Showing 47 publications by Allyson Lister
"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.
David R, Rybina A, Burel J-M, Heriche J-K, Audergon P et al. (2023), The EMBO journal, e115008
BibTeX
@article{besustainableeo-2023/11,
title={"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling. },
author={David R, Rybina A, Burel J-M, Heriche J-K, Audergon P et al.},
journal={The EMBO journal},
pages={e115008},
year = "2023"
}
"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.
David R, Rybina A, Burel J-M, Heriche J-K, Audergon P et al. (2023), The EMBO journal, e115008
BibTeX
@article{besustainableeo-2023/11,
title={"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.},
author={David R, Rybina A, Burel J-M, Heriche J-K, Audergon P et al.},
journal={The EMBO journal},
pages={e115008},
publisher={EMBO},
year = "2023"
}
“Be sustainable”: EOSC-Life recommendations for implementation of FAIR principles in life science data handling
David R, Rybina A, Burel J-M, Lister A & Sansone S (2023), The EMBO Journal, 42(23)
BibTeX
@article{besustainableeo-2023/11,
title={“Be sustainable”: EOSC-Life recommendations for implementation of FAIR principles in life science data handling},
author={David R, Rybina A, Burel J-M, Lister A & Sansone S},
journal={The EMBO Journal},
volume={42},
number={e115008},
publisher={EMBO Press},
year = "2023"
}
The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary
Steffens S, Schröder K, Krüger M, Maack C, Streckfuss-Bömeke K et al. (2023), Clinical Research in Cardiology, 113(5), 672-679
BibTeX
@article{thechallengesof-2023/10,
title={The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary},
author={Steffens S, Schröder K, Krüger M, Maack C, Streckfuss-Bömeke K et al.},
journal={Clinical Research in Cardiology},
volume={113},
pages={672-679},
publisher={Springer},
year = "2023"
}
Umbrella data management plans to integrate FAIR data: lessons from the ISIDORe and BY-COVID Consortia for Pandemic Preparedness
David R, Richard AS, Connellan C, Lister A, Romano P et al. (2023), Data Science Journal, 22
BibTeX
@article{umbrelladataman-2023/9,
title={Umbrella data management plans to integrate FAIR data: lessons from the ISIDORe and BY-COVID Consortia for Pandemic Preparedness},
author={David R, Richard AS, Connellan C, Lister A, Romano P et al.},
journal={Data Science Journal},
volume={22},
number={35},
publisher={Ubiquity Press},
year = "2023"
}
The FAIR Cookbook - the essential resource for and by FAIR doers.
Rocca-Serra P, Gu W, Ioannidis V, Abbassi-Daloii T, Capella-Gutierrez S et al. (2023), Scientific data, 10(1), 292
BibTeX
@article{thefaircookbook-2023/5,
title={The FAIR Cookbook - the essential resource for and by FAIR doers.},
author={Rocca-Serra P, Gu W, Ioannidis V, Abbassi-Daloii T, Capella-Gutierrez S et al.},
journal={Scientific data},
volume={10},
pages={292},
year = "2023"
}
The FAIR Cookbook - the essential resource for and by FAIR doers
Rocca-Serra P, Gu W, Ioannidis V, Abbassi-Daloii T, Capella-Gutierrez S et al. (2023), Scientific Data, 10
BibTeX
@article{thefaircookbook-2023/5,
title={The FAIR Cookbook - the essential resource for and by FAIR doers},
author={Rocca-Serra P, Gu W, Ioannidis V, Abbassi-Daloii T, Capella-Gutierrez S et al.},
journal={Scientific Data},
volume={10},
number={292},
publisher={Springer Nature},
year = "2023"
}
SBML level 3: An extensible format for the exchange and reuse of biological models
Keating SM, Waltemath D, König M, Zhang F, Dräger A et al. (2020), Molecular Systems Biology, 16(8)
BibTeX
@article{sbmllevelanexte-2020/8,
title={SBML level 3: An extensible format for the exchange and reuse of biological models},
author={Keating SM, Waltemath D, König M, Zhang F, Dräger A et al.},
journal={Molecular Systems Biology},
volume={16},
number={e9110},
publisher={EMBO Press},
year = "2020"
}
Helping the Consumers and Producers of Standards, Repositories and Policies to Enable FAIR Data
McQuilton P, Batista D, Beyan O, Granell R, Coles S et al. (2020), Data Intelligence, 2(1-2), 151-157
BibTeX
@article{helpingtheconsu-2020/1,
title={Helping the Consumers and Producers of Standards, Repositories and Policies to Enable FAIR Data},
author={McQuilton P, Batista D, Beyan O, Granell R, Coles S et al.},
journal={Data Intelligence},
volume={2},
pages={151-157},
publisher={MIT Press},
year = "2020"
}
FAIRsharing as a community approach to standards, repositories and policies
Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M et al. (2019), Nature Biotechnology, 37(4), 358-367
BibTeX
@article{fairsharingasac-2019/4,
title={FAIRsharing as a community approach to standards, repositories and policies},
author={Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M et al.},
journal={Nature Biotechnology},
volume={37},
pages={358-367},
publisher={Springer Nature},
year = "2019"
}
Mapping subjects and domains across the humanities and natural sciences in FAIRsharing
Lister AL, McQuilton P, Thurston M & Sansone SA (2019), CEUR Workshop Proceedings, 2849, 133-134
BibTeX
@inproceedings{mappingsubjects-2019/1,
title={Mapping subjects and domains across the humanities and natural sciences in FAIRsharing},
author={Lister AL, McQuilton P, Thurston M & Sansone SA},
pages={133-134},
year = "2019"
}
FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies
Sansone S-A, McQuilton PETER, Rocca-Serra PHILIPPE, Gonzalez-Beltran ALEJANDRA, Izzo MASSIMILIANO et al. (2018), NATURE BIOTECHNOLOGY(4)
BibTeX
@article{fairsharingacoh-2018/1,
title={FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies},
author={Sansone S-A, McQuilton PETER, Rocca-Serra PHILIPPE, Gonzalez-Beltran ALEJANDRA, Izzo MASSIMILIANO et al.},
journal={NATURE BIOTECHNOLOGY},
publisher={Cold Spring Harbor Laboratory},
year = "2018"
}
BioSharing: harnessing metadata standards for the data commons
Sansone S-A, Gonzalez-Beltran A, Rocca-Serra P, McQuilton P, Izzo M et al. (2017), bioRxiv
BibTeX
@article{biosharingharne-2017/5,
title={BioSharing: harnessing metadata standards for the data commons},
author={Sansone S-A, Gonzalez-Beltran A, Rocca-Serra P, McQuilton P, Izzo M et al.},
journal={bioRxiv},
publisher={Cold Spring Harbor Laboratory},
year = "2017"
}
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.
McQuilton P, Gonzalez-Beltran A, Rocca-Serra P, Thurston M, Lister A et al. (2016), Database, 2016
BibTeX
@article{biosharingcurat-2016/5,
title={BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.},
author={McQuilton P, Gonzalez-Beltran A, Rocca-Serra P, Thurston M, Lister A et al.},
journal={Database},
volume={2016},
publisher={Oxford University Press},
year = "2016"
}
The Ontology for Biomedical Investigations.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B et al. (2016), PloS one, 11(4), e0154556
BibTeX
@article{theontologyforb-2016/1,
title={The Ontology for Biomedical Investigations.},
author={Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B et al.},
journal={PloS one},
volume={11},
pages={e0154556},
year = "2016"
}
Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES).
Relton CL, Gaunt T, McArdle W, Ho K, Duggirala A et al. (2015), International journal of epidemiology, 44(4), 1181-1190
BibTeX
@article{dataresourcepro-2015/8,
title={Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES).},
author={Relton CL, Gaunt T, McArdle W, Ho K, Duggirala A et al.},
journal={International journal of epidemiology},
volume={44},
pages={1181-1190},
year = "2015"
}
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
Malone J, Brown A, Lister AL, Ison J, Hull D et al. (2014), Journal of biomedical semantics, 5, 25
BibTeX
@article{thesoftwareonto-2014/1,
title={The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.},
author={Malone J, Brown A, Lister AL, Ison J, Hull D et al.},
journal={Journal of biomedical semantics},
volume={5},
pages={25},
year = "2014"
}
Enhancing systems biology models through semantic data integration
Lister AL (2012)
BibTeX
@misc{enhancingsystem-2012/,
title={Enhancing systems biology models through semantic data integration},
author={Lister AL},
year = "2012"
}
Controlled vocabularies and semantics in systems biology.
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A et al. (2011), Molecular systems biology, 7, 543
BibTeX
@article{controlledvocab-2011/10,
title={Controlled vocabularies and semantics in systems biology.},
author={Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A et al.},
journal={Molecular systems biology},
volume={7},
pages={543},
year = "2011"
}
Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects.
Addinall SG, Holstein E-M, Lawless C, Yu M, Chapman K et al. (2011), PLoS genetics, 7(4), e1001362
BibTeX
@article{quantitativefit-2011/4,
title={Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects.},
author={Addinall SG, Holstein E-M, Lawless C, Yu M, Chapman K et al.},
journal={PLoS genetics},
volume={7},
pages={e1001362},
year = "2011"
}
MIREOT: The minimum information to reference an external ontology term
Courtot M, Gibson F, Lister AL, Malone J, Schober D et al. (2011), Applied ontology, 6(1), 23-33
BibTeX
@article{mireottheminimu-2011/1,
title={MIREOT: The minimum information to reference an external ontology term},
author={Courtot M, Gibson F, Lister AL, Malone J, Schober D et al.},
journal={Applied ontology},
volume={6},
pages={23-33},
year = "2011"
}
Modeling biomedical experimental processes with OBI
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y et al. (2010), Journal of Biomedical Semantics, 1(Suppl 1), s7
BibTeX
@inproceedings{modelingbiomedi-2010/6,
title={Modeling biomedical experimental processes with OBI},
author={Brinkman RR, Courtot M, Derom D, Fostel JM, He Y et al.},
pages={s7},
year = "2010"
}
Annotation of SBML models through rule-based semantic integration.
Lister AL, Lord P, Pocock M & Wipat A (2010), Journal of biomedical semantics, 1 Suppl 1, S3
BibTeX
@article{annotationofsbm-2010/6,
title={Annotation of SBML models through rule-based semantic integration.},
author={Lister AL, Lord P, Pocock M & Wipat A},
journal={Journal of biomedical semantics},
volume={1 Suppl 1},
pages={S3},
year = "2010"
}
Semantic Integration in the Life Sciences
Lister AL (2010), Ontogenesis
BibTeX
@article{semanticintegra-2010/1,
title={Semantic Integration in the Life Sciences},
author={Lister AL},
journal={Ontogenesis},
year = "2010"
}
Live Coverage of Intelligent Systems for Molecular Biology/European Conference on computational biology (ISMB/ECCB) 2009.
Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M et al. (2010), PLoS computational biology, 6(1), e1000640
BibTeX
@article{livecoverageofi-2010/1,
title={Live Coverage of Intelligent Systems for Molecular Biology/European Conference on computational biology (ISMB/ECCB) 2009.},
author={Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M et al.},
journal={PLoS computational biology},
volume={6},
pages={e1000640},
year = "2010"
}
Live coverage of scientific conferences using web technologies.
Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M et al. (2010), PLoS computational biology, 6(1), e1000563
BibTeX
@article{livecoverageofs-2010/1,
title={Live coverage of scientific conferences using web technologies.},
author={Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M et al.},
journal={PLoS computational biology},
volume={6},
pages={e1000563},
year = "2010"
}
Managing experimental data using FuGE.
Jones AR & Lister AL (2010), Methods in molecular biology (Clifton, N.J.), 604, 333-343
BibTeX
@article{managingexperim-2010/1,
title={Managing experimental data using FuGE.},
author={Jones AR & Lister AL},
journal={Methods in molecular biology (Clifton, N.J.)},
volume={604},
pages={333-343},
year = "2010"
}
The OWL of biomedical investigations
Courtot M, Bug W, Gibson F, Lister AL, Malone J et al. (2009), CEUR Workshop Proceedings, 432
BibTeX
@inproceedings{theowlofbiomedi-2009/12,
title={The OWL of biomedical investigations},
author={Courtot M, Bug W, Gibson F, Lister AL, Malone J et al.},
year = "2009"
}
Saint: a lightweight integration environment for model annotation.
Lister AL, Pocock M, Taschuk M & Wipat A (2009), Bioinformatics (Oxford, England), 25(22), 3026-3027
BibTeX
@article{saintalightweig-2009/11,
title={Saint: a lightweight integration environment for model annotation.},
author={Lister AL, Pocock M, Taschuk M & Wipat A},
journal={Bioinformatics (Oxford, England)},
volume={25},
pages={3026-3027},
year = "2009"
}
MIREOT: the Minimum Information to Reference an External Ontology Term
Courtot M, Gibson F, Lister AL, Malone J, Schober D et al. (2009), International Conference on Biomedical Ontology, 87-90
BibTeX
@inproceedings{mireottheminimu-2009/7,
title={MIREOT: the Minimum Information to Reference an External Ontology Term},
author={Courtot M, Gibson F, Lister AL, Malone J, Schober D et al.},
pages={87-90},
year = "2009"
}
Annotation of SBML Models Through Rule-Based Semantic Integration
Lister AL, Lord P, Pocock M & Wipat A (2009), The 12th Annual Bio-Ontologies Meeting, ISMB 2009, 49+-49+
BibTeX
@inproceedings{annotationofsbm-2009/6,
title={Annotation of SBML Models Through Rule-Based Semantic Integration},
author={Lister AL, Lord P, Pocock M & Wipat A},
pages={49+-49+},
year = "2009"
}
Modeling and managing experimental data using FuGE.
Jones AR, Lister AL, Hermida L, Wilkinson P, Eisenacher M et al. (2009), Omics : a journal of integrative biology, 13(3), 239-251
BibTeX
@article{modelingandmana-2009/6,
title={Modeling and managing experimental data using FuGE.},
author={Jones AR, Lister AL, Hermida L, Wilkinson P, Eisenacher M et al.},
journal={Omics : a journal of integrative biology},
volume={13},
pages={239-251},
year = "2009"
}
Saint: a lightweight SBML annotation integration environment
Lister AL, Pocock M & Wipat A (2009), BioSysBio 2009
BibTeX
@inproceedings{saintalightweig-2009/3,
title={Saint: a lightweight SBML annotation integration environment},
author={Lister AL, Pocock M & Wipat A},
year = "2009"
}
Interfacing systems biology and synthetic biology.
Lister A, Charoensawan V, De S, James K, Janga SC et al. (2009), Genome biology, 10(6), 309
BibTeX
@article{interfacingsyst-2009/1,
title={Interfacing systems biology and synthetic biology.},
author={Lister A, Charoensawan V, De S, James K, Janga SC et al.},
journal={Genome biology},
volume={10},
pages={309},
year = "2009"
}
Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.
Field D, Glöckner FO, Garrity GM, Gray T, Sterk P et al. (2008), Omics : a journal of integrative biology, 12(2), 101-108
BibTeX
@article{meetingreportth-2008/6,
title={Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.},
author={Field D, Glöckner FO, Garrity GM, Gray T, Sterk P et al.},
journal={Omics : a journal of integrative biology},
volume={12},
pages={101-108},
year = "2008"
}
XSL transformations for FuGE and FuGE extension documents for HTML and tab-delimited rendering
Rocca-Serra P, Sansone S, Jones A, Lister A, Gibson F et al. (2008)
BibTeX
@misc{xsltransformati-2008/6,
title={XSL transformations for FuGE and FuGE extension documents for HTML and tab-delimited rendering},
author={Rocca-Serra P, Sansone S, Jones A, Lister A, Gibson F et al.},
year = "2008"
}
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Sansone S-A, Rocca-Serra P, Brandizi M, Brazma A, Field D et al. (2008), Omics : a journal of integrative biology, 12(2), 143-149
BibTeX
@inproceedings{thefirstrsbiisa-2008/6,
title={The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".},
author={Sansone S-A, Rocca-Serra P, Brandizi M, Brazma A, Field D et al.},
pages={143-149},
year = "2008"
}
The minimum information about a genome sequence (MIGS) specification.
Field D, Garrity G, Gray T, Morrison N, Selengut J et al. (2008), Nature biotechnology, 26(5), 541-547
BibTeX
@article{theminimuminfor-2008/5,
title={The minimum information about a genome sequence (MIGS) specification.},
author={Field D, Garrity G, Gray T, Morrison N, Selengut J et al.},
journal={Nature biotechnology},
volume={26},
pages={541-547},
year = "2008"
}
The minimum information about a genome sequence (MIGS) specification
Field D, Garrity G, Gray T, Morrison N, Selengut J et al. (2008), Nature Biotechnology, 26(5), 541-547
BibTeX
@article{theminimuminfor-2008/5,
title={The minimum information about a genome sequence (MIGS) specification},
author={Field D, Garrity G, Gray T, Morrison N, Selengut J et al.},
journal={Nature Biotechnology},
volume={26},
pages={541-547},
year = "2008"
}
Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models
Lister AL, Pocock M & Wipat A (2007), Journal of Integrative Bioinformatics, 4(3), 252-263
BibTeX
@article{integrationofco-2007/12,
title={Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models},
author={Lister AL, Pocock M & Wipat A},
journal={Journal of Integrative Bioinformatics},
volume={4},
pages={252-263},
publisher={De Gruyter},
year = "2007"
}
CS-TR Number 1016: Implementing the FuGE Object Model: a Systems Biology Data Portal and Integrator
Lister AL, Jones AR, Pocock M, Shaw O & Wipat A (2007)
BibTeX
@misc{cstrnumberimple-2007/4,
title={CS-TR Number 1016: Implementing the FuGE Object Model: a Systems Biology Data Portal and Integrator},
author={Lister AL, Jones AR, Pocock M, Shaw O & Wipat A},
year = "2007"
}
eGenomics: Cataloguing Our Complete Genome Collection III
Field D, Garrity G, Gray T, Selengut J, Sterk P et al. (2007), International Journal of Genomics, 2007, 47304
BibTeX
@article{egenomicscatalo-2007/,
title={eGenomics: Cataloguing Our Complete Genome Collection III},
author={Field D, Garrity G, Gray T, Selengut J, Sterk P et al.},
journal={International Journal of Genomics},
volume={2007},
pages={47304},
publisher={Hindawi},
year = "2007"
}
Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models
Lister AL, Pocock M & Wipat A (2007), Journal of Integrative Bioinformatics, 4, 80+-80+
BibTeX
@article{integrationofco-2007/,
title={Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models},
author={Lister AL, Pocock M & Wipat A},
journal={Journal of Integrative Bioinformatics},
volume={4},
number={3},
pages={80+-80+},
year = "2007"
}
Biological Databases: Infrastructure, Content and Integration
Williams AL, Kersey PJ, Pruess M & Apweiler R (2005), 11-28
BibTeX
@misc{biologicaldatab-2005/3,
title={Biological Databases: Infrastructure, Content and Integration},
author={Williams AL, Kersey PJ, Pruess M & Apweiler R},
year = "2005"
}
The International Protein Index: an integrated database for proteomics experiments.
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E et al. (2004), Proteomics, 4(7), 1985-1988
BibTeX
@article{theinternationa-2004/7,
title={The International Protein Index: an integrated database for proteomics experiments.},
author={Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E et al.},
journal={Proteomics},
volume={4},
pages={1985-1988},
year = "2004"
}
SBML Level 3 Package Proposal: Annotation
Hucka M, Laibe C, Juty N, Liebermeister W, Keating S et al. (0), 1-1
BibTeX
@article{sbmllevelpackag-/,
title={SBML Level 3 Package Proposal: Annotation},
author={Hucka M, Laibe C, Juty N, Liebermeister W, Keating S et al.},
journal={},
pages={1-1},
publisher={Springer Nature}
}
OBI Ontology
Consortium TOBI (0)
BibTeX
@misc{obiontology-/,
title={OBI Ontology},
author={Consortium TOBI}
}