Adam Siepel

Summary

Affiliation: Cornell University
Country: USA

Publications

  1. doi request reprint Darwinian alchemy: Human genes from noncoding DNA.
    Adam Siepel
    Department of Biological Statistics and Computational Biology, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 19:1693-5. 2009
  2. pmc Targeted discovery of novel human exons by comparative genomics
    Adam Siepel
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 17:1763-73. 2007
  3. pmc Phylogenomics of primates and their ancestral populations
    Adam Siepel
    Department of Biological Statistics and Computational Biology, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 19:1929-41. 2009
  4. pmc PHAST and RPHAST: phylogenetic analysis with space/time models
    Melissa J Hubisz
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Brief Bioinform 12:41-51. 2011
  5. pmc Genome-wide inference of natural selection on human transcription factor binding sites
    Leonardo Arbiza
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
    Nat Genet 45:723-9. 2013
  6. pmc Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells
    Charles G Danko
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Mol Cell 50:212-22. 2013
  7. pmc Identification of active transcriptional regulatory elements from GRO-seq data
    Charles G Danko
    1 Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA 2 Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA 3 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Nat Methods 12:433-8. 2015
  8. pmc GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters
    Nicholas J Fuda
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 11:e1005108. 2015
  9. pmc Bayesian inference of ancient human demography from individual genome sequences
    Ilan Gronau
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Nat Genet 43:1031-4. 2011
  10. pmc Replacing and additive horizontal gene transfer in Streptococcus
    Sang Chul Choi
    Department of Biological Statistics and Computational Biology, Cornell University
    Mol Biol Evol 29:3309-20. 2012

Collaborators

Detail Information

Publications28

  1. doi request reprint Darwinian alchemy: Human genes from noncoding DNA.
    Adam Siepel
    Department of Biological Statistics and Computational Biology, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 19:1693-5. 2009
  2. pmc Targeted discovery of novel human exons by comparative genomics
    Adam Siepel
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 17:1763-73. 2007
    ..However, they suggest that hundreds-not thousands-of protein-coding genes are completely missing from the current gene catalogs...
  3. pmc Phylogenomics of primates and their ancestral populations
    Adam Siepel
    Department of Biological Statistics and Computational Biology, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 19:1929-41. 2009
    ..Finally, I discuss remaining challenges and future prospects at this nexus of phylogenetics, population genetics, and genomics...
  4. pmc PHAST and RPHAST: phylogenetic analysis with space/time models
    Melissa J Hubisz
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Brief Bioinform 12:41-51. 2011
    ..0 are available for download at http://compgen.bscb.cornell.edu/phast, under the terms of an unrestrictive BSD-style license. RPHAST can also be obtained from the Comprehensive R Archive Network (CRAN; http://cran.r-project.org)...
  5. pmc Genome-wide inference of natural selection on human transcription factor binding sites
    Leonardo Arbiza
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
    Nat Genet 45:723-9. 2013
    ..Overall, regulatory elements seem to contribute substantially to both adaptive substitutions and deleterious polymorphisms with key implications for human evolution and disease. ..
  6. pmc Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells
    Charles G Danko
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Mol Cell 50:212-22. 2013
    ..Collectively, our results identify previously uncharacterized variation in the rate of transcription and highlight elongation as an important, variable, and regulated rate-limiting step during transcription...
  7. pmc Identification of active transcriptional regulatory elements from GRO-seq data
    Charles G Danko
    1 Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA 2 Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA 3 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Nat Methods 12:433-8. 2015
    ..Using dREG, we surveyed TREs in eight human cell types and provide new insights into global patterns of TRE function...
  8. pmc GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters
    Nicholas J Fuda
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 11:e1005108. 2015
    ..Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters. ..
  9. pmc Bayesian inference of ancient human demography from individual genome sequences
    Ilan Gronau
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Nat Genet 43:1031-4. 2011
    ....
  10. pmc Replacing and additive horizontal gene transfer in Streptococcus
    Sang Chul Choi
    Department of Biological Statistics and Computational Biology, Cornell University
    Mol Biol Evol 29:3309-20. 2012
    ..Additive transfers are also found to be associated with evidence of positive selection. These findings shed new light on the manner in which HGT has shaped pathogenic bacterial genomes...
  11. pmc Error and error mitigation in low-coverage genome assemblies
    Melissa J Hubisz
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS ONE 6:e17034. 2011
    ..Our error-mitigated alignments are available for download...
  12. pmc Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila
    Jaaved Mohammed
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA Tri Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
    RNA 20:1195-209. 2014
    ..Altogether, our findings reveal a surprising tissue-directed influence of miRNA evolution, involving a distinct mode of miRNA function connected to adaptive gene regulation in the testis. ..
  13. pmc Patterns of positive selection in six Mammalian genomes
    Carolin Kosiol
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 4:e1000144. 2008
    ..This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection...
  14. pmc Contrasting X-linked and autosomal diversity across 14 human populations
    Leonardo Arbiza
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Am J Hum Genet 94:827-44. 2014
    ..Further reductions can be predicted by more extreme demographic events in excess of those captured by the latest studies but, in the absence of these, also by historical sex-biased demographic events or other processes. ..
  15. pmc The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution
    Jaaved Mohammed
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    RNA 19:1295-308. 2013
    ..These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class. ..
  16. pmc A method for calculating probabilities of fitness consequences for point mutations across the human genome
    Brad Gulko
    Graduate Field of Computer Science, Cornell University, Ithaca, New York, USA
    Nat Genet 47:276-83. 2015
    ..2-7.5% of nucleotides in the human genome have influenced fitness since the human-chimpanzee divergence, and they suggest that recent evolutionary turnover has had limited impact on the functional content of the genome. ..
  17. pmc Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
    Leighton J Core
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
    Nat Genet 46:1311-20. 2014
    ..These results support a unified model of transcription initiation at promoters and enhancers. ..
  18. pmc Genome-wide inference of ancestral recombination graphs
    Matthew D Rasmussen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 10:e1004342. 2014
    ..The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective sweeps...
  19. pmc Inference of natural selection from interspersed genomic elements based on polymorphism and divergence
    Ilan Gronau
    Department of Biological Statistics and Computational Biology, Cornell University, USA
    Mol Biol Evol 30:1159-71. 2013
    ..To demonstrate the usefulness of INSIGHT, we apply it to several classes of human noncoding RNAs and to GATA2-binding sites in the human genome...
  20. pmc Diverse modes of evolutionary emergence and flux of conserved microRNA clusters
    Jaaved Mohammed
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA Tri Institutional Training Program in Computational Biology and Medicine, Sloan Kettering Institute, New York, New York 10065, USA
    RNA 20:1850-63. 2014
    ....
  21. pmc Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution
    Haruo Suzuki
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
    Genome Biol Evol 3:168-85. 2011
    ....
  22. pmc Cis-regulatory elements and human evolution
    Adam Siepel
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA Electronic address
    Curr Opin Genet Dev 29:81-9. 2014
    ..We consider inferences based on primate divergence, human polymorphism, and combinations of divergence and polymorphism. We then consider 'new frontiers' in this field stemming from recent research on transcriptional regulation. ..
  23. doi request reprint Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation
    Leonardo Campagna
    Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
    Mol Ecol 24:4238-51. 2015
    ..Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans. ..
  24. pmc A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells
    Nasun Hah
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Cell 145:622-34. 2011
    ..Collectively, our results provide the most comprehensive measurement of the primary and immediate estrogen effects to date and a resource for understanding rapid signal-dependent transcription in other systems...
  25. pmc Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
    Jiayu Wen
    Department of Developmental Biology, Sloan Kettering Institute, New York, New York 10065, USA
    Genome Res 24:1236-50. 2014
    ..These data should encourage broader usage of fly cell lines, beyond the few that are presently in common usage. ..
  26. pmc Accurate prediction of inducible transcription factor binding intensities in vivo
    Michael J Guertin
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 8:e1002610. 2012
    ..These findings provide new insights into the interplay between the genomic sequence and the chromatin landscape in determining transcription factor binding intensity...
  27. pmc Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing
    Srikanth Gottipati
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    Nat Genet 43:741-3. 2011
    ..This relative reduction is most parsimoniously explained by differences in demographic history without the need to invoke natural selection...
  28. pmc A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
    Aaron E Tenney
    Laboratory for Computational Genomics and Department of Computer Science, Washington University, St Louis, Missouri 63130, USA
    Genome Res 17:212-8. 2007
    ..We also present a method for mapping double-insertion events in a random insertional-mutagenesis library...