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Siepel, Adam
Cornell Faculty Member
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Positions
- Associate Professor, Biological Statistics and Computational Biology (BSCB), College of Agriculture and Life Sciences (CALS)
- Dir Assoc Acad, Institute of Biotechnology, Office of the Vice Provost for Research
My expertise is in computational genomics, especially in sequence analysis, phylogeny reconstruction, molecular evolution, and comparative mammalian genomics. I am trained as an engineer and computer scientist, but have been working closely with molecular and evolutionary biologists since 1994. I joined the Cornell faculty in 2006, after finishing my PhD in computer science and bioinformatics at UC Santa Cruz. Before my PhD, I worked for several years as a software engineer in a bioinformatics research institute (NCGR, Santa Fe).
Research Areas
Websites
- Affiliations
- Research
- Publications
- Teaching
- Service
- Background
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Affiliations
administrative responsibilities
- Director of Graduate Studies - Field of Computational Biology
member of graduate field
other Cornell affiliations
advisory group member
Research
research overview
- comparative and evolutionary genomics, bioinformatics
research activities
principal investigator on
- 2009 ALFRED P. SLOAN RESEARCH FELLOWS awarded by SLOAN FOUNDATION 2009 - 2013
- CAREER: MODELS OF EVOLUTION AND DISCOVERY OF FUNCTIONAL ELEMENTS IN MAMMALS AND DROSOPHILA awarded by DIRECTORATE FOR BIOLOGICAL SCIENCES NSF 2007 - 2013
- PACKARD FELLOWSHIP FOR SCIENCE AND ENGINEERING: IDENTIFICATION OF FUNCTIONAL ELEMENTS IN MAMMALIAN GENOMES awarded by DAVID & LUCILE PACKARD FND 2007 - 2014
- PHMRA POST DOCTORAL FELLOWSHIP IN INFORMATICS awarded by PHARMACEUTICAL RESEARCH & MANUFACTURES OF AMERICA FDN, IN 2010 - 2012
- WHAT MADE US HUMAN? awarded by NATL INST OF HEALTH DHHS 2008 - 2012
co-principal investigator on
area(s) of concentration/expertise
keywords
- bayesian statistics
- conerved noncoding sequences
- gene prediction
- genomics
- molecular evolution
- phylogeny reconstruction
- population genetics
- probabilistic graphical models
submitted impact statement
Publications
individual publications
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academic article
- Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo. PLoS Genetics. 8. 2012
- Accurate prediction of inducible transcription factor binding intensities in vivo.. PLoS Genetics. 8. 2012
- A high-resolution map of evolutionary constraint in the human genome based on 29 eutherian mammals.. Nature. 478:476-482. 2011
- A rapid,extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 145:622-634. 2011
- Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing.. Nature. 43:741-743. 2011
- Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics. 43:1031-1034. 2011
- Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biology and Evolution. 3:168-185. 2011
- Error and error mitigation in low-coverage genome assemblies. PLoS ONE. 6. 2011
- PHAST and RPHAST: Phylogenetic analysis with space/time models. Briefings in Bioinformatics. 12:41-51. 2011
- The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Molecular Biology and Evolution. 29:1047-1057. 2011
- Three different periods of regulatory innovation during vertebrate evolution. Science. 333:1019-1024. 2011
- Widespread regulatory activity of vertebrate microRNA* species. RNA. 17:312-326. 2011
- A simple genetic architecture underlies morphological variation in dogs. PLoS Biology. 8. 2010
- Detection of non-neutral substitution rates on Mammalian phylogenies. Genome Research. 20:110-121. 2010
- Positive selection on apoptosis related genes. FEBS Lett. 584:469-476. 2010
- Reconstructing histories of complex gene clusters on a phylogeny. Journal of Computational Biology. 17:1267-1279. 2010
- Darwinian alchemy: human genes from noncoding DNA. Genome Research. 19:1693-1695. 2009
- Phylogenomics of primates and their ancestral populations. Genome Research. 19:1929-1941. 2009
- Adaptive evolution drives accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res. 18:1592-1601. 2008
- Patterns of positive selection in six mammalian genomes. PLoS Genetics. 4. 2008
- Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics. 180:391-408. 2008
- 28-way vertebrate alignment and conservation track in the UCSC genome browser. Genome Res. 17:1797-1808. 2007
- Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17:760-774. 2007
- Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Molecular Biology of the Cell. 27:90-104. 2007
- Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Molecular and Cellular Biology. 27:5090-5104. 2007
- Targeted discovery of novel human exons by comparative genomics. Genome Res. 17:1763-1773. 2007
- The UCSC genome browser database: update 2007. Nucleic Acids Research. 35. 2007
- A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441:87-90. 2006
- An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 443:167-172. 2006
- Forces shaping the fastest evolving regions in the human genome. PLoS Genetics. 2. 2006
- Identification and classification of conserved RNA secondary structures in the human genome. PLoS Computational Biology. 2. 2006
- The UCSC Genome Browser Database: update 2006. Nucleic Acids Research. 34. 2006
- Computational screening of conserved genomic DNA in search of functional noncoding elements. Nature Methods. 2:535-545. 2005
- Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15:1034-1050. 2005
- Combining phylogenetic and hidden Markov models in biosequence analysis. J. Comput. Biol. 11:413-428. 2004
- Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Molecular Biology and Evolution. 21:468-488. 2004
- An algorithm to enumerate sorting reversals for signed permutations. J Comput Biol. 10. 2003
- Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 424:788-793. 2003
- A Simplified Hillslope Erosion Model with Vegetation Elements for Practical Applications. Journal of Hydrology. 258:111-121. 2002
- An integration platform for heterogeneous bioinformatics software components. IBM Systems Journal. 40. 2001
- ISYS: A decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics. 17:83-94. 2001
- The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Research. 27:35-38. 1999
- The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Research. 26. 1998
- The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Research. 25. 1997
- A computer program designed to screen rapidly for HIV Type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses. 11. 1995
-
chapter
- Phylogenetic hidden Markov models. Statistical Methods in Molecular Evolution. 2005
-
conference paper
- Reconstructing the evolutionary history of complex human gene clusters. Proceedings of the 12th International Conference on Research in Computational Molecular Biology. 2008
- New methods for detecting lineage-specific selection. Proceedings of the 10th International Conference on Research in Computational Molecular Biology. 2006
- Computational identification of evolutionarily conserved exons. Proceedings of the 8th International Conference on Research in Computational Molecular Biology. 2004
- Efficient approximations for learning phylogenetic HMM models from data. Intelligent Systems for Molecular Biology (ISMB) 2004 and Bioinformatics. 2004
- Combining phylogenetic and hidden Markov models in biosequence analysis. Proceeding of the 7th International Conference on Research in Computational Molecular Biology. 2003
- An algorithm to find all sorting reversals. Proceeding of the 6th International Conference on Research in Computational Molecular Biology. 2002
- Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. Proceeding of the 2nd International Workshop on Algorithms in Bioinformatics, Lecture Notes in Computer Science. 2002
- Bioinformatics for rice resources. Novartis Found Symp. 59-81. 2001
- Finding an optimal inversion median: experimental results. Proceeding of the 1st International Workshop on Algorithms in Bioinformatics, Lecture Notes in Computer Science. 2001
presentations
featured in archived article
- Cornell launches Center for Comparative and Population Genomics
- From mice to men, evidence of evolutionary selection is found in 544 genes in analysis going back 80 million years
- In major advancement for medical research, Cornell scientists help analyze the rhesus macaque genome
- Peng Chen, Liam McAllister and Adam Siepel are named Sloan fellows
Teaching
teaching overview
- computational genomics, bioinformatics machine learning (graphical models)
teaching activities
- BTRY-6970: Individual Graduate Study in Biometry and Statistics - Spring 2013
- BTRY-7980: Graduate Supervised Teaching - Spring 2013
- BTRY-8900: Master's Level Thesis Research - Spring 2013
- BTRY-9900: Doctoral-Level Dissertation Research - Spring 2013
- CS-7999: Independent Research - Spring 2013
- BTRY-6970: Individual Graduate Study in Biometry and Statistics - Fall 2012
- BTRY-7900: Graduate-Level Dissertation Research - Fall 2012
- BTRY-7980: Graduate Supervised Teaching - Fall 2012
- BTRY-8900: Master's Level Thesis Research - Fall 2012
- BTRY-9900: Doctoral-Level Dissertation Research - Fall 2012
- CS-7999: Independent Research - Fall 2012
- BTRY-6970: Individual Graduate Study in Biometry and Statistics - Spring 2012
- BTRY-7980: Graduate Supervised Teaching - Spring 2012
- BTRY-8900: Master's Level Thesis Research - Spring 2012
- BTRY-9900: Doctoral-Level Dissertation Research - Spring 2012
- CS-7999: Independent Research - Spring 2012
- BTRY-4840: Computational Genomics - Fall 2011
- BTRY-6700: Applied Bioinformatics and Systems Biology - Fall 2011
- BTRY-6840: Computational Genomics - Fall 2011
- BTRY-6970: Individual Graduate Study in Biometry and Statistics - Fall 2011
- BTRY-7900: Graduate-Level Dissertation Research - Fall 2011
- BTRY-7980: Graduate Supervised Teaching - Fall 2011
- BTRY-8900: Master's-Level Thesis Research - Fall 2011
- BTRY-9900: Doctoral-Level Dissertation Research - Fall 2011
- CS-7999: Independent Research - Fall 2011
Service
current professional activities
-
- Member of Rhesus Macaque Sequencing and Analysis Consortium (2006–present)
- Member of ENCyclopedia Of DNA Elements (ENCODE) Consortium (2004–present)
- Participant in Mammalian Gene Collection (MGC) project (2004–present)
- Member of International Human Genome Sequencing Consortium (2004)
- Member of International Chicken Genome Sequencing Consortium (2003–2004)
- Member of graduate fields of Computational Biology, Biometry, Computer Science, and Genetics & Development at Cornell University, 2006–present
- Developer of freely available software package called PHAST (PHylogenetic Analysis with Space/Time models), 2003–present (>150 downloads)
- Contributor to UC Santa Cruz Genome Browser (conservation, ExoniPhy, and DLESS tracks), 2003–present
- Reviewer for PLoS Biology, Genome Research, Molecular Biology and Evolution, PLoS Computational Biology,
- PLoS Genetics, Bioinformatics, BMC Bioinformatics, and The Plant Cell
- Program Committees for Workshop on Algorithms in Bioinformatics (WABI), 2006–2007; Intelligent Systems for Molecular Biology (ISMB) / European Conference on Computational Biology (ECCB), 2004–2007;
- International Conference on Machine Learning (ICML), 2007
- Committees at Cornell: Graduate student admissions committee, field of Computational Biology, 2006–2007;
- Undergraduate Biology Curriculum Task Force, 2007; Advisory Committee for Cornell Institute for Cell and Molecular Biology, 2007
- Advisory committee on sequencing of primate genomes, National Human Genome Research Institute, 2007
service to the profession
- 2x Mammals Sequencing and Analysis Consortium Member 2008 -
- Orangutan Sequencing and Analysis Consortium Member 2008 -
- Advisory Committee for sequencing of primate genomes, National Human Genome Research Institute Committee Member 2007 -
- Mammalian Gene Collection Project Member 2004 -
- Ho-Nun-De-Kah, Cornell University Agriculture and Life Sciences Honor Society Member 1993 -
- Tau Beta Pi, National Engineering Honor Society Member 1993 -
- Program Committees, Workshop on Algorithms in Bioinformatics (WABI) Committee Member 2006 - 2008
- Rhesus Macaque Sequencing and Analysis Consortium Member 2006 - 2007
- ENCyclopedia Of DNA Elements (ENCODE) Consortium Member 2004 - 2007
- Program Committee, Intelligent Systems for Molecular Biology (ISMB) / European Conference on Computational Biology (ECCB) Committee Member 2004 - 2007
- Program Committee, International Conference on Machine Learning (ICML) Committee Member - 2007
- International Chicken Genome Sequencing Consortium Member 2003 - 2004
- International Human Genome Sequencing Consortium Member - 2004
reviewer or editor for
Background
education and training
- Ph.D. in Computer Science, University of California, Santa Cruz 2005
- M.S. in Computer Science, University of New Mexico 2001
- B.S. in Agricultural and Biological Engineering, Cornell University 1994
awards and honors
- Sloan Research Fellowship, 2009
- Packard Fellowship, 2007
- Microsoft Research New Faculty Fellowship, 2007
- NSF CAREER Award, 2007
- Tomorrow’s PIs, 2007
- Graduate Research and Education in Adaptive bio-Technology (GREAT) Fellowship, 2005
- Achievement Rewards for College Scientists (ARCS) Scholarship, 2004
- Best Student Paper, 2002
- UC Santa Cruz Chancellor’s Fellowship, 2002
- Sustained Performance Award, 1999
- Empire State Scholarship, 1990
- Valedictorian, 1990
awards and distinctions listing
-
- NSF CAREER Award, 2007
- Microsoft Research New Faculty Fellowship, 2007 (1 of 5)
- Named one of “Tomorrow’s PIs,” Genome Technology magazine, 2007 (1 of 30)
- Graduate Research and Education in Adaptive bio-Technology (GREAT) Fellowship, University of California
- Biotechnology Research and Education Program (UCBREP), 2004-2005
- Achievement Rewards for College Scientists (ARCS) Scholarship, 2003–2004
- Best Student Paper, 6th Int’l Conf. on Research in Computational Molecular Biology, 2002
- UC Santa Cruz Chancellor’s Fellowship, 2002
- Sustained Performance Award, National Center for Genome Resources, 1999
- Tau Beta Pi, National Engineering Honor Society, inducted 1993
- Ho-Nun-De-Kah, Cornell University Agriculture and Life Sciences Honor Society, inducted 1993
- Empire State Scholarship, 1990
- Valedictorian, West Valley Central School (NY), 1990
Other
college
- CALS
research keyword
- bayesian statistics
- conerved noncoding sequences
- gene prediction
- genomics
- molecular evolution
- phylogeny reconstruction
- population genetics
- probabilistic graphical models