next up previous
Next: The need for bioinformatics Up: No Title Previous: Bioinformatics extends beyond sequence

The present situation at UCD

Although UCD has great strengths in biology generally, it has been slow to develop concentrated strength in bioinformatics, computational molecular biology and their relationship with genomics. However, this is now changing.

There is now a cadre of biologists on campus who actively incorporate the use of bioinformatics tools into their work, at the sequence level, in structure modeling, and in linking together and simulating complex neurological structures. There is a growing number of biology and chemistry graduate students and post-docs who are attempting to learn the needed technical aspects of computer programming and bioinformatics by taking classes in the computer science department; the bio-technology program organized a widely-attended multi-day workshop on bioinformatics and genomics in summer 1998; there was a widely-attended seminar series on genomics/bioinformatics in agriculture in fall 1998; a graduate course on theoretical aspects of sequence-oriented computational biology is taught every other year in the computer science department, and a book published along the lines of that course [#!GUS97!#]; there will be three graduate courses given on the use of sequence-oriented bioinformatics tools in winter and spring 1999 (one in AES, one in DBS and one in the Medical School), and a course on the foundations of bioinformatics is being developed in computer science. There is a small group in the computer science department that studies, develops and implements sequence-oriented bioinformatics tools. That group has had eight postdoctoral students in the last several years, two who now have faculty positions and continue to focus on computational biology, one who won the DOE distinguished Human Genome Postdoc fellowship here, one who has continued with another postdoc position in a large bioinformatics group at the German Cancer institute, and one who is head of a 30 person bioinformatics unit at a biotech/genomics company; another bioinformatics Ph.d student (who actually received his degree at UC Berkeley) is now doing bioinformatics research in industry. The group also employed two UCD undergraduates who are now graduate students at Stanford focusing on bioinformatics, one in an MD/Ph.d. program, and the other in CS/MIS. Another group in computer science has been working with neurobiologists to build relational databases of brain structures, and graphical, visual tools; work is expected to continue with the submission of a major grant application. The biostatistics affinity group is moving more towards genetics and genomics, and a statistical geneticist has recently been hired in the Rowe program. There are faculty members in EVE who have developed web-accessible databases for evolutionary trees, and who incorporate the use of phylogenetic software in their courses. Evolution and Ecology and Ornamental Horticulture have also incorporated linkage analysis and QTL analysis software into some of their graduate courses. There is a computational biology group centered at ITD; superficially, their focus has very little intersection with computational molecular biology and bioinformatics, but at a deeper technical level, they face many of the same modeling and simulation issues that arise in some parts of computational molecular biology. There is an effort in medical informatics, and now an established masters program, which also has little superficial intersection with molecularly oriented and genomic-oriented bioinformatics, but again has some of the same technical problems, and the potential to fuse together with computational molecular biology and bioinformatics.

So despite the slow start of bioinformatics on campus, it is beginning, and the potential for bioinformatics and computational molecular biology is great at UCD due to the diversity and high number of biologists on campus. Davis has the additional potential of close collaboration with the genomics and bioinformatics efforts at the Human Genome Centers at the Lawrence Livermore National Lab and at the Lawrence Berkeley National Lab. Several faculty, and students on campus have had ties to those centers. There is additional potential for collaboration with local biotech companies who have an active interest in bioinformatics. Moreover, additional faculty in various areas outside of biology, such as Computer science, Engineering, Statistics and Mathematics, are eager to develop programs and positions that build on their different strengths and concentrate on different aspects of computational biology, and yet integrate and interface well with such efforts in DBS, AES, and the Medical School.


next up previous
Next: The need for bioinformatics Up: No Title Previous: Bioinformatics extends beyond sequence
Dan Gusfield
1999-11-03