People

Dr. Nicholas Chia | chia@guava.physics.uiuc.edu

- Postdoctoral Researcher, Institute for Genomic Biology
- Ph.D., Physics, Ohio State University

Personal Website

The focus of my research approaches biology along two main fronts – a physics approach to theoretical prediction in biology, and a bioinformatics/systems biology approach toward observation and hypothesis testing.

Dr. Cory Funk | cfunk@systemsbiology.org

- Postdoctoral Researcher, Institute for Systems Biology
- Ph.D., University of Illinois at Urbana-Champaign, 2010

Dr. Pan-Jun Kim | extutor@illinois.edu

- Postdoctoral Researcher, Institute for Genomic Biology
- Ph.D., Physics, KAIST, 2008

Interaction among many simple and identical elements as well as selective and nonlinear communication of different multifunctional elements with others leads to the system’s complex and coherent behavior. For the successful study on systems biology, we have to cope with the bewildering complexity of biological systems, covering a wide range of scales in time and space. Complex network theory within the extended scope of statistical physics, and nonlinear dynamics of spatio-temporally extended media, are extremely useful in investigating such biological complexity, and are the key tools I'm employing for my research.

Dr. Youn-Hee Ko | younko@illinois.edu

- Ph.D., CS, University of Illinois at Urbana-Champaign, 2010
- M.S., CSE, Korea University, 2003
- B.S., CSE, Korea University, 2001

Personal Website

My research interests are focused on devoloping statistical methods to understand complex biological mechanisms. I have applied grahical models to infer gene networks using Bayesian networks and mixture models. Currently I am working on identifying cell-type specific transcripts in the brain, which can be at core of discovering biomarkers for blood diagnostics.

Dr. Charu Gupta Kumar | cgkumar@illinois.edu

- Postdoctoral Researcher, Institute for Genomic Biology
- Ph.D., Animal Sciences, University of Illiniois, Urbana-Champaign, 2008

Curriculum Vitae | Personal Website

I am interested in using genomics and systems biology to explore questions related to transcriptional regulation and evolution of coding genes, non-coding RNA, and hard-to-annotate genes such as novel genes and metagenomic sequence. I would like to apply these interests specifically to the study of functions (and dysfunctions) within brain systems. My time outside of work is devoted to my family and reading. Beyond this I like to listen to music, cook, watch movies especially old classics, go for long walks...

Jaeyun Sung | sung4@illinois.edu

- Ph.D. Student (5^th year), Dept. of Chemical and Biomolecular Engineering
- M.S., Chemical and Biomolecular Engineering, UIUC, 2008,
- B.S., Chemical and Biomolecular Engineering, Georgia Institute of Technology, 2005

Curriculum Vitae

My research interests are in the field of systems medicine.  I use a combined computational-experimental approach to analyze global patterns in gene-expression and extracellular protein secretion from organ-specific disease specimens to drive the discovery of biomarkers that allow early detection and accurate classification.  Once the biomarkers are known, I aim to elucidate the causal perturbations inside intracellular networks.  This would allow us a better understanding of the molecular state of the cell during disease manifestation.  Apart from indulging myself with such academic endeavors, I look out for great places to eat and drink, or catch a good rock concert whenever I get the chance.

James Eddy | eddy2@illinois.edu

- Ph.D. Student (4^th year), Dept. of Bioengineering
- M.S., Bioengineering, UIUC, 2010
- B.S., Biomedical Engineering, University of Virginia, 2007

Curriculum Vitae

I'm interested in the application of systems biology models and tools in understanding, diagnosing, treating, and preventing human disease. In particular, I'd like to explore the power of in silico models to integrate different types of biological data and processes. Most of my current research is focused on cancer, but I also have a strong interest in immunology. I enjoy listening to lots of music (and writing/playing it when I have the time).

Caroline Milne | cmilne2@illinois.edu

- Ph.D. Student (4^th year), Dept. of Chemical and Biomolecular Engineering
- B.S., Chemical and Biomolecular Engineering, University of Cornell, 2007

Curriculum Vitae

I'm interested in using systems biology approaches to metabolically engineer organisms for biofuel production and in developing new methods for rapidly modeling lesser-characterized organisms. Outside of the lab I enjoy hanging out with friends, alpine and water skiing when I can, rock climbing, being outdoors, cooking, watching movies, listening to music, knitting...

Sriram Chandrasekaran | chandra6@illinois.edu

- Ph.D. Student (3^rd year), Dept. of Biophysics and Computational Biology
- B. Tech Biotechnology, Anna University, 2008

Personal Website

My current research focuses on reverse engineering and modeling cellular networks. I am coming up with new strategies for network inference and integrating it with metabolism in cancer and in the brain. Other projects include identifying candidate blood markers for brain cancer and studying criticality in biological systems. Outside the lab, I spend time playing cricket and racquet ball. I love trekking and have a penchant for outdoor photography. I sometimes help in organizing events for ASHA (a charity organization) and I also work for the IBS (Illinois Biophysics Society) newsletter.

Matthew Gonnerman | gonnerm1@illinois.edu

- Ph.D. Student (3^rd year), Dept. of Chemical and Biomolecular Engineering
- B.S., Chemical and Biomolecular Engineering, University of Nebraska, 2008

My current research concerns network scale kinetic models in biological systems.  Kinetic parameters cannot be measured accurately and consistently within organisms, which hinders traditional approaches to gathering in vivo kinetic data.  My research uses mathematical techniques along with available metabolomic and proteomic data of an organism to produce solution sets containing kinetic rate constants for the system.  Outside the lab, I enjoy golfing, bowling, watching movies (especially comedies), and cooking/baking.  If I have any time left, you can find me playing video games. 

Andrew Magis | magis1@illinois.edu

- Ph.D. Student (3^rd year), Center for Biophysics and Computational Biology
- M.S., Computer Science, University of Florida, 2008
- B.S., Computer Science, Harvey Mudd College, 2003

Curriculum Vitae

I am interested in using graphics processing units to accelerate the analysis of expression and network data for marker discovery and disease diagnosis. My current project is to develop novel algorithms for disease diagnosis from expression data implemented on the GPU. I am also interested in regulatory network inference using mutual information and regression. Outside of the lab I enjoy reading, playing guitar, and watching Masterpiece Mysteries!

Chunjing Wang | wang130@illinois.edu

- Ph.D. Student (3^rd year), Dept. of Chemical and Biomolecular Engineering
- BASc., Biomedical Engineering, University of Toronto, 2008 

Curriculum Vitae

I am interested in using system biology tools to identify potential diagnostic markers for cancer classification. More specifically, I hope to find efficient genetic markers to define previously unrecognized tumor subtypes (class discovery) and assign particular tumor samples to already-defined classes (class prediction). I like reading (especially Chinese martial arts novels), listening to music, watching movies, and swimming.

Daniel Baker | baker28@igb.uiuc.edu

- Ph.D. Student (2^nd year), Center for Biophysics and Computational Biology
- Predoctoral Fellowship, Beckman Institute for Advanced Technology (with Klaus Schulten)
- B.A., Physics and Biology (Pre-Med), Ball State University, 2008 (at age 18)

My research interests consist, in principle, of understanding complex biological systems through a lens of theoretical statistical physics and computational means. Specifically, these manifest in the lab's directions on the systems biology of cancer and synthetic biology/cellular engineering. Outside of the lab, I'm interested in particle physics, protein folding, and the neuropsychobiology of consciousness and spirituality. Outside of science, I love classical music, dystopian and classic literature, existentialism and aestheticism in the arts.

Matthew Benedict | benedic1@illinois.edu

- Ph.D. Student (2^nd year), Dept. of Chemical and Biomolecular Engineering
- B.S., Chemical Engineering, University of Connecticut, 2008

I am currently working on the development of an accurate metabolic and regulatory network reconstruction for M. acetivorans, a marine methane-producing archaea. Such a reconstruction will further our understanding of the global carbon cycle and help guide the development of biologically derived methane as an economically viable alternative energy source. Outside of the lab, I enjoy running, gardening, and reading.

Piyush Labhsetwar | labhset1@illinois.edu

- Ph.D. Student (2^nd year), Center for Biophysics and Computational Biology
- M. Tech., Biotechnology, Indian Institute of Technology, Madras, 2009
- B. Tech., Biotechnology, Indian Institute of Technology, Madras, 2009

Curriculum Vitae

I am working on integrating dynamic models for metabolic network with Flux Balance Analysis (FBA) models. Dynamic models include ordinary differential equation (ODE) models as well as stochastic models. In future, I aim to study how noise propagates in a biochemical network to produce cellular phenotypes. For this I will combine genome scale metabolic network with whole cell spatial models for stochastic modeling developed by Zan Schulten. Validation on E. coli will be followed by application in methanogens. My hobbies include travelling, running, hiking, adventure sports, music, reading about science, watching documentaries and most importantly partying and hanging out with friends.

Shuyi Ma | shuyima1@illinois.edu

- Ph.D. Student (2^nd year), Dept. of Chemical and Biomolecular Engineering
- B.S., Chemical Engineering, California Institute of Technology, 2009

Curriculum Vitae

I am interested in how biochemical networks evolve within organisms and the effect of network perturbations on the physiological state of the organism. My current work on lung disease diagnosis seeks to probe telltale expression signatures in the transcriptome that are indicative of different lung health states. Outside the lab, I enjoy reading, skating, and drawing.

Yuliang Wang | wang341@illinois.edu

- Ph.D. Student (2^nd year), Dept. of Chemical and Biomolecular Engineering
- B.S., Bioengineering, Tianjin University, 2009

Curriculum Vitae

I am interested in using various machine learning methods to mine omics data, especially microarray data, in order to find potential biomarkers for human disease diagnosis and treatment. I also have a huge interest in biological network analysis. My current research is to mine liver microarray data to find unique transcriptomic signatures for various liver diseases that may lead to potential biomarkers.

John Earls | earls3@illinois.edu

- Ph.D. Student (-0.4 year), Dept. of Computer Science
- M.S. Bioinformatics Student, Dept. of Computer Science, Degree in Spring 2011
- B.S., Computer Science, Illinois State University, 2008

Curriculum Vitae

I was raised in Spring Valley, IL. I originally went to the UIC as an English major, but dropped out to pursue software development. After several years, I went to Illinois State and graduated with Honors in 2008. I then came to the U of I to get a Masters Degree in Bioinformatics which I will receive this Spring.   I will start a Ph.D. in Computer Science in the Fall.  My interests include machine learning, pattern matching and software engineering. Since then UIUC I have TA'd CS 225, Data Structures in C++, for 4 semesters and instructed the course last summer.  I enjoy bringing together biology and computation.  I believe this work can make a real difference in the world.

Matthew Richards | maricha2@illinois.edu

- Ph.D. Student (1^st year), Dept. of Chemical and Biomolecular Engineering
- B.S., Chemical and Biomolecular Engineering, University of California, Berkeley, 2010

My work is currently focused on developing an algorithm that can determine minimal growth media based on limited genomic data. A successful model could greatly expand the very limited number of organisms that could be grown in a laboratory setting. When I'm not working, I enjoy baking, trying new foods, collecting different kinds of hot sauce, and playing foosball and underwater hockey.

Bozena Sawicka | sawicka3@illinois.edu

- Ph.D. Student (1^st year), Dept. of Chemical and Biomolecular Engineering
- B.S., Chemical and Biomolecular Engineering, UIUC, 2010

I was born and raised in Poland. At the age of 19, I moved to the United States. My research interests are in the field of systems medicine. Throughout my graduate education I will use the combined computational-experimental approach to develop models for disease diagnostics. My current project is focused on the regulatory and signaling networks of glioblastoma (brain cancer). Outside of the lab, I enjoy running, baking and watching Big Bang Theory. Also, I have the sweetest Shih Tzu puppy called Laplace.

Soroush Ardekani | sardek2@illinois.edu

- Dept. of Chemical and Biomolecular Engineering (Class of 2011)

I am currently working with Shuyi Ma and James Eddy on the global study of disease. My project specifically targets lung disease and consists of using gene expression data to determine pathway conservation and perturbation within those diseases. In the future this information could be used to help clinical patients with disease classification. Outside of my academics and research I enjoy watching movies, staying active, and catching up with friends on the quad.

Bobak Hadidi | bhadidi2@illinois.edu

- Undergraduate (Class of 2011), Dept. of Computer Science

I am principally interested in the application of computational and quantitative methods to understanding questions of biological significance, with an eye towards the treatment of terminal illness. My current work focuses on adaption of the Differential Rank Conservation (DIRAC) technique developed by James Eddy for use without a priori-known pathways or networks. To this end, I am using novel clustering techniques in conjunction with massive microarray datasets and protein-protein interaction information integrated from several sources. With these tools, we can identify network-scale pertubations in a phenotype-variable population, say, those with or without carcinoma in distinct stages. As a member of the Illinois iGEM team, I am also involved in developing software tools for the nascent field of Synthetic Biology. Computer Science and Biology aside, most every field of human inquiry which exists under the sun, formal or not, provokes my curiosity. My free time is often spent playing my guitar (or resisting the urge to), enjoying music, reading, running, hiking, or playing the beautiful game (soccer).

Austin Lee-Richerson | aleeric2@illinois.edu

- Undergraduate (Class of 2011), Dept. of Bioengineering

I am currently working with James Eddy to develop a metabolic reconstruction of glial cells and glioblastoma multiforme (GBM).  This project will hopefully be a precursor to a full in silico model of GBM, which can be used to potentially locate metabolic targets for therapy.  Outside of the lab I am heavily involved in the local chapter of the Biomedical Engineering Society and reviving the Chi Phi fraternity on the Illinois campus.  I enjoy reading (my favorite author is David Sedaris), canoeing, and playing cards.

Nassim Ajami | najami2@illinois.edu

- Undergraduate (Class of 2012), Dept. of Chemical and Biomolecular Engineering

I am currently working with Matthew Richards in developing an algorithm that can determine media components necessary to grow an organism culture, given genomic information on that organism. If successful, the algorithm could dramatically expand the number of organisms that are able to be studied in vitro, which would allow researchers to explore new avenues in microbiology. Working on this project has exposed me to a new way of thinking about biology that I find exciting and inspiring. Outside of research, I enjoy playing music, staying active, and learning new things.

Andrea Herrmann | aherrmann1989@gmail.com

- Undergraduate (Class of 2012), Dept. of Chemical and Biomolecular Engineering

I am working under Matt Richards and am helping research organisms and the media they grow in for the algorithm that he's developing. I enjoy horseback riding and cooking.