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ORCIDBibTeX records: Jakob Skou Pedersen
@article{DBLP:journals/nature/RheinbayNAWSTHH20,
author = {Esther Rheinbay and
Morten Muhlig Nielsen and
Federico Abascal and
Jeremiah Wala and
Ofer Shapira and
Grace Tiao and
Henrik Hornsh{\o}j and
Julian M. Hess and
Randi Istrup Juul and
Ziao Lin and
Lars Feuerbach and
Radhakrishnan Sabarinathan and
Tobias Madsen and
Jaegil Kim and
Loris Mularoni and
Shimin Shuai and
Andr{\'{e}}s Lanz{\'{o}}s and
Carl Herrmann and
Yosef E. Maruvka and
Ciyue Shen and
Samirkumar B. Amin and
Pratiti Bandopadhayay and
Johanna Bertl and
Keith A. Boroevich and
John Busanovich and
Joana Carlevaro{-}Fita and
Dimple Chakravarty and
Calvin Wing Yiu Chan and
David Craft and
Priyanka Dhingra and
Klev Diamanti and
Nuno A. Fonseca and
Abel Gonzalez{-}Perez and
Qianyun Guo and
Mark P. Hamilton and
Nicholas J. Haradhvala and
Chen Hong and
Keren Isaev and
Todd A. Johnson and
Malene Juul and
Andr{\'{e}} Kahles and
Abdullah Kahraman and
Youngwook Kim and
Jan Komorowski and
Kiran Kumar and
Sushant Kumar and
Donghoon Lee and
Kjong{-}Van Lehmann and
Yilong Li and
Eric Minwei Liu and
Lucas Lochovsky and
Keunchil Park and
Oriol Pich and
Nicola D. Roberts and
Gordon Saksena and
Steven E. Schumacher and
Nikos Sidiropoulos and
Lina Sieverling and
Nasa Sinnott{-}Armstrong and
Chip Stewart and
David Tamborero and
Jose M. C. Tubio and
Husen M. Umer and
Liis Uusk{\"{u}}la{-}Reimand and
Claes Wadelius and
Lina Wadi and
Xiaotong Yao and
Cheng{-}Zhong Zhang and
Jing Zhang and
James E. Haber and
Asger Hobolth and
Marcin Imielinski and
Manolis Kellis and
Michael S. Lawrence and
Christian von Mering and
Hidewaki Nakagawa and
Benjamin J. Raphael and
Mark A. Rubin and
Chris Sander and
Lincoln D. Stein and
Joshua M. Stuart and
Tatsuhiko Tsunoda and
David A. Wheeler and
Rory Johnson and
J{\"{u}}ri Reimand and
Mark Gerstein and
Ekta Khurana and
Peter J. Campbell and
N{\'{u}}ria L{\'{o}}pez{-}Bigas and
Gary D. Bader and
Jonathan Barenboim and
Rameen Beroukhim and
S{\o}ren Brunak and
Ken Chen and
Jung Kyoon Choi and
Jordi Deu{-}Pons and
J. Lynn Fink and
Joan Frigola and
Carlo Gambacorti Passerini and
Dale W. Garsed and
Gad Getz and
Ivo Glynne Gut and
David Haan and
Arif Ozgun Harmanci and
Mohamed Helmy and
Ermin Hodzic and
Jos{\'{e}} M. G. Izarzugaza and
Jong K. Kim and
Jan O. Korbel and
Erik Larsson and
Shantao Li and
Xiaotong Li and
Shaoke Lou and
Kathleen Marchal and
I{\~{n}}igo Martincorena and
Alexander Mart{\'{\i}}nez{-}Fundichely and
Patrick D. McGillivray and
William Meyerson and
Ferran Mui{\~{n}}os and
Marta Paczkowska and
Kiejung Park and
Jakob Skou Pedersen and
Tirso Pons and
Sergio Pulido{-}Tamayo and
Iker Reyes{-}Salazar and
Matthew A. Reyna and
Carlota Rubio{-}Perez and
S{\"{u}}leyman Cenk Sahinalp and
Leonidas Salichos and
Mark Shackleton and
Raunak Shrestha and
Alfonso Valencia and
Miguel Vazquez and
Lieven P. C. Verbeke and
Jiayin Wang and
Jonathan Warrell and
Sebastian M. Waszak and
Joachim Weischenfeldt and
Guanming Wu and
Jun Yu and
Xuanping Zhang and
Yan Zhang and
Zhongming Zhao and
Lihua Zou and
Kadir C. Akdemir and
Eva G. Alvarez and
Adrian Baez{-}Ortega and
Paul C. Boutros and
David D. L. Bowtell and
Benedikt Brors and
Kathleen H. Burns and
Kin Chan and
Isidro Cort{\'{e}}s{-}Ciriano and
Ana Dueso{-}Barroso and
Andrew J. Dunford and
Paul A. Edwards and
Xavier Estivill and
Dariush Etemadmoghadam and
Milana Frenkel{-}Morgenstern and
Dmitry A. Gordenin and
Barbara Hutter and
David T. W. Jones and
Young Seok Ju and
Marat D. Kazanov and
Leszek J. Klimczak and
Youngil Koh and
Eunjung Alice Lee and
Jake June{-}Koo Lee and
Andy G. Lynch and
Geoff MacIntyre and
Florian Markowetz and
Matthew Meyerson and
Satoru Miyano and
Fabio C. P. Navarro and
Stephan Ossowski and
Peter J. Park and
John V. Pearson and
Montserrat Puiggr{\`{o}}s and
Karsten Rippe and
Steven A. Roberts and
Bernardo Rodriguez{-}Martin and
Ralph Scully and
David Torrents and
Izar Villasante and
Nicola Waddell and
Jeremiah A. Wala and
Lixing Yang and
Sung{-}Soo Yoon and
Jorge Zamora},
title = {Analyses of non-coding somatic drivers in 2,658 cancer whole genomes},
journal = {Nat.},
volume = {578},
number = {7793},
pages = {102--111},
year = {2020},
url = {https://doi.org/10.1038/s41586-020-1965-x},
doi = {10.1038/S41586-020-1965-X},
timestamp = {Thu, 11 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/RheinbayNAWSTHH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/CalabreseDDFHKL20,
author = {Claudia Calabrese and
Natalie R. Davidson and
Deniz Demircioglu and
Nuno A. Fonseca and
Yao He and
Andr{\'{e}} Kahles and
Kjong{-}Van Lehmann and
Fenglin Liu and
Yuichi Shiraishi and
Cameron M. Soulette and
Lara Urban and
Liliana Greger and
Siliang Li and
Dongbing Liu and
Marc D. Perry and
Qian Xiang and
Fan Zhang and
Junjun Zhang and
Peter Bailey and
Serap Erkek and
Katherine A. Hoadley and
Yong Hou and
Matthew R. Huska and
Helena Kilpinen and
Jan O. Korbel and
Maximillian G. Marin and
Julia Markowski and
Tannistha Nandi and
Qiang Pan{-}Hammarstr{\"{o}}m and
Chandra Sekhar Pedamallu and
Reiner Siebert and
Stefan G. Stark and
Hong Su and
Patrick Tan and
Sebastian M. Waszak and
Christina K. Yung and
Shida Zhu and
Philip Awadalla and
Matthew Meyerson and
B. F. Francis Ouellette and
Kui Wu and
Huanming Yang and
Samirkumar B. Amin and
Aur{\'{e}}lien Chateigner and
Isidro Cort{\'{e}}s{-}Ciriano and
Brian Craft and
Milana Frenkel{-}Morgenstern and
Mary Goldman and
Ekta Khurana and
Fabien C. Lamaze and
Chang Li and
Xiaobo Li and
Xinyue Li and
Xingmin Liu and
Morten Muhlig Nielsen and
Akinyemi I. Ojesina and
Peter J. Park and
Jakob Skou Pedersen and
Bin Tean Teh and
Jian Wang and
Heng Xiong and
Sergei Yakneen and
Chen Ye and
Xiuqing Zhang and
Liangtao Zheng and
Jingchun Zhu and
Chad Creighton and
Jonathan G{\"{o}}ke and
Roland F. Schwarz and
Oliver Stegle and
Zemin Zhang and
Alvis Brazma and
Gunnar R{\"{a}}tsch and
Angela N. Brooks},
title = {Genomic basis for {RNA} alterations in cancer},
journal = {Nat.},
volume = {578},
number = {7793},
pages = {129--136},
year = {2020},
url = {https://doi.org/10.1038/s41586-020-1970-0},
doi = {10.1038/S41586-020-1970-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/CalabreseDDFHKL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JuulMGBHKP19,
author = {Malene Juul and
Tobias Madsen and
Qianyun Guo and
Johanna Bertl and
Asger Hobolth and
Manolis Kellis and
Jakob Skou Pedersen},
title = {ncdDetect2: improved models of the site-specific mutation rate in
cancer and driver detection with robust significance evaluation},
journal = {Bioinform.},
volume = {35},
number = {2},
pages = {189--199},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty511},
doi = {10.1093/BIOINFORMATICS/BTY511},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JuulMGBHKP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NielsenTMHP18,
author = {Morten Muhlig Nielsen and
Paula Tataru and
Tobias Madsen and
Asger Hobolth and
Jakob Skou Pedersen},
title = {Regmex: a statistical tool for exploring motifs in ranked sequence
lists from genomics experiments},
journal = {Algorithms Mol. Biol.},
volume = {13},
number = {1},
pages = {17:1--17:11},
year = {2018},
url = {https://doi.org/10.1186/s13015-018-0135-2},
doi = {10.1186/S13015-018-0135-2},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/NielsenTMHP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BertlGJBNHPH18,
author = {Johanna Bertl and
Qianyun Guo and
Malene Juul and
S{\o}ren Besenbacher and
Morten Muhlig Nielsen and
Henrik Hornsh{\o}j and
Jakob Skou Pedersen and
Asger Hobolth},
title = {A site specific model and analysis of the neutral somatic mutation
rate in whole-genome cancer data},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {147:1--147:15},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2141-2},
doi = {10.1186/S12859-018-2141-2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BertlGJBNHPH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MadsenHJP17,
author = {Tobias Madsen and
Asger Hobolth and
Jens Ledet Jensen and
Jakob Skou Pedersen},
title = {Significance evaluation in factor graphs},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {199:1--199:12},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1614-z},
doi = {10.1186/S12859-017-1614-Z},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MadsenHJP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SwitnickiJMSP16,
author = {Michal P. Switnicki and
Malene Juul and
Tobias Madsen and
Karina D. S{\o}rensen and
Jakob Skou Pedersen},
title = {{PINCAGE:} probabilistic integration of cancer genomics data for perturbed
gene identification and sample classification},
journal = {Bioinform.},
volume = {32},
number = {9},
pages = {1353--1365},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv758},
doi = {10.1093/BIOINFORMATICS/BTV758},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SwitnickiJMSP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SahooSP16,
author = {Sudhakar Sahoo and
Michal P. Switnicki and
Jakob Skou Pedersen},
title = {ProbFold: a probabilistic method for integration of probing data in
{RNA} secondary structure prediction},
journal = {Bioinform.},
volume = {32},
number = {17},
pages = {2626--2635},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw175},
doi = {10.1093/BIOINFORMATICS/BTW175},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SahooSP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarolchikKBBCDGHHHKMPPRRRSSTTWZHK08,
author = {Donna Karolchik and
Robert M. Kuhn and
Robert Baertsch and
Galt P. Barber and
Hiram Clawson and
Mark Diekhans and
Belinda Giardine and
Rachel A. Harte and
Angela S. Hinrichs and
Fan Hsu and
Kord M. Kober and
Webb Miller and
Jakob Skou Pedersen and
Andy Pohl and
Brian J. Raney and
Brooke L. Rhead and
Kate R. Rosenbloom and
Kayla E. Smith and
Mario Stanke and
Archana Thakkapallayil and
Heather Trumbower and
Ting Wang and
Ann S. Zweig and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser Database: 2008 update},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Database-Issue},
pages = {773--779},
year = {2008},
url = {https://doi.org/10.1093/nar/gkm966},
doi = {10.1093/NAR/GKM966},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarolchikKBBCDGHHHKMPPRRRSSTTWZHK08.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}
}
@article{DBLP:journals/bioinformatics/PedersenH03,
author = {Jakob Skou Pedersen and
Jotun Hein},
title = {Gene finding with a hidden Markov model of genome structure and evolution},
journal = {Bioinform.},
volume = {19},
number = {2},
pages = {219--227},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/19.2.219},
doi = {10.1093/BIOINFORMATICS/19.2.219},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PedersenH03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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