David Haussler

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David Haussler

David Haussler (born October 1953 ) is an American bioinformatician .

Life

Haussler is the son of an engineer and grew up in Los Angeles . He was initially interested in painting, which he studied for a few months in 1971 at the Academy of Arts in San Francisco , and psychology, which he studied for two years in Los Angeles at Immaculate Heart College (IHC). From 1973 he studied mathematics at Connecticut College with a bachelor's degree in 1975. After a vacation job in the laboratory of his older brother Mark, who was a biochemist at the University of Arizona , he began to be interested in biology, but also realized that laboratory work was not his Strength was. But the stay led to a first publication in Science on the metabolism of vitamin D . In 1979 he received his Masters in Mathematics from California Polytechnic State University in San Luis Obispo . He then went on to study computer science at the University of Colorado at Boulder , where he received his doctorate in 1982 under Andrzej Ehrenfeucht ( Insertion and Iterated Insertion as Operations on Formal Languages ) In Colorado, other leading bioinformaticians such as Eugene Myers , who soon afterwards at the Was involved in developing the BLAST algorithm , and Gary Stormo . Haussler himself initially dealt with artificial intelligence and statistics . In the 1990s he turned back to genetics and joined the Human Genome Project at the University of California, Santa Cruz (UCSC) . He is currently researching at the Howard Hughes Medical Institute (HHMI).

He is also Professor (Biomolecular Engineering) at UCSC, and Director of the Center for Biomolecular Science and Engineering there. He is Co-Director of the California Institute for Quantitative Biomedical Research and Consulting Professor at Stanford University School of Medicine and the University of California, San Francisco (Department of Biopharmacy).

He is a member of the National Academy of Sciences (2006), the California Academy of Science, the American Association for the Advancement of Science , the American Academy of Arts and Sciences and, since 2018, the National Academy of Engineering . He received the Dickson Prize in Science and the Allen Newell Award from the Association for Computing Machinery (ACM) and the AAAI. In 2005 he won the Classic Paper Award from the American Association of Artificial Intelligence (AAAI). He is a member of the AAAI and the American Society of Human Genetics . In 2008 he received the Senior Scientist Accomplishment Award from the International Society for Computational Biology and the Curt Stern Award from the American Society for Human Genetics. In 2001 he was named Scientist of the Year by Research and Development Magazine. For 2015 he was awarded the Dan David Prize .

Yoav Freund is one of his doctoral students .

Haussler is married and has two children.

plant

In the 1990s he developed key algorithms for the large gene sequencing projects using Hidden Markov Models . This enabled genes coding for proteins to be filtered from the wealth of information in the sequencing data. In 1999 he joined the Human Genome Project . His student Jim Kent developed a GigAssembler program with which the DNA of the human genome (from around 3 billion base pairs) is assembled from many snippets (some of which were faulty) of base sequences of up to a few thousand bases in length (at that time around 400,000 from laboratories worldwide) could. They were able to catch up (with much less funds) at the University of California, Santa Cruz (UCSC) compared to the private project of Celera Genomics (where Eugene Myers led the computer science). On July 2, 2000, the entire sequence of the human genome was posted on the Internet. Haussler and colleagues then developed the UCSC browser, which enabled the interactive viewing of the sequence enriched with background information.

Haussler's team was then also involved in other sequencing projects ( mouse , Drosophila , chimpanzee , macaque , chicken , rat ). Conclusions about evolution could also be drawn from the comparison of the genetic material. Haussler and colleagues found little changed gene sequences during evolution - 481 segments with more than 200 base pairs (and 5000 with over 100 base pairs), which were completely identical between humans, rats and mice (and almost identical to the corresponding sections in chickens and dogs) . The role of these regions is not entirely clear. They do not code for proteins and are part of what has been derogatoryly called junk DNA , but a change in them is associated with high negative selection. Haussler and colleagues are researching their role in gene regulation .

By comparing genes, Haussler and colleagues were able to reconstruct the genetic material of the common mammalian ancestor (a type of shrew) that lived 100 million years ago with 98 percent accuracy.

In addition, they were able to find sections that had changed particularly in humans ( human accelerated regions , HAR), including a region HAR 1, which is particularly read out in the Cajal-Retzius neurons during the embryonic development of the first 7 to 19 weeks and plays a key role plays in the development of the neocortex.

Most recently (2008) he has been working on the evolution of entire genomes.

Web links

Individual evidence

  1. ↑ Jones, Pevzner An introduction to bioinformatics algorithms , 2004, p. 403
  2. ↑ Portrait at the HMMI
  3. ^ Mathematics Genealogy Project
  4. ↑ D. Haussler, A. Krogh, IS Mian: A Hidden Markov Model that Finds Genes in E. Coli DNA . In: Nucleic Acids Res. , Vol. 22, 1994, PMID 7984429 , p. 4768
  5. ↑ Kent, Haussler: Assembly of the working draft of the human genome with GigAssembler . In: Genome Res. , Vol. 11, 2001, pp. 1541-1548.
  6. ↑ Beierano, Pheasant, Makunin, Stephen, Kent, Mattick, Haussner: Ultraconserved elements in the human genome . In: Science , Volume 304, 2004, PMID 15131266 , p. 1321.
  7. ↑ Katzman, Haussler et al. a .: Human genome ultraconserved elements are ultraselected . In: Science , Volume 317, 2007, PMID 17702936 , p. 915.
  8. ↑ Report on this at the HHMI; Report to the UCSC; Darwin's spiritual grandchildren . In: Zeit Online , 2009
  9. ↑ Pollard, Haussler et al. a .: An RNA gene expressed during cortical development evolved rapidly in humans . In: Nature , Volume 443, 2006, p. 167
  10. ^ M Blanchette, ED Green, W Miller, D. Haussler: Reconstructing large regions of an ancestral mammalian genome in silico . In: Genome Res. , Volume 14, 2004, pp. 2412–2423, PMC 534665 (free full text)
personal data
SURNAME Haussler, David
BRIEF DESCRIPTION American computer scientist
DATE OF BIRTH October 1953