Research

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

Professor & Chair

Emi Sei

Research Group Leader

Shanshan Bai

Supv, Laboratory & Research

Kaile Wang

Instructor

Tuan Tran

Research Laboratory Manager

Jerome Lin

Computational Scientist

Jianzhuo Li

Research Investigator

Min Hu

Sr Computational Scientist

Anna K. Casasent

Computational Scientist

Mitchell Rao

Computational Scientist

Zhenna Xiao

Postdoctoral Fellow

Runmin Wei

Postdoctoral Fellow

Yuehui Zhao

Postdoctoral Fellow

Nicolaas Baudoin

Postdoctoral Fellow

Rachel Dittmar

Postdoctoral Fellow

Aatish Thennavan

Postdoctoral Fellow

Ryan Mulqueen

Postdoctoral Fellow

Andres Nevarez

Postdoctoral Fellow

Haijing Jin

Postdoctoral Fellow

Jake Leighton

Graduate Student

Rui Ye

Graduate Student

Yun Yan

Graduate Student

Hanghui Ye

Graduate Student

Jie Ye

Graduate Student

Yiyun Lin

Graduate Student

Siyuan He

Graduate Student

Junke (Kris) Wang

Graduate Student

Ping Xu

Graduate Student

Lei Yang

Graduate Student

Heba Elgamal

Masters Student

ALUMNI

Yong Wang, Ph.D, Senior Postdoctoral Fellow
Ruli Gao, Ph.D, Senior Postdoctoral Fellow
Charissa Kim, MD / Ph.D. Student
Naveen Ramesh, Ph.D Student
Marco Leung, Ph.D. Student
Alexander Davis, Ph.D. Student
Alexander Davis, Ph.D. Student
Aislyn Shalck, Ph.D. Student
Darlan Minussi, Ph.D. Student
Tapsi Kumar, Ph.D. Student
Yuwei Lin, Masters Student
Mashiat Rabbani, Masters Student
Haowei Du, Masters Student
Cheng Peng, Masters Student

Pictures

Selected publications

Breast tumours maintain a reservoir of subclonal diversity during expansion

Nature
  • Darlan C. Minussi
  • Michael D. Nicholson
  • Hanghui Ye
  • Alexander Davis
  • Kaile Wang
  • Toby Baker
  • Maxime Tarabich
  • Emi Sei
  • Haowei Du
  • Mashiat Rabbani
  • Cheng Peng
  • Min Hu
  • Shanshan Bai
  • Yu-wei Lin
  • Aislyn Schalck
  • ...
  • Nicholas Navin
2021Mar

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

Cell
  • Charissa Kim
  • Ruli Gao
  • Emi Sei
  • Rachel Brandt
  • Johan Hartman
  • Thomas Hatschek
  • Nicola Crosetto
  • Theodoros Foukakis
  • Nicholas Navin
2018Apr

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

Cell
  • Anna K. Casasent
  • Ruli Gao
  • Emi Sei
  • William Pangburn
  • Tod Casasent
  • Anna K. Casasent
  • FundaMeric Bernstam
  • Mary E.Edgerton
  • Nicholas Navin
2018Jan

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 Navin
2016Oct

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

Nature
  • 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 Navin
2014Jul

Lab News

Code

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

Spatial charting of single-cell transcriptomes in tissues  (Nature Biotechnology)

  • Runmin Wei
  • Siyuan He
  • Shanshan Bai
  • Emi Sei
  • Min Hu
  • Alastair Thompson
  • Ken Chen
  • Savitri Krishnamurthy
  • Nicholas Navin
2022Mar

CopyKat: Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes  (Nature Biotechnology)

  • Ruli Gao
  • Bai Shanshan
  • Ying C. Henderson
  • Yiyun Lin
  • Aislyn Schalck
  • Yun Yan
  • Tapsi Kumar
  • Min Hu
  • Emi Sei
  • ...
  • Nicholas Navin
2021JAN

SCOPIT: sample size calculations for single-cell sequencing experiments  (BMC Bioinformatics)

Weblink
  • Alexander Davis
  • Ruli Gao
  • Nicholas Navin
2019Nov

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
2017May

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

  • Hamim Zafar
  • Yong Wang
  • Luay Nakhleh
  • Nicholas Navin
  • Ken Chen
2016Jun

Videos

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

‘Nicholas Navin answers: How are multi-omics approaches helping us decipher human cancer biology?'.

‘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 Senior Research Assistant that will work on the processing human tissue samples and prepare them for various single cell sequencing library preparations (10x Genomics), including DNA, RNA and ATAC data. Please see the description for more details.

Requirements: BS in natural sciences or related field with 3+ years experience.

Preferred: MS or Ph.D. in natural sciences or related field with experience in NGS, qPCR, PCR and tissue culture experience.

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

Contact Us

Nicholas Navin, Professor

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

nnavin (at) mdanderson.org