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Herbert M. Sauro - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
Systems Biology, Synthetic Biology
Website:
https://sites.google.com/site/bioindica2016/news-and-updates/speaker-herbert-m-sauro
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Year Citation  Score
2023 Ma S, Fan L, Konanki SA, Liu E, Gennari JH, Smith LP, Hellerstein JL, Sauro HM. VSCode-Antimony: A Source Editor for Building, Analyzing, and Translating Antimony Models. Bioinformatics (Oxford, England). PMID 38096590 DOI: 10.1093/bioinformatics/btad753  0.628
2023 Shin W, Gennari JH, Hellerstein JL, Sauro HM. An automated model annotation system (AMAS) for SBML models. Bioinformatics (Oxford, England). 39. PMID 37882737 DOI: 10.1093/bioinformatics/btad658  0.626
2023 Jardine BE, Smith LP, Sauro HM. MakeSBML: A tool for converting between Antimony and SBML. Arxiv. PMID 37731653  0.316
2023 Shin W, Gennari JH, Hellerstein JL, Sauro HM. An Automated Model Annotation System (AMAS) for SBML Models. Biorxiv : the Preprint Server For Biology. PMID 37503075 DOI: 10.1101/2023.07.19.549722  0.626
2023 Shin J, Porubsky V, Carothers J, Sauro HM. Standards, dissemination, and best practices in systems biology. Current Opinion in Biotechnology. 81: 102922. PMID 37004298 DOI: 10.1016/j.copbio.2023.102922  0.314
2022 Xu J, Jiang J, Sauro HM. SBMLDiagrams: A python package to process and visualize SBML layout and render. Bioinformatics (Oxford, England). PMID 36370074 DOI: 10.1093/bioinformatics/btac730  0.306
2022 Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, ... ... Sauro HM, et al. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research. PMID 35524558 DOI: 10.1093/nar/gkac331  0.682
2021 Smith LP, Bergmann FT, Garny A, Helikar T, Karr J, Nickerson D, Sauro H, Waltemath D, König M. The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. Journal of Integrative Bioinformatics. 18: 20210021. PMID 35330701 DOI: 10.1515/jib-2021-0021  0.535
2021 Welsh C, Nickerson DP, Rampadarath A, Neal ML, Sauro HM, Gennari JH. libOmexMeta: Enabling semantic annotation of models to support FAIR principles. Bioinformatics (Oxford, England). PMID 34132740 DOI: 10.1093/bioinformatics/btab445  0.651
2021 Baig H, Fontanarossa P, Kulkarni V, McLaughlin J, Vaidyanathan P, Bartley B, Bhakta S, Bhatia S, Bissell M, Clancy K, Cox RS, Goñi Moreno A, Gorochowski T, Grunberg R, Lee J, ... ... Sauro H, et al. Synthetic biology open language visual (SBOL Visual) version 2.3. Journal of Integrative Bioinformatics. PMID 34098590 DOI: 10.1515/jib-2020-0045  0.707
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, ... ... Sauro HM, 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  0.544
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  0.407
2020 Baig H, Fontanarossa P, Kulkarni V, McLaughlin J, Vaidyanathan P, Bartley B, Bhatia S, Bhakta S, Bissell M, Clancy K, Cox RS, Moreno AG, Gorochowski T, Grunberg R, Luna A, ... ... Sauro H, et al. Synthetic biology open language visual (SBOL visual) version 2.2. Journal of Integrative Bioinformatics. PMID 32543457 DOI: 10.1515/jib-2020-0014  0.716
2020 Medley JK, Hellerstein J, Sauro HM. libsbmljs-Enabling web-based SBML tools. Bio Systems. 104150. PMID 32339626 DOI: 10.1016/J.Biosystems.2020.104150  0.415
2019 Beal J, Nguyen T, Gorochowski TE, Goñi-Moreno A, Scott-Brown J, McLaughlin JA, Madsen C, Aleritsch B, Bartley B, Bhakta S, Bissell M, Castillo-Hair SM, Clancy K, Luna A, Le Novere N, ... ... Sauro H, et al. Communicating Structure and Function in Synthetic Biology Diagrams. Acs Synthetic Biology. PMID 31348656 DOI: 10.1021/Acssynbio.9B00139  0.745
2019 Madsen C, Goñi Moreno A, P U, Palchick Z, Roehner N, Atallah C, Bartley B, Choi K, Cox RS, Gorochowski T, Grünberg R, Macklin C, McLaughlin J, Meng X, Nguyen T, ... ... Sauro H, et al. Synthetic Biology Open Language (SBOL) Version 2.3. Journal of Integrative Bioinformatics. PMID 31199770 DOI: 10.1515/Jib-2019-0025  0.824
2019 Madsen C, Goni Moreno A, Palchick Z, P U, Roehner N, Bartley B, Bhatia S, Bhakta S, Bissell M, Clancy K, Cox RS, Gorochowski T, Grunberg R, Luna A, McLaughlin J, ... ... Sauro H, et al. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. Journal of Integrative Bioinformatics. PMID 31199768 DOI: 10.1515/jib-2018-0101  0.717
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, ... ... Sauro HM, et al. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. PMID 30462164 DOI: 10.1093/Bib/Bby087  0.644
2018 Bartley B, Choi K, Samineni M, Zundel Z, Nguyen T, Myers CJ, Sauro H. pySBOL: A Python Package for Genetic Design Automation and Standardization. Acs Synthetic Biology. PMID 30424601 DOI: 10.1021/Acssynbio.8B00336  0.762
2018 Choi K, Medley JK, König M, Stocking K, Smith L, Gu S, Sauro HM. Tellurium: An extensible python-based modeling environment for systems and synthetic biology. Bio Systems. PMID 30053414 DOI: 10.1016/J.Biosystems.2018.07.006  0.414
2018 Medley JK, Choi K, König M, Smith L, Gu S, Hellerstein J, Sealfon SC, Sauro HM. Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology. Plos Computational Biology. 14: e1006220. PMID 29906293 DOI: 10.1371/Journal.Pcbi.1006220  0.405
2018 Bedaso Y, Bergmann FT, Choi K, Medley K, Sauro HM. A Portable Structural Analysis Library for Reaction Networks. Bio Systems. PMID 29857031 DOI: 10.1016/J.Biosystems.2018.05.008  0.556
2018 Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, ... ... Sauro H, et al. Synthetic Biology Open Language (SBOL) Version 2.2.0. Journal of Integrative Bioinformatics. PMID 29605823 DOI: 10.1515/Jib-2018-0001  0.815
2018 Cox RS, Madsen C, McLaughlin J, Nguyen T, Roehner N, Bartley B, Bhatia S, Bissell M, Clancy K, Gorochowski T, Grünberg R, Luna A, Le Novere N, Pocock M, Sauro H, et al. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. Journal of Integrative Bioinformatics. PMID 29549707 DOI: 10.1515/Jib-2017-0074  0.739
2017 Bartley BA, Kim K, Medley JK, Sauro HM. Synthetic Biology: Engineering Living Systems from Biophysical Principles. Biophysical Journal. 112: 1050-1058. PMID 28355534 DOI: 10.1016/J.Bpj.2017.02.013  0.734
2017 Sauro HM. Control and regulation of pathways via negative feedback. Journal of the Royal Society, Interface. 14. PMID 28202588 DOI: 10.1098/Rsif.2016.0848  0.306
2017 Cox Iii RS, McLaughlin JA, Gruenberg R, Beal J, Wipat A, Sauro H. A Visual Language for Protein Design. Acs Synthetic Biology. PMID 28173698 DOI: 10.1021/Acssynbio.6B00286  0.375
2016 Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, ... ... Sauro H, et al. Synthetic Biology Open Language (SBOL) Version 2.1.0. Journal of Integrative Bioinformatics. 13: 30-132. PMID 29215992 DOI: 10.1515/jib-2016-291  0.814
2016 Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, ... ... Sauro H, et al. Synthetic Biology Open Language (SBOL) Version 2.1.0. Journal of Integrative Bioinformatics. 13: 291. PMID 28187407 DOI: 10.2390/biecoll-jib-2016-291  0.814
2016 Choi K, Smith LP, Medley JK, Sauro HM. phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. Journal of Bioinformatics and Computational Biology. 1650035. PMID 27774871 DOI: 10.1142/S0219720016500359  0.35
2016 Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Gruenberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, ... ... Sauro H, et al. Sharing Structure and Function in Biological Design with SBOL 2.0. Acs Synthetic Biology. PMID 27111421 DOI: 10.1021/Acssynbio.5B00215  0.809
2016 Misirli G, Hallinan J, Pocock M, Lord P, McLaughlin JA, Sauro H, Wipat A. Data Integration and Mining for Synthetic Biology Design. Acs Synthetic Biology. PMID 27110921 DOI: 10.1021/Acssynbio.5B00295  0.427
2015 Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics. 12: 902-991. PMID 29220967 DOI: 10.1515/jib-2015-272  0.82
2015 Quinn JY, Cox RS, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari AJ, McLaughlin JA, Myers CJ, P U, ... ... Sauro HM, et al. SBOL Visual: A Graphical Language for Genetic Designs. Plos Biology. 13: e1002310. PMID 26633141 DOI: 10.1371/Journal.Pbio.1002310  0.785
2015 Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics. 12: 272. PMID 26528570 DOI: 10.1515/Jib-2016-291  0.827
2015 Kim KH, Choi K, Bartley B, Sauro HM. Controlling E. coli Gene Expression Noise. Ieee Transactions On Biomedical Circuits and Systems. PMID 26372647 DOI: 10.1109/Tbcas.2015.2461135  0.679
2015 Somogyi ET, Bouteiller JM, Glazier JA, König M, Medley JK, Swat MH, Sauro HM. libRoadRunner: A High Performance SBML Simulation and Analysis Library. Bioinformatics (Oxford, England). PMID 26085503 DOI: 10.1093/Bioinformatics/Btv363  0.377
2015 Galdzicki M, Kahl LJ, Endy D, Sauro HM. Reply to Intellectual property issues and synthetic biology standards. Nature Biotechnology. 33: 25. PMID 25574632 DOI: 10.1038/Nbt.3114  0.756
2015 Myers C, Clancy K, Misirli G, Oberortner E, Pocock M, Quinn J, Roehner N, Sauro HM. The synthetic biology open language. Methods in Molecular Biology (Clifton, N.J.). 1244: 323-36. PMID 25487105 DOI: 10.1007/978-1-4939-1878-2_16  0.462
2015 Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ. Proposed data model for the next version of the synthetic biology open language. Acs Synthetic Biology. 4: 57-71. PMID 24896221 DOI: 10.1021/Sb500176H  0.415
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  0.578
2014 Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. A reappraisal of how to build modular, reusable models of biological systems. Plos Computational Biology. 10: e1003849. PMID 25275523 DOI: 10.1371/Journal.Pcbi.1003849  0.585
2014 Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, ... ... Sauro HM, et al. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology. 32: 545-50. PMID 24911500 DOI: 10.1038/Nbt.2891  0.78
2014 Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Dream Six and Seven Parameter Estimation Consortium, Sauro HM, et al. Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. Bmc Systems Biology. 8: 13. PMID 24507381 DOI: 10.1186/1752-0509-8-13  0.577
2014 Smith LP, Butterworth E, Bassingthwaighte JB, Sauro HM. SBML and CellML translation in antimony and JSim. Bioinformatics (Oxford, England). 30: 903-7. PMID 24215024 DOI: 10.1093/Bioinformatics/Btt641  0.373
2014 Neal ML, Galdzicki M, Gallimore JT, Sauro HM. A C library for retrieving specific reactions from the BioModels database. Bioinformatics (Oxford, England). 30: 129-30. PMID 24078714 DOI: 10.1093/Bioinformatics/Btt567  0.774
2014 Myers CJ, Sauro H, Wipat A. Introduction to the special issue on computational synthetic biology Acm Journal On Emerging Technologies in Computing Systems. 11. DOI: 10.1145/2668126  0.37
2013 Sleight SC, Sauro HM. Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits. Acs Synthetic Biology. 2: 519-28. PMID 24004180 DOI: 10.1021/Sb400055H  0.3
2013 Sleight SC, Sauro HM. Randomized BioBrick assembly: a novel DNA assembly method for randomizing and optimizing genetic circuits and metabolic pathways. Acs Synthetic Biology. 2: 506-18. PMID 23841916 DOI: 10.1021/Sb4000542  0.304
2013 Sauro HM, Kim KH. Synthetic biology: It's an analog world. Nature. 497: 572-3. PMID 23676675 DOI: 10.1038/Nature12246  0.333
2012 Chandran D, Sauro HM. Hierarchical modeling for synthetic biology. Acs Synthetic Biology. 1: 353-64. PMID 23651289 DOI: 10.1021/Sb300033Q  0.64
2012 Copeland WB, Bartley BA, Chandran D, Galdzicki M, Kim KH, Sleight SC, Maranas CD, Sauro HM. Computational tools for metabolic engineering. Metabolic Engineering. 14: 270-80. PMID 22629572 DOI: 10.1016/J.Ymben.2012.03.001  0.753
2012 Sleight SC, Sauro HM. Design and construction of a prototype CMY (Cyan-Magenta-Yellow) genetic circuit as a mutational readout device to measure evolutionary stability dynamics and determine design principles for robust synthetic systems Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 481-488. DOI: 10.7551/978-0-262-31050-5-Ch063  0.301
2012 Neal ML, Sauro HM. SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database Nature Precedings. 7: 1-1. DOI: 10.1038/Npre.2012.7028.1  0.328
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, ... ... Sauro HM, et al. Minimum Information About a Simulation Experiment (MIASE). Plos Computational Biology. 7: e1001122. PMID 21552546 DOI: 10.1371/Journal.Pcbi.1001122  0.538
2011 Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. Standard biological parts knowledgebase. Plos One. 6: e17005. PMID 21390321 DOI: 10.1371/Journal.Pone.0017005  0.78
2011 Peccoud J, Anderson JC, Chandran D, Densmore D, Galdzicki M, Lux MW, Rodriguez CA, Stan GB, Sauro HM. Essential information for synthetic DNA sequences. Nature Biotechnology. 29: 22; discussion 22-3. PMID 21221092 DOI: 10.1038/Nbt.1753  0.755
2010 Chandran D, Bergmann FT, Sauro HM. Computer-aided design of biological circuits using TinkerCell. Bioengineered Bugs. 1: 274-81. PMID 21327060 DOI: 10.4161/Bbug.1.4.12506  0.72
2010 Sleight SC, Bartley BA, Lieviant JA, Sauro HM. Designing and engineering evolutionary robust genetic circuits. Journal of Biological Engineering. 4: 12. PMID 21040586 DOI: 10.1186/1754-1611-4-12  0.688
2010 Shen SY, Bergmann F, Sauro HM. SBML2TikZ: supporting the SBML render extension in LaTeX. Bioinformatics (Oxford, England). 26: 2794-5. PMID 20829443 DOI: 10.1093/Bioinformatics/Btq512  0.602
2010 Sleight SC, Bartley BA, Lieviant JA, Sauro HM. In-Fusion BioBrick assembly and re-engineering. Nucleic Acids Research. 38: 2624-36. PMID 20385581 DOI: 10.1093/Nar/Gkq179  0.709
2010 Sauro HM, Bergmann FT. Software Tools for Systems Biology Systems Biomedicine. 289-314. DOI: 10.1016/B978-0-12-372550-9.00012-2  0.485
2009 Chandran D, Bergmann FT, Sauro HM. TinkerCell: modular CAD tool for synthetic biology. Journal of Biological Engineering. 3: 19. PMID 19874625 DOI: 10.1186/1754-1611-3-19  0.735
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, ... ... Sauro H, et al. The Systems Biology Graphical Notation. Nature Biotechnology. 27: 735-41. PMID 19668183 DOI: 10.1038/Nbt.1558  0.453
2009 Smith LP, Bergmann FT, Chandran D, Sauro HM. Antimony: a modular model definition language. Bioinformatics (Oxford, England). 25: 2452-4. PMID 19578039 DOI: 10.1093/Bioinformatics/Btp401  0.712
2008 Chandran D, Copeland WB, Sleight SC, Sauro HM. Mathematical modeling and synthetic biology. Drug Discovery Today. Disease Models. 5: 299-309. PMID 27840651 DOI: 10.1016/J.Ddmod.2009.07.002  0.642
2008 Sauro HM, Bergmann FT. Standards and ontologies in computational systems biology. Essays in Biochemistry. 45: 211-22. PMID 18793134 DOI: 10.1042/Bse0450211  0.613
2008 Bergmann FT, Sauro HM. Comparing simulation results of SBML capable simulators. Bioinformatics (Oxford, England). 24: 1963-5. PMID 18579569 DOI: 10.1093/Bioinformatics/Btn319  0.497
2008 Chandran D, Copeland WB, Sleight SC, Sauro HM. Mathematical modeling and synthetic biology Drug Discovery Today: Disease Models. 5: 299-309. DOI: 10.1016/j.ddmod.2009.07.002  0.768
2007 Entus R, Aufderheide B, Sauro HM. Design and implementation of three incoherent feed-forward motif based biological concentration sensors. Systems and Synthetic Biology. 1: 119-28. PMID 19003446 DOI: 10.1007/S11693-007-9008-6  0.321
2007 Vallabhajosyula RR, Sauro HM. Stochastic simulation GUI for biochemical networks. Bioinformatics (Oxford, England). 23: 1859-61. PMID 17586553 DOI: 10.1093/Bioinformatics/Btm231  0.352
2006 Deckard A, Bergmann FT, Sauro HM. Supporting the SBML layout extension. Bioinformatics (Oxford, England). 22: 2966-7. PMID 17038346 DOI: 10.1093/Bioinformatics/Btl520  0.581
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  0.394
2006 Vallabhajosyula RR, Chickarmane V, Sauro HM. Conservation analysis of large biochemical networks. Bioinformatics (Oxford, England). 22: 346-53. PMID 16317075 DOI: 10.1093/Bioinformatics/Bti800  0.324
2006 Bergmann FT, Vallabhajosyula RR, Sauro HM. Computational tools for modeling protein networks Current Proteomics. 3: 181-197. DOI: 10.2174/157016406779475380  0.52
2006 Bergmann FT, Sauro HM. SBW - A modular framework for systems biology Proceedings - Winter Simulation Conference. 1637-1645. DOI: 10.1109/WSC.2006.322938  0.441
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  0.375
2005 Chickarmane V, Paladugu SR, Bergmann F, Sauro HM. Bifurcation discovery tool. Bioinformatics (Oxford, England). 21: 3688-90. PMID 16081475 DOI: 10.1093/Bioinformatics/Bti603  0.558
2004 Sauro HM, Ingalls B. Conservation analysis in biochemical networks: computational issues for software writers. Biophysical Chemistry. 109: 1-15. PMID 15059656 DOI: 10.1016/J.Bpc.2003.08.009  0.339
2004 Sauro H. The Computational Versatility of Proteomic Signaling Networks Current Proteomics. 1: 67-81. DOI: 10.2174/1570164043488315  0.314
2004 Rao CV, Sauro HM, Arkin AP. Putting the “Control” in Metabolic Control Analysis Ifac Proceedings Volumes. 37: 1001-1006. DOI: 10.1016/S1474-6670(17)31939-0  0.31
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  0.444
2003 Ingalls BP, Sauro HM. Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. Journal of Theoretical Biology. 222: 23-36. PMID 12699732 DOI: 10.1016/S0022-5193(03)00011-0  0.323
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  0.682
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  0.319
1997 Woods JH, Sauro HM. Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions. Computer Applications in the Biosciences : Cabios. 13: 123-30. PMID 9146958 DOI: 10.1093/Bioinformatics/13.2.123  0.307
1995 Sauro HM, Barrett J. In vitro control analysis of an enzyme system: experimental and analytical developments. Molecular and Cellular Biochemistry. 145: 141-50. PMID 7675034 DOI: 10.1007/Bf00935486  0.301
1994 Sauro HM. Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channelling. Bio Systems. 33: 55-67. PMID 7803701 DOI: 10.1016/0303-2647(94)90061-2  0.302
1993 Sauro HM. SCAMP: a general-purpose simulator and metabolic control analysis program. Computer Applications in the Biosciences : Cabios. 9: 441-50. PMID 8402211 DOI: 10.1093/Bioinformatics/9.4.441  0.406
1991 Sauro HM, Fell DA. SCAMP: A metabolic simulator and control analysis program Mathematical and Computer Modelling. 15: 15-28. DOI: 10.1016/0895-7177(91)90038-9  0.606
1990 Sauro HM, Kacser H. Enzyme-enzyme interactions and control analysis. 2. The case of non-independence: heterologous associations. European Journal of Biochemistry / Febs. 187: 493-500. PMID 2406133 DOI: 10.1111/J.1432-1033.1990.Tb15330.X  0.631
1990 Kacser H, Sauro HM, Acerenza L. Enzyme-enzyme interactions and control analysis. 1. The case of non-additivity: monomer-oligomer associations. European Journal of Biochemistry / Febs. 187: 481-91. PMID 2406132 DOI: 10.1111/J.1432-1033.1990.Tb15329.X  0.764
1990 Fell DA, Sauro HM. Metabolic control analysis. The effects of high enzyme concentrations. European Journal of Biochemistry / Febs. 192: 183-7. PMID 2401290 DOI: 10.1111/J.1432-1033.1990.Tb19212.X  0.569
1990 Fell DA, Sauro HM. Metabolic control analysis by computer: progress and prospects. Biomedica Biochimica Acta. 49: 811-6. PMID 2082924  0.534
1989 Acerenza L, Sauro HM, Kacser H. Control analysis of time-dependent metabolic systems. Journal of Theoretical Biology. 137: 423-44. PMID 2626059 DOI: 10.1016/S0022-5193(89)80038-4  0.769
1987 Sauro HM, Small JR, Fell DA. Metabolic control and its analysis. Extensions to the theory and matrix method. European Journal of Biochemistry / Febs. 165: 215-21. PMID 3569295 DOI: 10.1111/J.1432-1033.1987.Tb11214.X  0.57
1987 SAURO HM, FELL DA. The role of co-operativity in metabolism Biochemical Society Transactions. 15: 234-235. DOI: 10.1042/Bst0150234  0.535
1986 FELL DA, SAURO HM. Non-equilibrium/equilibrium reactions: which controls? Biochemical Society Transactions. 14: 624-625. DOI: 10.1042/Bst0140624  0.526
1985 Fell DA, Sauro HM. Metabolic control and its analysis. Additional relationships between elasticities and control coefficients. European Journal of Biochemistry / Febs. 148: 555-61. PMID 3996393 DOI: 10.1111/J.1432-1033.1985.Tb08876.X  0.583
1985 FELL DA, SAURO HM. Substrate cycles: do they really cause amplification? Biochemical Society Transactions. 13: 762-763. DOI: 10.1042/Bst0130762  0.521
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