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

Tuan Tran

Research Laboratory Manager

Jerome Lin

Computational Scientist

Heba Elgamal

Senior Research Assistant

Jianzhuo Li

Research Scientist

Mitchell Rao

Computational Scientist

Chenling Tang

Computational Scientist

Zhenna Xiao

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

Rui Ye

Postdoctoral Fellow

Sidi Zhao

Postdoctoral Fellow

Yun Yan

Graduate Student

Jie Ye

Graduate Student

Siyuan He

Graduate Student

Junke (Kris) Wang

Graduate Student

Ping Xu

Graduate Student

Lei Yang

Graduate Student

Mariam Mosaad

Graduate Student

Reem Elghaish

Graduate Student

Chante Bethell

Graduate Student

ALUMNI

Yiyun Lin, Ph.D. Student
Hanghui Ye, Ph.D. Student
Darlan Minussi, Ph.D. Student
Tapsi Kumar, Ph.D. Student
Jake Leighton, Ph.D. Student
Aislyn Shalck, Ph.D. Student
Naveen Ramesh, Ph.D Student
Alexander Davis, Ph.D. Student
Charissa Kim, M.D. / Ph.D. Student
Marco Leung, Ph.D. Student
Kaile Wang, Ph.D., Research Assistant Professor
Anna K. Casasent, Ph.D., Senior Computational Scientist
Runmin Wei, Ph.D., Senior Postdoctoral Fellow
Yuehui Zhao, Ph.D., Senior Postdoctoral Fellow
Yong Wang, Ph.D., Senior Postdoctoral Fellow
Ruli Gao, Ph.D., Senior Postdoctoral Fellow
Yuwei Lin, Masters Student
Mashiat Rabbani, Masters Student
Haowei Du, Masters Student
Cheng Peng, Masters Student

Pictures

Selected publications

Normal breast tissues harbour rare populations of aneuploid epithelial cells

Nature
  • Yiyun Lin
  • Junke Wang
  • Kaile Wang
  • Shanshan Bai
  • Aatish Thennavan
  • Runmin Wei
  • Yun Yan
  • Jianzhuo Li
  • Heba Elgamal
  • Emi Sei
  • ...
  • Nicholas Navin
2024Nov

Archival single-cell genomics reveals persistent subclones during DCIS progression

Cell
  • Kaile Wang
  • Tapsi Kumar
  • Junke Wang
  • Darlan Conterno Minussi
  • Emi Sei
  • Jianzhuo Li
  • Tuan M. Tran
  • Aatish Thennavan
  • Min Hu
  • Anna K. Casasent
  • Zhenna Xiao
  • Shanshan Bai
  • Lei Yang
  • ...
  • Nicholas Navin
2023Aug

A spatially resolved single-cell genomic atlas of the adult human breast

Nature
  • Tapsi Kumar
  • Kevin Nee
  • Runmin Wei
  • Siyuan He
  • Quy H. Nguyen
  • Shanshan Bai
  • Kerrigan Blake
  • Maren Pein
  • Yanwen Gong
  • ...
  • Devon A. Lawson
  • Kai Kessenbrock
  • Nicholas Navin
2023Jun

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

Lab News

Code

Resolving clonal substructure from single cell genomic data using CopyKit  (Preprint)

  • Darlan Conterno Minussi
  • Alexander Davis
  • Junke Wang
  • ...
  • Nicholas Navin
2022Mar

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

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 Systems Biology
The University of Texas MD Anderson Cancer Center
1664 Moursund Street, Zayed Building 10th floor
Houston, Tx, 77030

nnavin (at) mdanderson.org