Director

Keith Dunker
Professor
Department of Biochemistry and Molecular Biology
(317) 278-9220
kedunker@iupui.edu
Dunker Lab
Publications

Director of the Center for Computational Biology and Bioinformatics; Professor of Biochemistry and Molecular Biology. After receiving his B.S. in Chemistry from UCBerkeley in 1965, he went on to the University of Wisconsin at Madison to earn his M.S. in Physics and his Ph.D. in Biophysics under the direction of Dr. Roland Rueckert. From 1969-1973, he carried out postdoctoral research at Yale University in the laboratory of Donald Marvin where he worked on the structure and cell penetration of the filamentous phage fd. His bioinformatics research goals over the next several years include the improvement of intrinsic disorder predictions, especially with respect to identifying different types of disorder (flavors) and then to understand the relationships between the different types of disorder and protein function, i.e., to understand flavor-function relationships.

Faculty

Jake Chen
Assistant Professor
Department of Informatics and Computer Science
(317) 278-7604
jchen@iupui.edu
Chen Lab

Dr. Jake Chen is an assistant Professor of Informatics and Assistant Professor of Computer Science. He is an IEEE senior member, and co-founder/vice president of Chinese Association of Bioinformatics. After receiving his B.S. in Biochemistry and Molecular Biology from Peking University, he went on to the University of Minnesota to earn both his M.S. and Ph.D. in Computer Science and Engineering. Between 1995 and 2004, he worked at various positions including: the University of Minnesota Computational Biology Center in Minneapolis, MN, Affymetrix, Inc, Santa Clara, CA, and Myriad Proteomics (Prolexys Pharmaceuticals), Inc., Salt Lake City, UT, rising from a research scientist to an industrial bioinformatics department head. His current research interests are biological data management, proteomics, systems and network biology, computational drug discovery, and integrated discovery informatics that combines bioinformatics with molecular diagnosis in human diseases.

Jeesun Jung
Assistant Professor
Department of Medical and Molecular Genetics
(317) 274-3688
jeejung@iupui.edu
Jung Lab
Publications

Assistant Professor of Medical and Molecular Genetics. I received my Ph.D. in statistics from Texas A&M University in 2004, and was trained as a postdoctoral research associate in statistical genetic group of Human Genetics department at the University of Pittsburgh. The main research I am interested in is to develop statistical methodologies for finding susceptibility genes of human complex disease traits and statistical frameworks for genome-wide based genetic linkage and association study.

Xiaoman Shawn Li
Assistant Professor
Department of Medicine, Division of Biostatistics
(317) 278-7273
shawnli@iupui.edu
Li Lab
Publications

Assistant Professor of Medicine, Division of Biostatistics. After receiving his PhD in Mathematics from the University of Southern California under the supervision of Dr. Michael S. Waterman, Dr. Li carried out his postdoctoral research at the Wong Lab at Harvard University then at Stanford University from 2003 to 2005. His research focuses on gene regulation, developmental biology and evolution.

Lang Li
Associate Professor
Division of Biostatistics, Department of Medicine
Indiana Univeristy School of Medicine
(317) 274-4332
lali@iupui.edu
www.biostat.iupui.edu/%7Elangli/

Dr. Li is a full member of the Indiana University Cancer Center. The laboratory is focused on research and training in pharmacokinetics, pharmacogenetics, and system biology. Our pharmacokinetics research covers statistical and computational method and tool development for physiologically based pharmacokinetics model for drug-drug interaction prediction, pharmacokinetics/pharmacodynamics model based trial simulation and study design, and pharmacology data mining. Our pharmacogenetics research focuses on bioinformatical and statistical method and tool development for pharmacology functional and genetic variation definition of drug metabolic enzymes, transporters, and drug targets; and their associations with intermediate biomarkers and clinical outcomes. Our system biology research focuses on bioinformatical and computational method and tool development for estrogen metabolic pathway and estrogen regulation pathway. We currently are developing an integrated system consists of SNPs, gene expression, DNA methylation, histone modifications, transcription regulation, microRNA, and estrogen metabolites.

Yunlong Liu
Assistant Professor
Department of Medicine, Division of Biostatistics
(317) 278-9222
yunliu@iupui.edu
Liu Lab
Publications

Assistant Professor of Medicine, Division of Biostatistics. Dr. Liu received his Ph.D. degree from Weldon School of Biomedical Engineering at Purdue University, and fulfilled his postdoctoral training in Dr. Howard Edenberg's laboratory at Indiana University School of Medicine. During his doctoral and postdoctoral research, Dr. Liu developed a series of mathematical models to identify transcription-factor binding motifs from array-derived gene expression data and genomic DNA sequences. The models demonstrated great potentials in aiding drug development, immunotherapeutics and gene therapy. Dr. Liu's current research interest focuses on developing computational and statistical methodologies in understanding transcriptional and post-transcriptional mechanisms underlying global gene and protein expression patterns.

Samy Meroueh
Assistant Professor
Department of Biochemistry and Molecular Biology
(317) 274-8315
smeroueh@iupui.edu
Meroueh Lab
Publications

Assistant Professor of Biochemistry and Molecular Biology. Samy Meroueh studied chemistry at Wayne State University where he received his Ph.D. under the supervision of William L. Hase. He then joined the group of Shahriar Mobashery as a Walther Cancer Institute Fellow at the University of Notre Dame in South Bend, Indiana. During his tenure in the Mobashery lab he used computational and experimental tools towards understanding the catalytic machinery of enzymes that are involved in antimicrobial resistance and various pathological processes such as cancer. He was also involved in the design and discovery of molecules that would target those enzymes as potential therapeutic agents. His current interests lie in the development and implementation of a more robust scoring function for the purpose of virtual screening, and the use of this scoring function in the search of small molecules that would disrupt macromolecular interactions for the discovery of lead molecules with the potential of becoming clinically relevant. Surface plasmon resonance, isothermal titration calorimetry, as well as various computational tools will be used to characterize the kinetics and thermodynamics of binding for these compounds. His research will focus on three targets, namely the urokinase plasminogen activator system, the bacterial sortases, and the acyltransfer site of the bacterial ribosome.

Sean Mooney
Assistant Professor
Department of Medical and Molecular Genetics
(317) 278-9221
mooney@mail.compbio.iupui.edu
Mooney Lab
Publications

Assistant Professor of Medical Genetics. In 1997, Dr. Mooney received his B.S. with Distinction in Biochemistry and Molecular Biology from the University of Wisconsin at Madison. He received his Ph.D. in 2001 under the advisement of Dr. Teri Klein at the University of California in San Francisco. In 2001, he was awarded an American Cancer Society John Peter Hoffman Fellowship under the advisement of Dr. Russ Altman at Stanford University. His research focuses on sequence and structural approaches to important post-genomic problems by developing and applying computational chemistry and bioinformatics tools.

Pedro Romero
Assistant Professor
School of Informatics
(317) 278-4101
promero@indiana.edu
informatics.iupui.edu

Dr. Romero joined the field of Bioinformatics in 1996, while at Washington State University. During his doctoral studies, he developed the first successful predictors of protein intrinsic disorder from amino acid sequence. As a postdoctoral fellow at SRI International, in Menlo Park, CA, he worked on the development and analysis of pathway-genome databases comprising the BioCyc resource (http://biocyc.org). At SRI International he was involved in the development of pathway-genome databases for several organisms, including HumanCyc, which contain the first version of the human metabolic network predicted entirely from the human genome. Dr. Romero is a member of the BioPathways Consortium, and was Co-chair of the session on Genomes, Pathways and Interactions Bioinformatics at the Pacific Symposium on Biocomputing (PSB) for the years 2001, 2002, and 2003. He recently joined the Center for Computational Biology and Bioinformatics at IUPUI as a visiting scientist, previous to joining the School of Informatics starting in the Fall of 2004. His research interests include the computational analyses of intrinsic disorder in proteins as related to function and evolution, and the computational management and analysis of metabolomics data.

Li Shen
Assistant Professor
Department of Radiology
(317) 278-0498
shenli@iupui.edu
Shen Lab

Assistant Professor of Radiology, Division of Imaging Sciences. Dr. Shen received his Ph.D. degree in Computer Science from Dartmouth College in 2004. From 2004-2007, he was an Assistant Professor of Computer Science and the Director of the Image and Pattern Analysis Lab at UMass Dartmouth. Dr. Shen's research is focused on studying computational methods in the areas of biomedical imaging and bioinformatics. One current emphasis is to develop algorithms for bridging neuroimaging and genomics (e.g., identifying genetic risk factors using imaging as phenotypes). General computational methods of his interest include (1) image & vision computing, (2) data mining & pattern recognition, (3) geometric modeling & graphics.

Yaoqi Zhou
Professor
School of Informatics
(317) 278-7674
yqzhou@iupui.edu
Zhou Lab

Professor, School of Informatics and Center for Computational Biology, School of Medicine. Trained as a theoretical physicist in a chemistry department, Dr. Zhou's research area moves to Chemical Engineering and Computational Biophysics during postdoctoral studies and to Bioinformatics when he became an independent researcher as an Assistant Professor in 2000 at State University of New York at Buffalo. His multidisciplinary training allows him to approach bioinformatic problems from the angle of physics. A recent example is the development of a knowledge-based energy function (called DFIRE) for proteins using the principle of physics rather than pure statistical information of protein structures. His group developed many freely available bioinformatic tools including SPARKS and SP3 for fold recognition and structure prediction, SPEM for multiple sequence alignment, SPINE for secondary and accessible surface area prediction, PINUP for binding-site prediction, MC2 for module identification from network of protein-protein interactions, and THUMBUP for topology prediction of transmembrane helical proteins. The long-term goal of the research in Dr. Zhou's group is to elucidate the relations between the sequence, structure, and function of proteins and to uncover the molecular mechanisms underlying various diseases. This will be accomplished by designing simple (yet realistic) models and by developing statistical mechanics theories and bioinformatic tools.

Staff

Associates

Marcos Betancourt
Assistant Professor
Department of Physics
(317) 274-6910
mrbetanc@iupui.edu
www.physics.iupui.edu

Dr. Betancourt is an Assistant Professor in the Department of Physics. He has a Ms. in Physics and a Ph.D. in Biophysics from University of California, San Diego. He has held postdoctoral positions at the University of Maryland College Park and at SUNY Center of Excellence in Bioinformatics. Dr. Betancourt's current research interest/goal involves the theoretical development of protein coarse-grained models, including the systematic development of effective free energies that can be used for simulating their structure and long time-scale dynamics, and the theory of protein sequence design.

Ernst Dow
Sr. Information Consultant
Eli Lilly and Company
(317) 443-5814
dow@lilly.com
elililly.com

Principle Research Scientist in Bioinformatics. After receiving his B.S. in Chemistry with a Computer Science option from the University of Pittsburgh in 1988, Dr. Dow joined Eli Lilly and Company focusing on computational chemistry. Following an AI Fellowship with Digital Equipment Corporation in neural networks he worked on QSAR and then took an educational leave, obtaining his Ph.D. from the University of Illinois at Urbana-Champaign in Biophysics and Computational Biology under Dr. Thomas Anastasio in 1999. He has been in Bioinformatics leading the effort to gain insight into biology from microarray and other high information content studies.

Birong Liao
Principal Research Scientist
Eli Lilly and Company
(317) 655-1717
liaobi@lilly.com
elililly.com

Dr. Birong Liao is currently a Principal Research Scientist at Integrative Biology Core of Lilly Research Laboratories, coordinating and implementing Informatics technology on the area of Biomarker discovery. Previously, He was the group leader of Expression Profiling Informatics in Pfizer - Ann Arbor laboratories. His research interests are in the area of date integration using principles and theories of mathematics / statistics /physics on data from genetics, genomics, proteomics, metabolomics, in combination with literature mining and network analysis to understand the mechanisms of efficacy and toxicity resulting from drug intervention on disease models, with the goal of predicating better drug targets and biomarkers. Most recently, he is applying these technologies in two therapeutic areas, i. e. atherosclerosis / cardiovascular disease and cancer. He frequently presents his research in academics and industry forums.

Predrag Radivojac
Assistant Professor
School of Informatics
(812) 856-1851
predrag@indiana.edu
informatics.iupui.edu

Assistant Professor of Informatics, Indiana University. Predrag Radivojac received his Ph.D. degree in Computer and Information Sciences from Temple University in 2003 under the direction of Zoran Obradovic. In 2004 he held a pos-doctoral position in Keith Dunker's lab at Indiana University School of Medicine, after which he joined School of Informatics, Indiana University at Bloomington. Prof. Radivojac's research interests are in protein bioinformatics, proteomics, and machine learning/data mining.

Chen Su
Principal Research Scientist
Eli Lilly and Company
(317) 277-9657
chen_su@lilly.com
elililly.com

Dr. Chen Su joined Eli Lilly and company as a senior biologist in 2000 and was promoted to principal research scientist in 2003. She received her Ph.D. in computational biology in 2000 from Penn State, where she established relationships between genetic polymorphism of immune system genes and immune functions. She earned her B.S. in biochemistry and molecular biology from Beijing University in 1995. Dr. Su has focused on combining computational, statistical, and biological approaches to analyze genomic, proteomic, and physiological data in large-scale genomics experiments. She has successfully applied these methodologies to support multiple discovery programs, toxicology studies, and clinical trials. Her work has contributed to increased efficiency of bench labs; identification of novel drug targets; and putative biomarkers for obesity, cancer, and toxicology. Dr. Su currently leads several multidisciplinary efforts in biomarker identification and drug mechanisms of action. Dr. Su holds a publication record with 21 peer-reviewed original research papers and numerous conference presentations. She has won multiple prestigious awards from Lilly Research Laboratories and has been invited to teach at Lilly University and major academic institutes. She is also the recipient of '2004 Young Innovator' awarded by the Science Spectrum magazine.