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ORCIDBibTeX records: Misha Kapushesky
@article{DBLP:journals/nar/CulhaneSSPMKHKPFPGPOCQ12,
author = {Aed{\'{\i}}n C. Culhane and
Markus S. Schr{\"{o}}der and
Razvan Sultana and
Shaita C. Picard and
Enzo N. Martinelli and
Caroline Kelly and
Benjamin Haibe{-}Kains and
Misha Kapushesky and
Anne{-}Alyssa St Pierre and
William Flahive and
Kermshlise C. Picard and
Daniel Gusenleitner and
Gerald Papenhausen and
Niall O'Connor and
Mick Correll and
John Quackenbush},
title = {GeneSigDB: a manually curated database and resource for analysis of
gene expression signatures},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {1060--1066},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr901},
doi = {10.1093/NAR/GKR901},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CulhaneSSPMKHKPFPGPOCQ12.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/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/bioinformatics/KurbatovaAKSK11,
author = {Natalja Kurbatova and
Tomasz Adamusiak and
Pavel Kurnosov and
Morris A. Swertz and
Misha Kapushesky},
title = {ontoCAT: an {R} package for ontology traversal and search},
journal = {Bioinform.},
volume = {27},
number = {17},
pages = {2468--2470},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr375},
doi = {10.1093/BIOINFORMATICS/BTR375},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KurbatovaAKSK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AdamusiakBKVAAKPS11,
author = {Tomasz Adamusiak and
Tony Burdett and
Natalja Kurbatova and
K. Joeri van der Velde and
Niran Abeygunawardena and
Despoina Antonakaki and
Misha Kapushesky and
Helen E. Parkinson and
Morris A. Swertz},
title = {OntoCAT - simple ontology search and integration in Java, {R} and
REST/JavaScript},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {218},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-218},
doi = {10.1186/1471-2105-12-218},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AdamusiakBKVAAKPS11.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/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}
}
@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/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}
}
@inproceedings{DBLP:conf/semweb/MaloneAHKP08,
author = {James Malone and
Tomasz Adamusiak and
Ele Holloway and
Misha Kapushesky and
Helen E. Parkinson},
editor = {Rinke Hoekstra and
Peter F. Patel{-}Schneider},
title = {Developing an Ontology from the Application Up},
booktitle = {Proceedings of the 5th International Workshop on {OWL:} Experiences
and Directions {(OWLED} 2009), Chantilly, VA, United States, October
23-24, 2009},
series = {{CEUR} Workshop Proceedings},
volume = {529},
publisher = {CEUR-WS.org},
year = {2009},
url = {https://ceur-ws.org/Vol-529/owled2009\_submission\_49.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:05 +0100},
biburl = {https://dblp.org/rec/conf/semweb/MaloneAHKP08.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/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}
}
@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/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/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/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}
}
@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}
}
@inproceedings{DBLP:conf/wabi/SoinovKK04,
author = {Lev Soinov and
Alexander Kanapin and
Misha Kapushesky},
editor = {Inge Jonassen and
Junhyong Kim},
title = {Supervised Learning-Aided Optimization of Expert-Driven Functional
Protein Sequence Annotation},
booktitle = {Algorithms in Bioinformatics, 4th International Workshop, {WABI} 2004,
Bergen, Norway, September 17-21, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3240},
pages = {159--169},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30219-3\_14},
doi = {10.1007/978-3-540-30219-3\_14},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SoinovKK04.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}
}
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