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ORCIDBibTeX records: Erik L. L. Sonnhammer
@article{DBLP:journals/bioinformatics/HillertonSNS22,
author = {Thomas Hillerton and
Deniz Se{\c{c}}ilmis and
Sven Nelander and
Erik L. L. Sonnhammer},
title = {Fast and accurate gene regulatory network inference by normalized
least squares regression},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2263--2268},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac103},
doi = {10.1093/BIOINFORMATICS/BTAC103},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HillertonSNS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PerssonS22,
author = {Emma Persson and
Erik L. L. Sonnhammer},
title = {InParanoid-DIAMOND: faster orthology analysis with the InParanoid
algorithm},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2918--2919},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac194},
doi = {10.1093/BIOINFORMATICS/BTAC194},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PerssonS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SecilmisHS22,
author = {Deniz Se{\c{c}}ilmis and
Thomas Hillerton and
Erik L. L. Sonnhammer},
title = {GRNbenchmark - a web server for benchmarking directed gene regulatory
network inference methods},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {398--404},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac377},
doi = {10.1093/NAR/GKAC377},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SecilmisHS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/NeversJJYFPCCMV22,
author = {Yannis Nevers and
Tamsin E. M. Jones and
Dushyanth Jyothi and
Bethan Yates and
Meritxell Ferret and
Laura Portell{-}Silva and
Laia Cod{\'{o}} and
Salvatore Cosentino and
Marina Marcet{-}Houben and
Anna Vlasova and
Laetitia Poidevin and
Arnaud Kress and
Mark Hickman and
Emma Persson and
Ivana Pilizota and
Cristina Guijarro{-}Clarke and
Adrian M. Altenhoff and
Elspeth A. Bruford and
Christophe Dessimoz and
Ingo Ebersberger and
David M. Emms and
Toni Gabald{\'{o}}n and
Natasha M. Glover and
Yanhui Hu and
Wataru Iwasaki and
Odile Lecompte and
Benjamin Linard and
Mar{\'{\i}}a J. Mart{\'{\i}}n and
David S. Roos and
Erik Sonhammer and
Paul D. Thomas and
David Thybert and
Klaas Vandepoele and
Salvador Capella{-}Guti{\'{e}}rrez and
Asier Gonzalez{-}Uriarte and
Javier Garrayo{-}Ventas and
Dmitry Repchevsky and
Vicky Sundesha and
Erik L. L. Sonnhammer},
title = {The Quest for Orthologs orthology benchmark service in 2022},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {623--632},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac330},
doi = {10.1093/NAR/GKAC330},
timestamp = {Sun, 19 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/NeversJJYFPCCMV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SecilmisHNS21,
author = {Deniz Se{\c{c}}ilmis and
Thomas Hillerton and
Sven Nelander and
Erik L. L. Sonnhammer},
title = {Inferring the experimental design for accurate gene regulatory network
inference},
journal = {Bioinform.},
volume = {37},
number = {20},
pages = {3553--3559},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab367},
doi = {10.1093/BIOINFORMATICS/BTAB367},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SecilmisHNS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MistryCWQSSTPRR21,
author = {Jaina Mistry and
Sara Chuguransky and
Lowri Williams and
Matloob Qureshi and
Gustavo A. Salazar and
Erik L. L. Sonnhammer and
Silvio C. E. Tosatto and
Lisanna Paladin and
Shriya Raj and
Lorna J. Richardson and
Robert D. Finn and
Alex Bateman},
title = {Pfam: The protein families database in 2021},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D412--D419},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa913},
doi = {10.1093/NAR/GKAA913},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MistryCWQSSTPRR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GualaOMS20,
author = {Dimitri Guala and
Christoph Ogris and
Nikola M{\"{u}}ller and
Erik L. L. Sonnhammer},
title = {Genome-wide functional association networks: background, data {\&}
state-of-the-art resources},
journal = {Briefings Bioinform.},
volume = {21},
number = {4},
pages = {1224--1237},
year = {2020},
url = {https://doi.org/10.1093/bib/bbz064},
doi = {10.1093/BIB/BBZ064},
timestamp = {Sun, 11 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GualaOMS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AltenhoffGCEGHN20,
author = {Adrian M. Altenhoff and
Javier Garrayo{-}Ventas and
Salvatore Cosentino and
David Emms and
Natasha M. Glover and
Ana Hern{\'{a}}ndez{-}Plaza and
Yannis Nevers and
Vicky Sundesha and
Damian Szklarczyk and
Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and
Laia Cod{\'{o}} and
The Quest for Orthologs Consortium and
Josep Lluis Gelp{\'{\i}} and
Jaime Huerta{-}Cepas and
Wataru Iwasaki and
Steven Kelly and
Odile Lecompte and
Matthieu Muffato and
Maria Jesus Martin and
Salvador Capella{-}Guti{\'{e}}rrez and
Paul D. Thomas and
Erik L. L. Sonnhammer and
Christophe Dessimoz},
title = {The Quest for Orthologs benchmark service and consensus calls in 2020},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Webserver-Issue},
pages = {W538--W545},
year = {2020},
url = {https://doi.org/10.1093/nar/gkaa308},
doi = {10.1093/NAR/GKAA308},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AltenhoffGCEGHN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MorganTNS19,
author = {Daniel Morgan and
Andreas Tj{\"{a}}rnberg and
Torbj{\"{o}}rn E. M. Nordling and
Erik L. L. Sonnhammer},
title = {A generalized framework for controlling {FDR} in gene regulatory network
inference},
journal = {Bioinform.},
volume = {35},
number = {6},
pages = {1026--1032},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty764},
doi = {10.1093/BIOINFORMATICS/BTY764},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MorganTNS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PerssonKFS19,
author = {Emma Persson and
Mateusz Kaduk and
Sofia K. Forslund and
Erik L. L. Sonnhammer},
title = {Domainoid: domain-oriented orthology inference},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {523:1--523:12},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-3137-2},
doi = {10.1186/S12859-019-3137-2},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PerssonKFS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/El-GebaliMBELPQ19,
author = {Sara El{-}Gebali and
Jaina Mistry and
Alex Bateman and
Sean R. Eddy and
Aurelien Luciani and
Simon C. Potter and
Matloob Qureshi and
Lorna J. Richardson and
Gustavo A. Salazar and
Alfredo Smart and
Erik L. L. Sonnhammer and
Layla Hirsh and
Lisanna Paladin and
Damiano Piovesan and
Silvio C. E. Tosatto and
Robert D. Finn},
title = {The Pfam protein families database in 2019},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D427--D432},
year = {2019},
url = {https://doi.org/10.1093/nar/gky995},
doi = {10.1093/NAR/GKY995},
timestamp = {Mon, 26 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/El-GebaliMBELPQ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForslundPCSAHMP18,
author = {Kristoffer Forslund and
C{\'{e}}cile Pereira and
Salvador Capella{-}Guti{\'{e}}rrez and
Alan W. Sousa da Silva and
Adrian M. Altenhoff and
Jaime Huerta{-}Cepas and
Matthieu Muffato and
Mateus Patricio and
Klaas Vandepoele and
Ingo Ebersberger and
Judith A. Blake and
Jesualdo Tom{\'{a}}s Fern{\'{a}}ndez{-}Breis and
The Quest for Orthologs Consortium and
Brigitte Boeckmann and
Toni Gabald{\'{o}}n and
Erik L. L. Sonnhammer and
Christophe Dessimoz and
Suzanna Lewis},
title = {Gearing up to handle the mosaic nature of life in the quest for orthologs},
journal = {Bioinform.},
volume = {34},
number = {2},
pages = {323--329},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx542},
doi = {10.1093/BIOINFORMATICS/BTX542},
timestamp = {Fri, 08 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForslundPCSAHMP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OgrisGKS18,
author = {Christoph Ogris and
Dimitri Guala and
Mateusz Kaduk and
Erik L. L. Sonnhammer},
title = {FunCoup 4: new species, data, and visualization},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D601--D607},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1138},
doi = {10.1093/NAR/GKX1138},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/OgrisGKS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KadukS17,
author = {Mateusz Kaduk and
Erik L. L. Sonnhammer},
title = {Improved orthology inference with Hieranoid 2},
journal = {Bioinform.},
volume = {33},
number = {8},
pages = {1154--1159},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw774},
doi = {10.1093/BIOINFORMATICS/BTW774},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KadukS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KadukRLS17,
author = {Mateusz Kaduk and
Christian Riegler and
Oliver Lemp and
Erik L. L. Sonnhammer},
title = {HieranoiDB: a database of orthologs inferred by Hieranoid},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D687--D690},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw923},
doi = {10.1093/NAR/GKW923},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KadukRLS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaiderKS16,
author = {Christian Haider and
Marina Kavic and
Erik L. L. Sonnhammer},
title = {TreeDom: a graphical web tool for analysing domain architecture evolution},
journal = {Bioinform.},
volume = {32},
number = {15},
pages = {2384--2385},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw140},
doi = {10.1093/BIOINFORMATICS/BTW140},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaiderKS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SaripellaSF16,
author = {Ganapathi Varma Saripella and
Erik L. L. Sonnhammer and
Kristoffer Forslund},
title = {Benchmarking the next generation of homology inference tools},
journal = {Bioinform.},
volume = {32},
number = {17},
pages = {2636--2641},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw305},
doi = {10.1093/BIOINFORMATICS/BTW305},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SaripellaSF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OgrisHS16,
author = {Christoph Ogris and
Thomas Helleday and
Erik L. L. Sonnhammer},
title = {PathwAX: a web server for network crosstalk based pathway annotation},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Webserver-Issue},
pages = {W105--W109},
year = {2016},
url = {https://doi.org/10.1093/nar/gkw356},
doi = {10.1093/NAR/GKW356},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/OgrisHS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SonnhammerO15,
author = {Erik L. L. Sonnhammer and
Gabriel {\"{O}}stlund},
title = {InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {234--239},
year = {2015},
url = {https://doi.org/10.1093/nar/gku1203},
doi = {10.1093/NAR/GKU1203},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SonnhammerO15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StudhamTNNS14,
author = {Matthew Studham and
Andreas Tj{\"{a}}rnberg and
Torbj{\"{o}}rn E. M. Nordling and
Sven Nelander and
Erik L. L. Sonnhammer},
title = {Functional association networks as priors for gene regulatory network
inference},
journal = {Bioinform.},
volume = {30},
number = {12},
pages = {130--138},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu285},
doi = {10.1093/BIOINFORMATICS/BTU285},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StudhamTNNS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GualaSS14,
author = {Dimitri Guala and
Erik Sj{\"{o}}lund and
Erik L. L. Sonnhammer},
title = {MaxLink: network-based prioritization of genes tightly linked to a
disease seed set},
journal = {Bioinform.},
volume = {30},
number = {18},
pages = {2689--2690},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu344},
doi = {10.1093/BIOINFORMATICS/BTU344},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GualaSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SonnhammerGSMRBTDa14,
author = {Erik L. L. Sonnhammer and
Toni Gabald{\'{o}}n and
Alan W. Sousa da Silva and
Maria Jesus Martin and
Marc Robinson{-}Rechavi and
Brigitte Boeckmann and
Paul D. Thomas and
Christophe Dessimoz and
The Quest for Orthologs Consortium},
title = {Big data and other challenges in the quest for orthologs},
journal = {Bioinform.},
volume = {30},
number = {21},
pages = {2993--2998},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu492},
doi = {10.1093/BIOINFORMATICS/BTU492},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SonnhammerGSMRBTDa14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FinnBCCEEHHHMSTP14,
author = {Robert D. Finn and
Alex Bateman and
Jody Clements and
Penelope Coggill and
Ruth Y. Eberhardt and
Sean R. Eddy and
Andreas Heger and
Kirstie Hetherington and
Liisa Holm and
Jaina Mistry and
Erik L. L. Sonnhammer and
John G. Tate and
Marco Punta},
title = {Pfam: the protein families database},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {222--230},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1223},
doi = {10.1093/NAR/GKT1223},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FinnBCCEEHHHMSTP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SchmittOS14,
author = {Thomas Schmitt and
Christoph Ogris and
Erik L. L. Sonnhammer},
title = {FunCoup 3.0: database of genome-wide functional coupling networks},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {380--388},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt984},
doi = {10.1093/NAR/GKT984},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SchmittOS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/TjarnbergNSS13,
author = {Andreas Tj{\"{a}}rnberg and
Torbj{\"{o}}rn E. M. Nordling and
Matthew Studham and
Erik L. L. Sonnhammer},
title = {Optimal Sparsity Criteria for Network Inference},
journal = {J. Comput. Biol.},
volume = {20},
number = {5},
pages = {398--408},
year = {2013},
url = {https://doi.org/10.1089/cmb.2012.0268},
doi = {10.1089/CMB.2012.0268},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/TjarnbergNSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DessimozGRSH12,
author = {Christophe Dessimoz and
Toni Gabald{\'{o}}n and
David S. Roos and
Erik L. L. Sonnhammer and
Javier Herrero},
title = {Toward community standards in the quest for orthologs},
journal = {Bioinform.},
volume = {28},
number = {6},
pages = {900--904},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts050},
doi = {10.1093/BIOINFORMATICS/BTS050},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DessimozGRSH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PuntaCEMTBPFCCHHSEBF12,
author = {Marco Punta and
Penny C. Coggill and
Ruth Y. Eberhardt and
Jaina Mistry and
John G. Tate and
Chris Boursnell and
Ningze Pang and
Kristoffer Forslund and
Goran Ceric and
Jody Clements and
Andreas Heger and
Liisa Holm and
Erik L. L. Sonnhammer and
Sean R. Eddy and
Alex Bateman and
Robert D. Finn},
title = {The Pfam protein families database},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {290--301},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr1065},
doi = {10.1093/NAR/GKR1065},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PuntaCEMTBPFCCHHSEBF12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AlexeyenkoSTGFS12,
author = {Andrey Alexeyenko and
Thomas Schmitt and
Andreas Tj{\"{a}}rnberg and
Dimitri Guala and
Oliver Frings and
Erik L. L. Sonnhammer},
title = {Comparative interactomics with Funcoup 2.0},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {821--828},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr1062},
doi = {10.1093/NAR/GKR1062},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AlexeyenkoSTGFS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ForslundSTS11,
author = {Kristoffer Forslund and
Fabian Schreiber and
Nattaphon Thanintorn and
Erik L. L. Sonnhammer},
title = {OrthoDisease: tracking disease gene orthologs across 100 species},
journal = {Briefings Bioinform.},
volume = {12},
number = {5},
pages = {463--473},
year = {2011},
url = {https://doi.org/10.1093/bib/bbr024},
doi = {10.1093/BIB/BBR024},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ForslundSTS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SchmittMSS11,
author = {Thomas Schmitt and
David N. Messina and
Fabian Schreiber and
Erik L. L. Sonnhammer},
title = {Letter to the Editor: SeqXML and OrthoXML: standards for sequence
and orthology information},
journal = {Briefings Bioinform.},
volume = {12},
number = {5},
pages = {485--488},
year = {2011},
url = {https://doi.org/10.1093/bib/bbr025},
doi = {10.1093/BIB/BBR025},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SchmittMSS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ForslundPS11,
author = {Kristoffer Forslund and
Isabella Pekkari and
Erik L. L. Sonnhammer},
title = {Domain architecture conservation in orthologs},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {326},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-326},
doi = {10.1186/1471-2105-12-326},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ForslundPS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OstlundSFKMRFS10,
author = {Gabriel {\"{O}}stlund and
Thomas Schmitt and
Kristoffer Forslund and
Tina K{\"{o}}stler and
David N. Messina and
Sanjit Roopra and
Oliver Frings and
Erik L. L. Sonnhammer},
title = {InParanoid 7: new algorithms and tools for eukaryotic orthology analysis},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Database-Issue},
pages = {196--203},
year = {2010},
url = {https://doi.org/10.1093/nar/gkp931},
doi = {10.1093/NAR/GKP931},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/OstlundSFKMRFS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FinnMTCHPGGCFHSEB10,
author = {Robert D. Finn and
Jaina Mistry and
John G. Tate and
Penny C. Coggill and
Andreas Heger and
Joanne E. Pollington and
O. Luke Gavin and
Prasad Gunasekaran and
Goran Ceric and
Kristoffer Forslund and
Liisa Holm and
Erik L. L. Sonnhammer and
Sean R. Eddy and
Alex Bateman},
title = {The Pfam protein families database},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Database-Issue},
pages = {211--222},
year = {2010},
url = {https://doi.org/10.1093/nar/gkp985},
doi = {10.1093/NAR/GKP985},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FinnMTCHPGGCFHSEB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForslundS09,
author = {Kristoffer Forslund and
Erik L. L. Sonnhammer},
title = {Predicting protein function from domain content},
journal = {Bioinform.},
volume = {25},
number = {9},
pages = {1214},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp186},
doi = {10.1093/BIOINFORMATICS/BTP186},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForslundS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MessinaS09,
author = {David N. Messina and
Erik L. L. Sonnhammer},
title = {DASher: a stand-alone protein sequence client for DAS, the Distributed
Annotation System},
journal = {Bioinform.},
volume = {25},
number = {10},
pages = {1333--1334},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp153},
doi = {10.1093/BIOINFORMATICS/BTP153},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MessinaS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForslundS09a,
author = {Kristoffer Forslund and
Erik L. L. Sonnhammer},
title = {Benchmarking homology detection procedures with low complexity filters},
journal = {Bioinform.},
volume = {25},
number = {19},
pages = {2500--2505},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp446},
doi = {10.1093/BIOINFORMATICS/BTP446},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForslundS09a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BjorkholmS09,
author = {Patrik Bj{\"{o}}rkholm and
Erik L. L. Sonnhammer},
title = {Comparative analysis and unification of domain-domain interaction
networks},
journal = {Bioinform.},
volume = {25},
number = {22},
pages = {3020--3025},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp522},
doi = {10.1093/BIOINFORMATICS/BTP522},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BjorkholmS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KlammerMSS09,
author = {Martin Klammer and
David N. Messina and
Thomas Schmitt and
Erik L. L. Sonnhammer},
title = {MetaTM - a consensus method for transmembrane protein topology prediction},
journal = {{BMC} Bioinform.},
volume = {10},
pages = {314},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-314},
doi = {10.1186/1471-2105-10-314},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KlammerMSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChalkS08,
author = {Alistair M. Chalk and
Erik L. L. Sonnhammer},
title = {siRNA specificity searching incorporating mismatch tolerance data},
journal = {Bioinform.},
volume = {24},
number = {10},
pages = {1316--1317},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn121},
doi = {10.1093/BIOINFORMATICS/BTN121},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChalkS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KlammerRS08,
author = {Martin Klammer and
Sanjit Roopra and
Erik L. L. Sonnhammer},
title = {jSquid: a Java applet for graphical on-line network exploration},
journal = {Bioinform.},
volume = {24},
number = {12},
pages = {1467--1468},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn213},
doi = {10.1093/BIOINFORMATICS/BTN213},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KlammerRS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForslundS08,
author = {Kristoffer Forslund and
Erik L. L. Sonnhammer},
title = {Predicting protein function from domain content},
journal = {Bioinform.},
volume = {24},
number = {15},
pages = {1681--1687},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn312},
doi = {10.1093/BIOINFORMATICS/BTN312},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForslundS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForslundS08a,
author = {Kristoffer Forslund and
Erik L. L. Sonnhammer},
title = {Predicting protein function from domain content},
journal = {Bioinform.},
volume = {24},
number = {19},
pages = {2275},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn447},
doi = {10.1093/BIOINFORMATICS/BTN447},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForslundS08a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/DaubS08,
author = {Carsten O. Daub and
Erik L. L. Sonnhammer},
title = {Employing conservation of co-expression to improve functional inference},
journal = {{BMC} Syst. Biol.},
volume = {2},
pages = {81},
year = {2008},
url = {https://doi.org/10.1186/1752-0509-2-81},
doi = {10.1186/1752-0509-2-81},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/DaubS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BerglundSOS08,
author = {Ann{-}Charlotte Berglund and
Erik Sj{\"{o}}lund and
Gabriel {\"{O}}stlund and
Erik L. L. Sonnhammer},
title = {InParanoid 6: eukaryotic ortholog clusters with inparalogs},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Database-Issue},
pages = {263--266},
year = {2008},
url = {https://doi.org/10.1093/nar/gkm1020},
doi = {10.1093/NAR/GKM1020},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BerglundSOS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FinnTMCSHCFESB08,
author = {Robert D. Finn and
John G. Tate and
Jaina Mistry and
Penny C. Coggill and
Stephen John Sammut and
Hans{-}Rudolf Hotz and
Goran Ceric and
Kristoffer Forslund and
Sean R. Eddy and
Erik L. L. Sonnhammer and
Alex Bateman},
title = {The Pfam protein families database},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Database-Issue},
pages = {281--288},
year = {2008},
url = {https://doi.org/10.1093/nar/gkm960},
doi = {10.1093/NAR/GKM960},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FinnTMCSHCFESB08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HollichS07,
author = {Volker Hollich and
Erik L. L. Sonnhammer},
title = {PfamAlyzer: domain-centric homology search},
journal = {Bioinform.},
volume = {23},
number = {24},
pages = {3382--3383},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm521},
doi = {10.1093/BIOINFORMATICS/BTM521},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HollichS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LassmannS07,
author = {Timo Lassmann and
Erik L. L. Sonnhammer},
title = {Automatic extraction of reliable regions from multiple sequence alignments},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-5}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S5-S9},
doi = {10.1186/1471-2105-8-S5-S9},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LassmannS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KallKS07,
author = {Lukas K{\"{a}}ll and
Anders Krogh and
Erik L. L. Sonnhammer},
title = {Advantages of combined transmembrane topology and signal peptide prediction
- the Phobius web server},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Web-Server-Issue},
pages = {429--432},
year = {2007},
url = {https://doi.org/10.1093/nar/gkm256},
doi = {10.1093/NAR/GKM256},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KallKS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FinnMSGHLMMKDESB06,
author = {Robert D. Finn and
Jaina Mistry and
Benjamin Schuster{-}B{\"{o}}ckler and
Sam Griffiths{-}Jones and
Volker Hollich and
Timo Lassmann and
Simon Moxon and
Mhairi Marshall and
Ajay Khanna and
Richard Durbin and
Sean R. Eddy and
Erik L. L. Sonnhammer and
Alex Bateman},
title = {Pfam: clans, web tools and services},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {247--251},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj149},
doi = {10.1093/NAR/GKJ149},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FinnMSGHLMMKDESB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LassmannS06,
author = {Timo Lassmann and
Erik L. L. Sonnhammer},
title = {Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Web-Server-Issue},
pages = {596--599},
year = {2006},
url = {https://doi.org/10.1093/nar/gkl191},
doi = {10.1093/NAR/GKL191},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/LassmannS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/AlexeyenkoTLS06,
author = {Andrey Alexeyenko and
Ivica Tamas and
Gang Liu and
Erik L. L. Sonnhammer},
title = {Automatic clustering of orthologs and inparalogs shared by multiple
proteomes},
booktitle = {Proceedings 14th International Conference on Intelligent Systems for
Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006},
pages = {9--15},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl213},
doi = {10.1093/BIOINFORMATICS/BTL213},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/AlexeyenkoTLS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WistrandS05,
author = {Markus Wistrand and
Erik L. L. Sonnhammer},
title = {Improved profile {HMM} performance by assessment of critical algorithmic
features in {SAM} and {HMMER}},
journal = {{BMC} Bioinform.},
volume = {6},
pages = {99},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-99},
doi = {10.1186/1471-2105-6-99},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WistrandS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SonnhammerH05,
author = {Erik L. L. Sonnhammer and
Volker Hollich},
title = {\emph{Scoredist}: {A} simple and robust protein sequence distance
estimator},
journal = {{BMC} Bioinform.},
volume = {6},
pages = {108},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-108},
doi = {10.1186/1471-2105-6-108},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SonnhammerH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LassmannS05,
author = {Timo Lassmann and
Erik L. L. Sonnhammer},
title = {Kalign - an accurate and fast multiple sequence alignment algorithm},
journal = {{BMC} Bioinform.},
volume = {6},
pages = {298},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-298},
doi = {10.1186/1471-2105-6-298},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LassmannS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ChalkWGS05,
author = {Alistair M. Chalk and
Richard E. Warfinge and
Patrick Georgii{-}Hemming and
Erik L. L. Sonnhammer},
title = {siRNAdb: a database of siRNA sequences},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Database-Issue},
pages = {131--134},
year = {2005},
url = {https://doi.org/10.1093/nar/gki136},
doi = {10.1093/NAR/GKI136},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ChalkWGS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AbhimanS05,
author = {Saraswathi Abhiman and
Erik L. L. Sonnhammer},
title = {FunShift: a database of function shift analysis on protein subfamilies},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Database-Issue},
pages = {197--200},
year = {2005},
url = {https://doi.org/10.1093/nar/gki067},
doi = {10.1093/NAR/GKI067},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AbhimanS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OBrienRS05,
author = {Kevin P. O'Brien and
Maido Remm and
Erik L. L. Sonnhammer},
title = {Inparanoid: a comprehensive database of eukaryotic orthologs},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Database-Issue},
pages = {476--480},
year = {2005},
url = {https://doi.org/10.1093/nar/gki107},
doi = {10.1093/NAR/GKI107},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/OBrienRS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KallKS05,
author = {Lukas K{\"{a}}ll and
Anders Krogh and
Erik L. L. Sonnhammer},
title = {An {HMM} posterior decoder for sequence feature prediction that includes
homology information},
booktitle = {Proceedings Thirteenth International Conference on Intelligent Systems
for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005},
pages = {251--257},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti1014},
doi = {10.1093/BIOINFORMATICS/BTI1014},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/KallKS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EkdahlS04,
author = {Sven Ekdahl and
Erik L. L. Sonnhammer},
title = {ChromoWheel: a new spin on eukaryotic chromosome visualization},
journal = {Bioinform.},
volume = {20},
number = {4},
pages = {576--577},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/btg448},
doi = {10.1093/BIOINFORMATICS/BTG448},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/EkdahlS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChalkWS04,
author = {Alistair M. Chalk and
Martin Wennerberg and
Erik L. L. Sonnhammer},
title = {Sfixem - graphical sequence feature display in Java},
journal = {Bioinform.},
volume = {20},
number = {15},
pages = {2488--2490},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth265},
doi = {10.1093/BIOINFORMATICS/BTH265},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChalkWS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Camps-VallsCSMS04,
author = {Gustavo Camps{-}Valls and
Alistair M. Chalk and
Antonio J. Serrano{-}L{\'{o}}pez and
Jos{\'{e}} David Mart{\'{\i}}n{-}Guerrero and
Erik L. L. Sonnhammer},
title = {Profiled support vector machines for antisense oligonucleotide efficacy
prediction},
journal = {{BMC} Bioinform.},
volume = {5},
pages = {135},
year = {2004},
url = {https://doi.org/10.1186/1471-2105-5-135},
doi = {10.1186/1471-2105-5-135},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Camps-VallsCSMS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/WistrandS04,
author = {Markus Wistrand and
Erik L. L. Sonnhammer},
title = {Transition Priors for Protein Hidden Markov Models: An Empirical Study
towards Maximum Discrimination},
journal = {J. Comput. Biol.},
volume = {11},
number = {1},
pages = {181--193},
year = {2004},
url = {https://doi.org/10.1089/106652704773416957},
doi = {10.1089/106652704773416957},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/WistrandS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BatemanCDFHGKMMSSYE04,
author = {Alex Bateman and
Lachlan James M. Coin and
Richard Durbin and
Robert D. Finn and
Volker Hollich and
Sam Griffiths{-}Jones and
Ajay Khanna and
Mhairi Marshall and
Simon Moxon and
Erik L. L. Sonnhammer and
David J. Studholme and
Corin Yeats and
Sean R. Eddy},
title = {The Pfam protein families database},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Database-Issue},
pages = {138--141},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh121},
doi = {10.1093/NAR/GKH121},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BatemanCDFHGKMMSSYE04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StormS02,
author = {Christian E. V. Storm and
Erik L. L. Sonnhammer},
title = {Automated ortholog inference from phylogenetic trees and calculation
of orthology reliability},
journal = {Bioinform.},
volume = {18},
number = {1},
pages = {92--99},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.1.92},
doi = {10.1093/BIOINFORMATICS/18.1.92},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StormS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HollichSS02,
author = {Volker Hollich and
Christian E. V. Storm and
Erik L. L. Sonnhammer},
title = {OrthoGUI: graphical presentation of Orthostrapper results},
journal = {Bioinform.},
volume = {18},
number = {9},
pages = {1272--1273},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.9.1272},
doi = {10.1093/BIOINFORMATICS/18.9.1272},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HollichSS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChalkS02,
author = {Alistair M. Chalk and
Erik L. L. Sonnhammer},
title = {Computational antisense oligo prediction with a neural network model},
journal = {Bioinform.},
volume = {18},
number = {12},
pages = {1567--1575},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.12.1567},
doi = {10.1093/BIOINFORMATICS/18.12.1567},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChalkS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BatemanBCDEEGHMS03,
author = {Alex Bateman and
Ewan Birney and
Lorenzo Cerutti and
Richard Durbin and
Laurence Ettwiller and
Sean R. Eddy and
Sam Griffiths{-}Jones and
Kevin L. Howe and
Mhairi Marshall and
Erik L. L. Sonnhammer},
title = {The Pfam Protein Families Database},
journal = {Nucleic Acids Res.},
volume = {30},
number = {1},
pages = {276--280},
year = {2002},
url = {https://doi.org/10.1093/nar/30.1.276},
doi = {10.1093/NAR/30.1.276},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BatemanBCDEEGHMS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StormS01,
author = {Christian E. V. Storm and
Erik L. L. Sonnhammer},
title = {{NIFAS:} visual analysis of domain evolution in proteins},
journal = {Bioinform.},
volume = {17},
number = {4},
pages = {343--348},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.4.343},
doi = {10.1093/BIOINFORMATICS/17.4.343},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StormS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PodowskiS01,
author = {Raf M. Podowski and
Erik L. L. Sonnhammer},
title = {{MEDUSA:} large scale automatic selection and visual assessment of
{PCR} primer pairs},
journal = {Bioinform.},
volume = {17},
number = {7},
pages = {656--657},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.7.656},
doi = {10.1093/BIOINFORMATICS/17.7.656},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PodowskiS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BatemanBDEHS00,
author = {Alex Bateman and
Ewan Birney and
Richard Durbin and
Sean R. Eddy and
Kevin L. Howe and
Erik L. L. Sonnhammer},
title = {The Pfam Protein Families Database},
journal = {Nucleic Acids Res.},
volume = {28},
number = {1},
pages = {263--266},
year = {2000},
url = {https://doi.org/10.1093/nar/28.1.263},
doi = {10.1093/NAR/28.1.263},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BatemanBDEHS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ElofssonS99,
author = {Arne Elofsson and
Erik L. L. Sonnhammer},
title = {A comparison of sequence and structure protein domain families as
a basis for structural genomics},
journal = {Bioinform.},
volume = {15},
number = {6},
pages = {480--500},
year = {1999},
url = {https://doi.org/10.1093/bioinformatics/15.6.480},
doi = {10.1093/BIOINFORMATICS/15.6.480},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ElofssonS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BatemanBDEFS99,
author = {Alex Bateman and
Ewan Birney and
Richard Durbin and
Sean R. Eddy and
Robert D. Finn and
Erik L. L. Sonnhammer},
title = {Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority
of proteins},
journal = {Nucleic Acids Res.},
volume = {27},
number = {1},
pages = {260--262},
year = {1999},
url = {https://doi.org/10.1093/nar/27.1.260},
doi = {10.1093/NAR/27.1.260},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BatemanBDEFS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SonnhammerEBBD98,
author = {Erik L. L. Sonnhammer and
Sean R. Eddy and
Ewan Birney and
Alex Bateman and
Richard Durbin},
title = {Pfam: multiple sequence alignments and HMM-profiles of protein domains},
journal = {Nucleic Acids Res.},
volume = {26},
number = {1},
pages = {320--322},
year = {1998},
url = {https://doi.org/10.1093/nar/26.1.320},
doi = {10.1093/NAR/26.1.320},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SonnhammerEBBD98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/SonnhammerHK98,
author = {Erik L. L. Sonnhammer and
Gunnar von Heijne and
Anders Krogh},
editor = {Janice I. Glasgow and
Timothy G. Littlejohn and
Fran{\c{c}}ois Major and
Richard H. Lathrop and
David Sankoff and
Christoph W. Sensen},
title = {A Hidden Markov Model for Predicting Transmembrane Helices in Protein
Sequences},
booktitle = {Proceedings of the 6th International Conference on Intelligent Systems
for Molecular Biology (ISMB-98), Montr{\'{e}}al, Qu{\'{e}}bec,
Canada, June 28 - July 1, 1998},
pages = {175--182},
publisher = {{AAAI}},
year = {1998},
url = {http://www.aaai.org/Library/ISMB/1998/ismb98-021.php},
timestamp = {Thu, 27 Jun 2019 11:28:34 +0200},
biburl = {https://dblp.org/rec/conf/ismb/SonnhammerHK98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SonnhammerD94,
author = {Erik L. L. Sonnhammer and
Richard Durbin},
title = {A workbench for large-scale sequence homology analysis},
journal = {Comput. Appl. Biosci.},
volume = {10},
number = {3},
pages = {301--307},
year = {1994},
url = {https://doi.org/10.1093/bioinformatics/10.3.301},
doi = {10.1093/BIOINFORMATICS/10.3.301},
timestamp = {Fri, 15 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SonnhammerD94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/SonnhammerD94,
author = {Erik L. L. Sonnhammer and
Richard Durbin},
editor = {Russ B. Altman and
Douglas L. Brutlag and
Peter D. Karp and
Richard H. Lathrop and
David B. Searls},
title = {An Expert System for Processing Sequence Homology Data},
booktitle = {Proceedings of the Second International Conference on Intelligent
Systems for Molecular Biology, August 14-17, 1994, Stanford University,
Stanford, California, {USA}},
pages = {363--368},
publisher = {{AAAI}},
year = {1994},
url = {http://www.aaai.org/Library/ISMB/1994/ismb94-045.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/SonnhammerD94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StoffersSBRW92,
author = {H. J. Stoffers and
Erik L. L. Sonnhammer and
G. J. Blommestijn and
N. J. Raat and
Hans V. Westerhoff},
title = {{METASIM:} object-oriented modelling of cell regulation},
journal = {Comput. Appl. Biosci.},
volume = {8},
number = {5},
pages = {443--449},
year = {1992},
url = {https://doi.org/10.1093/bioinformatics/8.5.443},
doi = {10.1093/BIOINFORMATICS/8.5.443},
timestamp = {Fri, 15 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StoffersSBRW92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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