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1.

Design patterns of biological cells.

Andrews, Steven S; Wiley, H Steven; Sauro, Herbert M.

Bioessays ; 46(3): e2300188, 2024 03.

Article in English | MEDLINE | ID: mdl-38247191

2.

SBMLDiagrams: a python package to process and visualize SBML layout and render.

Xu, Jin; Jiang, Jessie; Sauro, Herbert M.

Bioinformatics ; 39(1)2023 01 01.

Article in English | MEDLINE | ID: mdl-36370074

3.

libRoadRunner 2.0: a high performance SBML simulation and analysis library.

Welsh, Ciaran; Xu, Jin; Smith, Lucian; König, Matthias; Choi, Kiri; Sauro, Herbert M.

Bioinformatics ; 39(1)2023 01 01.

Article in English | MEDLINE | ID: mdl-36478036

4.

An automated model annotation system (AMAS) for SBML models.

Shin, Woosub; Gennari, John H; Hellerstein, Joseph L; Sauro, Herbert M.

Bioinformatics ; 39(11)2023 11 01.

Article in English | MEDLINE | ID: mdl-37882737

5.

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.

Ma, Steve; Fan, Longxuan; Konanki, Sai Anish; Liu, Eva; Gennari, John H; Smith, Lucian P; Hellerstein, Joseph L; Sauro, Herbert M.

Bioinformatics ; 39(12)2023 12 01.

Article in English | MEDLINE | ID: mdl-38096590

6.

Tissue Forge: Interactive biological and biophysics simulation environment.

Sego, T J; Sluka, James P; Sauro, Herbert M; Glazier, James A.

PLoS Comput Biol ; 19(10): e1010768, 2023 Oct.

Article in English | MEDLINE | ID: mdl-37871133

7.

Publishing reproducible dynamic kinetic models.

Porubsky, Veronica; Smith, Lucian; Sauro, Herbert M.

Brief Bioinform ; 22(3)2021 05 20.

Article in English | MEDLINE | ID: mdl-32793969

8.

SBbadger: biochemical reaction networks with definable degree distributions.

Kochen, Michael A; Wiley, H Steven; Feng, Song; Sauro, Herbert M.

Bioinformatics ; 38(22): 5064-5072, 2022 11 15.

Article in English | MEDLINE | ID: mdl-36111865

9.

Adapting modeling and simulation credibility standards to computational systems biology.

Tatka, Lillian T; Smith, Lucian P; Hellerstein, Joseph L; Sauro, Herbert M.

J Transl Med ; 21(1): 501, 2023 07 26.

Article in English | MEDLINE | ID: mdl-37496031

10.

libOmexMeta: enabling semantic annotation of models to support FAIR principles.

Welsh, Ciaran; Nickerson, David P; Rampadarath, Anand; Neal, Maxwell L; Sauro, Herbert M; Gennari, John H.

Bioinformatics ; 37(24): 4898-4900, 2021 12 11.

Article in English | MEDLINE | ID: mdl-34132740

11.

Harmonizing semantic annotations for computational models in biology.

Neal, Maxwell Lewis; König, Matthias; Nickerson, David; Misirli, Göksel; Kalbasi, Reza; Dräger, Andreas; Atalag, Koray; Chelliah, Vijayalakshmi; Cooling, Michael T; Cook, Daniel L; Crook, Sharon; de Alba, Miguel; Friedman, Samuel H; Garny, Alan; Gennari, John H; Gleeson, Padraig; Golebiewski, Martin; Hucka, Michael; Juty, Nick; Myers, Chris; Olivier, Brett G; Sauro, Herbert M; Scharm, Martin; Snoep, Jacky L; Touré, Vasundra; Wipat, Anil; Wolkenhauer, Olaf; Waltemath, Dagmar.

Brief Bioinform ; 20(2): 540-550, 2019 03 22.

Article in English | MEDLINE | ID: mdl-30462164

12.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Keating, Sarah M; Waltemath, Dagmar; König, Matthias; Zhang, Fengkai; Dräger, Andreas; Chaouiya, Claudine; Bergmann, Frank T; Finney, Andrew; Gillespie, Colin S; Helikar, Tomás; Hoops, Stefan; Malik-Sheriff, Rahuman S; Moodie, Stuart L; Moraru, Ion I; Myers, Chris J; Naldi, Aurélien; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Swat, Maciej J; Thieffry, Denis; Watanabe, Leandro; Wilkinson, Darren J; Blinov, Michael L; Begley, Kimberly; Faeder, James R; Gómez, Harold F; Hamm, Thomas M; Inagaki, Yuichiro; Liebermeister, Wolfram; Lister, Allyson L; Lucio, Daniel; Mjolsness, Eric; Proctor, Carole J; Raman, Karthik; Rodriguez, Nicolas; Shaffer, Clifford A; Shapiro, Bruce E; Stelling, Joerg; Swainston, Neil; Tanimura, Naoki; Wagner, John; Meier-Schellersheim, Martin; Sauro, Herbert M; Palsson, Bernhard; Bolouri, Hamid; Kitano, Hiroaki; Funahashi, Akira; Hermjakob, Henning.

Mol Syst Biol ; 16(8): e9110, 2020 08.

Article in English | MEDLINE | ID: mdl-32845085

13.

A compiler for biological networks on silicon chips.

Medley, J Kyle; Teo, Jonathan; Woo, Sung Sik; Hellerstein, Joseph; Sarpeshkar, Rahul; Sauro, Herbert M.

PLoS Comput Biol ; 16(9): e1008063, 2020 09.

Article in English | MEDLINE | ID: mdl-32966274

14.

A brief note on the properties of linear pathways.

Sauro, Herbert M.

Biochem Soc Trans ; 48(4): 1379-1395, 2020 08 28.

Article in English | MEDLINE | ID: mdl-32830848

15.

Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

Medley, J Kyle; Choi, Kiri; König, Matthias; Smith, Lucian; Gu, Stanley; Hellerstein, Joseph; Sealfon, Stuart C; Sauro, Herbert M.

PLoS Comput Biol ; 14(6): e1006220, 2018 06.

Article in English | MEDLINE | ID: mdl-29906293

16.

SBOL Visual: A Graphical Language for Genetic Designs.

Quinn, Jacqueline Y; Cox, Robert Sidney; Adler, Aaron; Beal, Jacob; Bhatia, Swapnil; Cai, Yizhi; Chen, Joanna; Clancy, Kevin; Galdzicki, Michal; Hillson, Nathan J; Le Novère, Nicolas; Maheshwari, Akshay J; McLaughlin, James Alastair; Myers, Chris J; P, Umesh; Pocock, Matthew; Rodriguez, Cesar; Soldatova, Larisa; Stan, Guy-Bart V; Swainston, Neil; Wipat, Anil; Sauro, Herbert M.

PLoS Biol ; 13(12): e1002310, 2015 Dec.

Article in English | MEDLINE | ID: mdl-26633141

17.

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M.

Biophys J ; 112(6): 1050-1058, 2017 Mar 28.

Article in English | MEDLINE | ID: mdl-28355534

18.

libRoadRunner: a high performance SBML simulation and analysis library.

Somogyi, Endre T; Bouteiller, Jean-Marie; Glazier, James A; König, Matthias; Medley, J Kyle; Swat, Maciej H; Sauro, Herbert M.

Bioinformatics ; 31(20): 3315-21, 2015 Oct 15.

Article in English | MEDLINE | ID: mdl-26085503

19.

Improving reproducibility in computational biology research.

Papin, Jason A; Mac Gabhann, Feilim; Sauro, Herbert M; Nickerson, David; Rampadarath, Anand.

PLoS Comput Biol ; 16(5): e1007881, 2020 05.

Article in English | MEDLINE | ID: mdl-32427998

20.

SBML and CellML translation in antimony and JSim.

Smith, Lucian P; Butterworth, Erik; Bassingthwaighte, James B; Sauro, Herbert M.

Bioinformatics ; 30(7): 903-7, 2014 Apr 01.

Article in English | MEDLINE | ID: mdl-24215024

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