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Adam C. Siepel

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Adam Siepel
Born
Adam C. Siepel

(1972-06-24) June 24, 1972 (age 52)
NationalityUnited States
Alma mater
Known forevolutionarily conserved sequences
Awards
Scientific career
Fields
Institutions
ThesisComparative mammalian genomics: Models of evolution and detection of functional elements (2005)
Doctoral advisorDavid Haussler
Websitecompgen.bscb.cornell.edu/~acs

Adam C. Siepel (born 1972) is an American computational biologist known for his research in comparative genomics, particularly the development of statistical methods and software tools for identifying evolutionarily conserved sequences.[1][2][3][4] Siepel is currently an Associate Professor in the Department of Biological Statistics and Computational Biology at Cornell University. He also directs Cornell's Ph.D. program in Computational Biology and serves as an Associate Director for the Cornell Center for Comparative and Population Genomics where has been on the faculty since 2006.[5]

Education and Career

Siepel completed a B.S. in Agricultural and Biological Engineering at Cornell University in 1994, then worked at Los Alamos National Laboratory until 1996. From 1996 to 2001, he worked as a software developer at the National Center for Genome Resources in Santa Fe, while completing an M.S. in Computer Science at the University of New Mexico. He obtained a Ph.D. in Computer Science from the University of California, Santa Cruz in 2005.

Research

Siepel has worked on various problems at the intersection of computer science, statistics, evolutionary biology, and genomics. Working with Bette Korber and Gerry Myers at Los Alamos National Laboratory in the mid-1990s, he developed phylogenetic methods for detecting recombinant strains of HIV, which became fairly widely used in the HIV research community.[6] Later, at the National Center for Genome Resources, Siepel led the development of ISYS, a technology for integrating heterogeneous bioinformatics databases, analysis tools, and visualization programs.[7] He also did theoretical work on algorithms for phylogeny reconstruction based on genome rearrangements, working with Bernard Moret at the University of New Mexico.[8]

In 2002, Siepel joined David Haussler's laboratory at the University of California, Santa Cruz and began to work on computational problems in comparative genomics. With Haussler, he developed a program called ExoniPhy for identifying protein-coding genes based on their distinctive patterns of molecular evolution, which was later used to discover several hundred human genes.[9][10] Siepel also developed a method called phastCons for identifying evolutionarily conserved sequences in genomic sequences.[11] PhastCons was the original engine behind the widely used evolutionary conservation tracks in the UCSC Genome Browser. Siepel developed a freely available software package called PHAST (PHylogenetic Analysis with Space Time models) that includes ExoniPhy, phastCons, and several other tools for statistical phylogenetics and comparative genomics.[12]

Siepel's research group at Cornell has continued to work on the identification and characterization of conserved non-coding sequences. They have also studied fast-evolving sequences in both coding[13] and noncoding[14] regions, including human accelerated regions. Much of their recent work has focused on primate genomes,[15] although they have studied various other species as well. Recently, Siepel's research group has developed methods to estimate the times in early human history when major population groups first diverged, based on complete genome sequence data.[16][17][18]

A common theme in Siepel's research is the development of precise mathematical models for the complex processes by which genomes evolve over time. His research group uses these models, together with techniques from computer science and statistics, both to peer into the past, and to address questions of practical importance for human health.[19]

Awards and honours

Siepel was a recipient of a Guggenheim Fellowship in 2012.[19] He was also awarded a David and Lucile Packard Fellowship for Science and Engineering in 2007, a Microsoft Research Faculty Fellowship in 2007, and a Sloan Research Fellowship in 2009.


References

  1. ^ a b Adam C. Siepel publications indexed by Google Scholar
  2. ^ Adam C. Siepel's publications indexed by the Scopus bibliographic database. (subscription required)
  3. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1002/cpe.3231, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1002/cpe.3231 instead.
  4. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 17571346, please use {{cite journal}} with |pmid=17571346 instead.
  5. ^ Adam Siepel's CV.
  6. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 8573400, please use {{cite journal}} with |pmid=8573400 instead.
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  8. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 12935346, please use {{cite journal}} with |pmid=12935346 instead.
  9. ^ Dublin, Matthew. With New Biofx Approach, Researchers Find 300 Novel Human Genes. Genome Technology. February 2008.
  10. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1101/gr.7128207, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1101/gr.7128207 instead.
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  12. ^ PHAST website.
  13. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1371/journal.pgen.1000144, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1371/journal.pgen.1000144 instead.
  14. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1101/gr.097857.109, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1101/gr.097857.109 instead.
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  16. ^ Ramanujan, Krishna. "Researchers use genome sequences to peer into early human history." Cornell Chronicle. September 19, 2011.
  17. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1038/ng.937, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1038/ng.937 instead.
  18. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1038/ng.953, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1038/ng.953 instead.
  19. ^ a b Guggenheim profile.

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