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

My laboratory uses a combination of genomics, computational, and genetic approaches to investigate large-scale networks of factors that control gene expression during development and disease. A major challenge in the “genomic era” of biology is to assemble the thousands of genes and proteins encoded within each genome into comprehensive subsets that specify particular developmental events or physiological processes. We are approaching this challenge using Drosophila melanogaster as a model and in the human genome directly. We are continually seeking new ways to combine genomics, computation, molecular genetics and biochemistry to identify and functionally characterize both individual molecules and large-scale molecular patterns that contribute to multi-genic phenotypes.  In the process we have developed novel experimental tools and analytical approaches to elucidate transcriptional regulatory networks that control biological processes ranging from metamorphosis in Drosophila to cancer in humans.  While our work has consistently pursued development of a comprehensive regulatory architecture map of the Drosophila genome during development and evolution, we have recently shifted a considerable amount of our focus into parallel approaches for studying the human cancer genome, while still leveraging the Drosophila model in order to couple target discovery to biological validation.  In addition to our own individual research programs, our lab participates in large consortia such as the modENCODE, human ENCODE, and The Cancer Genome Atlas.  Instead of relying on traditional genetic or molecular screens to identify and characterized novel molecules driving normal development and oncogenesis, we are pursuing a unique approach that relies on the interplay of computational and statistical modeling methods with experimentation using a combination of Drosophila, human cell lines, primary tumors, genome sequencing and genomic association studies, and mouse xenograft models; this approach has already yielded several novel, potentially druggable candidates whose roles in both Drosophila development and in human tumor biology were previously overlooked by more traditional methods.  Our goal is to pinpoint and then functionally characterize the most biologically relevant and druggable individual and pathway targets, and to ultimately develop clinically useful tools for modulating them. 

Ci, W., et al., SPOP promotes tumorigenesis by acting as a key regulatory hub in kidney cancer. submitted.

TCGA, T.C.G.A.N., Comprehensive Molecular Portraits of Human Breast Tumors. Nature, in press.

Kittler, R., et al., A Comprehensive Map of Nuclear Receptor Networks in Breast Cancer Cells. Cell Rep. 2013 Feb 21;3(2):538-51. doi: 10.1016/j.celrep.2013.01.004. Epub 2013 Jan 31.

Ni X, Zhang YE, Nègre N, Chen S, Long M, White KP. Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome. 2012 Nov;10(11):e1001420. doi: 10.1371/journal.pbio.1001420. Epub 2012 Nov 6.

ENCODE Project Consortium, et al. An integrated encyclopedia of DNA elements in the human genome.Nature. 2012. Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

Dore, L.C., et al., Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis. Blood, 2012. 119(16): p. 3724-33.

Cancer Genome Atlas Research, N., Integrated genomic analyses of ovarian carcinoma. Nature, 2011. 474(7353): p. 609-15.

Negre, N., et al., A cis-regulatory map of the Drosophila genome. Nature, 2011. 471(7339): p. 527-31.

Al-Dhaheri, M., et al., CARM1 is an important determinant of ERalpha-dependent breast cancer cell differentiation and proliferation in breast cancer cells. Cancer Res, 2011. 71(6): p. 2118-28.

Godley, L.A., et al., An integrated genomic approach to the assessment and treatment of acute myeloid leukemia. Semin Oncol, 2011. 38(2): p. 215-24.

Consortium, E.P., A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol, 2011. 9(4): p. e1001046.

Hah, N., et al., A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 2011. 145(4): p. 622-34.

Negre, N., et al., A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet, 2010. 6(1): p. e1000814.

modEncode, et al., Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 2010. 330(6012): p. 1787-97.

Hua, S., R. Kittler, and K.P. White, Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell, 2009. 137(7): p. 1259-71.

Liu, J., et al., Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer. Science, 2009. 323(5918): p. 1218-22.

Celniker, S.E., et al., Unlocking the secrets of the genome. Nature, 2009. 459(7249): p. 927-30.

Gauhar, Z., et al., Genomic mapping of binding regions for the Ecdysone receptor protein complex. Genome Res, 2009. 19(6): p. 1006-13.

Tian, F., et al., Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. Bioinformatics, 2009. 25(22): p. 3001-4.

Hua, S., et al., Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Mol Syst Biol, 2008. 4: p. 188.

Cancer Genome Atlas Research, N., Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 2008. 455(7216): p. 1061-8.

Hooper, S.D., et al., Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Mol Syst Biol, 2007. 3: p. 72.

Negre, N., et al., Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol, 2006. 4(6): p. e170.

Moorman, C., et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A, 2006. 103(32): p. 12027-32.

Rifkin, S.A., et al., A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature, 2005. 438(7065): p. 220-3.

Stolc, V., et al., A gene expression map for the euchromatic genome of Drosophila melanogaster. Science, 2004. 306(5696): p. 655-60.

Li, T.R. and K.P. White, Tissue-specific gene expression and ecdysone-regulated genomic networks in Drosophila. Dev Cell, 2003. 5(1): p. 59-72.

Michaut, L., et al., Analysis of the eye developmental pathway in Drosophila using DNA microarrays. Proc Natl Acad Sci U S A, 2003. 100(7): p. 4024-9.

Rifkin, S.A., J. Kim, and K.P. White, Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet, 2003. 33(2): p. 138-44.

Sun, L.V., et al., Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc Natl Acad Sci U S A, 2003. 100(16): p. 9428-33.

Arbeitman, M.N., et al., Gene expression during the life cycle of Drosophila melanogaster. Science, 2002. 297(5590): p. 2270-5.

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