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ORCIDBibTeX records: Thomas M. Keane
@article{DBLP:journals/nar/ThakurBBFHHKKLLMMOPVVWZM23,
author = {Matthew Thakur and
Alex Bateman and
Cath Brooksbank and
Mallory Ann Freeberg and
Melissa Harrison and
Matthew Hartley and
Thomas M. Keane and
Gerard J. Kleywegt and
Andrew Leach and
Maria Levchenko and
Sarah L. Morgan and
Ellen M. McDonagh and
Sandra E. Orchard and
Irene Papatheodorou and
Sameer Velankar and
Juan Antonio Vizca{\'{\i}}no and
Rick Witham and
Barbara Zdrazil and
Johanna R. McEntyre},
title = {EMBL's European Bioinformatics Institute {(EMBL-EBI)} in 2022},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {9--17},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac1098},
doi = {10.1093/NAR/GKAC1098},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ThakurBBFHHKKLLMMOPVVWZM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FreebergFDRCJKM22,
author = {Mallory Ann Freeberg and
Lauren A. Fromont and
Teresa D'altri and
Anna Foix Romero and
Jorge Izquierdo Ciges and
Aina Jene and
Giselle Kerry and
Mauricio Moldes and
Roberto Ariosa and
Silvia Bahena and
Daniel Barrowdale and
Marcos Casado Barbero and
Dietmar Fern{\'{a}}ndez{-}Orth and
Carles Garcia{-}Linares and
Emilio Garcia{-}Rios and
Fr{\'{e}}d{\'{e}}ric Haziza and
Bela Juhasz and
Oscar Martinez Llobet and
Gemma Milla and
Anand Mohan and
Manuel Rueda and
Aravind Sankar and
Dona Shaju and
Ashutosh Shimpi and
Babita Singh and
Coline Thomas and
Sabela de la Torre and
Umuthan Uyan and
Claudia Vasallo and
Paul Flicek and
Roderic Guig{\'{o}} and
Arcadi Navarro and
Helen E. Parkinson and
Thomas M. Keane and
Jordi Rambla},
title = {The European Genome-phenome Archive in 2021},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {980--987},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab1059},
doi = {10.1093/NAR/GKAB1059},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/FreebergFDRCJKM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CezardCHKKSSSTV22,
author = {Timothee Cezard and
Fiona Cunningham and
Sarah E. Hunt and
Baron Koylass and
Nitin Kumar and
Gary Saunders and
April Shen and
Andres f Silva and
Kirill Tsukanov and
Sundararaman Venkataraman and
Paul Flicek and
Helen E. Parkinson and
Thomas M. Keane},
title = {The European Variation Archive: a {FAIR} resource of genomic variation
for all species},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {1216--1220},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab960},
doi = {10.1093/NAR/GKAB960},
timestamp = {Sun, 06 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CezardCHKKSSSTV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SenfDHMTHK21,
author = {Alexander Senf and
Robert Davies and
Fr{\'{e}}d{\'{e}}ric Haziza and
John Marshall and
Juan Ram{\'{o}}n Troncoso{-}Pastoriza and
Oliver Hofmann and
Thomas M. Keane},
title = {Crypt4GH: a file format standard enabling native access to encrypted
data},
journal = {Bioinform.},
volume = {37},
number = {17},
pages = {2753--2754},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab087},
doi = {10.1093/BIOINFORMATICS/BTAB087},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SenfDHMTHK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YatesACDLLNSHK21,
author = {Andrew D. Yates and
Jeremy Adams and
Somesh Chaturvedi and
Robert Davies and
Matthew R. Laird and
Rasko Leinonen and
Rishi Nag and
Nathan C. Sheffield and
Oliver Hofmann and
Thomas M. Keane},
title = {Refget: standardized access to reference sequences},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {299--300},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab524},
doi = {10.1093/BIOINFORMATICS/BTAB524},
timestamp = {Thu, 25 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YatesACDLLNSHK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DrysdaleCPGBGGH20,
author = {Rachel Drysdale and
Charles E. Cook and
Robert Petryszak and
Vivienne Baillie Gerritsen and
Mary Barlow and
Elisabeth Gasteiger and
Franziska Gruhl and
J{\"{u}}rgen Haas and
Jerry Lanfear and
Rodrigo Lopez and
Nicole Redaschi and
Heinz Stockinger and
Daniel Teixeira and
Aravind Venkatesan and
Alex Bateman and
Alan J. Bridge and
Guy Cochrane and
Robert D. Finn and
Frank Oliver Gl{\"{o}}ckner and
Marc Hanauer and
Thomas M. Keane and
Andrew Leach and
Luana Licata and
Per Oksvold and
Sandra E. Orchard and
Christine A. Orengo and
Helen E. Parkinson and
Bengt Persson and
Pablo Porras and
Jordi Rambla and
Ana Rath and
Charlotte Rodwell and
Ugis Sarkans and
Dietmar Schomburg and
Ian Sillitoe and
J. Dylan Spalding and
Mathias Uhl{\'{e}}n and
Sameer Velankar and
Juan Antonio Vizca{\'{\i}}no and
Kalle von Feilitzen and
Christian von Mering and
Andrew D. Yates and
Niklas Blomberg and
Christine Durinx and
Johanna R. McEntyre},
title = {The {ELIXIR} Core Data Resources: fundamental infrastructure for the
life sciences},
journal = {Bioinform.},
volume = {36},
number = {8},
pages = {2636--2642},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz959},
doi = {10.1093/BIOINFORMATICS/BTZ959},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DrysdaleCPGBGGH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AmidAKBBFHHHIJK20,
author = {Clara Amid and
Blaise T. F. Alako and
Vishnukumar Balavenkataraman Kadhirvelu and
Tony Burdett and
Josephine Burgin and
Jun Fan and
Peter W. Harrison and
Sam Holt and
Abdulrahman Hussein and
Eugene Ivanov and
Suran Jayathilaka and
Simon Kay and
Thomas M. Keane and
Rasko Leinonen and
Xin Liu and
Josu{\'{e}} Mart{\'{\i}}nez{-}Villacorta and
Annalisa Milano and
Amir Pakseresht and
Nadim Rahman and
Jeena Rajan and
Kethi Reddy and
Edward Richards and
Dmitriy Smirnov and
Alexey Sokolov and
Senthilnathan Vijayaraja and
Guy Cochrane},
title = {The European Nucleotide Archive in 2019},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D70--D76},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz1063},
doi = {10.1093/NAR/GKZ1063},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/AmidAKBBFHHHIJK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KelleherLABDGGG19,
author = {Jerome Kelleher and
Mike Lin and
Carl H. Albach and
Ewan Birney and
Robert Davies and
Marina Gourtovaia and
David Glazer and
Cristina Y. Gonz{\'{a}}lez and
David K. Jackson and
Aaron Kemp and
John Marshall and
Andrew Nowak and
Alexander Senf and
Jaime M. Tovar{-}Corona and
Alexander Vikhorev and
Thomas M. Keane and
GA4GH Streaming Task Team},
title = {htsget: a protocol for securely streaming genomic data},
journal = {Bioinform.},
volume = {35},
number = {1},
pages = {119--121},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty492},
doi = {10.1093/BIOINFORMATICS/BTY492},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KelleherLABDGGG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HarrisonAACCHHJ19,
author = {Peter W. Harrison and
Blaise T. F. Alako and
Clara Amid and
Ana Cerde{\~{n}}o{-}T{\'{a}}rraga and
Iain Cleland and
Sam Holt and
Abdulrahman Hussein and
Suran Jayathilaka and
Simon Kay and
Thomas M. Keane and
Rasko Leinonen and
Xin Liu and
Josu{\'{e}} Mart{\'{\i}}nez{-}Villacorta and
Annalisa Milano and
Nima Pakseresht and
Jeena Rajan and
Kethi Reddy and
Edward Richards and
Marc Rossello and
Nicole Silvester and
Dmitriy Smirnov and
Ana Luisa Toribio and
Senthilnathan Vijayaraja and
Guy Cochrane},
title = {The European Nucleotide Archive in 2018},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D84--D88},
year = {2019},
url = {https://doi.org/10.1093/nar/gky1078},
doi = {10.1093/NAR/GKY1078},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/HarrisonAACCHHJ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SilvesterAACCCH18,
author = {Nicole Silvester and
Blaise T. F. Alako and
Clara Amid and
Ana Cerde{\~{n}}o{-}T{\'{a}}rraga and
Laura Clarke and
Iain Cleland and
Peter W. Harrison and
Suran Jayathilaka and
Simon Kay and
Thomas M. Keane and
Rasko Leinonen and
Xin Liu and
Josu{\'{e}} Mart{\'{\i}}nez{-}Villacorta and
Manuela Menchi and
Kethi Reddy and
Nima Pakseresht and
Jeena Rajan and
Marc Rossello and
Dmitriy Smirnov and
Ana Luisa Toribio and
Daniel Vaughan and
Vadim Zalunin and
Guy Cochrane},
title = {The European Nucleotide Archive in 2017},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D36--D40},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1125},
doi = {10.1093/NAR/GKX1125},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SilvesterAACCCH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KeaneWA13,
author = {Thomas M. Keane and
Kim Wong and
David J. Adams},
title = {RetroSeq: transposable element discovery from next-generation sequencing
data},
journal = {Bioinform.},
volume = {29},
number = {3},
pages = {389--390},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/bts697},
doi = {10.1093/BIOINFORMATICS/BTS697},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KeaneWA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jpdc/PageKN10,
author = {Andrew J. Page and
Thomas M. Keane and
Thomas J. Naughton},
title = {Multi-heuristic dynamic task allocation using genetic algorithms in
a heterogeneous distributed system},
journal = {J. Parallel Distributed Comput.},
volume = {70},
number = {7},
pages = {758--766},
year = {2010},
url = {https://doi.org/10.1016/j.jpdc.2010.03.011},
doi = {10.1016/J.JPDC.2010.03.011},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jpdc/PageKN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AssefaKONB09,
author = {Samuel A. Assefa and
Thomas M. Keane and
Thomas D. Otto and
Chris Newbold and
Matthew Berriman},
title = {{ABACAS:} algorithm-based automatic contiguation of assembled sequences},
journal = {Bioinform.},
volume = {25},
number = {15},
pages = {1968--1969},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp347},
doi = {10.1093/BIOINFORMATICS/BTP347},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AssefaKONB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jpdc/PageKN08,
author = {Andrew J. Page and
Thomas M. Keane and
Thomas J. Naughton},
title = {Scheduling in a dynamic heterogeneous distributed system using estimation
error},
journal = {J. Parallel Distributed Comput.},
volume = {68},
number = {11},
pages = {1452--1462},
year = {2008},
url = {https://doi.org/10.1016/j.jpdc.2008.07.004},
doi = {10.1016/J.JPDC.2008.07.004},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jpdc/PageKN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KeaneNM07,
author = {Thomas M. Keane and
Thomas J. Naughton and
James O. McInerney},
title = {MultiPhyl: a high-throughput phylogenomics webserver using distributed
computing},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Web-Server-Issue},
pages = {33--37},
year = {2007},
url = {https://doi.org/10.1093/nar/gkm359},
doi = {10.1093/NAR/GKM359},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KeaneNM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/KeanePNTM06,
author = {Thomas M. Keane and
Andrew J. Page and
Thomas J. Naughton and
Simon A. A. Travers and
James O. McInerney},
title = {Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines},
journal = {Algorithmica},
volume = {45},
number = {3},
pages = {285--300},
year = {2006},
url = {https://doi.org/10.1007/s00453-006-1215-0},
doi = {10.1007/S00453-006-1215-0},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithmica/KeanePNTM06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/PageCKNMW06,
author = {Andrew J. Page and
Shirley Coyle and
Thomas M. Keane and
Thomas J. Naughton and
Charles Markham and
Tom{\'{a}}s E. Ward},
title = {Distributed Monte Carlo simulation of light transportation in tissue},
booktitle = {20th International Parallel and Distributed Processing Symposium {(IPDPS}
2006), Proceedings, 25-29 April 2006, Rhodes Island, Greece},
publisher = {{IEEE}},
year = {2006},
url = {https://doi.org/10.1109/IPDPS.2006.1639511},
doi = {10.1109/IPDPS.2006.1639511},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/PageCKNMW06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KeaneNTMM05,
author = {Thomas M. Keane and
Thomas J. Naughton and
Simon A. A. Travers and
James O. McInerney and
Grace P. McCormack},
title = {DPRml: distributed phylogeny reconstruction by maximum likelihood},
journal = {Bioinform.},
volume = {21},
number = {7},
pages = {969--974},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti100},
doi = {10.1093/BIOINFORMATICS/BTI100},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KeaneNTMM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KeaneN05,
author = {Thomas M. Keane and
Thomas J. Naughton},
title = {{DSEARCH:} sensitive database searching using distributed computing},
journal = {Bioinform.},
volume = {21},
number = {8},
pages = {1705--1706},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti163},
doi = {10.1093/BIOINFORMATICS/BTI163},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KeaneN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cbms/KeanePMN05,
author = {Thomas M. Keane and
Andrew J. Page and
James O. McInerney and
Thomas J. Naughton},
title = {A High-Throughput Bioinformatics Distributed Computing Platform},
booktitle = {18th {IEEE} Symposium on Computer-Based Medical Systems {(CBMS} 2005),
23-24 June 2005, Dublin, Ireland},
pages = {377--382},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CBMS.2005.11},
doi = {10.1109/CBMS.2005.11},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cbms/KeanePMN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/PageKN05,
author = {Andrew J. Page and
Thomas M. Keane and
Thomas J. Naughton},
title = {Bioinformatics on a Heterogeneous Java Distributed System},
booktitle = {19th International Parallel and Distributed Processing Symposium {(IPDPS}
2005), {CD-ROM} / Abstracts Proceedings, 4-8 April 2005, Denver, CO,
{USA}},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/IPDPS.2005.127},
doi = {10.1109/IPDPS.2005.127},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/PageKN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ispdc/PageKN04,
author = {Andrew J. Page and
Thomas M. Keane and
Thomas J. Naughton},
title = {Adaptive Scheduling across a Distributed Computation Platform},
booktitle = {3rd International Symposium on Parallel and Distributed Computing
{(ISPDC} 2004), 3rd International Workshop on Algorithms, Models and
Tools for Parallel Computing on Heterogenous Networks (HeteroPar 2004),
5-7 July 2004, Cork, Ireland},
pages = {141--148},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/ISPDC.2004.8},
doi = {10.1109/ISPDC.2004.8},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ispdc/PageKN04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pppj/PageKANW03,
author = {Andrew J. Page and
Thomas M. Keane and
Richard Allen and
Thomas J. Naughton and
John Waldron},
editor = {James F. Power and
John Waldron},
title = {Multi-tiered distributed computing platform},
booktitle = {Proceedings of the 2nd International Symposium on Principles and Practice
of Programming in Java, {PPPJ} 2003, Kilkenny City, Ireland, June
16-18, 2003},
series = {{ACM} International Conference Proceeding Series},
volume = {42},
pages = {191--194},
publisher = {{ACM}},
year = {2003},
url = {https://dl.acm.org/citation.cfm?id=957347},
timestamp = {Mon, 26 Nov 2018 15:05:58 +0100},
biburl = {https://dblp.org/rec/conf/pppj/PageKANW03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fidji/KeaneANMW02,
author = {Thomas M. Keane and
Richard Allen and
Thomas J. Naughton and
James O. McInerney and
John Waldron},
editor = {Nicolas Guelfi and
Egidio Astesiano and
Gianna Reggio},
title = {Distributed Java Platform with Programmable {MIMD} Capabilities},
booktitle = {Scientific Engineering for Distributed Java Applications, International
Workshop, {FIDJI} 2002, Luxembourg-Kirchberg, Luxembourg, November
28-29, 2002, Revised Papers},
series = {Lecture Notes in Computer Science},
volume = {2604},
pages = {122--131},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-36520-6\_11},
doi = {10.1007/3-540-36520-6\_11},
timestamp = {Tue, 14 May 2019 10:00:45 +0200},
biburl = {https://dblp.org/rec/conf/fidji/KeaneANMW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pppj/KeaneANMW02,
author = {Thomas M. Keane and
Richard Allen and
Thomas J. Naughton and
James O. McInerney and
John Waldron},
editor = {John Waldron and
James F. Power},
title = {Distributed computing for {DNA} analysis},
booktitle = {Proceedings of the naugural International Symposium on Principles
and Practice of Programming in Java, {PPPJ} 2002, and Proceedings
of the second workshop on Intermediate representation engineering
for virtual machines, Dublin, Ireland, June 13-14, 2002},
series = {{ACM} International Conference Proceeding Series},
volume = {25},
pages = {65--70},
publisher = {{ACM}},
year = {2002},
url = {https://dl.acm.org/citation.cfm?id=638490},
timestamp = {Mon, 26 Nov 2018 15:05:58 +0100},
biburl = {https://dblp.org/rec/conf/pppj/KeaneANMW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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