An Overview of CellML 1.1, a Biological Model Description Language. - Autumn A. Cuellar; Catherine M. Lloyd; Poul M. F. Nielsen; David P. Bullivant; David P. Nickerson; Peter J. Hunter (Simul., 2003)

Multi-scale and multi-physics visualization. - Shane Blackett; David P. Bullivant; David P. Nickerson; Peter J. Hunter (SIGGRAPH Posters, 2005)

A Computational Model of Cardiac Electromechanics. - David P. Nickerson; Steven A. Niederer; Carey Stevens; Martyn P. Nash; Peter J. Hunter (EMBC, 2006)

Toward a Curated CellML Model Repository. - David P. Nickerson; Carey Stevens; Matt D. B. Halstead; Peter J. Hunter; Poul M. F. Nielsen (EMBC, 2006)

Computational multiscale modeling in the IUPS Physiome Project: Modeling cardiac electromechanics. - David P. Nickerson; Martyn P. Nash; Poul M. F. Nielsen; Nicolas Smith; Peter J. Hunter (IBM J. Res. Dev., 2006)

Reference descriptions of cellular electrophysiology models. - David P. Nickerson; Alberto Corrias; Martin L. Buist (Bioinform., 2008)

An overview of the CellML API and its implementation. - Andrew K. Miller; Justin Marsh; Adam Reeve; Alan Garny; Randall Britten; Matt D. B. Halstead; Jonathan Cooper; David P. Nickerson; Poul M. F. Nielsen (BMC Bioinform., 2010)

The Physiome Model Repository 2. - Tommy Yu; Catherine M. Lloyd; David P. Nickerson; Mike T. Cooling; Andrew K. Miller; Alan Garny; Jonna R. Terkildsen; James R. Lawson; Randall Britten; Peter J. Hunter; Poul M. F. Nielsen (Bioinform., 2011)

Revision history aware repositories of computational models of biological systems. - Andrew K. Miller; Tommy Yu; Randall Britten; Mike T. Cooling; James R. Lawson; Dougal Cowan; Alan Garny; Matt D. B. Halstead; Peter J. Hunter; David P. Nickerson; Geoff Nunns; Sarala M. Wimalaratne; et al. (BMC Bioinform., 2011)

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. - Dagmar Waltemath; Richard R. Adams; Frank T. Bergmann; Michael Hucka; Fedor A. Kolpakov; Andrew K. Miller; Ion I. Moraru; David P. Nickerson; Sven Sahle; Jacky L. Snoep; Nicolas Le Novère (BMC Syst. Biol., 2011)

Minimum Information About a Simulation Experiment (MIASE). - Dagmar Waltemath; Richard R. Adams; Daniel A. Beard; Frank T. Bergmann; Upinder S. Bhalla; Randall Britten; Vijayalakshmi Chelliah; Mike T. Cooling; Jonathan Cooper; Edmund J. Crampin; Alan Garny; Stefan Hoops; et al. (PLoS Comput. Biol., 2011)

Standards and tools supporting collaborative development of the virtual physiological human. - David P. Nickerson; Alan Garny; Poul M. F. Nielsen; Peter J. Hunter (EMBC, 2013)

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. - Frank T. Bergmann; Richard R. Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (BMC Bioinform., 2014)

COMBINE archive: One File To Share Them All. - Frank T. Bergmann; Richard Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (CoRR, 2014)

Physiome Repository. - Tommy Yu; Randall D. Britten; David P. Nickerson; Peter J. Hunter; Poul M. F. Nielsen (Encyclopedia of Computational Neuroscience, 2014)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. - Frank T. Bergmann; Jonathan Cooper; Nicolas Le Novère; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2015)

The CellML 1.1 Specification. - Autumn A. Cuellar; Warren Hedley; Melanie Nelson; Catherine M. Lloyd; Matt D. B. Halstead; David P. Bullivant; David P. Nickerson; Peter J. Hunter; Poul M. F. Nielsen (J. Integr. Bioinform., 2015)

Specifications of Standards in Systems and Synthetic Biology. - Falk Schreiber; Gary D. Bader; Martin Golebiewski; Michael Hucka; Benjamin Kormeier; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath; Stephan Weise (J. Integr. Bioinform., 2015)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. - Falk Schreiber; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath (J. Integr. Bioinform., 2016)

Introducing the Physiome Journal: Improving Reproducibility, Reuse, and Discovery of Computational Models. - David Phillip Nickerson; Peter John Hunter (eScience, 2017)

A brief history of COMBINE. - Chris J. Myers; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; David P. Nickerson; Falk Schreiber; Dagmar Waltemath (WSC, 2017)

SED-ML web tools: generate, modify and export standard-compliant simulation studies. - Frank T. Bergmann; David P. Nickerson; Dagmar Waltemath; Martin Scharm (Bioinform., 2017)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). - Frank T. Bergmann; Jonathan Cooper; Matthias König 003; Ion I. Moraru; David P. Nickerson; Nicolas Le Novère; Brett G. Olivier; Sven Sahle; Lucian P. Smith; Dagmar Waltemath (J. Integr. Bioinform., 2018)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. - Falk Schreiber; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath (J. Integr. Bioinform., 2018)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

Community-driven roadmap for integrated disease maps. - Marek Ostaszewski; Stephan Gebel; Inna Kuperstein; Alexander Mazein; Andrei Yu. Zinovyev; Ugur Dogrusoz; Jan Hasenauer; Ronan M. T. Fleming; Nicolas Le Novère; Piotr Gawron; Thomas S. Ligon; Anna Niarakis; et al. (Briefings Bioinform., 2019)

Model annotation and discovery with the Physiome Model Repository. - Dewan M. Sarwar; Reza Kalbasi; John H. Gennari; Brian E. Carlson; Maxwell Lewis Neal; Bernard de Bono; Koray Atalag; Peter J. Hunter; David P. Nickerson (BMC Bioinform., 2019)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. - Falk Schreiber; Björn Sommer 001; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2019)

CellML 2.0. - Michael Clerx; Michael T. Cooling; Jonathan Cooper; Alan Garny; Keri R. Moyle; David P. Nickerson; Poul M. F. Nielsen; Hugh Sorby (J. Integr. Bioinform., 2020)

Open modeling and exchange (OMEX) metadata specification version 1.0. - Maxwell Lewis Neal; John H. Gennari; Dagmar Waltemath; David P. Nickerson; Matthias König 003 (J. Integr. Bioinform., 2020)

Specifications of standards in systems and synthetic biology: status and developments in 2020. - Falk Schreiber; Björn Sommer 001; Tobias Czauderna; Martin Golebiewski; Thomas E. Gorochowski; Michael Hucka; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2020)

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). - Dagmar Waltemath; Martin Golebiewski; Michael L. Blinov; Padraig Gleeson; Henning Hermjakob; Michael Hucka; Esther Thea Inau; Sarah M. Keating; Matthias König 003; Olga Krebs; Rahuman S. Malik-Sheriff; David P. Nickerson; et al. (J. Integr. Bioinform., 2020)

Improving reproducibility in computational biology research. - Jason A. Papin; Feilim Mac Gabhann; Herbert M. Sauro; David P. Nickerson; Anand K. Rampadarath (PLoS Comput. Biol., 2020)

libOmexMeta: enabling semantic annotation of models to support FAIR principles. - Ciaran M. Welsh; David P. Nickerson; Anand K. Rampadarath; Maxwell Lewis Neal; Herbert M. Sauro; John H. Gennari (Bioinform., 2021)

OMEX metadata specification (version 1.2). - John H. Gennari; Matthias König 003; Goksel Misirli; Maxwell Lewis Neal; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2021)

Specifications of standards in systems and synthetic biology: status and developments in 2021. - Falk Schreiber; Padraig Gleeson; Martin Golebiewski; Thomas E. Gorochowski; Michael Hucka; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath (J. Integr. Bioinform., 2021)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2021)

Hierarchical semantic composition of biosimulation models using bond graphs. - Niloofar Shahidi; Michael Pan; Soroush Safaei; Kenneth Tran; Edmund J. Crampin; David P. Nickerson (PLoS Comput. Biol., 2021)

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. - Anna Niarakis; Dagmar Waltemath; James A. Glazier; Falk Schreiber; Sarah M. Keating; David P. Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomás Helikar; Sylvain Soliman; et al. (Briefings Bioinform., 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

PhysioMed: A Semantic Web based Framework for Linking Healthcare Information with Computational Physiology Models. - Reza Kalbasi; David P. Nickerson; Koray Atalag (BCB, 2023)

Vision for the 12 LABOURS Digital Twin Platform. - Thiranja P. Babarenda Gamage; Ayah Elsayed; Chinchien Lin; Alan Wu; Yuan Feng; Jianwei Yu; Linkun Gao; Savindi Wijenayaka; Martyn P. Nash; Anthony J. Doyle; David P. Nickerson (EMBC, 2023)

Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE). - Yuda Munarko; Anand K. Rampadarath; David P. Nickerson (F1000Research, 2023)

CellML 2.0.1. - Michael Clerx; Michael T. Cooling; Jonathan Cooper; Alan Garny; Keri R. Moyle; David P. Nickerson; Poul M. F. Nielsen; Hugh Sorby (J. Integr. Bioinform., 2023)

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. - Matthias König 003; Padraig Gleeson; Martin Golebiewski; Thomas E. Gorochowski; Michael Hucka; Sarah M. Keating; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath; Falk Schreiber (J. Integr. Bioinform., 2023)

CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities. - Yuda Munarko; Anand K. Rampadarath; David P. Nickerson (Frontiers Bioinform., 2023)

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. - Martin Golebiewski; Gary D. Bader; Padraig Gleeson; Thomas E. Gorochowski; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath; Falk Schreiber (J. Integr. Bioinform., 2024)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2024)