Meritxell Oliva Pavia

Postdoc,
- Stranger lab / Genetic Medicine Department / IGSB
- PostDoctoral Scholar

Contact Information

KCBD 10132

Phone: +1-917-822-02-64
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Andrew Skol


- Senior Statistical Geneticist
- Stranger Lab and CDIS (Center for Data Intensive Science)

Contact Information

KCBD 10132

Phone: 773-834-3003
Email: .(JavaScript must be enabled to view this email address)

Bio

Dr. Skol is interested in the relationship between genetics and phenotype, especially as it relates to cancer and other disease related phenotypes. He is currently working towards better understand how genetic and genomics variation explains sex difference in cancer incidence, progression, prognosis and response to therapy. 


Research Papers

Elizabeth Lipschultz


- Undergraduate Research Assistant

Contact Information

Phone: 402-305-2088
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Marian Fernando


- Research Specialist

Contact Information

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Eve Grumish, M.S.

Research Professional,
- Research Specialist I

Contact Information

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Ian J. Begeman

Research Professional,
- Research Specialist

Contact Information

Email: .(JavaScript must be enabled to view this email address)

Bio

I research protein expression in human tissues as part of the NIH's Genotype-Tissue Expression Program in Dr. Barbara Stranger’s lab at the Institute for Systems Biology. I measure protein expression in human tissues using state-of-the-art robotic microwestern and reverse phase protein array systems and analyze protein expression data using R.


Research Papers

Alan Selewa

PhD Student,
- PhD Student
- Savas Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Phone: (773) 834-1877
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Parthiv Patel

PhD Student,
- PhD Student
- Savas Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Hoang Van Phan

PhD Student,
- PhD Student
- Savas Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Christian Jordi

PhD Student,
- PhD Student
- Savas Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Jing Lin

PhD Student,
- PhD Student
- Savas Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Navid Ghorashian

Postdoc,
- Postdoc
- Savas Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Ce Zhang

Postdoc,
- Postdoc
- Savas Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Hsiung-Lin Tu

Postdoc,
- Postdoc
- Savas Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Email: .(JavaScript must be enabled to view this email address)

Bio

I am interested in understanding (1) the potential source of cell-to-cell variability and (2) how the temporal modulation of input signal affects NF-kappaB signaling. In collaboration with Ce, we are developing microfluidic tools to study embryonic neuron stem cells.


Research Papers

Jun Huang

PhD Student,
- Moellering Lab / Biological Sciences Division
- PhD Candidate / Department of Biochemistry and Molecular Biophysics

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Phone: 7738348900
Fax: 773-834-2877
Email: .(JavaScript must be enabled to view this email address)
Website: http://moelleringlab.uchicago.edu


Research Papers

Nir Drayman

Postdoc,
- Savas Tay Lab
- Post-Doc

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Fax: 773-834-2877
Email: .(JavaScript must be enabled to view this email address)

Bio

Nir Drayman obtained his PhD in Virology from the Hebrew University of Jerusalem, Israel in 2014. Then joined the lab of Uri Alon at the Weizmann Institute for a short post-doc working on Herpes Simplex virus and am currently with Savas Tay, trying to learn cool things about viruses and the cells they infect.


Research Papers

Michael Junkin

Staff Scientist,
- Savas Tay Lab
- Senior Scientist at the Institute for Molecular Engineering

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637
 

Fax: 773-834-2877
Email: .(JavaScript must be enabled to view this email address)
Website: http://ime.uchicago.edu/tay_group/


Research Papers

Administrative Specialist

Staff,
- Administrative Specialist

Contact Information

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

Phone: (773) 702-6685
Fax: (773) 834-2877
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Gengjie Jia

Postdoc,
- Medicine and Human Genetics, Institute for Genomics and Systems Biology, Computation Institute
- Postdoctoral Scholar
- Rzhetsky Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
KCBD 10160b
Chicago, IL 60637

Phone: +1 312-459-8103
Email: .(JavaScript must be enabled to view this email address)
Email: .(JavaScript must be enabled to view this email address)

Bio

Dr. JIA’s key expertise lies in Reverse Engineering using system-level biological/biomedical data.
In 2008, he obtained a B.Sc. degree in Biological Science from University of Science and Technology of China and his undergraduate thesis focused on Genetic Engineering, Biochemistry and Structural Immunology; In 2013, a Ph.D. degree from Singapore-MIT Alliance (a joint degree of National University of Singapore and Massachusetts Institute of Technology) with research interests on Bioinformatics, Systems Biology, Parameter Estimation, Biological Network Modeling and Metabolic Engineering. After graduation, he acquired three-year industrial experience in Data Analysis, Signal Processing, and Modeling in CGG.
Starting from 2016, as a Postdoctoral Researcher with Prof. Andrey Rzhetsky in the Department of Medicine, Institute for Genomics and Systems Biology, Computation Institute at the University of Chicago, he is conducting research on Biomedical Informatics, Dynamic Modeling, Medical Genetics and Systems Pharmacology. Specifically, two undergoing projects include (1) Dynamic modeling of cancer pathways for designing strategies for combinatorial drug interventions in the treatment of cancer; (2) Statistical analysis of the existing insurance claims and clinical records for identification of groups of etiologically distinct forms of asthma.

CV can be accessed here.


Research Papers

Tonya Brunetti

Postdoc,
- Post doctoral scholar, Computational Biologist
- Kevin White Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637

Email: .(JavaScript must be enabled to view this email address)

Bio

Tonya graduated with her BA from the University of Colorado in molecular cell and developmental biology.  She attended the University of New Mexico for gradate school and obtained her PhD in genetics and developmental biology and simultaneously obtained a MS in computer science.  Her current research project is in collaboration with the Chicago Pancreatic Cancer Initiative (CPCI) and involves the genetic analysis of somatic mutations in patients diagnosed with pancreatic cancer and its relationship to clinical outcome and survival.  Tonya's second research project is in collaboration with the PsychENCODE consortium to analyze RNA-seq data and ATAC-seq data from post-mortem brain tissue across various psychiatric disorders.


Research Papers

Jing Lin

PhD Student,
- Tay Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637

Phone: 3128045877
Email: .(JavaScript must be enabled to view this email address)

Bio

Jing Lin came from Sichuan China, the biggest natural habitat for giant pandas in the world. She obtained her BE degree from the National University of Singapore, majoring in Electrical Engineering, specifying in micro-fabrications. Then, she moved to ETH Zurich for the pursuit of a master degree in Biomedical Engineering. After that, she joined Savas Tay's group in D-BSSE, ETH Zurich as a Ph.D. student.


Research Papers

Marlin Amy Halder


- Research Specialist, Chicago Pancreatic Cancer Initiative
- Kevin White Lab

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637

Email: .(JavaScript must be enabled to view this email address)
Email: 312-887-9171

Bio

I am part of the Chicago Pancreatic Cancer Initiative group. My job duties include DNA/RNA isolation from frozen tissue, FFPE slides, blood and cell culture. I coordinate data delivery between sequencing core and bioinformaticians and maintain records. I also serve as a backup to the clinical team in patient recruitment and specimen collection.


Research Papers

Haneen Ammouri

Alumni, Research Technician,
- Research Technician
- Kevin White Lab

Contact Information

modERN Research Technician
Kevin White’s Lab
Institute for Genomics and Systems Biology
University of Chicago
900 E57th St. KCBD 10240
Chicago, IL 60637

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)
Website: https://www.linkedin.com/in/haneen-ammouri-35094628

Bio

I am currently part of the ModENCODE project where we conduct ChIP-seq experiments on  Drosophila melanogaster transgenic lines to understand the role of transcription factors in regulation and development. I graduated with a M.S. degree from Lund University in molecular biology where I had studied the relationship between microRNAs and metastasis in prostate cancer cell lines.


Research Papers

Sujun Hua

IGSB, Alumni,

Contact Information


Research Papers

Joelle Perusse

IGSB, Alumni,

Contact Information


Research Papers

Beth Russell

IGSB, Alumni, PhD Student,

Contact Information


Research Papers

Savas Tay

IGSB, Core Member,
- Associate Professor in Molecular Engineering

Contact Information

Institute for Genomics & Systems Biology
The University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
KCBD 10130
Chicago, IL 60637

Phone: 773-702-4511
Email: .(JavaScript must be enabled to view this email address)
Email: http://www.microfluidics.uchicago.edu/index.html
Website: http://ime.uchicago.edu/savas_tay/

Bio

Postdoctoral openings at the Tay Lab. Please see career opportunities.

Research

Savas Tay is a systems biologist and bioengineer who works at the interface of biology, physics, and engineering. His overarching goal is to understand how biological systems work from an engineer’s perspective, and use this knowledge to manipulate cells and gene pathways to help cure diseases. On the technology front, his lab develops high-throughput and high-content single-cell analysis devices by integrating microfluidics and optics.

Prof. Tay is joining University of Chicago as an Associate Professor in the summer of 2016 from ETH Zurich in Switzerland. A main focus for Savas Tay in Chicago will be to understand the role of molecular pathway dynamics in cellular information processing, pathogen sensing and recognition, and signaling. His Lab performs precision dynamic measurements on living cells and develops predictive models of complex biological systems like the immune system. Such models can serve as a rapid test-bed for drug studies and genome editing applications.

Microfluidic technologies developed by the Tay Lab create realistic environments that mimic living tissue, and measure dynamic processes in individual cells with extreme precision and throughput, adding majorly to the systems biology push at the Tay Lab. Tay is also interested in translating such technologies to real-life biomedical applications.
His work on NF-κB, a key transcription factor that regulates thousands of immune genes, was published in leading scientific journals such as Nature, Cell and PNAS. He discovered that cells activate NF-κB in an all-or-none fashion, similar to a digital switch. Recently, he discovered that molecular noise improves cellular signal transmission, and showed how oscillatory inputs control transcriptional dynamics by synergizing with molecular noise.

Before becoming interested in biological research, Dr. Tay was an optical physicist. His achievements in optics include the development of the first updateable holographic 3-D display, infrared-sensitive holographic materials for optical communications and bioimaging, tunable photonic crystal devices, and plasmonic thermal emitters for infrared imaging.

More on Tay’s research and publications can be found in his ETH website.


Research Papers

Lucas Eppel

Staff,
- White Lab
- Systems Administrator

Contact Information

The University of Chicago

900 East 57th Street

Chicago, IL 60637

Phone: 312-344-3056
Email: .(JavaScript must be enabled to view this email address)

Bio

Luke has worked across many different enterprise Forbes top 50 companies, and is now excited to work in academia. He is fluent in all variants of Linux and virtualization, as well as programming across many major programming languages.


Research Papers

Miguel A. Brown


- Kevin White Lab
- Programmer, IGSB

Contact Information

KCBD

900 E 57th Street

Office number 1015A

Chicago, IL 60637

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Amber Thomas

Alumni, Research Technician,
- Kevin White Lab
- Research Technician

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637
Room:10240D

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)
Website: https://www.linkedin.com/pub/amber-thomas/78/ab1/a8


Research Papers

Isabel Romero Calvo


- Kevin White Lab
- Research Professional

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
 

Phone: 3125208818
Email: mailto:iromerocalvo@uchicago.edu


Research Papers

Gihoon Lee

Student,
- Raymond Moellering Laboratory
- Department of Chemistry
- Graduate student

Contact Information

Institute for Genomics & Systems Biology

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637

Phone: 773-834-8900
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Jeff Montgomery

Lab Technician,
- Raymond Moellering Lab
- Technician

Contact Information

Institute for Genomics & Systems Biology

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637

Phone: 773-834-8900
Email: .(JavaScript must be enabled to view this email address)

Bio

In the Moellering Lab, I am setting up molecular biology and biochemistry workflows while also initiating projects in peptidomimetics, focusing on novel cyclization strategies.
I graduated in 2014 from the University of Chicago with degrees in Biochemistry and Chemistry, conducting research in biocatalysis and directed evolution and TAing for several biology courses.


Research Papers

JAE WON CHANG

Postdoc,
- Raymond Moellering Laboratory
- Department of Chemistry
- Postdoc

Contact Information

Institute for Genomics & Systems Biology

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637
 

Phone: 773-834-8900
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Sarah Fazal

Research Professional, Staff, CSC,
- Cellular Screening Center
- Research Technologist

Contact Information

Cellular Screening Center (CSC)
The University of Chicago
Gordon Center for Integrative Sciences
Room WSB03
929 E. 57th St.
Chicago, IL 60637
Phone: 773.256.9772
Fax: 773.256.9183
Phone: 773.256-9772

Phone: 773 256 9190
Email: .(JavaScript must be enabled to view this email address)

Bio

Sarah recently joined the CSC. Her prior experience was in a start-up laboratory where she gained valuable experience in molecular and cell biology techniques. She runs screening projects and also plays a role in maintaining the lab.


Research Papers

Ekaterina (Katya) Khramtsova

Postdoc,
- Postdoctoral Scholar
- Department of Medicine
- Section of Genetic Medicine
- Barbara Stranger lab

Contact Information

900 East 57th Street
Chicago, IL 60637

Email: .(JavaScript must be enabled to view this email address)

Bio

Ekaterina’s work focuses on characterizing the contribution of the sex chromosomes and sexually dimorphic expression quantitative trait loci to sex-biased neuropsychiatric disease polygenic risk. More specifically, her work in the Stranger laboratory in collaboration with Dr. Lea Davis focuses on Tourette syndrome and obsessive compulsive disorder.


Research Papers

Rachel D. Melamed

Postdoc,
- Rzhetsky Lab
- Postdoc

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL. 60637
Room:10160B

Phone: 857-498-0044
Email: .(JavaScript must be enabled to view this email address)
Website: http://home.uchicago.edu/~melamed


Research Papers

Raymond Moellering

IGSB, Core Member,
- Assistant Professor
- Department of Chemistry

Contact Information

900 East 57th Street
KCBD 10118
Chicago, IL 60637
The University of Chicago

Phone: 773-834-5650
Fax: 773-834-2877
Email: .(JavaScript must be enabled to view this email address)
Website: https://chemistry.uchicago.edu/faculty/faculty/person/member/raymond-moellering.html

Bio

Research in the Moellering Lab lies at the interface of chemistry and biology, with an eye towards understanding and intervening in human disease. By integrating chemical synthesis, cell biology and mass spectrometry platforms, our research aims to identify novel biological mechanisms underlying diseases such as diabetes and cancer, and to subsequently develop innovative diagnostic and therapeutic modalities to impact these disorders. We are specifically interested in developing new chemical tools and technologies to study complexity and dynamics in the proteome, thus enabling targeted manipulation of protein targets and the pathways they govern. We are actively pursuing projects in the following research areas:

Research

Metabolic signaling and protein post-translational modifications in disease: Control of protein structure and function via reversible small molecule binding and covalent post-translational modifications are well-established and conserved biochemical regulatory mechanisms in cell biology. These events integrate diverse signaling pathways in the cell and also allow for significant expansion of the chemical and functional diversity afforded by finite genetic products (~23,000) by more than an order of magnitude (~1,000,000 unique proteins). While these mechanisms are involved in all aspects of biology, we lack a complete map of these chemical modifications, including their tissue-, cell- and temporal regulation and, importantly, their regulatory roles in normal and pathologic cell signaling. Our group has several areas of active research into the origins and roles of novel protein modification networks in the regulation of metabolic homeostasis, particularly within the contexts of aging, metabolic disease and cancer. For example, we have discovered several novel protein post-translational modifications resulting from the interactions between proteins and reactive primary metabolites formed by glucose, a ubiquitous energy source in life. These non-enzymatic modifications represent a direct connection between glycolytic flux and alterations in the structure and function of key proteins, including glycolytic enzymes themselves, pointing to the existence of an ancient and likely biomedically important intrinsic feedback pathway in mammalian cells. Using a combination of cell biology, mass spectrometry and chemical probe development, we are exploring the fundamental biochemical processes that regulate the formation and removal of these modifications, their effects on target protein structure and function, and their ability to serve as a novel form of intracellular signaling, integrating glucose metabolism with other pathways in normal as well as diseased processes.

Harnessing chemical proteomic technologies for discovery biology and chemical probe development: Our group is developing novel chemical proteomic technology platforms with applications ranging from basic biology to drug discovery. One area of active research is the development of proteomic platforms for the discovery and mapping of protein-ligand (e.g. protein-metabolite, protein-drug, protein-protein) interaction networks in native cellular environments. Connecting ligands to their biologically relevant binding partner(s) is a major challenge in unraveling cellular signaling events as well as understanding the mechanism of action for chemical probes and even existing drugs. We are developing chemical proteomic platforms that will enable systems-level views of ligand interactions proteome-wide. Specific interest areas included: development of label-free chemical proteomic platforms; development of novel chemical probes for poorly characterized protein families; application of proteomic platforms in relevant disease models to discover new diagnostic and/or therapeutic targets in cancer.

Synthetic protein and peptide therapeutics: Nature employs a myriad of chemical modifications to control protein structure and function. For example, subtle chemical transformations like disulfide bridge formation and protein acetylation can have profound effects on protein structure, stability and half-life. In addition to our exploration of natural protein modification networks in cellular biochemistry and physiology, our group is interested in drawing upon these strategies to develop synthetically-modified protein- and peptide-based chemical probes. These efforts compliment our interests in disease associated biological pathways by enabling chemical probe development for classes of biomolecules that have proven difficult to target with conventional small molecules. Protein-based drugs have become a major area of drug discovery in the past few decades, mainly owing to their ability to bind protein targets with exceptional potency and specificity relative to traditional small molecule drugs. These desirable properties, however, are often accompanied by limitations in target space, route of administration and stability. Our group is developing novel approaches to synthetically modify or mimic proteins and peptides to improve their drug-like properties, which include protease-resistance, in vivo half-life, and the ability to access intracellular targets. Through total- and semi-synthesis, we are employing these strategies to develop novel classes of peptide and protein mimetics to address difficult biological targets in human diseases such as diabetes and cancer.


Research Papers

Matthew Tirrell

Executive Advisory Committee Member,
- Dean and Founding Pritzker Director of the Institute for Molecular Engineering

Contact Information

The University of Chicago
Institute for Molecular Engineering
5747 South Ellis Avenue,
Jones Laboratory 222
Chicago, IL, 60637

Phone: 773.834.2001
Email: mtirrell at uchicago.edu
Website: http://ime.uchicago.edu/tirrell_lab/

Bio

Professor Tirrell received a BS degree in Chemical Engineering from Northwestern University and a PhD in Polymer Science and Engineering from the University of Massachusettes. He began his academic career as an Assistant Professor in the Department of Chemical and Materials Engineering at the University of Minnesota where he later served as Head of the Department. He then moved to the University of California at Santa Barbara where he served as Dean of Engineering. After serving as Dean for 10 years, Professor Tirrell moved to the University of California at Berkeley where he served as Chair for the Department of Bioengineering. In 2011 he accepted the position of Founding Pritzker Director of the Institute for Molecular Engineering.

Research

Matthew Tirrell is a pioneering researcher in the fields of biomolecular engineering and nanotechnology, specializing in the manipulation and measurement of the surface properties of polymers, materials that consist of long, flexible chain molecules. His work combines microscopic measurements of intermolecular forces with the creation of new structures. His work has provided new insight into polymer properties, especially surface phenomena, such as adhesion, friction, and biocompatibility, and new materials based on self-assembly of synthetic and bioinspired materials.
 


Research Papers

Melissa Dsouza

Postdoc,
- MBL-UChicago Postdoctoral Scholar
- Gilbert Lab, Department of Ecology and Evolution

Contact Information

The University of Chicago

Institute for Genomics & Systems Biology 

900 East 57th Street

KCBD 10121C/D

Chicago, IL 60637

Phone: 312-618-7475
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Vineet Dhiman

IGSB, Postdoc,
- Postdoctoral Scholar
- Kevin White Laboratory

Contact Information

Institute for Genomics and Systems Biology
KCBD Room 10240D
900 E. 57th St.
Chicago, IL, 60637

Phone: 773-834-0074
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Yuan Ji

Fellow,
- Assistant Vice President
- Director, Program of Computational Genomics & Medicine
- NorthShore University HealthSystem

Contact Information

Yuan Ji, Ph.D.
Assistant Vice President
Director, Program of Computational Genomics & Medicine
NorthShore University HealthSystem
1001 University Place
Evanston, IL 60201

Associate Professor (Biostatistics, part-time),
Department of Public Health Sciences
The University of Chicago Biological Sciences
5841 S. Maryland Ave. |  Room W239, MC2000 | Chicago, IL  60637

Phone: 224-364-7312
Fax: 773-702-1979
Email: .(JavaScript must be enabled to view this email address)
Email: http://health.bsd.uchicago.edu/yji/
Website: http://compgenome.org/

Bio

Dr. Ji is a statistician, bioinformatician, and computational biologist. His research focuses on Bayesian statistical models and designs for big genomics data and cancer clinical trials. He is interested in develop innovative statistical models for analyzing high dimensional and complex data from micrsarrarys, single-cell genomics and proteomics, and next-generation sequencing experiments. He also spends equal amount of effort on developing adaptive designs for cancer clinical trials and studies, to enable translational and precise patient care.


Research Papers

Abraham A. Palmer

Fellow,
- Department of Psychiatry and Behavioral Neuroscience
- Department of Human Genetics
- Associate Professor

Contact Information

920 E 58th St. CLSC-507D
Chicago, IL 60637

Phone: (773) 834-2897
Fax: (773) 834-0505
Email: .(JavaScript must be enabled to view this email address)
Email: http://pgtg.uchicago.edu
Email: http://www.ratgenes.org
Website: http://www.palmerlab.org

Bio

My laboratory is devoted to elucidating the influence of genetics on behavior. One main objective of the lab is to use Genome Wide Association Studies (GWAS) in mice and rats to identify novel genes that modulate behavior. We use these discoveries to delve into the mechanism by which these genes influence behavior. We are also using similar techniques to examine normal (non-pathological) variability in human behavior.

http://genes.uchicago.edu/contents/faculty/palmer-abraham.html

https://psychiatry.uchicago.edu/directory/abraham-palmer-phd

http://neuroscience.uchicago.edu/?p=neuro/profile&id=28&c=0


Research Papers

Xin He

Fellow,
- Department of Human Genetics
- Assistant Professor

Contact Information

Cummings Life Science Center (CLSC)

420, 920 E. 58th St, Chicago, IL 60637

Phone: 773-834-7678
Email: .(JavaScript must be enabled to view this email address)
Website: xinhelab.org

Research

Our lab uses computational approaches to study the genetics of human diseases. We are particularly interested in developing novel methods that integrate multiple genomic datasets to have better power of detecting disease genes and gain deeper insights into the disease mechanisms.


Research Papers

Jared Bischof, M.S.

IGSB,
- Folker Meyer Lab
- Senior Software Engineer, Computation Institute, University of Chicago

Contact Information

Phone: 630-252-1277
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Naseer Sangwan

Argonne,
- Bio-Sciences Division Argonne National Laboratory
- Post-Doctoral Research Associate

Contact Information

Phone: 630 854 7656
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Kim M. Handley

Alumni,
- Postdoctoral Research Associate, Department of Ecology and Evolution
- Gilbert Lab

Contact Information

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Eric R. Johnston

Research Technician,
- Dion Antonopoulos Laboratory, Argonne National Laboratory
- Research Technician

Contact Information

9700 S. Cass Avenue
Bldg 202, Room A-341
Argonne, IL 60439


Research Papers

Aaron Garoutte

Alumni,
- Dion Antonopoulos Laboratory, Argonne National Laboratory
- Research Technician

Contact Information

9700 S. Cass Avenue
Bldg 202, Room A-341
Argonne, IL 60439


Research Papers

Dr. Jennifer Brulc, PhD

Alumni, Postdoc,
- Senior Scientist for Global Scientific & Regulatory Affairs
- Current Affiliation: The Bell Institute of Health and Nutrition at General Mills
- Previous Affiliation: Dion Antonopoulos Laboratory, Argonne National Laboratory

Contact Information

9700 S. Cass Avenue
Bldg 202, Room A-341
Argonne, IL 60439

Phone: 217-417-6349
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Brandon Bates

Alumni,
- Dion Antonopoulos Laboratory, Argonne National Laboratory
- Research Technician

Contact Information

9700 S. Cass Avenue
Bldg 202, Room A-341
Argonne, IL 60439


Research Papers

Theodore Flynn


- Dion Antonopoulos Laboratory, Biosciences Division at Argonne National Laboratory
- Computation Institute at The University of Chicago
- Research Scientist

Contact Information

9700 S. Cass Avenue
Bldg 202, Room A-341
Argonne, IL 60439

Phone: (630) 252-1181
Email: .(JavaScript must be enabled to view this email address)
Website: http://scholar.google.com/citations?user=bQ8_dQcAAAAJ

Research

Flynn TM, O’Loughlin EJ, Mishra B, DiChristina TJ, Kemner KM (2014) “Sulfur-mediated electron shuttling during bacterial iron reduction,” Science, Vol. 344(6187) p. 1039–1042. 
(link)

Dong Y, Kumar CG, Chia N, Kim P-J, Miller PA, Price ND, Cann IKO, Flynn TM, Sanford RA, Krapac IG, Locke RA, Hong P-Y, Tamaki H, Liu W-T, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Mackie RI, Fouke BW (2014) “Halomonas sulfidaeris-dominated microbial communities inhabits a 1.8 km-deep subsurface Cambrian sandstone reservoir,” Environmental Microbiology, Vol. 16(6), p. 1695–1708. 
(link)

Flynn TM, Sanford RA, Ryu H, Bethke CM, Levine AD, Ashbolt NJ, Santo Domingo JW (2013) “Functional microbial diversity and substrate utilization explain groundwater chemistry in a pristine aquifer,” BMC Microbiology, Vol. 13(1), p. 146(1–15). 
(link)

O’Loughlin EJ, Boyanov MI, Flynn TM, Gorski CA, Hofmann SM, McCormick ML, Scherer MM, Kemner KM (2013) “Effects of bound phosphate on the bioreduction of lepidocrocite (γ-FeOOH) and maghemite (γ-Fe2O3) and the formation of secondary minerals,” Environmental Science & Technology, Vol. 47(16), p. 9157–9166. 
(link)

Flynn TM, Sanford RA, Bethke CM, Iker B, Levine AD, Ashbolt NJ, Santo Domingo JW (2012) “The active bacterial community in a pristine, confined aquifer,” Water Resources Research, Vol. 48, p. W09510. 
(link)

Bethke CM, Sanford RA, Kirk MF, Jin Q, Flynn TM (2011) “The thermodynamic ladder in geomicrobiology,” American Journal of Science, Vol. 311(3), p. 183–210. 
(link)

Flynn TM, Sanford RA, Bethke CM (2008) “Attached and suspended microbial communities in a pristine confined aquifer,” Water Resources Research, Vol. 44, p. W07425. (link)

Locock AJ, Burns PC, Flynn TM (2005) “The role of water in the structures of synthetic hallimondite, Pb2[(UO2)(AsO4)2](H2O)n and synthetic parsonsite, Pb2[(UO2)(PO4)2](H2O)n, 0 ≤ n ≤ 0.5,” American Mineralogist, Vol. 90(1), p. 240–246. (link)

Locock AJ, Burns PC, Flynn TM (2005) “Structures of strontium- and barium-dominant compounds that contain the autunite-type sheet,” Canadian Mineralogist, Vol. 43, p. 721–733. (link)

Locock AJ, Burns PC, Duke MJM, Flynn TM (2004) “Monovalent cations in structures of the meta-autunite group,” Canadian Mineralogist, Vol. 42, p. 973–996. (link)

Locock AJ, Burns PC, Flynn TM (2004) “Divalent transition metals and magnesium in structures that contain the autunite-type sheet,” Canadian Mineralogist, Vol. 42, p. 1699–1718. (link)


Research Papers

Jason C. Koval

Research Technician,
- Dion Antonopoulos Laboratory, Argonne National Laboratory
- Research Technician

Contact Information

9700 S. Cass Avenue
Bldg 202, Room A-341
Argonne, IL 60439


Research Papers

Iratxe Zarraonaindia Martinez

Alumni,
- Post-doctoral Researcher
- Current Affiliation: Research Associate Genomics University of the Basque-Country, Spain
- Previous Affiliation: Jack Gilbert Lab

Contact Information

Genetics; Fac. Science & Technology

Dpt. Genetics, Physical Anthropology & Animal Physiology

University of the Basque Country (UPV/EHU)

Bº Sarriena s/n 48940 Leioa; Bilbao; Spain

Phone: +34-946015503
Email: .(JavaScript must be enabled to view this email address)
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Mark Applebaum

Clinical Associate,
- Department of Pediatrics, Section of Hematology/Oncology
- Susan Cohn Lab and Barbara Stranger Lab

Contact Information

The University of Chicago
KCBD 10th Floor
900 E. 57th St.
Chicago, IL 60637

Phone: (773) 702-6808
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Justin Chew

Student,
- Genetics, Genomics & Systems Biology
- Medical Sciences Training Program
- Michael Rust Laboratory

Contact Information

The University of Chicago - IGSB
900 E. 57th St. KCBD 10th Floor
Chicago, IL 60628

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Kevin Loeser

Alumni, Student,
- Summer Intern: Andrey Rzhetsky Lab

Contact Information

Knapp Center for Biomedical Discovery
Institute for Genomics and Systems Biology
900 East 57th Street
Chicago, IL 60637
Room:10160


Research Papers

Ishanu Chattopadhyay


- Assistant Professor, Department of Medicine, Section of Hospital Medicine
- Computation Institute

Contact Information

Knapp Center for Biomedical Discovery
Institute for Genomics and Systems Biology
900 East 57th Street
Chicago, IL 60637
 

Phone: (814) 441-1296
Email: .(JavaScript must be enabled to view this email address)
Website: http://home.uchicago.edu/~/ishanu/

Research

Publications 


Research Papers

Kanix Wang

PhD Student,
- Andrey Rzhetsky Laboratory

Contact Information

Knapp Center for Biomedical Discovery
Institute for Genomics and Systems Biology
900 East 57th Street
Chicago, IL 60637
Room:10160

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Ilya Mayzus

Programmer,
- Andrey Rzhetsky Laboratory

Contact Information

Knapp Center for Biomedical Discovery
Institute for Genomics and Systems Biology
900 East 57th Street
Chicago, IL 60637
Room:10160

Phone: (773) 702-6799
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Ryan Mork

Student,
- Graduate Student- 3rd Year
- Rzhetsky Lab

Contact Information

Knapp Center for Biomedical Discovery
Institute for Genomics and Systems Biology
900 East 57th Street
Chicago, IL 60637
Room:10160

Phone: 763-807-9413
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Mimi Brown

Alumni, Research Technician, Staff, MWAC,
- Microwestern Array Core Facility
- Research Technologist

Contact Information

Microwestern Array Core Facility (MWAC)
The University of Chicago
Knapp Center for Biomedical Discovery
Room 10126
900 E. 57th St.
Chicago, IL 60637

Phone: 773.702.8651
Fax: 773.834.2877
Email: .(JavaScript must be enabled to view this email address)

Bio

Mimi conducts the assay development and runs the Microwestern Arrays in the core.  She is also responsible for all of the daily operations of the Microwestern Array Core.


Research Papers

Nicole Re

Alumni, Research Technician,
- Cellular Screening Center
- Research Technologist

Contact Information

Cellular Screening Center
Institute for Genomics & Systems Biology
Gordon Center for Integrative Sciences
The University of Chicago
929 East 57th Street Chicago, IL 60637
Room: GCIS WSB 03

Email: .(JavaScript must be enabled to view this email address)

Bio

Nicole conducts high-throughput screens, cell culture, and performs all details of lab management in the CSC.


Research Papers

Eugene Leypunskiy

PhD Student,
- Rust Lab

Contact Information

Phone: 773.795.5650
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Matt Szynkarek

Alumni, Lab Technician, Staff, GEC,
- GEC
- Lab Technician

Contact Information

Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
Room:10230A

Phone: 773-834-0074
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Jonathan Spring


- Robert Grossman Lab
- Systems Administrator – The Center for Data Intensive Science

Contact Information

Laboratory for Advanced Computing
Center for Data Intensive Science
University of Chicago, KCBD 10128
900 E. 57th Street
Chicago, IL 60637

Phone: 312-771-0392
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Stuti Agrawal


- Center for Data Intensive Science
- Robert Grossman Lab
- Bioinformatician

Contact Information

University of Chicago - IGSB
900 E. 57th, KDBD 10240
Chicago, IL 60637

Email: .(JavaScript must be enabled to view this email address)


Research Papers

Patrick Reed

Alumni,
- White Lab
- PhD Student
- Committee on Neurobiology

Contact Information

University of Chicago - IGSB
900 E. 57th, KDBD 10240
Chicago, IL 60637

Phone: 773-490-6241
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Marty Forde

Alumni, Research Technician,
- Conte Center Core C
- Technologist

Marty Forde

Contact Information

Phone: 847-791-7413
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Mohana Ray

Postdoc,
- Kevin White Lab
- Postdoctoral Scholar

Mohana Ray

Contact Information

University of Chicago - IGSB
900 E. 57th, KDBD 10240
Chicago, IL 60637

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Shenglan Cindy Gao

Alumni, Postdoc,
- Kevin White Laboratory
- Postdoctoral Researcher

Contact Information

University of Chicago - IGSB
900 E. 57th, KDBD 10240
Chicago, IL 60637

Phone: 517-290-9791
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Liza Holtzman

Alumni, Staff,
- Business Administrator , Institute for Genomics & Systems Biology

Contact Information

Institute for Genomics & Systems Biology
The University of Chicago
900 East 57th Street
Chicago, IL 60637

Phone: (773) 834-3913
Fax: (773) 834-2877

Bio

Liza Holtzman was the IGSB Business Administrator and is responsible for administrative functions in the IGSB.


Research Papers

Barry Aprison

Education & Outreach Director,
- Sr. Lecturer, Biological Sciences Collegiate Division
- Education & Outreach Director, GGSB, CCSB, and Conte Center

Contact Information

Institute for Genomics & Systems Biology
Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637

Phone: (773) 834-2787
Email: .(JavaScript must be enabled to view this email address)

Research

The IGSB Education & Outreach Director is Dr. Barry Aprison who develops and oversees academic training programs through the auspices of the P50 NIH Conte Center for Computational Neuropsychiatric Genomics, the P50 NIH NIDA Center of Excellence, and the Ph.D. program in Genetics, Genomics, & Systems Biology (GGSB). Dr. Aprison’s biomedical research areas of interest are developmental genetics, molecular evolution, genomics, systems biology, and neurogenetics behavior. His education research areas of interest are cognitive science, interactive learning, and scientific teaching. 

EDUCATION & OUTREACH

Dr. Aprison designs and produces a portfolio of education and training programs for high school students, teachers, undergraduates, graduate students, post-doctoral fellows, and faculty.  He has partnerships with scholars at the University of Chicago, Northwestern University, the Field Museum, the Museum of Science & Industry, Chicago-area K-12 schools, the Collegiate Scholars Program, Urban Teacher Education Program, Research in the Biological Sciences, and  Post-Baccalaureate Research Education Program.  As a Senior Lecturer in the Biological Sciences Collegiate Division of the College, Dr. Aprison produces courses and lectures. They include classes for Systems Biology & Disease (MD-Ph.D. students), Systems & Networks in Cancer (grad students), Synthetic Biology & Regulation of Genes (undergrad students), and Topics in Immunology, Cancer, and Systems Biology (MD-Ph.D. students), and a system biology Journal Club and grant writing course (M.D. Ph. D. students..  Dr. Aprison works on campus-wide initiatives as a member of the Graduate Minority Committee.  He assists in the development of underrepresented minority (URM) recruitment and training programs. Dr. Aprison helps manage the applicant recruitment and course development of the Committee on Genetics, Genomics, & Systems Biology's Ph.D. program in coordination with the Chair.  Dr. Aprison leads a program he designed to support Molecular Biosciences graduate students to teach science in high schools and science museum exhibitions. They receive TA credit for 1-quarter's worth of planning, formative development, and teaching.

Prior to his coming to the University of Chicago in 2008, Dr. Aprison was Associate Professor of Education and Director of Science, Technology, Engineering, and Mathematics (STEM) Education Initiatives in the School of Education at Johns Hopkins University.  He joined the Hopkins faculty in 2007.  Dr. Aprison worked with teachers, principals, superintendents, curriculum specialists, engineers, scientists, evaluators, and designers to produce STEM education projects for Maryland schools.  His areas of specialization in education are:
a) designing, formatively developing, and implementing integrated STEM (iSTEM) K-16 education experiences;
b) producing narrative-based, goal-based learning STEM experiments;
c) generating elegant engineering challenges in classrooms and museum exhibitions;
d) producing phenomena-based interactives in classrooms and science exhibitions; and
e) designing, formatively developing, and producing education outreach program and hands-on exhibitions for science museums and centers.

Prior to joining Johns Hopkins University, Dr. Aprison was Director of Science and Technology at the Chicago Museum of Science and Industry for nineteen years (1988-2007). His leadership resulted in the production of award-winning exhibitions and education programs for millions of visitors, students, teachers and parents. Dr. Aprison led project teams to design, fabricate, and install highly successful interactive exhibitions (i.e., Imaging: The Tools of Science, Advanced Photon Source, AIDS: The War Within, NetWorld: The Internet, Genetics: Decoding Life, & Science Storms; total >27,000-sq. ft.; >$13-million).  He also designed and implemented high school outreach education programs linked to these exhibitions.  Dr Aprison received NSF, NIH, Centers for Disease Control and Prevention, HHMI, and other organization's support through competitive grant awards and funding programs. Three of Dr. Aprison's permanent exhibitions (Imaging: The Tools of Science, AIDS: The War Within, and Science Storms) won national award recognitions from the Curators' Committee of the American Association of Museums.

Dr. Aprison joined the Museum of Science and Industry in 1988 after being an NIH post-doctoral specific in the Indiana University Department of Biology.  As an NIH Postdoctral specific review studied the molecular genetics of sex-specific regulation of gene expression in Drosophila melanogaster.  Dr. Aprison also taught undergraduates genetics and developmental biology.  At Brandeis University he investigated the regulation of yolk protein gene expression and DNA synthesis in fully-defined, serum-free cultures of Xenopus laevis parenchymal liver cells.  Dr. Aprison taught undergraduates biology and received his Ph.D. in biology at Brandeis in 1984.


Research Papers

Shelly Wright

Alumni, Research Director,
- Director of Research & Operations, Institute for Genomics & Systems Biology

Shelly Wright

Contact Information

Institute for Genomics & Systems Biology
The University of Chicago
900 East 57th Street
Chicago, IL 60637

Phone: 773-834-0583
Fax: (773) 834-2877
Email: .(JavaScript must be enabled to view this email address)

Bio

Shelly Wright, Director of Research & Operations for the Institute for Genomics & Systems Biology, works with faculty and administrative leaders in the planning, initiation, and management of complex research initiatives across all areas of the IGSB. Her responsibilities include overseeing all areas of IGSB operations.


Research Papers

Danielle Troyer


- Program Manager
- Center for Data Intensive Science
- Robert Grossman Laboratory

Contact Information

University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
10th Floor
Chicago, IL 60637

Phone: (773) 834-0914
Email: .(JavaScript must be enabled to view this email address)>


Research Papers

Ravinesh A. Kumar, Ph.D.

Alumni,
- Director of Research for the Conte Center for Computational Neuropsychiatric Genomics

Contact Information

The University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
Room 10150

Phone: (773) 702-6799
Email: .(JavaScript must be enabled to view this email address)

Bio

Dr Kumar is interested in the genetic and environmental architecture of mental health and illness, including autism, schizophrenia, and psychopathology. As Director of Research for the Conte Center for Computational Neuropsychiatric Genomics, Dr. Kumar directs and manages the research activities, education & training, and major scientific and financial operations of this cross-disciplinary and multi-institutional enterprise, which includes The University of Chicago, Northwestern University, University of Illinois at Chicago, Stanford University, Harvard University, Columbia University, and University of Haifa in Israel. He also spearheads several research projects including 1) molecular genetic studies of conduct disorder, one of the most prevalent forms of child and adolescent psychopathology and 2) evaluating candidate genes for autism and schizophrenia using human induced pluripotent stem cells (iPSCs), neuronal progenitor cells and combinatorial RNA interference (RNAi).

Dr. Kumar joined The University of Chicago as a postdoctoral fellow in 2007 to investigate the genetics of neurodevelopmental disorders, including autism spectrum disorders, severe cortical malformations and epilepsy. He and others demonstrated that 16p11.2 microdeletions are among the most frequent chromosomal abnormalities associated with autism, a discovery that represented one of the top ten scientific achievements in autism research in 2008 (Kumar et al, Human Molecular Genetics, 2008). This work also received the prize for 'Best Biological Research Paper' awarded by the International Society for Autism Research at their annual meeting in 2009. Dr. Kumar was also part of the team that demonstrated that 16p11.2 chromosomal imbalances are implicated in schizophrenia (McCarthy et al, Nature Genetics, 2009) and infantile seizure disorder (Bedoyan et al, American Journal of Medical Genetics, 2010).


In his most recent work with the Conte Center, Dr. Kumar and collaborators Dr. Benjamin Lahey and Dr. Jean Decety are investigating the genetic and structural basis of conduct disorder using molecular genetics and functional magnetic resonance imaging (fMRI). Specifically, the team has selected candidate genes that include ESR1 (estrogen receptor), OXTR (oxytocin receptor), GABRA2 (GABA receptor), MAOA (monoamine oxidase A), 5-HTT (serotonin transporter), AVPR1(arginine vasopressin receptor), and COMT (catechol-O-methyltransferase). The team will look for associations between genetic variants in these genes and brain-behavioral phenotypes relevant to child and adolescent psychopathology.

During his doctoral work at The University of British Columbia in Vancouver, Ravinesh Kumar and colleagues demonstrated that pathologically violent 'fierce' mice are deleted for a single nuclear receptor gene called Nr2e1 (Kumar et al, Genesis, 2004). He went on to test the hypothesis that human NR2E1 underlies brain and behavioral development in neuropsychiatric and related disorders. To bolster this hypothesis, he used molecular, bioinformatic, and evolutionary genetic approaches to study NR2E1 in children with microcephaly (Kumar et al, Genes, Brain and Behavior, 2007), in children with microcepahtly, micropthalmia, ectrodactyly, and prognathism (MMEP) (Kumar et al, BMC Medical Genetics, 2007), and in adults with bipolar disorder, schizophrenia, and pathological aggression, including intermittent explosive disorder (Kumar et al, Neuropsychiatric Genetics, 2008).


During his postdoctoral studies, Dr. Kumar also identified three genetic risk factors for autism, including the seizure-related gene SEZ6L2 (Kumar et al , PLoS ONE, 2009) and two synaptic vesicle genes: APBA2 (Babatz et al, Autism Research, 2009) and RIMS3 (Kumar et al, Journal of Medical Genetics, 2010). In addition, he spearheaded a project that implicated mutations in the alpha tubulin gene TUBA1Awith wide spectrum lissencephaly, making this the first major gene associated with 'lissencephaly with cerebellar hypoplasia (LCH)' (Kumar et al, Human Molecular Genetics, 2010). His postdoctoral work also involved the development of integrated bioinformatics platforms and computational networks-based disease models to provide a conceptual framework for systems-level exploration of complex genotype-phenotype relations in complex disorders. Dr. Kumar hopes to combine his expertise and interests in neurodevelopmental and psychiatric genetics together with strong leadership and administrative skills to help lead the new Conte Center and establish its international identify as a cutting-edge institution for computational neurospsychiatric genomics.

Research


Click here for a complete list of publications


Research Papers

Tongjun Gu

Research Professional,
- Kevin White Laboratory

Contact Information

The Institute for Genomics and Systems Biology
White Lab
The University of Chicago
900 East 57th Street
Chicago, IL 60637

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)

Bio

Tongjun received her PhD. from Institute of Biophysics Chinese Academy of Sciences and did first turn of postdoc in The Jackson Lab. She joined in Kevin White lab in 2013 and works on developing pipelines for analysis of pancreatic cancer whole genome, exome, panel and RNA sequencing data to discover the factors that causing human cancer development. When she was in The Jackson Lab, she developed novel algorithms and pipelines for discovering and quantification of RNA editing (and gene expression) in mouse, further investigated the mechanisms/regulations of RNA editing using QTL (Quantitative Trait loci) mapping approach. She found Apobec1 is the major regulator of C->U editing and the secondary structure is more important than other factors for A->I editing and validated the results by experiments.


Research Papers

Maria Patterson

Research Professional,
- Robert Grossman Laboratory

Contact Information

Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
Room 10140

Phone: (773)-834-0914
Email: .(JavaScript must be enabled to view this email address)

Bio

Maria Patterson received her BA in Physics with a specialization in Astrophysics at the University of Chicago and MS and PhD in Astronomy at New Mexico State University.  As an Astronomy PhD student, she built 3D computer models of the morphology and kinematics of gaseous galaxy halos to study galaxy growth.  She was also Principal Investigator for a deep, wide-field optical survey of nearby galaxies that was able to recover faint star formation and signatures of galaxy mergers undetected in previous observations.

Research

Dr. Patterson currently works with the Open Science Data Cloud, which provides the scientific community with cloud-based storage and computing resources to easily share and manage data and data analysis algorithms.  She is also a lead for Project Matsu, developing cloud-based applications for the automatic processing and analysis of NASA satellite imagery. Matsu is responsible for tools such as the Namibia Early Warning Flood Dashboard, which uses ground and satellite measurements to monitor and evaluate the risk of flood and subsequent water-borne illness in southern Africa.  Dr. Patterson's is interested in using NASA satellite and other Earth science datasets for epidemiological studies.  She is currently studying possible environmental factors influencing the incidence rates of different diseases across the United States.


Research Papers

Trevar Simmons


- Office Assistant, Center for Data Intensive Science
- Robert Grossman Laboratory

Contact Information

Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
Room 10148

Phone: (773) 834-5358
Email: .(JavaScript must be enabled to view this email address)

Bio

Trevar is a graduate student in Religion at the Divinity School. He earned his BA from Palm Beach Atlantic University and an MA & MDiv from Gardner-Webb University.


Research Papers

Zhenyu Zhang


- Bioinformatician
- Robert Grossman Laboratory

Contact Information

The White Lab
Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
Room 10128

Email: .(JavaScript must be enabled to view this email address)

Bio

Zhenyu Zhang received his BA in Biochemistry and MS in Genetics at the Fudan University in China, and MS in Statistics and PhD in Cell and Molecular Biology at the University of Texas at Austin.  He has a wide variety of research experience in both statistical and experimental analysis of genetics, genomics, epigenetics, and pharmacogenomics.  As a PhD student in David Stein’s lab, he studied embryonic pattern formation in Drosophila and yeast gene evolution rate.  As a postdoctoral scholar in Bruce Lahn’s lab and Wei Du’s lab at the University of Chicago, he studied gene expression, DNA methylation and chromosome position in mammalian cells with RNA-seq and DNA deep sequencing, and gene-drug interaction with NCI60 and COSMIC mutation and drug-sensitivity data.  Zhenyu currently works as a bioinformatician in Robert Grossman’s lab at the Center for Data Intensive Science, specializing in analyzing deep sequencing and varies DNA array data.


Research Papers

Heather Scott

Alumni, Research Technician,
- Lab Manager, Kevin White Laboratory

Contact Information

The White Lab
Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
Room KCBD 10240

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)

Bio

I am an experienced Lab Manager who specializes in molecular biology and am always ready to learn new techniques. Currently I am working with various human cell lines and am investigating enhancer activities within those cell lines.


Research Papers

Michael Bolt, Ph.D.

IGSB, Alumni, Postdoc,
- Postdoctoral Scholar
- Kevin White Lab

Contact Information

The White Lab
Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
KCBD 10240

Phone: (713) 876-3484
Email: .(JavaScript must be enabled to view this email address)

Bio

Michael Bolt received his Ph.D. training at Baylor College of Medicine in the department of Molecular & Cellular Biology. During his graduate work he utilized high throughput microscopy to determine crosstalk between nuclear receptors and discover novel regulators of estrogen receptor. His primary research interests lie in transcription regulation and how dysfunction of transcription can lead to oncogenesis.

Research

My research has two primary focuses: 1) determining the function and oncogenic potential of recurrent missense mutations across cancer types using the CRISPR-Cas9 system and 2) defining functional relevance of nuclear receptor-bound and genome-wide enhancer regions.


Research Papers

Jeff Gersch

Alumni,
- Research Technician, Staff

Contact Information

The University of Chicago
Knapp Center for Biomedical Discovery
900 East 57th Street
Chicago, IL 60637
Room KCBD 10240

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)

Bio

I’m currently working as a lab technician on the modENCODE project. This project involves genome-wide mapping of transcription factor binding sites in Drosophila and is funded by NIH. I graduated from the University of Illinois in Urbana Champaign with a B.S. in Integrative Biology and from Southern Illinois University Carbondale with a M.S. in Zoology. My former research has included population genetics in the nurse shark, genetic identification of pallid and shovelnose sturgeon, and population genetics in golden mice.


Research Papers

David Toffey

Alumni, Lab Technician,
- Kevin White Laboratory

Contact Information

The White Lab
Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 E. 57th St.
Chicago, IL, 60637

Phone: 773-834-0074
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Mike Kreiser

Alumni, Lab Technician,
- Kevin White Laboratory

Contact Information

The White Lab
Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 E. 57th St.
Chicago, IL, 60637

Phone: 773-834-0074
Email: .(JavaScript must be enabled to view this email address)


Research Papers

Matthew Kirkey

Alumni, Research Technician,
- Research Technician, Kevin White Laboratory

Contact Information

The White Lab
Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 E. 57th St.
Chicago, IL, 60637

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)

Bio

I work on the ENCODE project, using Drosophila melanogaster as a model organism for ChIP-seq experiments.  I generate DNA libraries for next generation sequencing. With GFP-tagged transgenic fly lines, we elucidate the roles of transcription factors in development and regulation.


Research Papers

Pei-Chun Lin

Alumni, Postdoc,
- Kevin White Laboratory

Contact Information

The White Lab
Department of Human Genetics
The University of Chicago
Knapp Center for Biomedical Discovery
900 E. 57th St.
Chicago, IL, 60637

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)

Research

Research:


My research interests at the White Lab include (1) development of assays to characterize recurrent gene fusions in human cancer; (2) genomic profiling of pancreatic cancer; and (3) establishment of patient-derived xenograft mouse models for in vivo drug screening and biomarker development.


Research Papers

Sean Gibbons

Argonne,
- Dual-Advised Graduate Student; Resident Associate
- Jack Gilbert and Maureen Coleman Laboratories
- IGSB Argonne National Laboratory

Contact Information

Bldg 240, Room 4G17

Phone: 406-552-5677
Email: .(JavaScript must be enabled to view this email address)
Website: http://goo.gl/lM2MCt

Research

I study the ecology and evolution of microbial communities across fluctuating niche landscapes.  I am interested in how the interactions of constituent ensembles within a system coalesce to produce sophisticated emergent behaviors. In particular, I investigate the relationship between ecosystem disturbance and community diversity, the non-linear dynamics of ecological communities at transition points between alternative stable states, and metagenomic patterns along changing environmental gradients.


Research Papers

Daniel Smith

Argonne, Postdoc,
- Current Affiliation: Research Associate Alkek Center for Metagenomics and Microbiome Research
- Previous Affiliation: Jack Gilbert

Contact Information

Bldg 240, Room 4G13

Phone: (630) 252-6257
Email: .(JavaScript must be enabled to view this email address)
Website: http://www.bio.anl.gov/environmental_biology/microbial_lab.php

Research

Daniel uses high-throughput computing to analyze the functional and taxonomic profiles of next-generation sequencing data sets. Most recently he has applied his expertise to the Home Microbiome Project and Hospital Microbiome Projects to examine how humans shape indoor microbial ecosystems over the course of weeks and years.


Research Papers

Julia L. Woods

Alumni, Staff,
- Previous Affiliation: Project Assistant III, Institute for Genomics & Systems Biology
- Current Affiliation: Project Assistant, Martin Marty Center for the Advanced Study of Religion, Divinity School

Contact Information

University of Chicago - IGSB
900 E. 57th Street, KCBD 10100
Chicago, IL 60637

Phone: 773-834-5127
Fax: 773-834-2877
Email: .(JavaScript must be enabled to view this email address)

Bio

Julia Woods was the IGSB Project Assistant from 2012-2013. She left the IGSB for a position at the University of Chicago Divinity School.
 


Research Papers

Jason J. Pitt

PhD Student,
- Kevin White Laboratory

Contact Information

University of Chicago - IGSB
900 E. 57th, KDBD 10240
Chicago, IL 60637

Phone: 773-834-0074
Email: .(JavaScript must be enabled to view this email address)

Research

My broad research interests are in how data-intensive computing can help provide novel insights into biological processes, especially with respect to cancer genomics.

1) Despite decades of research, our understanding of cancer heritability and clonal evolution patterns are limited. Using large data repositories such as The Cancer Genome Atlas, I’m exploring how germline variation can influence the mutational landscape in a variety of malignancies. Elucidating the interplay between germline and somatic variation will provide us with a deeper understanding of cancer susceptibility and disease progression.
2) Processing terabytes of data is a significant burden both in terms of software and hardware. To help maximize resources and alleviate computational constraints on data analysis, I’m interested in developing parallel genomics workflows for high-performance and cloud computing systems.
3) Lastly, one of my longer standing interests is genetic ethics, particularly topics pertaining to genetic exceptionalism


Research Papers

Alex Strassman

Alumni, Staff,
- High-throughput Genomics Analysis Core

Contact Information

The University of Chicago - IGSB
900 E. 57th St., KCBD 10th Floor
Chicago, IL 60628

Email: .(JavaScript must be enabled to view this email address)

Bio

I am interested in research that examines diseases at the genomic level. I believe that a greater understanding of the genetic mutations that occur in disease like cancer will expand and improve the treatment options for patients.


Research Papers

Adam Didier

Alumni, Staff, HGAC,
- High-througput Genomic Analysis Core

Contact Information

The University of Chicago - IGSB
900 E. 57th St., KCBD 10th Floor
Chicago, IL 60628

Email: .(JavaScript must be enabled to view this email address)

Bio

I earned my bachelors at Loyola University in Molecular Biology.  I am interested in human genetics, particularly as it relates to the field of personalized medicine.  Other research interests include artificial chromosomes and cancer biology.


Research Papers

Matt Milton

Alumni, Research Technician,
- Kevin White Laboratory

Contact Information

Institute for Genomics and Systems Biology
The University of Chicago
KCBD Room 10240D
900 E. 57th St.
Chicago, IL, 60637

Phone: (773) 834-0074
Email: .(JavaScript must be enabled to view this email address)

Bio

My primary responsibility is to generate K562 cells stably expressing bacterial artificial chromosomes (BACs) for the ENCyclopedia of DNA Elements (ENCODE) project. Each BAC is engineered to tag a single transcription factor with GFP. After the BAC has been transfected, the expression of the fusion protein is validated via western blot and immunofluorescence staining.  Upon passing both validations, the transcription factors are fixed to DNA for chromatin immunoprecipitation followed by sequencing (ChIP-seq).  Identifying and cataloging the transcription factor binding sites for the known 1800 human transcription factors using ChIP-seq will provide a detailed repository to enable future experiments.


Research Papers

Gina Kuffel

Alumni, Research Technician, Staff,
- High-througput Genomics Analysis Core

Contact Information

The University of Chicago - IGSB
900 E. 57th St. KCBD 10th Floor
Chicago, IL 60637

Email: .(JavaScript must be enabled to view this email address)

Bio

I graduated from Loyola University Chicago with a bachelor’s degree in Bioinformatics and Molecular Biology and a minor in Biostatistics. My research interests include Human genetics, cancer biology, statistical analysis, object oriented programming, SAS programming, computational thinking in metagenomic studies, bioinformatics applications, DNA sequence analysis, and next generation sequencing platforms.


Research Papers

Amy Gill

Alumni, PhD Student,
- Committee on Cancer Biology

Contact Information

Institute for Genomics and Systems Biology
The University of Chicago
KCBD Room 10240D
900 E. 57th St.
Chicago, IL, 60637

Phone: (847) 477-3100
Email: .(JavaScript must be enabled to view this email address)

Research

Cells are continually receiving information about their environment and their health, and in order to survive they must make appropriate responses to this information. This information is gathered and processed using signaling networks, and this information is integrated to make decisions. Though many of the individual proteins in these networks are well-characterized, it is unknown how the cell integrates diverse information to make appropriate decisions.

Cancer is driven by rewiring of signaling networks, leading to inappropriate behavior. For example, cells may grow when they are supposed to remain quiescent, survive when they sustain damage and are expected to die, or migrate when they should stay put; these inappropriate behaviors are the essence of the malignant phenotype.

Using meso-scale proteomics via microwestern array technology, I am investigating the normal behavior of signaling networks and how these networks are deranged in leukemia. I intend to identify the driving forces that cause signaling networks to respond inappropriately in leukemic cells using data-driven modeling, and to identify the most sensitive nodes that could be disrupted to break down an expected response. These driving forces are likely to be excellent targets for therapy, since interfering with the machinery driving inappropriate responses could restore normal behavior to cancer cells. This research can also give insight into how normal signaling processes are deranged to contribute to oncogenesis.


Research Papers

Barbara Stranger

IGSB, Core Member, Fellow,
- Assistant Professor, Department of Medicine, Section of Genetic Medicine

Contact Information

Institute for Genomics and Systems Biology
The University of Chicago
900 E. 57th Street
KCBD 10134
Chicago, IL 60637

Phone: 773-702-4301
Email: .(JavaScript must be enabled to view this email address)
Website: https://aaa-uruk04.cri.uchicago.edu/profiles/display/915383

Bio

Dr. Barbara Stranger has a longstanding interest in population genetics and gene regulatory processes, and how these shape phenotypic variability. Her lab collects and analyzes multi-dimensional human genomics data, particularly transcriptome data and genetic variation data, in the context of health and disease. She had made many contributions to the field of expression QTL (eQTL) mapping in human populations, including large-scale genome-wide eQTL studies in humans, cross-tissue eQTL analysis of a single cohort, analysis of eQTLs in populations of diverse ancestry, sex-specific eQTLs in humans, and others. She has also successfully integrated eQTLs with disease, including cancer and inflammatory diseases, and published methods and resources for doing so. Current projects in her lab integrate regulatory genomics (including transcriptomics and proteomics) with human disease mapping, as well as characterizing the context-specificity of genetic and epigenetic effects on gene regulation (e.g., cell-type, sex, age).


Research Papers

Udaysankar Chockanathan

IGSB, Alumni, Research Technician,
- Previous Affiliation: Michael Rust Lab

Contact Information

The University of Chicago - IGSB
900 E. 57th St. KCBD 10th Floor
Chicago, IL 60628

Email: .(JavaScript must be enabled to view this email address)
Email: .(JavaScript must be enabled to view this email address)

Research

The KaiABC oscillator in cyanobacteria comprises the simplest known circadian rhythm in biology. The mechanism by which such rhythms evolved, however, is still largely unknown. Studying the fitness advantage conferred onto organisms with circadian clocks could elucidate how and why circadian rhythms became such a common feature of life.  By applying selective pressure in the form of interval lighting, I aim to determine the ability of each strain to predict future events (dawn and dusk) based on their circadian clock. I aim for this research to provide insights into both the evolutionary history of circadian rhythms, as well as the underlying biochemical mechanisms of the KaiABC oscillator.


Research Papers

Guillaume Lambert

Postdoc,
- Michael Rust Laboratory

Contact Information

The University of Chicago
KCBD 10123C
900 E 57th Street
Chicago, IL 60637

Phone: (773) 795-5650
Email: .(JavaScript must be enabled to view this email address)

Research

One of the most exciting developments in cell biology is the ability to study and quantify the stochastic variability of an organism’s behavior and phenotype. A fundamental question to ask is: can organisms exploit variations in gene expression, which are intrinsic to all biomolecular processes, to enhance the long-term fitness of populations as they respond to environmental perturbations? Over the next few years, I plan to use a physical approach that combines microfluidics technologies and single-cell biology to better understand the evolution and maintenance of regulatory mechanisms that anticipate fluctuating environments and test if they are beneficial, from an evolutionary point of view, to microorganisms. I particular, I am currently studying whether circadian rhythms—self-sustaining biomolecular clocks that coordinate an organism’s behavior and gene expression with the Earth’s 24 hour day—confer a significant and robust evolutionary advantage to populations of cyanobacteria as they are growing under cyclical light variations.


Research Papers

Jenny Lin

PhD Student,
- BMB, Michael Rust Laboratory

Contact Information

The University of Chicago-IGSB
900 E. 57th, St. KCBD 10th Floor
Chicago, IL 60637

Email: .(JavaScript must be enabled to view this email address)

Research

I am interested in the biochemical mechanism of the KaiABC circadian clock from the cyanobacterium S. elongatus. The three proteins KaiA, KaiC, and KaiC form a circadian oscillator independent of transcriptional/translational feedback mechanisms. The KaiABC clock can be reconstituted in vitro to generate sustained oscillations in the phosphorylation of KaiC with a 24 hour period. In the oscillator, KaiA binds KaiC to activate its kinase activity, leading to its autophosphorylation and KaiB negatively feedbacks on KaiC phosphorylation to inhibit KaiA activity. While it is known that this negative feedback involves the selective binding of KaiB to phosphorylated KaiC, how this leads to KaiA inhibition and KaiC dephosphorylation is still unclear. This is the current focus of my research; I am combining both experimental and computational approaches to define a clearer mechanistic model of the KaiABC oscillator.


Research Papers