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Genomics

The recent explosion of new knowledge about the essential properties of life--as gleaned from the Human Genome Project and other similar efforts--along with rapid-fire advances in computer technology have laid the foundation for the development of the rapidly emerging fields of bioinformatics and computational biology. These disciplines deal with the management, analysis, and visualization of the flood of information generated in molecular biology, genomics, and other areas of biology and biomedicine. These fields not only provide the tools and infrastructure necessary to support biological research into the next century, but are challenging areas of research in their own right. Progress in bioinformatics and computational biology requires that biologists, computer scientists, and mathematicians work in close collaboration, with significant cross-disciplinary training.

Bioinformatics at Penn

To provide an academic base for continuing research and education in this nascent field, a Center for Bioinformatics has been established at the University of Pennsylvania. The Center draws faculty from the Schools of Medicine (SOM), Engineering and Applied Science (SEAS), and Arts and Sciences (SAS). Among only a handful of academic groups dedicated strictly to bioinformatics, the new Center's base of operations rests in the Institute for Medicine and Engineering, an organizational blending of medical and engineering faculties to support enhanced research, educational and business initiatives for bioengineering projects. It is jointly sponsored by the Institute for Research in Cognitive Science (IRCS), and is directed by Susan Davidson (Computer and Information Science, SEAS), Interim-Director; and Warren Ewens (Biology, SAS), Associate Director in charge of education. The Center is housed in Blockley Hall, and provides a common ground for a number of research groups in bioinformatics. These research groups at present include CBIL (see below) and the Database Research Group (see http://db.cis.upenn.edu). In addition, it is the focus for education in genomics (see Education/Bioinformatics).

Computational Biology and Informatics Laboratory (CBIL)

Research in genomics at the Computational Biology and Informatics Laboratory (CBIL) is directed toward the building of databases and the development and application of data management and data analysis tools. At the genome level, computational and manual annotation of genomic sequence and transcribed sequences is underway for human and mouse. The annotation and sequence is now captured in a Genomics Unified Schema database which has merged prototype specialized databases developed at CBIL. The goal is to provide a comprehensive catalog of all human and mouse genes. This genome-wide effort provides a foundation for research at CBIL in functional genomics that is focused at the systems level (e.g., hematopoieis, CNS/behavior, pancreas development, endothelial cells). Gene expression data (EST libraries, arrays, SAGE) is used with annotated sequence to elucidate mechanisms of cellular development and differentiation.

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Penn Bioinformatics Forum

To foster closer collaboration with the pharmaceutical and biotech. industries, the Penn Bioinformatics Forum (PBF) was established in the fall of 1996. PBF is a seminar series whose purpose is to provide a neutral location for people involved in Bioinformatics to learn about recent advances from experts in the field, to exchange ideas and hold discussions about issues of common concern. Monthly speakers come from industry as well as academia, and draw visitors from the general bioinformatics community in the greater Philadelphia area and from as far away as Washington D.C.

Transcription Profiling

The technology to measure the expression of many genes from isolated tissues and even in single cells is well-developed at Penn. An NIH-funded Microarray Center is under development in the Department of Pathology and Laboratory Medicine, jointly with the University of Pennsylvania Cancer Center. RNA amplification for high-throughput transcription profiling in cells is conducted in the Department of Pharmacology, and at the Institute for Medicine and Engineering (IME) in a collaboration with AstraZeneca Pharmaceuticals.

For more information on Pennís Center for Bioinformatics, please visit http://www.pcbi.upenn.edu/

For more information on the Penn Bioinformatics Forum, please visit http://www.pcbi.upenn.edu/forum.php3

For more information on the Computational Biology and Informatics Laboratory (CBIL), please visit http://www.cbil.upenn.edu/

For more information on the University of Pennsylvania Cancer Center, please visit http://www.oncolink.upenn.edu/upcc/

For more information on Pennís Institute for Medicine and Engineering, please visit http://www.med.upenn.edu/ime/

For more information on Pennís Institute for Research on Cognitive Science, please visit http://www.ircs.upenn.edu/

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Biological Engineering Network at the University of Pennsylvania
1010 Vagelos Research Labs / 3340 Smith Walk / Philadelphia PA 19104-6383
tel. 215-573-6813 ~ fax. 215-573-6815 ~ e-mail: ben-penn@pobox.upenn.edu