Microarray technology allows researchers to study how genes interact with environmental factors, such as toxins or bacteria, to heighten susceptibility to disease. Bioinformatics helps to analyze the resulting data. The image above highlights genes important to the growth of Mycobacterium tuberculosis, the cause of tuberculosis.

"In the past, experiments did not involve such large data sets," observed Dyann Wirth, professor of infectious diseases in the Department of Immunology and Infectious Diseases and member of the advisory group for the core. "There has been a dramatic change in the past five to 10 years in the amount and availability of genomic data [or the DNA sequences themselves] and functional genomic data, [or the sequences’ purpose]." In the past five years alone, the genomes of humans, rats, and the malaria parasite Plasmodium Falciparum have been published, for example.

Simply defined, bioinformatics is the management of data derived from biological research. The field has come to the fore recently due to an exponential growth in data fueled by increasingly powerful computers and other technologies. Bioinformatics bridges computer science to fields as varied as statistics, genetics and genomics, biochemistry, immunology, and epidemiology.

"One of the purposes of bioinformatics is to reduce the number of experiments that need to be done to achieve reliable information," said L.J. Wei, professor of biostatistics in the Department of Biostatistics and member of the advisory group for the core. "However, an issue right now is that there are huge data sets that can be run through different kinds of software programs, ending up with many data points. Unless we understand and use bioinformatics well, we may not even know which of those data points are important."

In addition to Wirth and Wei, members of the Bioinformatics Core advisory group are:

• Xiaole (Shirley) Liu, assistant professor of biostatistics, Department of Biostatistics, and assistant professor of biostatistical sciences, Dana-Farber Cancer Institute

• Cheng Li,assistant professor of biostatistics, Department of Biostatistics, and assistant professor of biostatistical sciences, Dana-Farber Cancer Institute

• Peter Kraft, assistant professor of epidemiology, Department of Epidemiology

• Igor Kramnik, assistant professor of immunology and infectious diseases, Department of Immunology and Infectious Diseases

• Dieter Wolf, James Stevens Simmons Associate Professor of Molecular Oncology, Department of Genetics and Complex Diseases

• Alix Smullin, chief of staff, Office of the Dean

• Xin Lu, research scientist, Department of Biostatistics

Lu has been hired by the Office of the Dean as a part-time bioinformatics specialist to coordinate the core. Based in the Department of Biostatistics, he has helped develop http://www.hsph.harvard.edu/bioinfocore/, the core’s website. "This is a relatively nascent science," said Lu. "The idea is to create a community of researchers who represent varied fields and who are interested in becoming better-versed in bioinformatics. To some degree, we are all learning about this field. Why not learn together?"

The new core fulfills a number of functions:

Workshops–Monthly forums have been scheduled in which faculty members and researchers can discuss work in progress. Attendees can offer suggestions and insights, while learning more about how bioinformatics can help achieve specific research goals. Shirley Liu presented the first workshop on September 15, speaking about "Transcription Factor Sequence Motif Discovery and an Integrated Approach to Bacteria Operon Prediction." Slides for the talk are available on the core’s web site. The next workshop is on Wednesday, October 20 from 12:30 p.m. to 1:20 p.m. in FXB G-12. See below.

Training–Step-by-step tutorials on a number of software packages are available on the core’s web site.

Online resources–The core’s web site features links to databases for information on genetics, proteins, and transcription factors; web sites of other research groups involved in bioinformatics; and software for statistics, data integration, microarray analysis, SNPs haplotype analysis, linkage disequilibrium mapping, and motif finding.

Consulting services–Lu is available to offer suggestions on how to use bioinformatics tools in specific research projects. He has established office hours on Tuesdays and Wednesdays from 1 p.m. to 2 p.m. in SPHII-434 and can refer researchers to other bioinformatics specialists when necessary.

Collaborations–Through the workshops and consultations with Lu, the core is designed to help bring together scientists tackling similar research questions. The goal is to provide them with a forum to work together or exchange advice on methodologies.

A number of faculty are already seeking how the new core will be able to help advance their research agendas. Wolf heads the Kresge Center Proteomics Facility at HSPH and has received notice of funding through the Taplin Family Funds for Discovery for a Linux computer cluster. Once running, the cluster should provide reams of proteomics data, and Wolf is hoping that the bioinformatics core will help guide him on how to manage that information.

Kramnik, who studies immunity, is hoping the core will help him analyze data regarding host susceptibility to tuberculosis and to other infectious diseases. "I have been around the field of biology enough to see how it has changed in the past 10 years," said Kramnik. "Before, you could work in biology and not need the tools of bioinformatics but now, if you do not use them, I think you may miss out on potentially important data."

Questions can be directed to Xin Lu at 617-432-4915 and e-mailed to xinlu@hsph.harvard.edu.

Schedule of Monthly Workshops for Bioinformatics Core Announced

Wednesday, October 20

"Haplotype Inference, Haplotype Block Partition, and HtSNP Selection"

Speaker: Tianhua (Tim) Niu, assistant professor of medicine, Harvard Medical School, and research scientist, Department of Environmental Health

	Shirley Liu presented the first workshop in the Bioinformatics Core in September. The next workshop is on October 20.

Wednesday, November 17

"Analysis of the Intracellular Pathogen Resistance Gene 1 (Ipr1) Function in Macrophages Using Gene Expression Profiling"

Speakers: Cheng Li, assistant professor of biostatistics, Department of Biostatistics, and assistant professor of biostatistical sciences, Dana-Farber Cancer Institute, and Atabak Royaee, research fellow, Department of Immunology and Infectious Diseases

Wednesday, December 15

"SNP Selection for Candidate Gene Association Studies"

Speakers: Peter Kraft, assistant professor of epidemiology, Department of Epidemiology, and Rulla Tamimi, instructor in medicine, Brigham and Women’s Hospital, and instructor, Department of Epidemiology