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ORCIDBibTeX records: Adam C. Siepel
@article{DBLP:journals/bioinformatics/ZhaoDBTDS21,
author = {Yixin Zhao and
Noah Dukler and
Gilad Barshad and
Shushan Toneyan and
Charles G. Danko and
Adam C. Siepel},
title = {Deconvolution of expression for nascent RNA-sequencing data {(DENR)}
highlights pre-RNA isoform diversity in human cells},
journal = {Bioinform.},
volume = {37},
number = {24},
pages = {4727--4736},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab582},
doi = {10.1093/BIOINFORMATICS/BTAB582},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoDBTDS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/CougerPSPSPKMB14,
author = {M. Brian Couger and
Lenore Pipes and
Fabio Squina and
Rolf Prade and
Adam C. Siepel and
Robert Palermo and
Michael G. Katze and
Christopher E. Mason and
Philip D. Blood},
title = {Enabling large-scale next-generation sequence assembly with Blacklight},
journal = {Concurr. Comput. Pract. Exp.},
volume = {26},
number = {13},
pages = {2157--2166},
year = {2014},
url = {https://doi.org/10.1002/cpe.3231},
doi = {10.1002/CPE.3231},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/concurrency/CougerPSPSPKMB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HubiszPS11,
author = {Melissa J. Hubisz and
Katherine S. Pollard and
Adam C. Siepel},
title = {{PHAST} and {RPHAST:} phylogenetic analysis with space/time models},
journal = {Briefings Bioinform.},
volume = {12},
number = {1},
pages = {41--51},
year = {2011},
url = {https://doi.org/10.1093/bib/bbq072},
doi = {10.1093/BIB/BBQ072},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HubiszPS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/VinarBSS10,
author = {Tom{\'{a}}s Vinar and
Brona Brejov{\'{a}} and
Giltae Song and
Adam C. Siepel},
title = {Reconstructing Histories of Complex Gene Clusters on a Phylogeny},
journal = {J. Comput. Biol.},
volume = {17},
number = {9},
pages = {1267--1279},
year = {2010},
url = {https://doi.org/10.1089/cmb.2010.0090},
doi = {10.1089/CMB.2010.0090},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/VinarBSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ZhangSVGSM09,
author = {Yu Zhang and
Giltae Song and
Tom{\'{a}}s Vinar and
Eric D. Green and
Adam C. Siepel and
Webb Miller},
title = {Evolutionary History Reconstruction for Mammalian Complex Gene Clusters},
journal = {J. Comput. Biol.},
volume = {16},
number = {8},
pages = {1051--1070},
year = {2009},
url = {https://doi.org/10.1089/cmb.2009.0040},
doi = {10.1089/CMB.2009.0040},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ZhangSVGSM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/VinarBSS09,
author = {Tom{\'{a}}s Vinar and
Brona Brejov{\'{a}} and
Giltae Song and
Adam C. Siepel},
editor = {Francesca D. Ciccarelli and
Istv{\'{a}}n Mikl{\'{o}}s},
title = {Reconstructing Histories of Complex Gene Clusters on a Phylogeny},
booktitle = {Comparative Genomics, International Workshop, {RECOMB-CG} 2009, Budapest,
Hungary, September 27-29, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5817},
pages = {150--163},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04744-2\_13},
doi = {10.1007/978-3-642-04744-2\_13},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/VinarBSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0906-2635,
author = {Tom{\'{a}}s Vinar and
Brona Brejov{\'{a}} and
Giltae Song and
Adam C. Siepel},
title = {Bayesian History Reconstruction of Complex Human Gene Clusters on
a Phylogeny},
journal = {CoRR},
volume = {abs/0906.2635},
year = {2009},
url = {http://arxiv.org/abs/0906.2635},
eprinttype = {arXiv},
eprint = {0906.2635},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0906-2635.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ZhangSVGSM08,
author = {Yu Zhang and
Giltae Song and
Tom{\'{a}}s Vinar and
Eric D. Green and
Adam C. Siepel and
Webb Miller},
editor = {Martin Vingron and
Limsoon Wong},
title = {Reconstructing the Evolutionary History of Complex Human Gene Clusters},
booktitle = {Research in Computational Molecular Biology, 12th Annual International
Conference, {RECOMB} 2008, Singapore, March 30 - April 2, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4955},
pages = {29--49},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-78839-3\_4},
doi = {10.1007/978-3-540-78839-3\_4},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ZhangSVGSM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KuhnKZTTTSSSSRRRPPHHHDCBBBHK07,
author = {Robert M. Kuhn and
Donna Karolchik and
Ann S. Zweig and
Heather Trumbower and
Daryl J. Thomas and
Archana Thakkapallayil and
Charles W. Sugnet and
Mario Stanke and
Kayla E. Smith and
Adam C. Siepel and
Kate R. Rosenbloom and
Brooke L. Rhead and
Brian J. Raney and
Andy Pohl and
Jakob Skou Pedersen and
Fan Hsu and
Angela S. Hinrichs and
Rachel A. Harte and
Mark Diekhans and
Hiram Clawson and
Gill Bejerano and
Galt P. Barber and
Robert Baertsch and
David Haussler and
W. James Kent},
title = {The {UCSC} genome browser database: update 2007},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {668--673},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl928},
doi = {10.1093/NAR/GKL928},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KuhnKZTTTSSSSRRRPPHHHDCBBBHK07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HinrichsKBBBCDFHHHKPPRRSSSSTTWWZHK06,
author = {Angela S. Hinrichs and
Donna Karolchik and
Robert Baertsch and
Galt P. Barber and
Gill Bejerano and
Hiram Clawson and
Mark Diekhans and
Terrence S. Furey and
Rachel A. Harte and
Fan Hsu and
Jennifer Hillman{-}Jackson and
Robert M. Kuhn and
Jakob Skou Pedersen and
Andy Pohl and
Brian J. Raney and
Kate R. Rosenbloom and
Adam C. Siepel and
Kayla E. Smith and
Charles W. Sugnet and
A. Sultan{-}Qurraie and
Daryl J. Thomas and
Heather Trumbower and
Ryan J. Weber and
M. Weirauch and
Ann S. Zweig and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser Database: update 2006},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {590--598},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj144},
doi = {10.1093/NAR/GKJ144},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HinrichsKBBBCDFHHHKPPRRSSSSTTWWZHK06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/PedersenBSRLLKMH06,
author = {Jakob Skou Pedersen and
Gill Bejerano and
Adam C. Siepel and
Kate R. Rosenbloom and
Kerstin Lindblad{-}Toh and
Eric S. Lander and
Jim Kent and
Webb Miller and
David Haussler},
title = {Identification and Classification of Conserved {RNA} Secondary Structures
in the Human Genome},
journal = {PLoS Comput. Biol.},
volume = {2},
number = {4},
year = {2006},
url = {https://doi.org/10.1371/journal.pcbi.0020033},
doi = {10.1371/JOURNAL.PCBI.0020033},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/PedersenBSRLLKMH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SiepelPH06,
author = {Adam C. Siepel and
Katherine S. Pollard and
David Haussler},
editor = {Alberto Apostolico and
Concettina Guerra and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {New Methods for Detecting Lineage-Specific Selection},
booktitle = {Research in Computational Molecular Biology, 10th Annual International
Conference, {RECOMB} 2006, Venice, Italy, April 2-5, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3909},
pages = {190--205},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11732990\_17},
doi = {10.1007/11732990\_17},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SiepelPH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SiepelH04,
author = {Adam C. Siepel and
David Haussler},
title = {Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis},
journal = {J. Comput. Biol.},
volume = {11},
number = {2/3},
pages = {413--428},
year = {2004},
url = {https://doi.org/10.1089/1066527041410472},
doi = {10.1089/1066527041410472},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SiepelH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/JojicJMGSHH04,
author = {Vladimir Jojic and
Nebojsa Jojic and
Christopher Meek and
Dan Geiger and
Adam C. Siepel and
David Haussler and
David Heckerman},
title = {Efficient approximations for learning phylogenetic {HMM} models from
data},
booktitle = {Proceedings Twelfth International Conference on Intelligent Systems
for Molecular Biology/Third European Conference on Computational Biology
2004, Glasgow, UK, July 31-August 4, 2004},
pages = {161--168},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth917},
doi = {10.1093/BIOINFORMATICS/BTH917},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/JojicJMGSHH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SiepelH04,
author = {Adam C. Siepel and
David Haussler},
editor = {Philip E. Bourne and
Dan Gusfield},
title = {Computational identification of evolutionarily conserved exons},
booktitle = {Proceedings of the Eighth Annual International Conference on Computational
Molecular Biology, 2004, San Diego, California, USA, March 27-31,
2004},
pages = {177--186},
publisher = {{ACM}},
year = {2004},
url = {https://doi.org/10.1145/974614.974638},
doi = {10.1145/974614.974638},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SiepelH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Siepel03,
author = {Adam C. Siepel},
title = {An Algorithm to Enumerate Sorting Reversals for Signed Permutations},
journal = {J. Comput. Biol.},
volume = {10},
number = {3/4},
pages = {575--597},
year = {2003},
url = {https://doi.org/10.1089/10665270360688200},
doi = {10.1089/10665270360688200},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/Siepel03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SiepelH03,
author = {Adam C. Siepel and
David Haussler},
editor = {Martin Vingron and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman and
Webb Miller},
title = {Combining phylogenetic and hidden Markov models in biosequence analysis},
booktitle = {Proceedings of the Sventh Annual International Conference on Computational
Biology, {RECOMB} 2003, Berlin, Germany, April 10-13, 2003},
pages = {277--286},
publisher = {{ACM}},
year = {2003},
url = {https://doi.org/10.1145/640075.640111},
doi = {10.1145/640075.640111},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SiepelH03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/Siepel02,
author = {Adam C. Siepel},
editor = {Gene Myers and
Sridhar Hannenhalli and
David Sankoff and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {An algorithm to enumerate all sorting reversals},
booktitle = {Proceedings of the Sixth Annual International Conference on Computational
Biology, {RECOMB} 2002, Washington, DC, USA, April 18-21, 2002},
pages = {281--290},
publisher = {{ACM}},
year = {2002},
url = {https://doi.org/10.1145/565196.565233},
doi = {10.1145/565196.565233},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/Siepel02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MoretSTL02,
author = {Bernard M. E. Moret and
Adam C. Siepel and
Jijun Tang and
Tao Liu},
editor = {Roderic Guig{\'{o}} and
Dan Gusfield},
title = {Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction
from Gene-Order Data},
booktitle = {Algorithms in Bioinformatics, Second International Workshop, {WABI}
2002, Rome, Italy, September 17-21, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2452},
pages = {521--536},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45784-4\_40},
doi = {10.1007/3-540-45784-4\_40},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/MoretSTL02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SiepelFTZMBS01,
author = {Adam C. Siepel and
Andrew D. Farmer and
Andrew N. Tolopko and
Mingzhe Zhuang and
Pedro Mendes and
William D. Beavis and
Bruno W. S. Sobral},
title = {{ISYS:} a decentralized, component-based approach to the integration
of heterogeneous bioinformatics resources},
journal = {Bioinform.},
volume = {17},
number = {1},
pages = {83--94},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.1.83},
doi = {10.1093/BIOINFORMATICS/17.1.83},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SiepelFTZMBS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ibmsj/SiepelTFSSPB01,
author = {Adam C. Siepel and
Andrew N. Tolopko and
Andrew D. Farmer and
Peter A. Steadman and
Faye D. Schilkey and
B. Dawn Perry and
William D. Beavis},
title = {An integration platform for heterogeneous bioinformatics software
components},
journal = {{IBM} Syst. J.},
volume = {40},
number = {2},
pages = {570--591},
year = {2001},
url = {https://doi.org/10.1147/sj.402.0570},
doi = {10.1147/SJ.402.0570},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ibmsj/SiepelTFSSPB01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SiepelM01,
author = {Adam C. Siepel and
Bernard M. E. Moret},
editor = {Olivier Gascuel and
Bernard M. E. Moret},
title = {Finding an Optimal Inversion Median: Experimental Results},
booktitle = {Algorithms in Bioinformatics, First International Workshop, {WABI}
2001, Aarhus, Denmark, August 28-31, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2149},
pages = {189--203},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44696-6\_15},
doi = {10.1007/3-540-44696-6\_15},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SiepelM01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SkupskiBFHHIKKRSSSSTTWZH99,
author = {M. P. Skupski and
M. Booker and
Andrew D. Farmer and
M. Harpold and
Wen Huang and
Jeff T. Inman and
Donald Kiphart and
C. Kodira and
S. Root and
Faye D. Schilkey and
Jolene Schwertfeger and
Adam C. Siepel and
David Stamper and
Nina Thayer and
R. Thompson and
Jennifer R. Wortman and
J. J. Zhuang and
Carol Harger},
title = {The Genome Sequence DataBase: towards an integrated functional genomics
resource},
journal = {Nucleic Acids Res.},
volume = {27},
number = {1},
pages = {35--38},
year = {1999},
url = {https://doi.org/10.1093/nar/27.1.35},
doi = {10.1093/NAR/27.1.35},
timestamp = {Fri, 26 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/SkupskiBFHHIKKRSSSSTTWZH99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HargerSBFHHKKMSSSSSSTTWWZS98,
author = {Carol Harger and
M. P. Skupski and
J. Bingham and
Andrew D. Farmer and
S. Hoisie and
Peter T. Hraber and
Donald Kiphart and
L. Krakowski and
Mia McLeod and
Jolene Schwertfeger and
G. A. Seluja and
Adam C. Siepel and
Gautam Singh and
David Stamper and
Peter A. Steadman and
Nina Thayer and
R. Thompson and
P. Wargo and
Mark E. Waugh and
J. J. Zhuang and
Peter A. Schad},
title = {The Genome Sequence DataBase {(GSDB):} improving data quality and
data access},
journal = {Nucleic Acids Res.},
volume = {26},
number = {1},
pages = {21--26},
year = {1998},
url = {https://doi.org/10.1093/nar/26.1.21},
doi = {10.1093/NAR/26.1.21},
timestamp = {Mon, 12 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HargerSBFHHKKMSSSSSSTTWWZS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HargerSACCDEEFFFHKMMOPRRRRSSSS97,
author = {Carol Harger and
Marian Skupski and
Ethan Allen and
Christopher Clark and
David Crowley and
Emily Dickinson and
David Easley and
Ada Espinosa{-}Lujan and
Andrew D. Farmer and
Chris A. Fields and
Leandrita Flores and
Lynn Harris and
Gifford Keen and
Maurice Manning and
Michael P. McLeod and
John O'Neill and
Maria Pumilia and
Rhonda Reinert and
David Rider and
John Rohrlich and
Yolanda Romero and
Jolene Schwertfeger and
Gustavo Seluja and
Adam C. Siepel and
Gautam Singh and
Linda Smyth and
David Stamper and
Judy Stein and
Randy Suggs and
Rajini Takkallapalli and
Nina Thayer and
Gary Thompson and
Colleen Walsh and
Frederick Wedgeworth III and
Peter A. Schad},
title = {The Genome Sequence DataBase version 1.0 {(GSDB):} from low pass sequences
to complete genomes},
journal = {Nucleic Acids Res.},
volume = {25},
number = {1},
pages = {18--23},
year = {1997},
url = {https://doi.org/10.1093/nar/25.1.18},
doi = {10.1093/NAR/25.1.18},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HargerSACCDEEFFFHKMMOPRRRRSSSS97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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