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Stuart Brown, Director, Research Computing at NYU Medical Center


AT A GLANCE : PhD in Plant Molecular Biology from Cornell University, 1992 (laboratory of Olen Yoder, Plant Pathology).

Author of Bioinformatics: A Biologist’s Guide to Biocomputing and the Internet.

Enjoys playing hockey, Frisbee, soccer, and foosball with his kids.

QWhere will bioinformatics be in two years? Five years?

AIt will be more thoroughly integrated into the daily lives of most biologists and health care professionals.

QWhat are the biggest challenges the field of bioinformatics faces?

AThe biggest challenge is integration of various data sets — genome, gene expression, proteomics, protein-protein interactions, metabolic and regulatory pathways. There’s also the challenge of collaborative annotation — capturing the gene-specific knowledge of the community of biologists in our databases and making it available to everyone in a peer-reviewed fashion.

QHow does the near completion of the human genome project affect funding for university-based research?

AThis is a great time for biologists. The availability of all of this data makes so many new lines of research possible. Funding for academic biology research from agencies like NIH will continue to rise dramatically. Collaborations between the biotech/pharmaceutical industry and Universities will also continue to increase.

QHow do you compete with companies to attract and retain qualified bioinformaticists?

AWe don’t compete and we don’t retain. We take students/postdocs/early-stage faculty members and train them in bioinformatics. As they gain skills they leave for better paying jobs in industry. It takes a special sort of person to choose an academic career. We cannot hire trained bioinformatics staff people; there simply is no pool of qualified people. We can only hire biologists or people with computer science skills and put them to work on bioinformatics problems.

QWhere does your funding come from? How much funding do you have?

AOur group — Research Computing — is funded directly by NYU as a “Core Resource” for researchers. Individual faculty members pay an annual fee for access to our software and consulting services. We also obtain some grant funding as a consultant or co-PI in specific grants. We have obtained our own grant funding for specific equipment or projects — usually from the NSF.

QWhat hardware do you use?

AOur main server is a Compaq mainframe (a 4100 with four Alpha processors), which is about four years old now, but upgraded with the fastest Ultra 160 SCSI hard drives. We really need to buy a new server soon.

QWhat bioinformatics software do you use?

AOur main program is GCG running on Digital UNIX. We have about 800 user accounts. People access it via a web interface (SeqWeb), by X-Windows (SeqLab), or with a standard telnet command line. We also have site licenses for MacVector, OMIGA, and Sequencher — desktop computer programs that offer less power, but a simpler interface and better graphics than GCG. We do some in-house software development, but mostly by creating scripts that string together specific operations with these various programs and parse text files using C or PERL.

QHow would you compare the quality of publicly available and commercially available bioinformatics products?

ACommercial products generally offer a simpler, easier to use interface. Sometimes that enables people to make more complex or more thorough analyses by simplifying the process, but other times it limits you into a pre-defined analysis process. There are a few (very expensive) commercial bioinformatics products that also offer private data that cannot be accessed any other way — Incyte and Celera are examples. If you really need that data for your research, then there really is no alternative, eh?

QWhat non-existing technology do you most wish you had? What’s missing from the bioinformatics toolbox?

AI want a single public database that links ALL known information about genes, proteins, and genomic sequences — including expression, 3D structure, phylogenetic relationships, etc. — and a way for everyone to add new information and annotation into the database as they discover it.

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