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ORCIDBibTeX records: Alvis Brazma
@article{DBLP:journals/bioinformatics/UpchurchPABBNGKAHRGWABBB23,
author = {Sean Upchurch and
Emilio Palumbo and
Jeremy Adams and
David Bujold and
Guillaume Bourque and
Jared Nedzel and
Keenan Graham and
Meenakshi S. Kagda and
Pedro Assis and
Benjamin Hitz and
Emilio Righi and
Roderic Guig{\'{o}} and
Barbara J. Wold and
Alvis Brazma and
Julia Burchard and
Joe Capka and
Michael Cherry and
Laura Clarke and
Brian Craft and
Manolis Dermitzakis and
Mark Diekhans and
John Dursi and
Michael Sean Fitzsimons and
Zac Flaming and
Romina Garrido and
Alfred Gil and
Paul Godden and
Matt Green and
Mitch Guttman and
Brian Haas and
Max Haeussler and
Bo Li and
Sten Linnarsson and
Adam Lipski and
David Liu and
Simonne Longerich and
David Lougheed and
Jonathan Manning and
John C. Marioni and
Christopher Meyer and
Stephen B. Montgomery and
Alyssa Morrow and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Jared L. Nedzel and
David Nguyen and
Kevin Osborn and
Francis Ouellette and
Irene Papatheodorou and
Dmitri D. Pervouchine and
Arun K. Ramani and
Jordi Rambla and
Bashir Sadjad and
David Steinberg and
Jeremiah Talkar and
Timothy Tickle and
Kathy Tzeng and
Saman Vaisipour and
Sean Watford and
Barbara Wold and
Zhenyu Zhang and
Jing Zhu},
title = {RNAget: an {API} to securely retrieve {RNA} quantifications},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad126},
doi = {10.1093/BIOINFORMATICS/BTAD126},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/UpchurchPABBNGKAHRGWABBB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TheissHRHSREBU23,
author = {Maria Theiss and
Jean{-}Karim H{\'{e}}rich{\'{e}} and
Craig Russell and
David Helekal and
Alisdair Soppitt and
Jonas Ries and
Jan Ellenberg and
Alvis Brazma and
Virginie Uhlmann},
title = {Simulating structurally variable nuclear pore complexes for microscopy},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad587},
doi = {10.1093/BIOINFORMATICS/BTAD587},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TheissHRHSREBU23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MorenoFGMMMFFBB22,
author = {Pablo A. Moreno and
Silvie Fexova and
Nancy George and
Jonathan R. Manning and
Zhichao Miao and
Suhaib Mohammed and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Anja F{\"{u}}llgrabe and
Yalan Bi and
Natassja Bush and
Haider Iqbal and
Upendra Kumbham and
Andrey Solovyev and
Lingyun Zhao and
Ananth Prakash and
David Garc{\'{\i}}a{-}Seisdedos and
Deepti Jaiswal Kundu and
Shengbo Wang and
Mathias Walzer and
Laura Clarke and
David Osumi{-}Sutherland and
Marcela Karey Tello{-}Ruiz and
Sunita Kumari and
Doreen Ware and
Jana Eliasova and
Mark J. Arends and
Martijn C. Nawijn and
Kerstin B. Meyer and
Tony Burdett and
John C. Marioni and
Sarah A. Teichmann and
Juan Antonio Vizca{\'{\i}}no and
Alvis Brazma and
Irene Papatheodorou},
title = {Expression Atlas update: gene and protein expression in multiple species},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {129--140},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab1030},
doi = {10.1093/NAR/GKAB1030},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MorenoFGMMMFFBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Perez-RiverolBB22,
author = {Yasset P{\'{e}}rez{-}Riverol and
Jingwen Bai and
Chakradhar Bandla and
David Garc{\'{\i}}a{-}Seisdedos and
Suresh Hewapathirana and
Selvakumar Kamatchinathan and
Deepti Jaiswal Kundu and
Ananth Prakash and
Anika Frericks{-}Zipper and
Martin Eisenacher and
Mathias Walzer and
Shengbo Wang and
Alvis Brazma and
Juan Antonio Vizca{\'{\i}}no},
title = {The {PRIDE} database resources in 2022: a hub for mass spectrometry-based
proteomics evidences},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {543--552},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab1038},
doi = {10.1093/NAR/GKAB1038},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/Perez-RiverolBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SarkansF0ABDFGI21,
author = {Ugis Sarkans and
Anja F{\"{u}}llgrabe and
Ahmed Ali and
Awais Athar and
Ehsan Behrangi and
Nestor Diaz and
Silvie Fexova and
Nancy George and
Haider Iqbal and
Sandeep Kurri and
Jhoan Munoz and
Juan Camillo Rada and
Irene Papatheodorou and
Alvis Brazma},
title = {From ArrayExpress to BioStudies},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D1502--D1506},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1062},
doi = {10.1093/NAR/GKAA1062},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SarkansF0ABDFGI21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PapatheodorouMM20,
author = {Irene Papatheodorou and
Pablo A. Moreno and
Jonathan R. Manning and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Nancy George and
Silvie Fexova and
Nuno A. Fonseca and
Anja F{\"{u}}llgrabe and
Matthew Green and
Ni Huang and
Laura Huerta and
Haider Iqbal and
Monica Jianu and
Suhaib Mohammed and
Lingyun Zhao and
Andrew F. Jarnuczak and
Simon Jupp and
John C. Marioni and
Kerstin B. Meyer and
Robert Petryszak and
Cesar Augusto Prada Medina and
Carlos Talavera{-}L{\'{o}}pez and
Sarah A. Teichmann and
Juan Antonio Vizca{\'{\i}}no and
Alvis Brazma},
title = {Expression Atlas update: from tissues to single cells},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D77--D83},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz947},
doi = {10.1093/NAR/GKZ947},
timestamp = {Wed, 24 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PapatheodorouMM20.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/bmcbi/RuklisaBCSV19,
author = {Dace Ruklisa and
Alvis Brazma and
Karlis Cerans and
Thomas Schlitt and
Juris Viksna},
title = {Dynamics of gene regulatory networks and their dependence on network
topology and quantitative parameters - the case of phage {\(\lambda\)}},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {296:1--296:14},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-2909-z},
doi = {10.1186/S12859-019-2909-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RuklisaBCSV19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Perez-RiverolCB19,
author = {Yasset P{\'{e}}rez{-}Riverol and
Attila Csordas and
Jingwen Bai and
Manuel Bernal Llinares and
Suresh Hewapathirana and
Deepti Jaiswal Kundu and
Avinash Inuganti and
Johannes Griss and
Gerhard Mayer and
Martin Eisenacher and
Enrique P{\'{e}}rez and
Julian Uszkoreit and
Julianus Pfeuffer and
Timo Sachsenberg and
Sule Yilmaz and
Shivani Tiwary and
J{\"{u}}rgen Cox and
Enrique Audain and
Mathias Walzer and
Andrew F. Jarnuczak and
Tobias Ternent and
Alvis Brazma and
Juan Antonio Vizca{\'{\i}}no},
title = {The {PRIDE} database and related tools and resources in 2019: improving
support for quantification data},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D442--D450},
year = {2019},
url = {https://doi.org/10.1093/nar/gky1106},
doi = {10.1093/NAR/GKY1106},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/Perez-RiverolCB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AtharFGIHASFPPS19,
author = {Awais Athar and
Anja F{\"{u}}llgrabe and
Nancy George and
Haider Iqbal and
Laura Huerta and
Ahmed Ali and
Catherine Snow and
Nuno A. Fonseca and
Robert Petryszak and
Irene Papatheodorou and
Ugis Sarkans and
Alvis Brazma},
title = {ArrayExpress update - from bulk to single-cell expression data},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D711--D715},
year = {2019},
url = {https://doi.org/10.1093/nar/gky964},
doi = {10.1093/NAR/GKY964},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AtharFGIHASFPPS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SarkansGABMAMRS18,
author = {Ugis Sarkans and
Mikhail Gostev and
Awais Athar and
Ehsan Behrangi and
Olga Melnichuk and
Ahmed Ali and
Jasmine Minguet and
Juan Camillo Rada and
Catherine Snow and
Andrew Tikhonov and
Alvis Brazma and
Johanna R. McEntyre},
title = {The BioStudies database - one stop shop for all data supporting a
life sciences study},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D1266--D1270},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx965},
doi = {10.1093/NAR/GKX965},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SarkansGABMAMRS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PapatheodorouFK18,
author = {Irene Papatheodorou and
Nuno A. Fonseca and
Maria Keays and
Y. Amy Tang and
Elisabet Barrera and
Wojciech Bazant and
Melissa L. Burke and
Anja F{\"{u}}llgrabe and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Nancy George and
Laura Huerta and
Satu Koskinen and
Suhaib Mohammed and
Matthew J. Geniza and
Justin Preece and
Pankaj Jaiswal and
Andrew F. Jarnuczak and
Wolfgang Huber and
Oliver Stegle and
Juan Antonio Vizca{\'{\i}}no and
Alvis Brazma and
Robert Petryszak},
title = {Expression Atlas: gene and protein expression across multiple studies
and organisms},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D246--D251},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1158},
doi = {10.1093/NAR/GKX1158},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PapatheodorouFK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PetryszakFFHKTB17,
author = {Robert Petryszak and
Nuno A. Fonseca and
Anja F{\"{u}}llgrabe and
Laura Huerta and
Maria Keays and
Y. Amy Tang and
Alvis Brazma},
title = {The RNASeq-er {API} - a gateway to systematically updated analysis
of public RNA-seq data},
journal = {Bioinform.},
volume = {33},
number = {14},
pages = {2218--2220},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx143},
doi = {10.1093/BIOINFORMATICS/BTX143},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PetryszakFFHKTB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TorrenteB17,
author = {Aurora Torrente and
Alvis Brazma},
title = {clustComp, a bioconductor package for the comparison of clustering
results},
journal = {Bioinform.},
volume = {33},
number = {24},
pages = {4001--4003},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx532},
doi = {10.1093/BIOINFORMATICS/BTX532},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TorrenteB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/BrandiziMBKRSKK17,
author = {Marco Brandizi and
Olga Melnichuk and
Raffael Bild and
Florian Kohlmayer and
Benedicto Rodriguez{-}Castro and
Helmut Spengler and
Klaus A. Kuhn and
Wolfgang Kuchinke and
Christian Ohmann and
Timo Mustonen and
Mikael Linden and
Tommi H. Nyr{\"{o}}nen and
Ilkka Lappalainen and
Alvis Brazma and
Ugis Sarkans},
title = {Orchestrating differential data access for translational research:
a pilot implementation},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {17},
number = {1},
pages = {30:1--30:14},
year = {2017},
url = {https://doi.org/10.1186/s12911-017-0424-6},
doi = {10.1186/S12911-017-0424-6},
timestamp = {Sun, 06 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/midm/BrandiziMBKRSKK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BlomstedtDSBK16,
author = {Paul Blomstedt and
Ritabrata Dutta and
Sohan Seth and
Alvis Brazma and
Samuel Kaski},
title = {Modelling-based experiment retrieval: a case study with gene expression
clustering},
journal = {Bioinform.},
volume = {32},
number = {9},
pages = {1388--1394},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv762},
doi = {10.1093/BIOINFORMATICS/BTV762},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BlomstedtDSBK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PetryszakKTFBBF16,
author = {Robert Petryszak and
Maria Keays and
Y. Amy Tang and
Nuno A. Fonseca and
Elisabet Barrera and
Tony Burdett and
Anja F{\"{u}}llgrabe and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Simon Jupp and
Satu Koskinen and
Oliver Mannion and
Laura Huerta and
Karine Megy and
Catherine Snow and
Eleanor Williams and
Mitra Barzine and
Emma Hastings and
Hendrik Weisser and
James C. Wright and
Pankaj Jaiswal and
Wolfgang Huber and
Jyoti Choudhary and
Helen E. Parkinson and
Alvis Brazma},
title = {Expression Atlas update - an integrated database of gene and protein
expression in humans, animals and plants},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {746--752},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1045},
doi = {10.1093/NAR/GKV1045},
timestamp = {Tue, 26 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PetryszakKTFBBF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KirsanovaBRS15,
author = {Catherine Kirsanova and
Alvis Brazma and
Gabriella Rustici and
Ugis Sarkans},
title = {Cellular phenotype database: a repository for systems microscopy data},
journal = {Bioinform.},
volume = {31},
number = {16},
pages = {2736--2740},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv199},
doi = {10.1093/BIOINFORMATICS/BTV199},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KirsanovaBRS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KolesnikovHKMTWDKBBMPRTPPSB15,
author = {Nikolay Kolesnikov and
Emma Hastings and
Maria Keays and
Olga Melnichuk and
Y. Amy Tang and
Eleanor Williams and
Miroslaw Dylag and
Natalja Kurbatova and
Marco Brandizi and
Tony Burdett and
Karyn Megy and
Ekaterina Pilicheva and
Gabriella Rustici and
Andrew Tikhonov and
Helen E. Parkinson and
Robert Petryszak and
Ugis Sarkans and
Alvis Brazma},
title = {ArrayExpress update - simplifying data submissions},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {1113--1116},
year = {2015},
url = {https://doi.org/10.1093/nar/gku1057},
doi = {10.1093/NAR/GKU1057},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KolesnikovHKMTWDKBBMPRTPPSB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BlomstedtDSBK15,
author = {Paul Blomstedt and
Ritabrata Dutta and
Sohan Seth and
Alvis Brazma and
Samuel Kaski},
title = {Modelling-based experiment retrieval: {A} case study with gene expression
clustering},
journal = {CoRR},
volume = {abs/1505.05007},
year = {2015},
url = {http://arxiv.org/abs/1505.05007},
eprinttype = {arXiv},
eprint = {1505.05007},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/BlomstedtDSBK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FaulconbridgeBBGPVSBP14,
author = {Adam Faulconbridge and
Tony Burdett and
Marco Brandizi and
Mikhail Gostev and
Rui Pedro Pereira and
Drashtti Vasant and
Ugis Sarkans and
Alvis Brazma and
Helen E. Parkinson},
title = {Updates to BioSamples database at European Bioinformatics Institute},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {50--52},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1081},
doi = {10.1093/NAR/GKT1081},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FaulconbridgeBBGPVSBP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PetryszakBFFGHHJKKMMMMRTTWMPB14,
author = {Robert Petryszak and
Tony Burdett and
Benedetto Fiorelli and
Nuno A. Fonseca and
Mar Gonzalez{-}Porta and
Emma Hastings and
Wolfgang Huber and
Simon Jupp and
Maria Keays and
Nataliya Kryvych and
Julie A. McMurry and
John C. Marioni and
James Malone and
Karine Megy and
Gabriella Rustici and
Y. Amy Tang and
Jan Taubert and
Eleanor Williams and
Oliver Mannion and
Helen E. Parkinson and
Alvis Brazma},
title = {Expression Atlas update - a database of gene and transcript expression
from microarray- and sequencing-based functional genomics experiments},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {926--932},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1270},
doi = {10.1093/NAR/GKT1270},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PetryszakBFFGHHJKKMMMMRTTWMPB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hsb/BrazmaCRSV14,
author = {Alvis Brazma and
Karlis Cerans and
Dace Ruklisa and
Thomas Schlitt and
Juris Viksna},
editor = {Oded Maler and
{\'{A}}d{\'{a}}m M. Hal{\'{a}}sz and
Thao Dang and
Carla Piazza},
title = {Modeling and Analysis of Qualitative Behavior of Gene Regulatory Networks},
booktitle = {Hybrid Systems Biology - Second International Workshop, {HSB} 2013,
Taormina, Italy, September 2, 2013 and Third International Workshop,
{HSB} 2014, Vienna, Austria, July 23-24, 2014, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {7699},
pages = {51--66},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-27656-4\_3},
doi = {10.1007/978-3-319-27656-4\_3},
timestamp = {Tue, 03 Aug 2021 16:22:18 +0200},
biburl = {https://dblp.org/rec/conf/hsb/BrazmaCRSV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/LawlerHBC13,
author = {Katherine Lawler and
Kim E. Hammond{-}Kosack and
Alvis Brazma and
Richard M. R. Coulson},
title = {Genomic clustering and co-regulation of transcriptional networks in
the pathogenic fungus Fusarium graminearum},
journal = {{BMC} Syst. Biol.},
volume = {7},
pages = {52},
year = {2013},
url = {https://doi.org/10.1186/1752-0509-7-52},
doi = {10.1186/1752-0509-7-52},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/LawlerHBC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RusticiKBBDEFHIKKMMMPPRSTTTWWBPS13,
author = {Gabriella Rustici and
Nikolay Kolesnikov and
Marco Brandizi and
Tony Burdett and
Miroslaw Dylag and
Ibrahim Emam and
Anna Farne and
Emma Hastings and
Jon C. Ison and
Maria Keays and
Natalja Kurbatova and
James Malone and
Roby Mani and
Annalisa Mupo and
Rui Pedro Pereira and
Ekaterina Pilicheva and
Johan Rung and
Anjan Sharma and
Y. Amy Tang and
Tobias Ternent and
Andrew Tikhonov and
Danielle Welter and
Eleanor Williams and
Alvis Brazma and
Helen E. Parkinson and
Ugis Sarkans},
title = {ArrayExpress update - trends in database growth and links to data
analysis tools},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {987--990},
year = {2013},
url = {https://doi.org/10.1093/nar/gks1174},
doi = {10.1093/NAR/GKS1174},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RusticiKBBDEFHIKKMMMPPRSTTTWWBPS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaldasGKFRNKBK12,
author = {Jos{\'{e}} Caldas and
Nils Gehlenborg and
Eeva Kettunen and
Ali Faisal and
Mikko R{\"{o}}nty and
Andrew G. Nicholson and
Sakari Knuutila and
Alvis Brazma and
Samuel Kaski},
title = {Data-driven information retrieval in heterogeneous collections of
transcriptomics data links \emph{SIM2s} to malignant pleural mesothelioma},
journal = {Bioinform.},
volume = {28},
number = {2},
pages = {246--253},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/btr634},
doi = {10.1093/BIOINFORMATICS/BTR634},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaldasGKFRNKBK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XueBLTBP12,
author = {Vincent Xue and
Tony Burdett and
Margus Lukk and
Julie Taylor and
Alvis Brazma and
Helen E. Parkinson},
title = {MageComet - web application for harmonizing existing large-scale experiment
descriptions},
journal = {Bioinform.},
volume = {28},
number = {10},
pages = {1402--1403},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts148},
doi = {10.1093/BIOINFORMATICS/BTS148},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XueBLTBP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FonsecaRBM12,
author = {Nuno A. Fonseca and
Johan Rung and
Alvis Brazma and
John C. Marioni},
title = {Tools for mapping high-throughput sequencing data},
journal = {Bioinform.},
volume = {28},
number = {24},
pages = {3169--3177},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts605},
doi = {10.1093/BIOINFORMATICS/BTS605},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FonsecaRBM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GostevFBFSBP12,
author = {Mikhail Gostev and
Adam Faulconbridge and
Marco Brandizi and
Julio Fernandez{-}Banet and
Ugis Sarkans and
Alvis Brazma and
Helen E. Parkinson},
title = {The BioSample Database (BioSD) at the European Bioinformatics Institute},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {64--70},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr937},
doi = {10.1093/NAR/GKR937},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/GostevFBFSBP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KapusheskyABCFFHKKKKMMPPRTTWZPB12,
author = {Misha Kapushesky and
Tomasz Adamusiak and
Tony Burdett and
Aed{\'{\i}}n C. Culhane and
Anna Farne and
Alexey Filippov and
Ele Holloway and
Andrey Klebanov and
Nataliya Kryvych and
Natalja Kurbatova and
Pavel Kurnosov and
James Malone and
Olga Melnichuk and
Robert Petryszak and
Nikolay Pultsin and
Gabriella Rustici and
Andrew Tikhonov and
Ravensara S. Travillian and
Eleanor Williams and
Andrey Zorin and
Helen E. Parkinson and
Alvis Brazma},
title = {Gene Expression Atlas update - a value-added database of microarray
and sequencing-based functional genomics experiments},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {1077--1081},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr913},
doi = {10.1093/NAR/GKR913},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KapusheskyABCFFHKKKKMMPPRTTWZPB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1212-5932,
author = {Leo Lahti and
Aurora Torrente and
Laura Elo and
Alvis Brazma and
Johan Rung},
title = {Fully scalable online-preprocessing algorithm for short oligonucleotide
microarray atlases},
journal = {CoRR},
volume = {abs/1212.5932},
year = {2012},
url = {http://arxiv.org/abs/1212.5932},
eprinttype = {arXiv},
eprint = {1212.5932},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1212-5932.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GostevFRDPRMBK11,
author = {Mikhail Gostev and
Julio Fernandez{-}Banet and
Johan Rung and
Joern Dietrich and
Inga Prokopenko and
Samuli Ripatti and
Mark I. McCarthy and
Alvis Brazma and
Maria Krestyaninova},
title = {{SAIL} - a software system for sample and phenotype availability across
biobanks and cohorts},
journal = {Bioinform.},
volume = {27},
number = {4},
pages = {589--591},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btq693},
doi = {10.1093/BIOINFORMATICS/BTQ693},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GostevFRDPRMBK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GoncalvesTBK11,
author = {{\^{A}}ngela Gon{\c{c}}alves and
Andrew Tikhonov and
Alvis Brazma and
Misha Kapushesky},
title = {A pipeline for RNA-seq data processing and quality assessment},
journal = {Bioinform.},
volume = {27},
number = {6},
pages = {867--869},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr012},
doi = {10.1093/BIOINFORMATICS/BTR012},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GoncalvesTBK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ParkinsonSKABDEFHHKLMMPRSWABSB11,
author = {Helen E. Parkinson and
Ugis Sarkans and
Nikolay Kolesnikov and
Niran Abeygunawardena and
Tony Burdett and
Miroslaw Dylag and
Ibrahim Emam and
Anna Farne and
Emma Hastings and
Ele Holloway and
Natalja Kurbatova and
Margus Lukk and
James Malone and
Roby Mani and
Ekaterina Pilicheva and
Gabriella Rustici and
Anjan Sharma and
Eleanor Williams and
Tomasz Adamusiak and
Marco Brandizi and
Nataliya Sklyar and
Alvis Brazma},
title = {ArrayExpress update - an archive of microarray and high-throughput
sequencing-based functional genomics experiments},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {1002--1004},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1040},
doi = {10.1093/NAR/GKQ1040},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ParkinsonSKABDEFHHKLMMPRSWABSB11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaloneHAKZKZBP10,
author = {James Malone and
Ele Holloway and
Tomasz Adamusiak and
Misha Kapushesky and
Jie Zheng and
Nikolay Kolesnikov and
Anna Zhukova and
Alvis Brazma and
Helen E. Parkinson},
title = {Modeling sample variables with an Experimental Factor Ontology},
journal = {Bioinform.},
volume = {26},
number = {8},
pages = {1112--1118},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq099},
doi = {10.1093/BIOINFORMATICS/BTQ099},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaloneHAKZKZBP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShankarPBHLMSWBSSB10,
author = {Ravi Shankar and
Helen E. Parkinson and
Tony Burdett and
Emma Hastings and
Junmin Liu and
Michael Miller and
Rashmi Srinivasa and
Joseph White and
Alvis Brazma and
Gavin Sherlock and
Christian J. Stoeckert Jr. and
Catherine A. Ball},
title = {Annotare - a tool for annotating high-throughput biomedical investigations
and resulting data},
journal = {Bioinform.},
volume = {26},
number = {19},
pages = {2470--2471},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq462},
doi = {10.1093/BIOINFORMATICS/BTQ462},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShankarPBHLMSWBSSB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VainshteinSBHDM10,
author = {Yevhen Vainshtein and
Mayka Sanchez and
Alvis Brazma and
Matthias W. Hentze and
Thomas Dandekar and
Martina U. Muckenthaler},
title = {The IronChip evaluation package: a package of perl modules for robust
analysis of custom microarrays},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {112},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-112},
doi = {10.1186/1471-2105-11-112},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/VainshteinSBHDM10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KapusheskyEHKZMRWPB10,
author = {Misha Kapushesky and
Ibrahim Emam and
Ele Holloway and
Pavel Kurnosov and
Andrey Zorin and
James Malone and
Gabriella Rustici and
Eleanor Williams and
Helen E. Parkinson and
Alvis Brazma},
title = {Gene Expression Atlas at the European Bioinformatics Institute},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Database-Issue},
pages = {690--698},
year = {2010},
url = {https://doi.org/10.1093/nar/gkp936},
doi = {10.1093/NAR/GKP936},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KapusheskyEHKZMRWPB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icassp/PeltonenAGBK10,
author = {Jaakko Peltonen and
Helena Aidos and
Nils Gehlenborg and
Alvis Brazma and
Samuel Kaski},
title = {An information retrieval perspective on visualization of gene expression
data with ontological annotation},
booktitle = {Proceedings of the {IEEE} International Conference on Acoustics, Speech,
and Signal Processing, {ICASSP} 2010, 14-19 March 2010, Sheraton Dallas
Hotel, Dallas, Texas, {USA}},
pages = {2178--2181},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/ICASSP.2010.5495665},
doi = {10.1109/ICASSP.2010.5495665},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icassp/PeltonenAGBK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaldasGFBK09,
author = {Jos{\'{e}} Caldas and
Nils Gehlenborg and
Ali Faisal and
Alvis Brazma and
Samuel Kaski},
title = {Probabilistic retrieval and visualization of biologically relevant
microarray experiments},
journal = {Bioinform.},
volume = {25},
number = {12},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp215},
doi = {10.1093/BIOINFORMATICS/BTP215},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaldasGFBK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KauffmannRPKLBH09,
author = {Audrey Kauffmann and
Tim F. Rayner and
Helen E. Parkinson and
Misha Kapushesky and
Margus Lukk and
Alvis Brazma and
Wolfgang Huber},
title = {Importing ArrayExpress datasets into R/Bioconductor},
journal = {Bioinform.},
volume = {25},
number = {16},
pages = {2092--2094},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp354},
doi = {10.1093/BIOINFORMATICS/BTP354},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KauffmannRPKLBH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KrestyaninovaZVKRNGPKBLRPSMB09,
author = {Maria Krestyaninova and
Andris Zarins and
Juris Viksna and
Natalja Kurbatova and
Peteris Rucevskis and
Sudeshna Guha Neogi and
Mike Gostev and
Teemu Perheentupa and
Juha Knuuttila and
Amy Barrett and
Ilkka Lappalainen and
Johan Rung and
Karlis Podnieks and
Ugis Sarkans and
Mark I. McCarthy and
Alvis Brazma},
title = {A System for Information Management in BioMedical Studies - SIMBioMS},
journal = {Bioinform.},
volume = {25},
number = {20},
pages = {2768--2769},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp420},
doi = {10.1093/BIOINFORMATICS/BTP420},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KrestyaninovaZVKRNGPKBLRPSMB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CaldasGFBK09,
author = {Jos{\'{e}} Caldas and
Nils Gehlenborg and
Ali Faisal and
Alvis Brazma and
Samuel Kaski},
title = {Probabilistic retrieval and visualization of biologically relevant
microarray experiments},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-13}},
pages = {0},
year = {2009},
url = {http://www.biomedcentral.com/1471-2105/10/S13/P1},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CaldasGFBK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GehlenborgB09,
author = {Nils Gehlenborg and
Alvis Brazma},
title = {Visualization of large microarray experiments with space maps},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-13}},
pages = {0},
year = {2009},
url = {http://www.biomedcentral.com/1471-2105/10/S13/O7},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GehlenborgB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ParkinsonKKRSABDEFHLMMPRRSWBABBCKKMNRSSZSB09,
author = {Helen E. Parkinson and
Misha Kapushesky and
Nikolay Kolesnikov and
Gabriella Rustici and
Mohammadreza Shojatalab and
Niran Abeygunawardena and
Hugo B{\'{e}}rub{\'{e}} and
Miroslaw Dylag and
Ibrahim Emam and
Anna Farne and
Ele Holloway and
Margus Lukk and
James Malone and
Roby Mani and
Ekaterina Pilicheva and
Tim F. Rayner and
Faisal Ibne Rezwan and
Anjan Sharma and
Eleanor Williams and
Xiangqun Zheng Bradley and
Tomasz Adamusiak and
Marco Brandizi and
Tony Burdett and
Richard Coulson and
Maria Krestyaninova and
Pavel Kurnosov and
Eamonn Maguire and
Sudeshna Guha Neogi and
Philippe Rocca{-}Serra and
Susanna{-}Assunta Sansone and
Nataliya Sklyar and
Mengyao Zhao and
Ugis Sarkans and
Alvis Brazma},
title = {ArrayExpress update - from an archive of functional genomics experiments
to the atlas of gene expression},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Database-Issue},
pages = {868--872},
year = {2009},
url = {https://doi.org/10.1093/nar/gkn889},
doi = {10.1093/NAR/GKN889},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ParkinsonKKRSABDEFHLMMPRRSWBABBCKKMNRSSZSB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GiegerichBJUV08,
author = {Robert Giegerich and
Alvis Brazma and
Inge Jonassen and
Esko Ukkonen and
Martin Vingron},
title = {The {BREW} workshop series: a stimulating experience in PhD education},
journal = {Briefings Bioinform.},
volume = {9},
number = {3},
pages = {250--253},
year = {2008},
url = {https://doi.org/10.1093/bib/bbn002},
doi = {10.1093/BIB/BBN002},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GiegerichBJUV08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HaudryBLWGGKABBFWH08,
author = {Yannick Haudry and
Hugo B{\'{e}}rub{\'{e}} and
Ivica Letunic and
Paul{-}Daniel Weeber and
Julien Gagneur and
Charles Girardot and
Misha Kapushesky and
Detlev Arendt and
Peer Bork and
Alvis Brazma and
Eileen E. M. Furlong and
Joachim Wittbrodt and
Thorsten Henrich},
title = {4D\emph{Xpress}: a database for cross-species expression pattern comparisons},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Database-Issue},
pages = {847--853},
year = {2008},
url = {https://doi.org/10.1093/nar/gkm797},
doi = {10.1093/NAR/GKM797},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HaudryBLWGGKABBFWH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/BrazmaMA08,
author = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
editor = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
title = {Preface},
booktitle = {Proceedings of the 6th Asia-Pacific Bioinformatics Conference, {APBC}
2008, 14-17 January 2008, Kyoto, Japan},
series = {Advances in Bioinformatics and Computational Biology},
volume = {6},
publisher = {Imperial College Press},
year = {2008},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2008/apbc08preface.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/BrazmaMA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/HaudryOEBLKWWGGABBFWH08,
author = {Yannick Haudry and
Chuang Kee Ong and
Laurence Ettwiller and
Hugo B{\'{e}}rub{\'{e}} and
Ivica Letunic and
Misha Kapushesky and
Paul{-}Daniel Weeber and
Xi Wang and
Julien Gagneur and
Charles Girardot and
Detlev Arendt and
Peer Bork and
Alvis Brazma and
Eileen E. M. Furlong and
Joachim Wittbrodt and
Thorsten Henrich},
editor = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
title = {Comparing and Analysing Gene Expression Patterns Across Animal Species
Using 4DXpress},
booktitle = {Proceedings of the 6th Asia-Pacific Bioinformatics Conference, {APBC}
2008, 14-17 January 2008, Kyoto, Japan},
series = {Advances in Bioinformatics and Computational Biology},
volume = {6},
pages = {373--382},
publisher = {Imperial College Press},
year = {2008},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2008/apbc035a.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/HaudryOEBLKWWGGABBFWH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/apbc/2008,
editor = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
title = {Proceedings of the 6th Asia-Pacific Bioinformatics Conference, {APBC}
2008, 14-17 January 2008, Kyoto, Japan},
series = {Advances in Bioinformatics and Computational Biology},
volume = {6},
publisher = {Imperial College Press},
year = {2008},
isbn = {978-1-84816-108-5},
timestamp = {Mon, 15 Sep 2008 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/apbc/2008.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SchlittB07,
author = {Thomas Schlitt and
Alvis Brazma},
title = {Current approaches to gene regulatory network modelling},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-6}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S6-S9},
doi = {10.1186/1471-2105-8-S6-S9},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SchlittB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ViksnaCOPRZBNKMBS07,
author = {Juris Viksna and
Edgars Celms and
Martins Opmanis and
Karlis Podnieks and
Peteris Rucevskis and
Andris Zarins and
Amy Barrett and
Sudeshna Guha Neogi and
Maria Krestyaninova and
Mark I. McCarthy and
Alvis Brazma and
Ugis Sarkans},
title = {{PASSIM} - an open source software system for managing information
in biomedical studies},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-52},
doi = {10.1186/1471-2105-8-52},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ViksnaCOPRZBNKMBS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ParkinsonKSACFHKLLMRSWSB07,
author = {Helen E. Parkinson and
Misha Kapushesky and
Mohammadreza Shojatalab and
Niran Abeygunawardena and
Richard Coulson and
Anna Farne and
Ele Holloway and
Nikolay Kolesnykov and
P. Lilja and
Margus Lukk and
Roby Mani and
Tim F. Rayner and
Anjan Sharma and
E. William and
Ugis Sarkans and
Alvis Brazma},
title = {ArrayExpress - a public database of microarray experiments and gene
expression profiles},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {747--750},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl995},
doi = {10.1093/NAR/GKL995},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ParkinsonKSACFHKLLMRSWSB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/SamsonovaNRB07,
author = {Anastasia Samsonova and
Mahesan Niranjan and
Steven Russell and
Alvis Brazma},
title = {Prediction of Gene Expression in Embryonic Structures of \emph{Drosophila
melanogaster}},
journal = {PLoS Comput. Biol.},
volume = {3},
number = {7},
year = {2007},
url = {https://doi.org/10.1371/journal.pcbi.0030144},
doi = {10.1371/JOURNAL.PCBI.0030144},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/SamsonovaNRB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BlakeSKB06,
author = {Jonathon Blake and
Christian Schwager and
Misha Kapushesky and
Alvis Brazma},
title = {ChroCoLoc: an application for calculating the probability of co-localization
of microarray gene expression},
journal = {Bioinform.},
volume = {22},
number = {6},
pages = {765--767},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btk022},
doi = {10.1093/BIOINFORMATICS/BTK022},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BlakeSKB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RaynerRSCFHILMMPQSSWWWPSBB06,
author = {Tim F. Rayner and
Philippe Rocca{-}Serra and
Paul T. Spellman and
Helen C. Causton and
Anna Farne and
Ele Holloway and
Rafael A. Irizarry and
Junmin Liu and
Donald Maier and
Michael Miller and
Kjell Petersen and
John Quackenbush and
Gavin Sherlock and
Christian J. Stoeckert Jr. and
Joseph White and
Patricia L. Whetzel and
Farrell Wymore and
Helen E. Parkinson and
Ugis Sarkans and
Catherine A. Ball and
Alvis Brazma},
title = {A simple spreadsheet-based, MIAME-supportive format for microarray
data: {MAGE-TAB}},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {489},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-489},
doi = {10.1186/1471-2105-7-489},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RaynerRSCFHILMMPQSSWWWPSBB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SarkansPLOSACHRMSKSFRB05,
author = {Ugis Sarkans and
Helen E. Parkinson and
Gonzalo Garcia Lara and
Ahmet Oezcimen and
Anjan Sharma and
Niran Abeygunawardena and
Sergio Contrino and
Ele Holloway and
Philippe Rocca{-}Serra and
Gaurab Mukherjee and
Mohammadreza Shojatalab and
Misha Kapushesky and
Susanna{-}Assunta Sansone and
Anna Farne and
Tim F. Rayner and
Alvis Brazma},
title = {The ArrayExpress gene expression database: a software engineering
and implementation perspective},
journal = {Bioinform.},
volume = {21},
number = {8},
pages = {1495--1501},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti157},
doi = {10.1093/BIOINFORMATICS/BTI157},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SarkansPLOSACHRMSKSFRB05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DurinckMKDMBH05,
author = {Steffen Durinck and
Yves Moreau and
Arek Kasprzyk and
Sean R. Davis and
Bart De Moor and
Alvis Brazma and
Wolfgang Huber},
title = {BioMart and Bioconductor: a powerful link between biological databases
and microarray data analysis},
journal = {Bioinform.},
volume = {21},
number = {16},
pages = {3439--3440},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti525},
doi = {10.1093/BIOINFORMATICS/BTI525},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DurinckMKDMBH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TorrenteKB05,
author = {Aurora Torrente and
Misha Kapushesky and
Alvis Brazma},
title = {A new algorithm for comparing and visualizing relationships between
hierarchical and flat gene expression data clusterings},
journal = {Bioinform.},
volume = {21},
number = {21},
pages = {3993--3999},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti644},
doi = {10.1093/BIOINFORMATICS/BTI644},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TorrenteKB05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ParkinsonSSACCFLHKLMORRSSB05,
author = {Helen E. Parkinson and
Ugis Sarkans and
Mohammadreza Shojatalab and
Niran Abeygunawardena and
Sergio Contrino and
Richard Coulson and
Anna Farne and
Gonzalo Garcia Lara and
Ele Holloway and
Misha Kapushesky and
P. Lilja and
Gaurab Mukherjee and
Ahmet Oezcimen and
Tim F. Rayner and
Philippe Rocca{-}Serra and
Anjan Sharma and
Susanna{-}Assunta Sansone and
Alvis Brazma},
title = {ArrayExpress - a public repository for microarray gene expression
data at the {EBI}},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Database-Issue},
pages = {553--555},
year = {2005},
url = {https://doi.org/10.1093/nar/gki056},
doi = {10.1093/NAR/GKI056},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/ParkinsonSSACCFLHKLMORRSSB05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/GilksTB05,
author = {Walter R. Gilks and
Brian D. M. Tom and
Alvis Brazma},
title = {Fusing microarray experiments with multivariate regression},
booktitle = {ECCB/JBI'05 Proceedings, Fourth European Conference on Computational
Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas
de BioInform{\'{a}}tica), Palacio de Congresos, Madrid, Spain,
September 28 - October 1, 2005},
pages = {143},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti1123},
doi = {10.1093/BIOINFORMATICS/BTI1123},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/GilksTB05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KapusheskyKCDIKKTSVB04,
author = {Misha Kapushesky and
Patrick Kemmeren and
Aed{\'{\i}}n C. Culhane and
Steffen Durinck and
Jan Ihmels and
Christine K{\"{o}}rner and
Meelis Kull and
Aurora Torrente and
Ugis Sarkans and
Jaak Vilo and
Alvis Brazma},
title = {Expression Profiler: next generation - an online platform for analysis
of microarray data},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Web-Server-Issue},
pages = {465--470},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh470},
doi = {10.1093/NAR/GKH470},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KapusheskyKCDIKKTSVB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@book{DBLP:books/daglib/0014050,
author = {Helen C. Causton and
John Quackenbush and
Alvis Brazma},
title = {Microarray gene expression data analysis - a beginner's guide},
publisher = {Blackwell},
year = {2003},
isbn = {978-1-40510-682-5},
timestamp = {Fri, 15 Apr 2011 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/daglib/0014050.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BrooksbankCHMMMOPTABBHLSSC03,
author = {Catherine Brooksbank and
Evelyn Camon and
Midori A. Harris and
Michele Magrane and
Maria Jesus Martin and
Nicola J. Mulder and
Claire O'Donovan and
Helen E. Parkinson and
Mary Ann Tuli and
Rolf Apweiler and
Ewan Birney and
Alvis Brazma and
Kim Henrick and
Rodrigo Lopez and
Guenter Stoesser and
Peter Stoehr and
Graham Cameron},
title = {The European Bioinformatics Institute's data resources},
journal = {Nucleic Acids Res.},
volume = {31},
number = {1},
pages = {43--50},
year = {2003},
url = {https://doi.org/10.1093/nar/gkg066},
doi = {10.1093/NAR/GKG066},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BrooksbankCHMMMOPTABBHLSSC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BrazmaPSSVAHKKLORS03,
author = {Alvis Brazma and
Helen E. Parkinson and
Ugis Sarkans and
Mohammadreza Shojatalab and
Jaak Vilo and
Niran Abeygunawardena and
Ele Holloway and
Misha Kapushesky and
Patrick Kemmeren and
Gonzalo Garcia Lara and
Ahmet Oezcimen and
Philippe Rocca{-}Serra and
Susanna{-}Assunta Sansone},
title = {ArrayExpress - a public repository for microarray gene expression
data at the {EBI}},
journal = {Nucleic Acids Res.},
volume = {31},
number = {1},
pages = {68--71},
year = {2003},
url = {https://doi.org/10.1093/nar/gkg091},
doi = {10.1093/NAR/GKG091},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BrazmaPSSVAHKKLORS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BallSPRBCCGHHRSSSTBQ02,
author = {Catherine A. Ball and
Gavin Sherlock and
Helen E. Parkinson and
Philippe Rocca{-}Serra and
Catherine Brooksbank and
Helen C. Causton and
Duccio Cavalieri and
Terry Gaasterland and
Pascal Hingamp and
Frank C. P. Holstege and
Martin Ringwald and
Paul T. Spellman and
Christian J. Stoeckert Jr. and
Jason E. Stewart and
Ronald C. Taylor and
Alvis Brazma and
John Quackenbush},
title = {An open letter to the scientific journals},
journal = {Bioinform.},
volume = {18},
number = {11},
pages = {1409},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.11.1409},
doi = {10.1093/BIOINFORMATICS/18.11.1409},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BallSPRBCCGHHRSSSTBQ02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/PalinUBV02,
author = {Kimmo Palin and
Esko Ukkonen and
Alvis Brazma and
Jaak Vilo},
title = {Correlating gene promoters and expression in gene disruption experiments},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2002), October 6-9, 2002, Saarbr{\"{u}}cken, Germany},
pages = {172--180},
year = {2002},
timestamp = {Thu, 23 Jun 2016 15:53:27 +0200},
biburl = {https://dblp.org/rec/conf/eccb/PalinUBV02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/RungSBFV02,
author = {Johan Rung and
Thomas Schlitt and
Alvis Brazma and
K. Freivalds and
Jaak Vilo},
title = {Building and analysing genome-wide gene disruption networks},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2002), October 6-9, 2002, Saarbr{\"{u}}cken, Germany},
pages = {202--210},
year = {2002},
timestamp = {Fri, 09 Oct 2009 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/eccb/RungSBFV02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Brazma01,
author = {Alvis Brazma},
title = {On the Importance of Standardisation in Life Sciences},
journal = {Bioinform.},
volume = {17},
number = {1},
pages = {113--114},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.2.113},
doi = {10.1093/BIOINFORMATICS/17.2.113},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Brazma01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/ViloBJRU00,
author = {Jaak Vilo and
Alvis Brazma and
Inge Jonassen and
Alan J. Robinson and
Esko Ukkonen},
editor = {Philip E. Bourne and
Michael Gribskov and
Russ B. Altman and
Nancy Jensen and
Debra A. Hope and
Thomas Lengauer and
Julie C. Mitchell and
Eric D. Scheeff and
Chris Smith and
Shawn Strande and
Helge Weissig},
title = {Mining for Putative Regulatory Elements in the Yeast Genome Using
Gene Expression Data},
booktitle = {Proceedings of the Eighth International Conference on Intelligent
Systems for Molecular Biology, August 19-23, 2000, La Jolla / San
Diego, CA, {USA}},
pages = {384--394},
publisher = {{AAAI}},
year = {2000},
url = {http://www.aaai.org/Library/ISMB/2000/ismb00-039.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/ViloBJRU00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BrazmaJEG98,
author = {Alvis Brazma and
Inge Jonassen and
Ingvar Eidhammer and
David R. Gilbert},
title = {Approaches to the Automatic Discovery of Patterns in Biosequences},
journal = {J. Comput. Biol.},
volume = {5},
number = {2},
pages = {279--305},
year = {1998},
url = {https://doi.org/10.1089/cmb.1998.5.279},
doi = {10.1089/CMB.1998.5.279},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/BrazmaJEG98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/BrazmaJVU98,
author = {Alvis Brazma and
Inge Jonassen and
Jaak Vilo and
Esko Ukkonen},
title = {Predicting gene regulatory elements from their expression data in
the complete yeast genome},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1998,
University of Cologne, Germany, October 1998},
publisher = {Oxford University Press},
year = {1998},
timestamp = {Fri, 02 Aug 2019 15:48:14 +0200},
biburl = {https://dblp.org/rec/conf/gcb/BrazmaJVU98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icgi/BrazmaJVU98,
author = {Alvis Brazma and
Inge Jonassen and
Jaak Vilo and
Esko Ukkonen},
editor = {Vasant G. Honavar and
Giora Slutzki},
title = {Pattern Discovery in Biosequences},
booktitle = {Grammatical Inference, 4th International Colloquium, ICGI-98, Ames,
Iowa, USA, July 12-14, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1433},
pages = {257--270},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0054081},
doi = {10.1007/BFB0054081},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icgi/BrazmaJVU98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ngc/BrazmeC97,
author = {Alvis Brazma and
Karlis Cerans},
title = {Noise-Tolerant Efficient Inductive Synthesis of Regular Expressions
from Good Examples},
journal = {New Gener. Comput.},
volume = {15},
number = {1},
pages = {105--140},
year = {1997},
url = {https://doi.org/10.1007/BF03037562},
doi = {10.1007/BF03037562},
timestamp = {Thu, 14 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ngc/BrazmeC97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/BrazmaVU97,
author = {Alvis Brazma and
Jaak Vilo and
Esko Ukkonen},
title = {Finding transcription factor binding site combinations in the yeast
genome},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1997,
Kloster Irsee, Bavaria, Germany, September 1997},
pages = {57--59},
publisher = {Oxford University Press},
year = {1997},
timestamp = {Fri, 02 Aug 2019 15:48:15 +0200},
biburl = {https://dblp.org/rec/conf/gcb/BrazmaVU97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/BrazmaFMR97,
author = {Alvis Brazma and
Tomas P. Flores and
Peter Maccallum and
Alan J. Robinson},
title = {Data Mining and Visualisation in Molecular Biology Databases},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1997,
Kloster Irsee, Bavaria, Germany, September 1997},
pages = {127},
publisher = {Oxford University Press},
year = {1997},
timestamp = {Fri, 02 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/BrazmaFMR97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/BrazmaVUV97,
author = {Alvis Brazma and
Jaak Vilo and
Esko Ukkonen and
Kimmo Valtonen},
editor = {Terry Gaasterland and
Peter D. Karp and
Kevin Karplus and
Christos A. Ouzounis and
Chris Sander and
Alfonso Valencia},
title = {Data Mining for Regulatory Elements in Yeast Genome},
booktitle = {Proceedings of the 5th International Conference on Intelligent Systems
for Molecular Biology, Halkidiki, Greece, June 21-26, 1997},
pages = {65--74},
publisher = {{AAAI}},
year = {1997},
url = {http://www.aaai.org/Library/ISMB/1997/ismb97-009.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/BrazmaVUV97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/BrazmaUV96,
author = {Alvis Brazma and
Esko Ukkonen and
Jaak Vilo},
editor = {Tetsuo Asano and
Yoshihide Igarashi and
Hiroshi Nagamochi and
Satoru Miyano and
Subhash Suri},
title = {Discovering Unbounded Unions of Regular Pattern Languages from Positive
Examples (Extended Abstract)},
booktitle = {Algorithms and Computation, 7th International Symposium, {ISAAC} '96,
Osaka, Japan, December 16-18, 1996, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1178},
pages = {95--104},
publisher = {Springer},
year = {1996},
url = {https://doi.org/10.1007/BFb0009485},
doi = {10.1007/BFB0009485},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/BrazmaUV96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/BrazmaJUV96,
author = {Alvis Brazma and
Inge Jonassen and
Esko Ukkonen and
Jaak Vilo},
editor = {David J. States and
Pankaj Agarwal and
Terry Gaasterland and
Lawrence Hunter and
Randall Smith},
title = {Discovering Patterns and Subfamilies in Biosequences},
booktitle = {Proceedings of the Fourth International Conference on Intelligent
Systems for Molecular Biology, St. Louis, MO, USA, June 12-15 1996},
pages = {34--43},
publisher = {{AAAI}},
year = {1996},
url = {http://www.aaai.org/Library/ISMB/1996/ismb96-004.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/BrazmaJUV96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eurocolt/Brazma95,
author = {Alvis Brazma},
editor = {Paul M. B. Vit{\'{a}}nyi},
title = {Learning of regular expressions by pattern matching},
booktitle = {Computational Learning Theory, Second European Conference, EuroCOLT
'95, Barcelona, Spain, March 13-15, 1995, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {904},
pages = {392--403},
publisher = {Springer},
year = {1995},
url = {https://doi.org/10.1007/3-540-59119-2\_194},
doi = {10.1007/3-540-59119-2\_194},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/eurocolt/Brazma95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alt/BrazmaC94,
author = {Alvis Brazma and
Karlis Cerans},
editor = {Setsuo Arikawa and
Klaus P. Jantke},
title = {Efficient Learning of Regular Expressions from Good Examples},
booktitle = {Algorithmic Learning Theory, 4th International Workshop on Analogical
and Inductive Inference, {AII} '94, 5th International Workshop on
Algorithmic Learning Theory, {ALT} '94, Reinhardsbrunn Castle, Germany,
October 10-15, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {872},
pages = {76--90},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-58520-6\_55},
doi = {10.1007/3-540-58520-6\_55},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alt/BrazmaC94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alt/Brazma94,
author = {Alvis Brazma},
editor = {Setsuo Arikawa and
Klaus P. Jantke},
title = {Efficient Algorithm for Learning Simple Regular Expressions from Noisy
Examples},
booktitle = {Algorithmic Learning Theory, 4th International Workshop on Analogical
and Inductive Inference, {AII} '94, 5th International Workshop on
Algorithmic Learning Theory, {ALT} '94, Reinhardsbrunn Castle, Germany,
October 10-15, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {872},
pages = {260--271},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-58520-6\_69},
doi = {10.1007/3-540-58520-6\_69},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alt/Brazma94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gd/KaugarsRB94,
author = {Karlis Kaugars and
Juris Reinfelds and
Alvis Brazma},
editor = {Roberto Tamassia and
Ioannis G. Tollis},
title = {A Simple Algorithm for Drawing Large Graphs on Small Screens},
booktitle = {Graph Drawing, {DIMACS} International Workshop, {GD} '94, Princeton,
New Jersey, USA, October 10-12, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {894},
pages = {278--281},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-58950-3\_382},
doi = {10.1007/3-540-58950-3\_382},
timestamp = {Sun, 13 Nov 2022 09:57:39 +0100},
biburl = {https://dblp.org/rec/conf/gd/KaugarsRB94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/colt/Brazma93,
author = {Alvis Brazma},
editor = {Lenny Pitt},
title = {Efficient Identification of Regular Expressions from Representative
Examples},
booktitle = {Proceedings of the Sixth Annual {ACM} Conference on Computational
Learning Theory, {COLT} 1993, Santa Cruz, CA, USA, July 26-28, 1993},
pages = {236--242},
publisher = {{ACM}},
year = {1993},
url = {https://doi.org/10.1145/168304.168340},
doi = {10.1145/168304.168340},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/colt/Brazma93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/scai/Brazma93,
author = {Alvis Brazma},
editor = {Erik Sandewall and
Carl Gustaf Jansson},
title = {Learning a Subclass of Regular Expressions by Recognizing Periodic
Repetitions},
booktitle = {Fourth Scandinavian Conference on Artificial Intelligence, {SCAI}
1993, Stockholm, Sweden, May 4-7, 1993},
series = {Frontiers in Artificial Intelligence and Applications},
volume = {18},
pages = {137--146},
publisher = {{IOS} Press},
year = {1993},
timestamp = {Mon, 05 Aug 2019 17:00:40 +0200},
biburl = {https://dblp.org/rec/conf/scai/Brazma93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:conf/balt/Brazma91,
author = {Alvis Brazma},
editor = {Janis Barzdins and
Dines Bj{\o}rner},
title = {Inductive Synthesis of Dot Expressions},
booktitle = {Baltic Computer Science, Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {502},
pages = {156--212},
publisher = {Springer},
year = {1991},
url = {https://doi.org/10.1007/BFb0019359},
doi = {10.1007/BFB0019359},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/balt/Brazma91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jlp/KinbarB90,
author = {Efim B. Kinber and
Alvis Brazma},
title = {Models of Inductive Synthesis},
journal = {J. Log. Program.},
volume = {9},
number = {2{\&}3},
pages = {221--233},
year = {1990},
url = {https://doi.org/10.1016/0743-1066(90)90041-3},
doi = {10.1016/0743-1066(90)90041-3},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jlp/KinbarB90.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/BrazmaK86,
author = {Alvis Brazma and
Efim B. Kinber},
title = {Generalized Regular Expressions-A Language for Synthesis of Programs
with Braching in Loops},
journal = {Theor. Comput. Sci.},
volume = {46},
number = {3},
pages = {175--195},
year = {1986},
url = {https://doi.org/10.1016/0304-3975(86)90029-0},
doi = {10.1016/0304-3975(86)90029-0},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/BrazmaK86.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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