Kevin White Lab

Kevin White

James and Karen Frank Professor
Department of Human Genetics
Director, Institute for Genomics and Systems Biology
The University of Chicago

The Institute for Genomics and Systems Biology
The University of Chicago
900 East 57th Street
KCBD 10100A
Chicago, IL 60637

Phone: (773) 834-0074

About the Lab

The White lab studies the coordinated action of networks of genes that control developmental, disease and evolutionary processes. We have particular focus on discovery of genetic factors that contribute to cancer development and progression, and on building genome-wide models of transcriptional networks. We use an integrated approach that makes use of genome and transcriptome sequencing, large-scale protein-protein and protein-DNA interaction analyses, measurement of chromatin state, systematic RNAi and CRISPR mutational analysis, and high throughput functional analyses of genomic regulatory elements. By applying our methods to both closely and distantly related species, we are investigating how conserved molecular networks control basic developmental processes and how variation in molecular networks translates into variation in organismal phenotypes. We are also particularly interested in the transcriptional networks controlled by nuclear receptor proteins in development and disease. For example, we have produced genome-wide maps of the entire repertoire of nuclear receptors expressed in breast cancer cells, and this has led to the discovery of previously untargeted nuclear receptors that are promising drug candidates. We then test such candidates in mouse models, and we are attempting to ‘reverse engineer’ the nuclear receptor regulatory networks in breast cancer using a combination of genome-scale data generation, computational techniques and genomic engineering of cell lines and mice. We also have recently built novel algorithms for discovering tumor drivers and tumor risk factors from large-scale sequencing data, such as those available from The Cancer Genome Atlas. In those projects we have identified significantly co-occurring mutations and tested for genetic interactions in cell lines and in patient survival data, we have identified dozens of novel fusion genes and then synthesized them for testing in cell and mouse models, and we have systematically identified germline variants that may contribute to cancer risk and tested their functional roles using CRISPR engineered cell models.  Another focus of the lab is studying genetic regulatory programs that are highly conserved between fly and human. This has led to discoveries such as a role for the protein SPOP in both Drosophila embryogenesis and human kidney cancer, and to the identification of conserved targets of natural selection during adaptation to hypoxia (low oxygen) in both flies and humans. Related to this comparative work is our lab’s contributions to the ENCODE and modENCODE projects, where we have been systematically comparing the binding patterns of transcription factors genome-wide in flies, worms and humans. Our lab also contributes to the NIH GTEx and psychENCODE projects through our investigations of the relationship between genomic variation and variation in transcript and protein expression. Finally, we have recently embarked on an ambitious project in pancreatic cancer to co-analyze large numbers of tumor genomes, tens of thousands of electronic medical records, and literature databases to build predictive models of which patients might respond to which treatments. This work is facilitated by the use of patient-derived xenograft models, as well as mouse models developed using the CRISPR Cas9 system. Our goal is to develop algorithmic approaches to rapidly assess a tumor’s genomic and physiological state, then test drugs in mouse models that ultimately can be moved into patients.

Selected Papers

Rhee DY, et al. Transcription Factor Networks in Drosophila melanogaster
Cell Rep. 2014 Sep 17. [Epub ahead of print]
PMID: 25242320

Boyle AP, et al. Comparative analysis of regulatory information and circuits across distant species
Nature. 2014 Aug 28
PMID: 25164757

Hause RJ, et al. Identification and validation of genetic variants that influence transcription factor and cell signaling protein levels
Am J Hum Genet. 2014 Aug 7. Epub 2014 Jul 31.
PMID: 25087611

Seiwert TY, et al. Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas
Clin Cancer Res. 2014 Jul 23. [Epub ahead of print]
PMID: 25056374

Oh H, et al. Yorkie promotes transcription by recruiting a histone methyltransferase complex
Cell Rep. 2014 Jul 24. Epub 2014 Jul 10.
PMID: 25017066


Slattery M, et al. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
Genome Res. 2014 Jul
PMID: 24985916


Arthur RK, et al. Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification
Genome Res. 2014 Jul
PMID: 24985914


McNerney ME, et al. The spectrum of somatic mutations in high-risk acute myeloid leukaemia with -7/del(7q)
Br J Haematol. 2014 Aug. Epub 2014 Jun 13.
PMID: 24931631


VanderWeele DJ, et al. Low-grade prostate cancer diverges early from high grade and metastatic disease
Cancer Sci. 2014 Aug
PMID: 24890684

Lab Members

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A
Padma M. Akella

Padma M. Akella

Programmer,
Bioinformatician
(773) 834-7359
Noah Alexander

Noah Alexander

Alumni,
Undergraduate Student - Biological Sciences
(917) 628-4560
Rob Arthur

Rob Arthur

PhD Student,
Department of Ecology and Evolution
B
Chaitanya Bandlamudi

Chaitanya Bandlamudi

PhD Student,
Kevin White Laboratory
(773) 834-0074
Sam Bettis

Sam Bettis

Staff, CSC, Technical Director,
Cellular Screening Center
(773) 256-9772
Raj Bhanvadia

Raj Bhanvadia

Alumni,
Research Technician, Kevin White Laboratory
773-834-0074
Michael Bolt, Ph.D.

Michael Bolt, Ph.D.


Postdoctoral Scholar
Kevin White Lab
(713) 876-3484
Christopher Brown

Christopher Brown

Alumni,
Lily-LSRF Postdoctoral Fellow
(773) 834 0074
C
Alina Choudhury

Alina Choudhury

Alumni,
Research Technician, Kevin White Laboratory
(773) 834-0074
Alex Crofts

Alex Crofts

Alumni, Research Technician,
Previous Affiliation: Research Technician, Kevin White Laboratory
Current Affiliation: Graduate Student, University of Texas-Austin
(773) 834-0074
D
Ruby Dhar

Ruby Dhar

Alumni,
Research Associate
Assistant Professor
(773) 834 0074
Adam Didier

Adam Didier

Staff, HGAC,
High-througput Genomic Analysis Core
Erin Dybdahl

Erin Dybdahl

Alumni,
High-througput Genomic Analysis Core
773-834-0074
E
Sarah El Mouatassim Bih

Sarah El Mouatassim Bih

Alumni,
Research Technician, Kevin White Laboratory
(773) 834-0074
F
Elise Fletcher

Elise Fletcher

Alumni, Staff, CSC,
Cellular Screening Center
G
Jeff Gersch

Jeff Gersch

Research Technician,
Research Technician, Staff
(773) 834-0074
Jason Grundstad

Jason Grundstad

Programmer,
Senior Programmer, Kevin White Laboratory
(773) 834-0074
Tongjun Gu

Tongjun Gu


Postdoc
(773) 834-0074

Charles Guo

Alumni, Student,
Undergraduate Student
773-834-7359
J
Aashish Jha

Aashish Jha

IGSB, PhD Student,
Kevin White Laboratory
773.669.6744
Zifeng Jiang

Zifeng Jiang

Alumni, Staff,
Previous Affiliation: Research Professional, Kevin White Laboratory
Current Affiliation: Research Professional, Department of Pathology, The University of Chicago
(773) 834-0074
K
Madhura Kadaba

Madhura Kadaba

Alumni, Research Technician,
Recombineering Technician, Genome Engineering Core
773-834-0074
Subhradip Karmakar

Subhradip Karmakar

Alumni, Staff,
Research Associate Professional
(773) 834-0074
Aly Azeem Khan

Aly Azeem Khan

Postdoc,
Chicago Center for Systems Biology
773-834-0074
Matthew Kirkey

Matthew Kirkey

Research Technician,
Research Technician, Kevin White Laboratory
(773) 834-0074
Mike Kreiser

Mike Kreiser

Lab Technician,
Kevin White Laboratory
773-834-0074
L

Pei-Chun Lin

Postdoc,
Kevin White Laboratory
(773) 834-0074
Yuwen Liu

Yuwen Liu

PhD Student,
DRSB, Kevin White Laboratory
(773) 834-0074
M
Lijia Ma

Lijia Ma

Postdoc,
Kevin White Laboratory
(773) 834-0074
Matt Milton

Matt Milton

Research Technician,
Kevin White Laboratory
(773) 834-0074
Jennifer Moran

Jennifer Moran

Scientific Director, Staff, BRC,
Bac-Recombineering Core
773-834-0074
Erin Mowers

Erin Mowers

Alumni,
Medical Scientist Training Program
773-834-0074
N
Xiaochun Ni

Xiaochun Ni

Alumni,
Kevin White Laboratory
Current Affiliation: Postdoc, Harvard Medical School
(773) 834-0074
Dmitri Novikov

Dmitri Novikov

Alumni,
Director, Advanced Imaging Core (AIC)
(773) 834-0074
P
Elisha Pendleton

Elisha Pendleton

Research Technician,
Kevin White Laboratory
(773) 834-0074
April Peterson

April Peterson

Alumni, Research Technician,
Kevin White Laboratory
(773) 834-0074
Jason J. Pitt

Jason J. Pitt

PhD Student,
Kevin White Laboratory
773-834-0074
R
Edward (Jay) Rehm

Edward (Jay) Rehm

Alumni, Research Manager,
Kevin White Laboratory
(773) 702-7378
S
Heather Scott

Heather Scott

Research Technician,
Research Technician, Kevin White Laboratory
(773) 834-0074
Matt Slattery

Matt Slattery

Alumni, Postdoc,
Previous Affiliation: Kevin White Laboratory
Current Affiliation: Assistant Professor, University of Minnesota-Duluth
(773) 834-0074
Rebecca Spokony

Rebecca Spokony

Alumni, Postdoc,
Previous Afffiliation: Kevin White Laboratory
Current Affiliation: Assistant Professor, CUNY
(773) 834-0074
Thomas Stricker

Thomas Stricker

Alumni,
Previous Affiliation: Instructor, Department of Pathology
Current Affiliation: Assistant Professor, Vanderbilt
(773) 834-0074
T
David Toffey

David Toffey

Lab Technician,
Kevin White Laboratory
773-834-0074
V
David Vanderweele

David Vanderweele


Instructor, Department of Medicine, Section of Hematology/Oncology
(773) 834-0074
Alec Victorsen

Alec Victorsen

Staff,
Kevin White Laboratory
(773) 834-0074
W
Xiaoyue Wang

Xiaoyue Wang

Alumni, Postdoc,
Previous Affiliation: Kevin White Laboratory
Current Affiliation: Assistant Professor, Peking Union Medical College, China (March 2014)
(773) 834-0074
Kevin White

Kevin White

IGSB, Core Member, Sr. Fellow,
Director, Institute for Genomics & Systems Biology
Professor, Department of Human Genetics
(773) 834-3913
Y
Grace (Shan) Yu

Grace (Shan) Yu

PhD Student,
Kevin White Laboratory
(773) 251-1414
Z
Jie Zhou

Jie Zhou

PhD Student,
Kevin White Laboratory
(773) 834-0074

News

Audrey Fu Awarded K99 NIH Grant

IGSB Research Professional, Dr. Audrey Fu, was awarded a K99 NIH grant to support a research project entitled: Causal Inference of Gene Regulatory Networks with Application to Breast Cancer. The aim is to develop statistical models and computational methods for the inference of causal gene regulatory networks. The project will investigate how genetic variation acting on biological networks influences development and progression of diseases, using subtypes of breast cancer as a disease model.

IGSB Summer High School Student Accepted to Attend UChicago

Madison Olmsted, from Rio Americano High School in Sacramento, California, participated in a Research in Biological Sciences, Part 2 (RIBS-2) program in Kevin White’s lab last summer. 

Hormones and Microbes Interact to Modify Autoimmune Disease Progression

IGSB/CBC Postdoctoral Fellow Aly Khan co-authored a study on a previously unknown interaction between gut bacteria and gender bias in autoimmune diseases. The study proposes a novel two-signal model, in which hormones and microbes together influence the incidence and severity of autoimmune diseases. The results were published in Cell Immunity and are highlighted in a featured article in the issue.

Bionimbus Protected Data Cloud eliminates need for massive storage infrastructure

Bionimbus, an advanced cloud-based computing environment, helped Megan McNerney discover tumor suppressor gene, CUX1, is frequently inactivated in acute myeloid leukemia. The principal investigator for Bionimbus is Robert Grossman.

Gifts to boost University of Chicago as hub for biomedical ‘big data’

Two major gifts will build momentum behind the University of Chicago’s leadership in biomedical computation by assembling experts in the field and furnishing them with the tools to use “big data” to understand and treat disease.  Kevin White and Robert Grossman will lead the Pancreatic Cancer Genomic Medicine Initiative, which aims to improve care for patients with this disease using genomic and physiological data.

Tracing adaptive evolution of regulatory elements in the fly genome

Kevin White and colleagues determine the binding sites of the insulator protein CTCF in four Drosophila species whose divergence spans 25 million years in evolutionary time.  Their findings provide evidence for positive selection shaping the evolution of these regulatory sites and through them, the genes they control.

Aashish Jha was recently selected to receive a predoctoral fellowship from the University of Chicago

IGSB graduate student, Aashish Jha, in Kevin White?s lab, was recently selected to receive a predoctoral fellowship from the University of Chicago?s Center for Systems Biology of Oxygen Sensing.  An Institutional Training Grant, “Training in O2 Biology in Health & Disease,” will support his research training. This award is based on Aashish Jha?s academic record, scienti?c performance in the lab, and relevance of his thesis project to the ?eld of oxygen biology.

Research Papers