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Systems and Network Biology Laboratories (IU School of Informatics / Informatics Research Institute)

Led by Director Dr. Jake Chen and founding member Dr. Mathew Palakal, the two bioinformatics laboratories develop and maintains the most comprehensive biological knowledge on systems and network biology databases on campus. The laboratories provide users with the following uniquely developed database resources: BioMap, a PubMed literature-based data warehouse that provides a rapid ability for users to survey published literature and perform disease target and new drug discovery, a database of human annotated and predicted protein interactions (HAPPI), which contains more than 140,000 human protein interactions, and most recently, a database for healthy human individuals integrated plasma proteome (HIP2). Computational tools provided include ProteoLens, a visual data mining tool for network biology studies. For additional information about the laboratories, visit the web site here.

Macromolecular Sequence Analysis and Structure Genomics Lab (School of Informatics / Center for Computational Biology and Bioinformatics)

Led by co-director Dr. Yaoqi Zhou, the lab is the only facility on campus that provides a comprehensive collection of in-house bioinformatics tools for all aspects of sequence-structure-function analysis. The laboratory currently hosts SPEM for multiple sequence alignment & conserved motifs discovery in biological sequences, TUPS and SPINE for transmembrane helical topology finding and protein structural property findings, a suite of protein tertiary structure prediction/analysis tools, DFIRE for protein binding affinity and binding site prediction tools for protein interaction interface predictions, MC2 for protein interaction network functional module predictions, and TCD for protein folding kinetics predictions. For additional information about the lab, visit the web site here.

Bio-sample Repository (Clarian / Methodist Hospital)

Led by co-PI Frank Lloyd, MD, director of the Methodist Research Institute (MRI) and MRI’s bio-sample repository, the repository has been in continuous operation since 1998 and currently collects over 3,500 samples a year. It collects surgical tissues along with a wide variety of biological fluids according to the investigators’ criteria. It also collects cancer tissues, snap frozen and stored for future genomic/proteomic analysis. The Clarian Institutional Review Board along with the Bio-repository Ethical Committee oversees all of the Bio-repository operations. Patients are consented using HIPAA standards for both specimens and clinical data. A large secure database is used for tracing and annotation, which will be freely available for use by the CSBPM. A medical director and three full time procurement technicians are currently employed. A clinical annotated bio-repository will allow translational research to be integrated into the Center’s emphasis on biomedical research.

Translational Genomics Core (IU School of Medicine)

Led by co-director Sunil Badve, MD, the core provides consultation, technical advice, and collaboration to perform expression analysis from archival formalin-fixed paraffin-embedded tissues utilizing the DNA-annealation selection and ligation (DASL) technology, based on the Illumina platform. In addition, analyses of single nucleotide polymorphisms (SNPs) is also performed at the Core. The Core is capable of performing whole genome expression analysis. This Core also can help users gain access to the archival paraffin resources of the Clarian Pathology Laboratory, consisting of approximately 50,000 samples a year. For additional information, visit the web site here.

Center for Medical Genomics (IU School of Medicine)

Led by co-PI Dr. Edenberg, Center for Medical Genomics provides infrastructure and consulting for use of genomic technology in studies of disease and in other biomedical research. It will pursue further development of these technologies, and assist investigators in their use: 1) Microarrays. Experiments using microarray technology will provide clues to diagnoses and prognoses of diseases, treatment choices, drug design, and fundamental understanding of biology. 2) High-throughput Genotyping. Genes influence all of our physiological and pathological processes. Individual differences in gene sequence lead to differences in the risk for diseases and in the response to treatment. Experiments using high-throughput genotyping will enable us to study how genes influence disease and treatment in large populations. For additional information about the center, visit the web site here.

Proteomics Service Core (IU School of Medicine)

Led by co-director Dr. Mu Wang, the core is part of an IUSM Proteomics Core facility, it provides state-of-the-art proteomic tools for protein identification, quantification, and characterization on a fee-for-service basis. The facility is equipped with 3 ThermoFinnigan LTQ, 1 Micromass Q-TOF, 1 Micromass MALDI-TOF, and 1 ABI 4000 QTrap mass spectrometers. The facility currently has 9 scientific staff members. The Proteomics Core Facility will donate 300 consulting hours to CSBPM users who utilize more than one core facility for their project. For additional information, visit the web site here.

Biostatistics and Statistical Genetics Lab (IU Center for Computational Biology and Bioinformatics / Medical & Molecular Genetics)

Led by co-PI Dr. Jeesun Jung, the lab develops statistical, mathematical, and computational methods to help users solve scientific questions in biomedical genetics. The current research and services involve (1) development of reliable statistical models to identify genetic variants causing complex human disease such as asthma and hypertension, which have been longitudinally studied with the accumulation of a large amount of data, (2) genome-wide linkage analysis using 10K Affymetrix SNP chip technology and genome-wide association study genotyped by more than 100K SNP technology, and (3) establishing a statistical framework for association studies of SNP haplotype-based data. Biostatistics service and additional consulting are also available to develop new statistical methodologies for extracting valuable information from integrated system and omics results. For additional information about the research by Dr. Jung, visit the web site here.

Advanced Information Technology Core (IU University Information Technology Services)

Led by Dr. Bill Barnett, the Advanced IT Core (AITC) assists researchers in using advanced information technologies provided by the Research Technologies  (RT) division of University Information Technology Services (UITS).  As a liaison between researchers and RT services, the goal of this Core is to provide high performance technology solutions to problems confronted by IUSM research and partner in innovative approaches to medical research.  In particular, AITC helps researchers overcome the challenges of: exponential growth and increasing complexity of research data, the need for orders of magnitude increase in computational power for analysis, and requirements for robust and scalable applications for dissemination, and participation in national consortia. The AITC helps researchers in health care and related sciences to maximize data analysis, protect and store data, visualize information, and disseminate results nationally and internationally.  It provides access to IU supercomputers and parallel computing applications, high capacity data storage, visualization environments, and an secure and reliable cyberinfrastructure.