| Year |
Citation |
Score |
| 2023 |
König M, Gleeson P, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Schreiber F. Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. Journal of Integrative Bioinformatics. 20. PMID 36989443 DOI: 10.1515/jib-2023-0004 |
0.336 |
|
| 2021 |
Schreiber F, Gleeson P, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, König M, Myers CJ, Nickerson DP, Sommer B, Waltemath D. Specifications of standards in systems and synthetic biology: status and developments in 2021. Journal of Integrative Bioinformatics. 18. PMID 34674411 DOI: 10.1515/jib-2021-0026 |
0.311 |
|
| 2020 |
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, ... Hucka M, et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 16: e9110. PMID 32845085 DOI: 10.15252/Msb.20199110 |
0.584 |
|
| 2020 |
Smith LP, Moodie SL, Bergmann FT, Gillespie C, Keating SM, König M, Myers CJ, Swat MJ, Wilkinson DJ, Hucka M. Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. Journal of Integrative Bioinformatics. PMID 32750035 DOI: 10.1515/Jib-2020-0018 |
0.459 |
|
| 2020 |
Zhang F, Smith LP, Blinov ML, Faeder J, Hlavacek WS, Juan Tapia J, Keating SM, Rodriguez N, Dräger A, Harris LA, Finney A, Hu B, Hucka M, Meier-Schellersheim M. Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. Journal of Integrative Bioinformatics. PMID 32628633 DOI: 10.1515/Jib-2020-0015 |
0.438 |
|
| 2020 |
Schreiber F, Sommer B, Czauderna T, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. Specifications of standards in systems and synthetic biology: status and developments in 2020. Journal of Integrative Bioinformatics. PMID 32598316 DOI: 10.1515/Jib-2020-0022 |
0.373 |
|
| 2020 |
Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, et al. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). Journal of Integrative Bioinformatics. PMID 32598315 DOI: 10.1515/Jib-2020-0005 |
0.51 |
|
| 2019 |
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, ... Hucka M, et al. BioModels-15 years of sharing computational models in life science. Nucleic Acids Research. PMID 31701150 DOI: 10.1093/Nar/Gkz1055 |
0.548 |
|
| 2019 |
Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods in Molecular Biology (Clifton, N.J.). 2049: 285-314. PMID 31602618 DOI: 10.1007/978-1-4939-9736-7_17 |
0.533 |
|
| 2019 |
Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. Journal of Integrative Bioinformatics. PMID 31301675 DOI: 10.1515/Jib-2019-0035 |
0.472 |
|
| 2019 |
Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, et al. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of Integrative Bioinformatics. PMID 31219795 DOI: 10.1515/Jib-2019-0021 |
0.518 |
|
| 2019 |
Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, ... Hucka M, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/S41596-018-0098-2 |
0.443 |
|
| 2018 |
Neal ML, König M, Nickerson D, Misirli G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, ... Hucka M, et al. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. PMID 30462164 DOI: 10.1093/Bib/Bby087 |
0.692 |
|
| 2018 |
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, et al. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences. 13: 17. PMID 30117501 DOI: 10.1186/S40793-018-0320-4 |
0.375 |
|
| 2018 |
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. Journal of Integrative Bioinformatics. PMID 29596055 DOI: 10.1515/Jib-2018-0013 |
0.422 |
|
| 2018 |
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. Journal of Integrative Bioinformatics. PMID 29522418 DOI: 10.1515/jib-2017-0081 |
0.449 |
|
| 2018 |
Hucka M, Graham MJ. Software search is not a science, even among scientists: A survey of how scientists and engineers find software Journal of Systems and Software. 141: 171-191. DOI: 10.1016/J.Jss.2018.03.047 |
0.355 |
|
| 2017 |
Hucka M. SBMLPkgSpec: a LaTeX style file for SBML package specification documents. Bmc Research Notes. 10: 451. PMID 28877760 DOI: 10.1186/S13104-017-2788-1 |
0.494 |
|
| 2017 |
Rodriguez N, Hamm TM, Schulte R, Watanabe L, Vazirabad IY, Kofia V, Myers CJ, Funahashi A, Novère NL, Hucka M, Draeger A. The JSBML project: a fully featured Java API for working with systems biology models F1000research. 6. DOI: 10.7490/F1000Research.1114686.1 |
0.406 |
|
| 2016 |
Hucka M, Smith LP. SBML Level 3 package: Groups, Version 1 Release 1. Journal of Integrative Bioinformatics. 13: 8-29. PMID 29215993 DOI: 10.1515/jib-2016-290 |
0.304 |
|
| 2016 |
Hucka M, Smith LP. SBML Level 3 package: Groups, Version 1 Release 1. Journal of Integrative Bioinformatics. 13: 290. PMID 28187406 DOI: 10.2390/Biecoll-Jib-2016-290 |
0.411 |
|
| 2016 |
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. Journal of Integrative Bioinformatics. 13: 289. PMID 28187405 DOI: 10.2390/Biecoll-Jib-2016-289 |
0.395 |
|
| 2016 |
Waltemath D, Karr J, Bergmann F, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers C, Pir P, Alaybeyoglu B, Aranganathan N, Baghalian K, Bittig A, Burke P, et al. Toward community standards and software for whole-cell modeling. Ieee Transactions On Bio-Medical Engineering. PMID 27305665 DOI: 10.1109/Tbme.2016.2560762 |
0.47 |
|
| 2016 |
Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC. MOCCASIN: converting MATLAB ODE models to SBML. Bioinformatics (Oxford, England). PMID 26861819 DOI: 10.1093/Bioinformatics/Btw056 |
0.54 |
|
| 2015 |
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics. 12: 731-901. PMID 29220970 DOI: 10.1515/jib-2015-271 |
0.485 |
|
| 2015 |
Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Journal of Integrative Bioinformatics. 12: 382-549. PMID 29220965 DOI: 10.1515/jib-2015-266 |
0.462 |
|
| 2015 |
Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S. Specifications of Standards in Systems and Synthetic Biology. Journal of Integrative Bioinformatics. 12: 1-3. PMID 29220957 DOI: 10.1515/jib-2015-258 |
0.404 |
|
| 2015 |
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics. 12: 271. PMID 26528569 DOI: 10.2390/Biecoll-Jib-2015-271 |
0.561 |
|
| 2015 |
Smith LP, Hucka M, Hoops S, Finney A, Ginkel M, Myers CJ, Moraru I, Liebermeister W. SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. Journal of Integrative Bioinformatics. 12: 268. PMID 26528566 DOI: 10.2390/Biecoll-Jib-2015-268 |
0.502 |
|
| 2015 |
Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Journal of Integrative Bioinformatics. 12: 266. PMID 26528564 DOI: 10.1038/Npre.2010.4959.1 |
0.541 |
|
| 2015 |
Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S. Specifications of Standards in Systems and Synthetic Biology. Journal of Integrative Bioinformatics. 12: 258. PMID 26528556 DOI: 10.2390/Biecoll-Jib-2015-258 |
0.493 |
|
| 2015 |
Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157 |
0.342 |
|
| 2015 |
Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, ... ... Hucka M, et al. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (Oxford, England). PMID 26079347 DOI: 10.1093/Bioinformatics/Btv341 |
0.485 |
|
| 2015 |
Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N. Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. Frontiers in Bioengineering and Biotechnology. 3: 19. PMID 25759811 DOI: 10.3389/Fbioe.2015.00019 |
0.484 |
|
| 2015 |
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, et al. BioModels: ten-year anniversary. Nucleic Acids Research. 43: D542-8. PMID 25414348 DOI: 10.1093/Nar/Gku1181 |
0.525 |
|
| 2015 |
Gomez H, Hucka M, Keating S, Iber D, Sealfon S. MOCCASIN – a tool for converting MATLAB ODE models into reaction-based SBML F1000research. 6. DOI: 10.7490/F1000Research.1098305.1 |
0.378 |
|
| 2014 |
Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, et al. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. Bmc Bioinformatics. 15: 369. PMID 25494900 DOI: 10.1186/S12859-014-0369-Z |
0.531 |
|
| 2013 |
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, ... Hucka M, et al. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. Bmc Systems Biology. 7: 135. PMID 24321545 DOI: 10.1186/1752-0509-7-135 |
0.55 |
|
| 2013 |
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, et al. Path2Models: large-scale generation of computational models from biochemical pathway maps. Bmc Systems Biology. 7: 116. PMID 24180668 DOI: 10.1186/1752-0509-7-116 |
0.534 |
|
| 2013 |
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, ... Hucka M, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/Nbt.2488 |
0.363 |
|
| 2012 |
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, ... Hucka M, et al. The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942)) Nature Biotechnology. 30: 365. DOI: 10.1038/Nbt0412-365C |
0.318 |
|
| 2011 |
Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences. 5: 230-42. PMID 22180826 DOI: 10.4056/Sigs.5279417 |
0.473 |
|
| 2011 |
Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. Bmc Systems Biology. 5: 198. PMID 22172142 DOI: 10.1186/1752-0509-5-198 |
0.424 |
|
| 2011 |
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, ... Hucka M, et al. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology. 7: 543. PMID 22027554 DOI: 10.1038/Msb.2011.77 |
0.505 |
|
| 2011 |
Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M. JSBML: a flexible Java library for working with SBML. Bioinformatics (Oxford, England). 27: 2167-8. PMID 21697129 DOI: 10.1093/Bioinformatics/Btr361 |
0.467 |
|
| 2011 |
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, et al. Minimum Information About a Simulation Experiment (MIASE). Plos Computational Biology. 7: e1001122. PMID 21552546 DOI: 10.1371/Journal.Pcbi.1001122 |
0.643 |
|
| 2011 |
Waltemath D, Swainston N, Lister AL, Bergmann F, Henkel R, Hoops S, Hucka M, Juty N, Keating S, Knuepfer C, Krause F, Laibe C, Liebermeister W, Lloyd C, Misirli G, et al. SBML Level 3 Package Proposal: Annotation Nature Precedings. 6: 1-1. DOI: 10.1038/Npre.2011.5610.1 |
0.516 |
|
| 2010 |
Hucka M, Le Novère N. Software that goes with the flow in systems biology. Bmc Biology. 8: 140. PMID 21114874 DOI: 10.1186/1741-7007-8-140 |
0.461 |
|
| 2010 |
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, ... Hucka M, et al. The BioPAX community standard for pathway data sharing. Nature Biotechnology. 28: 935-42. PMID 20829833 DOI: 10.1038/Nbt.1666 |
0.373 |
|
| 2010 |
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. Bmc Systems Biology. 4: 92. PMID 20587024 DOI: 10.1186/1752-0509-4-92 |
0.591 |
|
| 2010 |
Smith LP, Hucka M. SBML Level 3 Hierarchical Model Composition Nature Precedings. DOI: 10.1038/Npre.2010.5133.1 |
0.375 |
|
| 2010 |
Hucka M, Bergmann F, Hoops S, Keating SM, Sahle S, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate) Nature Precedings. 1-1. DOI: 10.1038/Npre.2010.4123.1 |
0.493 |
|
| 2010 |
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, ... Hucka M, et al. Erratum: Corrigendum: The BioPAX community standard for pathway data sharing Nature Biotechnology. 28: 1308-1308. DOI: 10.1038/Nbt1210-1308C |
0.31 |
|
| 2009 |
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, et al. The Systems Biology Graphical Notation. Nature Biotechnology. 27: 735-41. PMID 19668183 DOI: 10.1038/Nbt.1558 |
0.473 |
|
| 2009 |
Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A. SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. Bioinformatics (Oxford, England). 25: 1455-6. PMID 19307240 DOI: 10.1093/Bioinformatics/Btp170 |
0.468 |
|
| 2009 |
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, et al. Erratum: The Systems Biology Graphical Notation Nature Biotechnology. 27: 864-864. DOI: 10.1038/Nbt0909-864D |
0.301 |
|
| 2008 |
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology. 26: 1155-60. PMID 18846089 DOI: 10.1038/Nbt1492 |
0.349 |
|
| 2008 |
Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: an API library for SBML. Bioinformatics (Oxford, England). 24: 880-1. PMID 18252737 DOI: 10.1093/Bioinformatics/Btn051 |
0.387 |
|
| 2008 |
Novere NL, Moodie S, Sorokin A, Hucka M, Schreiber F, Demir E, Mi H, Matsuoka Y, Wegner K, Kitano H. Systems Biology Graphical Notation: Process Diagram Level 1 Nature Precedings. 1-1. DOI: 10.1038/Npre.2008.2320.1 |
0.465 |
|
| 2007 |
Hucka M, Finney AM, Hoops S, Keating SM, Novère NL. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions Nature Precedings. 2: 1-1. DOI: 10.1038/Npre.2008.2715.1 |
0.566 |
|
| 2007 |
Hucka M. The Systems Biology Markup Language (SBML): Where It’s Been and Where It’s Going Nature Precedings. 1-1. DOI: 10.1038/Npre.2007.21.1 |
0.562 |
|
| 2007 |
Hucka M. Evolving standards and infrastructure for systems biology: SBML, SBGN, and BioModels.net Nature Precedings. 2: 1-1. DOI: 10.1038/Npre.2007.20.1 |
0.565 |
|
| 2007 |
Hucka M, Keating SM. The Systems Biology Markup Language (SBML) Level 2 Version 2 Nature Precedings. 2: 1-1. DOI: 10.1038/Npre.2007.19.1 |
0.573 |
|
| 2007 |
Shapiro BE, Finney A, Hucka M, Bornstein B, Funahashi A, Jouraku A, Keating SM, Le Novère N, Matthews J, Schilstra MJ. SBML models and MathSBML Introduction to Systems Biology. 395-421. DOI: 10.1007/978-1-59745-531-2_20 |
0.364 |
|
| 2006 |
Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W. Rules for modeling signal-transduction systems. Science's Stke : Signal Transduction Knowledge Environment. 2006: re6. PMID 16849649 DOI: 10.1126/Stke.3442006Re6 |
0.455 |
|
| 2006 |
Keating SM, Bornstein BJ, Finney A, Hucka M. SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics (Oxford, England). 22: 1275-7. PMID 16574696 DOI: 10.1093/Bioinformatics/Btl111 |
0.471 |
|
| 2006 |
Schilstra MJ, Li L, Matthews J, Finney A, Hucka M, Le Novère N. CellML2SBML: conversion of CellML into SBML. Bioinformatics (Oxford, England). 22: 1018-20. PMID 16473867 DOI: 10.1093/Bioinformatics/Btl047 |
0.515 |
|
| 2006 |
Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research. 34: D689-91. PMID 16381960 DOI: 10.1093/Nar/Gkj092 |
0.544 |
|
| 2006 |
Sauro HM, Harel D, Kwiatkowska M, Shaffer CA, Uhrmacher AM, Hucka M, Mendes P, Strömback L, Tyson JJ. Challenges for modeling and simulation methods in systems biology Proceedings - Winter Simulation Conference. 1720-1730. DOI: 10.1109/WSC.2006.322948 |
0.312 |
|
| 2005 |
Hucka M, Finney A. Escalating model sizes and complexities call for standardized forms of representation. Molecular Systems Biology. 1: 2005.0011. PMID 16729046 DOI: 10.1038/Msb4100015 |
0.471 |
|
| 2005 |
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology. 23: 1509-15. PMID 16333295 DOI: 10.1038/Nbt1156 |
0.7 |
|
| 2004 |
Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Systems Biology. 1: 41-53. PMID 17052114 DOI: 10.1049/sb:20045008 |
0.497 |
|
| 2004 |
Shapiro BE, Hucka M, Finney A, Doyle J. MathSBML: a package for manipulating SBML-based biological models. Bioinformatics (Oxford, England). 20: 2829-31. PMID 15087311 DOI: 10.1093/Bioinformatics/Bth271 |
0.564 |
|
| 2003 |
Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. Omics : a Journal of Integrative Biology. 7: 355-72. PMID 14683609 DOI: 10.1089/153623103322637670 |
0.495 |
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| 2003 |
Finney A, Hucka M. Systems biology markup language: Level 2 and beyond. Biochemical Society Transactions. 31: 1472-3. PMID 14641091 DOI: 10.1042/Bst0311472 |
0.515 |
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| 2003 |
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (Oxford, England). 19: 524-31. PMID 12611808 DOI: 10.1093/Bioinformatics/Btg015 |
0.541 |
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| 2002 |
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle J, Kitano H. The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 450-61. PMID 11928498 DOI: 10.1142/9789812799623_0042 |
0.39 |
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| 2002 |
Goddard NH, Beeman D, Cannon R, Cornelis H, Gewaltig MO, Hood G, Howell F, Rogister P, Schutter ED, Shankar K, Hucka M. NeuroML for plug and play neuronal modeling Neurocomputing. 44: 1077-1081. DOI: 10.1016/S0925-2312(02)00420-4 |
0.465 |
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| 2001 |
Goddard NH, Hucka M, Howell F, Cornelis H, Shankar K, Beeman D. Towards NeuroML: model description methods for collaborative modelling in neuroscience. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 356: 1209-28. PMID 11545699 DOI: 10.1098/Rstb.2001.0910 |
0.583 |
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