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 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.

Single Cell Genomics

Cancer Evolution

Liquid Biopsy Genomics

Computational Biology

The Team

Nicholas Navin

Principal Investigator

Emi Sei

Research Laboratory Manager

Ruli Gao

Senior Postdoctoral Fellow

Kaile Wang

Postdoctoral Fellow

Shanshan Bai

Sr. Research Assistant

Min Hu

Sr. Research Assistant

Alexander Davis

Graduate Student

Naveen Ramesh

Graduate Student

Aislyn Schalck

Graduate Student

Darlan Minussi

Graduate Student

Tapsi Kumar

Graduate Student

Jake Leighton

Graduate Student

Adnan Elhammali

Resident physician

Rui Ye

Graduate Student

Mashiat Rabbani

Master Student


Jill Waters, Laboratory Coordinator
Yong Wang, Ph.D, Senior Postdoctoral Fellow
Charissa Kim, MD / Ph.D. Student
Anna Unruh, Ph.D Student
Marco Leung, Ph.D. Student
Pei-Ching Tsai, Senior Research Assistant
Xiuqing Shi, M.D, Graduate Student
Antonio Giordano, MD, Ph.D Student
Jerry Jiang, Undergraduate Student
Jose Acevedo, Undergraduate Student
Rachael Brandt, Undergraduate Student
Jonathan Chen, Undergraduate Student
Annalyssa Long, Research Assistant
Will Pangburn, Undergraduate Student
Hossein Bakhshandeh, Undergraduate Student
Zuhal Oczan, Graduate Rotation Student
Haowei Du, Masters Student
Cheng Peng, Masters Student


Selected publications

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

  • Charissa Kim
  • Ruli Gao
  • Emi Sei
  • Rachel Brandt
  • Johan Hartman
  • Thomas Hatschek
  • Nicola Crosetto
  • Theodoros Foukakis
  • Nicholas E. Navin

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

  • Anna K. Casasent
  • Ruli Gao
  • Emi Sei
  • William Pangburn
  • Tod Casasent
  • Anna K. Casasent
  • FundaMeric Bernstam
  • Mary E.Edgerton
  • Nicholas E. Navin

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

Nature Genetics
  • Ruli Gao
  • Alexander Davis
  • Thomas O McDonald
  • Emi Sei
  • Xiuqing Shi
  • Yong Wang
  • Anna Casasent
  • Jill Waters
  • Hong Zhang
  • Franziska Michor
  • Nicholas E. Navin

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

  • Yong Wang
  • Jill Waters
  • Marco L. Leung
  • Anna Unruh
  • Whijae Roh
  • Xiuqing Shi
  • Ken Chen
  • Paul Scheet
  • Selina Vattathil
  • Han Liang
  • Hong Zhang
  • Rui Zhao
  • Franziska Michor
  • Funda Meric-Bernstam
  • Nicholas E. Navin

Lab News


We strive to develop innovative, well-tested, and well-documented tools for genome research.

SCOPIT: An interactive web tool for estimating the number of cells to sequence  (Preprint)

  • Alexander Davis
  • Ruli Gao
  • Nicholas Navin

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models   (Genome Biology)

  • Hamim Zafar
  • YAnthony Tzen
  • Nicholas Navin
  • Ken Chen
  • Luay Nakhleh

Monovar: single nucleotide variant detection in single cells  (Nature methods)

  • Hamim Zafar
  • Yong Wang
  • Luay Nakhleh
  • Nicholas Navin
  • Ken Chen


Meet Dr. Navin and his research program in single cell cancer genomics.

‘Sequencing the Single Cancer Cell’ (2015) ‘Adventures in Genomics’.

‘Sequencing the Single Cell’ (2015) ‘Adventures in Genomics’.

Funding support

We are very grateful for your generous funding support

We seek a talented individual with a strong background in computational biology, data science or bioinformatics. This individual will develop methods to analyze large-scale single cell sequencing datasets to understand cancer evolution. The ideal candidate will have experience in Unix/Linux, scripting languages (Perl, Python), statistical languages (R, Matlab) and experience with next-generation sequencing data analysis.

Requirements: Ph.D. in Bioinformatics, Computational Biology, Biostatistics or Data Science

The Navin laboratory has an open position for a postdoctoral fellow in cancer biology in the department of Genetics at the MD Anderson Cancer Center in Houston, TX.  We seek a talented individual with a strong background in experimental molecular biology and cancer biology techniques. This individual will work on projects that use single cell DNA and RNA sequencing to study cancer evolution, including invasion, metastasis or therapeutic resistance.  The ideal candidate will have strong scientific writing skills, experience in genomics and computational biology.

Requirements: Ph.D. in Molecular Biology, Genomics or Cancer Biology

The CPRIT Single Cell Genomics Center and Navin laboratory are seeking a data scientist/manager that will work on the processing and analysis of single cell sequencing dataset, including DNA, RNA and ATAC data. please see the description for more details.

Requirements: MS or Ph.D. in computer science, bioinformatics or data science


To apply please send a CV and cover letter to Nicholas Navin at 'nnavin' (at) mdanderson (dot) org.

Contact Us

Nicholas Navin, Associate Professor

Department of Genetics
The University of Texas MD Anderson Cancer Center
6767 Bertner Ave. Room BSRB S15.8412
Houston, Tx, 77030

nnavin (at)