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ORCIDBibTeX records: David J. Sherman
@article{DBLP:journals/bmcsb/ZhukovaS15,
author = {Anna Zhukova and
David James Sherman},
title = {Mimoza: web-based semantic zooming and navigation in metabolic networks},
journal = {{BMC} Syst. Biol.},
volume = {9},
pages = {10},
year = {2015},
url = {https://doi.org/10.1186/s12918-015-0151-5},
doi = {10.1186/S12918-015-0151-5},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/ZhukovaS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/LoiraZS15,
author = {Nicol{\'{a}}s Loira and
Anna Zhukova and
David James Sherman},
title = {Pantograph: {A} template-based method for genome-scale metabolic model
reconstruction},
journal = {J. Bioinform. Comput. Biol.},
volume = {13},
number = {2},
pages = {1550006:1--1550006:19},
year = {2015},
url = {https://doi.org/10.1142/S0219720015500067},
doi = {10.1142/S0219720015500067},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/LoiraZS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/AssarMMS14,
author = {Rodrigo Assar and
Mart{\'{\i}}n A. Montecino and
Alejandro Maass and
David J. Sherman},
title = {Modeling acclimatization by hybrid systems: Condition changes alter
biological system behavior models},
journal = {Biosyst.},
volume = {121},
pages = {43--53},
year = {2014},
url = {https://doi.org/10.1016/j.biosystems.2014.05.007},
doi = {10.1016/J.BIOSYSTEMS.2014.05.007},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biosystems/AssarMMS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/ZhukovaS14,
author = {Anna Zhukova and
David James Sherman},
title = {Knowledge-based generalization of metabolic networks: {A} practical
study},
journal = {J. Bioinform. Comput. Biol.},
volume = {12},
number = {2},
year = {2014},
url = {https://doi.org/10.1142/S0219720014410017},
doi = {10.1142/S0219720014410017},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/ZhukovaS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ZhukovaS14,
author = {Anna Zhukova and
David James Sherman},
title = {Knowledge-based Generalization of Metabolic Models},
journal = {J. Comput. Biol.},
volume = {21},
number = {7},
pages = {534--547},
year = {2014},
url = {https://doi.org/10.1089/cmb.2013.0143},
doi = {10.1089/CMB.2013.0143},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ZhukovaS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/amc/AssarS13,
author = {Rodrigo Assar and
David J. Sherman},
title = {Implementing biological hybrid systems: Allowing composition and avoiding
stiffness},
journal = {Appl. Math. Comput.},
volume = {223},
pages = {167--179},
year = {2013},
url = {https://doi.org/10.1016/j.amc.2013.08.012},
doi = {10.1016/J.AMC.2013.08.012},
timestamp = {Fri, 21 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/amc/AssarS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/AssarLGIMS12,
author = {Rodrigo Assar and
Andrea V. Leisewitz and
Alice Garcia and
Nibaldo C. Inestrosa and
Mart{\'{\i}}n A. Montecino and
David J. Sherman},
title = {Reusing and composing models of cell fate regulation of human bone
precursor cells},
journal = {Biosyst.},
volume = {108},
number = {1-3},
pages = {63--72},
year = {2012},
url = {https://doi.org/10.1016/j.biosystems.2012.01.008},
doi = {10.1016/J.BIOSYSTEMS.2012.01.008},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biosystems/AssarLGIMS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/LoiraDNS12,
author = {Nicol{\'{a}}s Loira and
Thierry Dulermo and
Jean{-}Marc Nicaud and
David James Sherman},
title = {A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia
lipolytica},
journal = {{BMC} Syst. Biol.},
volume = {6},
pages = {35},
year = {2012},
url = {https://doi.org/10.1186/1752-0509-6-35},
doi = {10.1186/1752-0509-6-35},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/LoiraDNS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/anb/AssarVS10,
author = {Rodrigo Assar and
Felipe A. Vargas and
David J. Sherman},
editor = {Katsuhisa Horimoto and
Masahiko Nakatsui and
Nikolaj Popov},
title = {Reconciling Competing Models: {A} Case Study of Wine Fermentation
Kinetics},
booktitle = {Algebraic and Numeric Biology - 4th International Conference, {ANB}
2010, Hagenberg, Austria, July 31- August 2, 2010, Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {6479},
pages = {98--116},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-28067-2\_6},
doi = {10.1007/978-3-642-28067-2\_6},
timestamp = {Tue, 14 May 2019 10:00:55 +0200},
biburl = {https://dblp.org/rec/conf/anb/AssarVS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NikolskiS09,
author = {Macha Nikolski and
David James Sherman},
title = {Family relationships: should consensus reign? - consensus clustering
for protein families},
journal = {Bioinform.},
volume = {25},
number = {17},
pages = {2294},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp440},
doi = {10.1093/BIOINFORMATICS/BTP440},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NikolskiS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/JeanSN09,
author = {G{\'{e}}raldine Jean and
David James Sherman and
Macha Nikolski},
title = {Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures},
journal = {J. Comput. Biol.},
volume = {16},
number = {9},
pages = {1267--1284},
year = {2009},
url = {https://doi.org/10.1089/cmb.2008.0046},
doi = {10.1089/CMB.2008.0046},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/JeanSN09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ShermanMNCSD09,
author = {David James Sherman and
Tiphaine C. Martin and
Macha Nikolski and
Cyril Cayla and
Jean{-}Luc Souciet and
Pascal Durrens},
title = {G{\'{e}}nolevures: protein families and synteny among complete
hemiascomycetous yeast proteomes and genomes},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Database-Issue},
pages = {550--554},
year = {2009},
url = {https://doi.org/10.1093/nar/gkn859},
doi = {10.1093/NAR/GKN859},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ShermanMNCSD09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gecco/VyahhiGNS09,
author = {Nikolay Vyahhi and
Adrien Go{\"{e}}ffon and
Macha Nikolski and
David James Sherman},
editor = {Franz Rothlauf},
title = {Swarming along the evolutionary branches sheds light on genome rearrangement
scenarios},
booktitle = {Genetic and Evolutionary Computation Conference, {GECCO} 2009, Proceedings,
Montreal, Qu{\'{e}}bec, Canada, July 8-12, 2009},
pages = {241--246},
publisher = {{ACM}},
year = {2009},
url = {https://doi.org/10.1145/1569901.1569935},
doi = {10.1145/1569901.1569935},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/gecco/VyahhiGNS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DurrensNS08,
author = {Pascal Durrens and
Macha Nikolski and
David James Sherman},
title = {Fusion and Fission of Genes Define a Metric between Fungal Genomes},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {10},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000200},
doi = {10.1371/JOURNAL.PCBI.1000200},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DurrensNS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gecco/GoeffonNS08,
author = {Adrien Go{\"{e}}ffon and
Macha Nikolski and
David James Sherman},
editor = {Conor Ryan and
Maarten Keijzer},
title = {An efficient probabilistic population-based descent for the median
genome problem},
booktitle = {Genetic and Evolutionary Computation Conference, {GECCO} 2008, Proceedings,
Atlanta, GA, USA, July 12-16, 2008},
pages = {315--322},
publisher = {{ACM}},
year = {2008},
url = {https://doi.org/10.1145/1389095.1389151},
doi = {10.1145/1389095.1389151},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/gecco/GoeffonNS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NikolskiS07,
author = {Macha Nikolski and
David James Sherman},
title = {Family relationships: should consensus reign? - consensus clustering
for protein families},
journal = {Bioinform.},
volume = {23},
number = {2},
pages = {71--76},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl314},
doi = {10.1093/BIOINFORMATICS/BTL314},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NikolskiS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BarriotSD07,
author = {Roland Barriot and
David J. Sherman and
Isabelle Dutour},
title = {How to decide which are the most pertinent overly-represented features
during gene set enrichment analysis},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-332},
doi = {10.1186/1471-2105-8-332},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BarriotSD07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ShermanDIBNS06,
author = {David James Sherman and
Pascal Durrens and
Florian Iragne and
Emmanuelle Beyne and
Macha Nikolski and
Jean{-}Luc Souciet},
title = {G{\'{e}}nolevures complete genomes provide data and tools for
comparative genomics of hemiascomycetous yeasts},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {432--435},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj160},
doi = {10.1093/NAR/GKJ160},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ShermanDIBNS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IragneNMAS05,
author = {Florian Iragne and
Macha Nikolski and
Bertrand Mathieu and
David Auber and
David James Sherman},
title = {ProViz: protein interaction visualization and exploration},
journal = {Bioinform.},
volume = {21},
number = {2},
pages = {272--274},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bth494},
doi = {10.1093/BIOINFORMATICS/BTH494},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/IragneNMAS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ShermanDBN04,
author = {David James Sherman and
Pascal Durrens and
Emmanuelle Beyne and
Macha Nikolski},
title = {G{\'{e}}nolevures: comparative genomics and molecular evolution
of hemiascomycetous yeasts},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Database-Issue},
pages = {315--318},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh091},
doi = {10.1093/NAR/GKH091},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ShermanDBN04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HermjakobMLMKOVRRVMABCSA04,
author = {Henning Hermjakob and
Luisa Montecchi{-}Palazzi and
Chris Lewington and
Sugath Mudali and
Samuel Kerrien and
Sandra E. Orchard and
Martin Vingron and
Bernd Roechert and
Peter Roepstorff and
Alfonso Valencia and
Hanah Margalit and
John Armstrong and
Amos Bairoch and
Gianni Cesareni and
David James Sherman and
Rolf Apweiler},
title = {IntAct: an open source molecular interaction database},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Database-Issue},
pages = {452--455},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh052},
doi = {10.1093/NAR/GKH052},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HermjakobMLMKOVRRVMABCSA04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fmcad/NikolskaiaRS98,
author = {Macha Nikolska{\"{\i}}a and
Antoine Rauzy and
David James Sherman},
editor = {Ganesh Gopalakrishnan and
Phillip J. Windley},
title = {Almana: {A} {BDD} Minimization Tool Integrating Heuristic and Rewriting
Methods},
booktitle = {Formal Methods in Computer-Aided Design, Second International Conference,
{FMCAD} '98, Palo Alto, California, USA, November 4-6, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1522},
pages = {100--114},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/3-540-49519-3\_8},
doi = {10.1007/3-540-49519-3\_8},
timestamp = {Tue, 14 May 2019 10:00:54 +0200},
biburl = {https://dblp.org/rec/conf/fmcad/NikolskaiaRS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/tacas/ShermanM98,
author = {David James Sherman and
Nicolas Magnier},
editor = {Bernhard Steffen},
title = {Factotum: Automatic and Systematic Sharing Support for Systems Analyzers},
booktitle = {Tools and Algorithms for Construction and Analysis of Systems, 4th
International Conference, {TACAS} '98, Held as Part of the European
Joint Conferences on the Theory and Practice of Software, ETAPS'98,
Lisbon, Portugal, March 28 - April 4, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1384},
pages = {249--262},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0054176},
doi = {10.1007/BFB0054176},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/tacas/ShermanM98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dagstuhl/MiniussiS96,
author = {Alain Miniussi and
David J. Sherman},
editor = {Olivier Danvy and
Robert Gl{\"{u}}ck and
Peter Thiemann},
title = {Squeezing Intermediate Construction in Equational Programs},
booktitle = {Partial Evaluation, International Seminar, Dagstuhl Castle, Germany,
February 12-16, 1996, Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {1110},
pages = {284--302},
publisher = {Springer},
year = {1996},
url = {https://doi.org/10.1007/3-540-61580-6\_14},
doi = {10.1007/3-540-61580-6\_14},
timestamp = {Mon, 23 Mar 2020 12:22:51 +0100},
biburl = {https://dblp.org/rec/conf/dagstuhl/MiniussiS96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/plilp/MetzemakersMSS94,
author = {Timo Metzemakers and
Alain Miniussi and
David J. Sherman and
Robert Strandh},
editor = {Manuel V. Hermenegildo and
Jaan Penjam},
title = {Improving Arithmetic Performance using Fine-Grain Unfolding},
booktitle = {Programming Language Implementation and Logic Programming, 6th International
Symposium, PLILP'94, Madrid, Spain, September 14-16, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {844},
pages = {324--339},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-58402-1\_23},
doi = {10.1007/3-540-58402-1\_23},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/plilp/MetzemakersMSS94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pepm/ShermanS92,
author = {David J. Sherman and
Robert Strandh},
title = {Call Unfolding Strategies for Equational Logic Programs},
booktitle = {PEPM'92, {ACM} {SIGPLAN} Workshop on Partial Evaluation and Semantics-Based
Program Manipulation, Fairmont Hotel, San Francisco, CA, USA, June
19-20, 1992, Proceedings {(TR} {YALEU/DCS/RR-909)}},
pages = {48--53},
publisher = {Yale University},
year = {1992},
timestamp = {Fri, 09 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/pepm/ShermanS92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pepm/ShermanSD91,
author = {David J. Sherman and
Robert Strandh and
Ir{\`{e}}ne Durand},
editor = {Charles Consel and
Olivier Danvy},
title = {Optimization of Equational Programs Using Partial Evaluation},
booktitle = {Proceedings of the Symposium on Partial Evaluation and Semantics-Based
Program Manipulation, PEPM'91, Yale University, New Haven, Connecticut,
USA, June 17-19, 1991},
pages = {72--82},
publisher = {{ACM}},
year = {1991},
url = {https://doi.org/10.1145/115865.115874},
doi = {10.1145/115865.115874},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/pepm/ShermanSD91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sas/DurandSS91,
author = {Ir{\`{e}}ne Durand and
David J. Sherman and
Robert Strandh},
editor = {Michel Billaud and
Pierre Cast{\'{e}}ran and
Marc{-}Michel Corsini and
Kaninda Musumbu and
Antoine Rauzy},
title = {Partial Evaluation of an Intermediate Language for Equational Programs},
booktitle = {Actes JTASPEFL'91 (Bordeaux, France), October 1991, Laboratoire Bordelais
de Recherche en Informatique (LaBRI), Proceedings},
series = {Series Bigre},
volume = {74},
pages = {98--106},
publisher = {Atelier Irisa, IRISA, Campus de Beaulieu},
year = {1991},
timestamp = {Fri, 09 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sas/DurandSS91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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