One of the earliest studies linking the Human Mutator Gene Homolog MSH2 to colon cancer featured Sequencher as the software of choice. Sequencher’s powerful algorithms and ease of use have made it a staple for genetic researchers all over the world. I got involved with sequence analysis and molecular databases and never looked back.Researchers have been finding variants and mutations using Sequencher software for a long time. It intrigued me and I joined it and worked on the project during its first five years. It was at that time that the GenBank Project started. After spending an additional three years managing my own NIH R01 grant, I decided we weren’t learning more about the genetics of complex traits using the genetic epidemiological tools available in the late 70s and early 80s. I was a mathematics major as an undergraduate and studied genetic epidemiology as a graduate student and postdoc. QWhat made you decide to become a bioinformaticist?Ī It was a natural progression for me. Software that is publicly available, especially those running under Unix, are more easily customizable. There is little room for customization when using commercial software. However, the functionality is often limited. QHow would you compare the quality of publicly available and commercially available bioinformatics products?ĪThe commercial products are generally easier to use because more emphasis has been put on the interface and documentation. On our Unix systems we use the standard set of tools - both WU Blast and NCBI Blast, EMBOSS, Genscan, HMMER, University of Washington sequence assembly programs, CLUSTALX and many others. We have several desktop products for the Macintosh and PC including but not limited to Sequencher, MacVector, LaserGene and VectorNTI. Given the directions in which research projects can move, we need to be ready to provide the necessary tools. Unfortunately there is no one solution to meet all needs of all researchers. We use both commercial and public domain software. QWhat bioinformatics software do you use?ĪWe try to acquire a wide variety of software. This seems more appealing to some than getting locked into one long-term project.ĪWe currently have several Sun servers and will shortly be implementing a Linux compute farm. Also people in my group get to move around on different projects. Excellent seminars are always available here and across the street at MIT. Whitehead provides a wonderful environment in which to learn and grow. We get to work with cutting edge researchers involved with state-of-the-art research. QHow do you compete with companies to attract and retain qualified bioinformaticists?ĪIn the part of Whitehead I support, there are 20 individual labs working in diverse areas of biomedical research. Other challenges include developing software to address some nagging questions: how to predict and characterize human promoter sequence, how to predict structure of a protein from the sequence, and how to evaluate the data gathered in microarray experiments. This includes not only teaching people what tools are available and how to use them, but teaching them how to interpret the results, the algorithms used, and the pros and cons of different methods. QWhat are the biggest challenges the field of bioinformatics faces?ĪI believe the biggest challenge is educating the biologists in the use of computational tools. We will have tools to identify the function of proteins and tools to understand protein-protein interactions. This will let us ask evolutionary questions which were not possible before and will let us look at the differences and similarities among species to gain a better understanding of ourselves. QWhere will bioinformatics be in two years? Five years?ĪWithin two to five years we’ll have the finished sequence of both human and mouse and probably some other primates and mammals. Built a biocomputing department to support Whitehead’s basic research labs.Įnjoys hiking, tennis, and playing the double bass. Co-founded the Genetic Counseling program at Brandeis University. Worked on the GenBank project during its first five years and the first release of the Genome Database. Advances in Clinical Genomics ProfilingĪT A GLANCE: PhD in human biology/ genetics from the University of Colorado, Boulder.
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