
- 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. PMID: 32296058.
- 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. PMID: 32302568.
- Davis A, Gao R, Navin N. SCOPIT: sample size calculations for single-cell sequencing experiments. BMC Bioinformatics 20(1):566, 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. 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. 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. 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. 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. PMID: 29307488.
- 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. PMID: 28546418.
- 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. PMID: 27479497.
- Zafar H, Wang Y, Nakhlem L, Navin N, Chen K. Monovar: Single Nucleotide Variant Detection in Single Cells. Nature Methods, 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.
- Leung M, Wang Y, Waters J, Navin N. SNES: Single Nuclei Exome Sequencing. Genome Biol 25(16):55, 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. 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. PMID: 25079324.
- 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. PMID: 22555242.
- 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. PMID: 21399628.
- 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. e-Pub 2021. PMID: 33462507.
- 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.
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.
- Wang Y, Navin N. Advances and Applications of Single-Cell Sequencing Technologies. Molecular Cell 58(4):598-609, 2015. PMID: 26000845.
Grant & Contract Support
| Title: | Investigating Chemoresistance Evolution in TNBC Breast Cancer Patients with Single Cell Sequencing |
| Funding Source: | Lefkofsky Foundation |
| Role: | Principal Investigator |
| Title: | Investigating Mutational Evolution and Intratumor Heterogeneity in TNBC |
| Funding Source: | American Cancer Society (ACS) |
| Role: | Principal Investigator |
| Title: | Integrated Single Cell Genomics Core Facility |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Principal Investigator |
| Title: | Characterizing cancer genome instability and translational impact using new sequencing technologies |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-Investigator |
| Title: | Omic and Multidimensional Spatial Atlas of Metastatic Breast and Prostate Cancers (OMS Atlas) |
| Funding Source: | NIH/NCI |
| Role: | Co-Investigator |
| Title: | Investigating Tumor Initiation and Invasion in Premalignant Breast Cancer with Spatial Single Cell Genomics |
| Funding Source: | NIH/NCI |
| Role: | Principal Investigator |
| Title: | Delineating the Evolution and Ecology of Chemoresistance in Breast Cancer with Single Cell Genomics |
| Funding Source: | NIH/NCI |
| Role: | Principal Investigator |
| Title: | Human Breast Cell Atlas Seed Network |
| Funding Source: | Chan Zuckerberg Initiative |
| Role: | Principal Investigator |
| Title: | Spatial-omic Analysis of Therapeutic Resistance in Metastatic Breast Cancer patients |
| Funding Source: | NIH/NCI |
| Role: | Co-Investigator |
| 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: | Principal Investigator |
| Title: | Translating Intestinal Radioprotection by EGLN Inhibition to Improve Clinical Outcomes in Unresectable Pancreatic Cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-Investigator |
| Title: | AML/MDS Moon Shot |
| Funding Source: | UTMDACC Moon Shot Program |
| Role: | Co-Investigator |
| Title: | Prostate Cancer Moon Shot |
| Funding Source: | UTMDACC Moon Shot Program |
| Role: | Co-Investigator |
| Title: | Breast Cancer Moon Shot |
| Funding Source: | UTMDACC Moon Shot Program |
| Role: | Co-Investigator |
| Title: | LC170171 Tumor heterogeneity and therapeutic resistance in small cell lung cancer (SCLC) |
| Funding Source: | Department of Defense (DOD) |
| Role: | Co-Investigator |
| Title: | Prevent Ductal Carcinoma in Situ Invasive Overtreatment Now – PRECISION |
| Funding Source: | Cancer Research UK |
| Role: | Co-Investigator |