World's Best Scientists 2026 revealed!

D-Index & Metrics

Computer Science

D-Index
46
Citations
14294
World Ranking
6682
National Ranking
2949

Research.com Recognitions

  • 2020 - Fellow of the Indian National Academy of Engineering (INAE)

Overview

Herbert M. Sauro is affiliated with the University of Washington in the United States. Their research primarily falls within Biochemistry, Genetics and Molecular Biology, with a significant focus on Molecular Biology. Additional subfields of study include Information Systems and Management, Biophysics, Artificial Intelligence, and Management Science and Operations Research.

The main topics covered in their work encompass Gene Regulatory Network Analysis, Microbial Metabolic Engineering and Bioproduction, Bioinformatics and Genomic Networks, Scientific Computing and Data Management, Genetics, Bioinformatics and Biomedical Research, Cell Image Analysis Techniques, and Protein Structure and Dynamics.

Recent papers by Herbert M. Sauro include:

  • SBML Level 3: an extensible format for the exchange and reuse of biological models, 2020, Molecular Systems Biology
  • Best Practices for Making Reproducible Biochemical Models, 2020, Cell Systems
  • libRoadRunner 2.0: a high performance SBML simulation and analysis library, 2022, Bioinformatics
  • Improving reproducibility in computational biology research, 2020, PLoS Computational Biology
  • The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE), 2020, Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics

Frequent co-authors collaborating with Herbert M. Sauro include:

  • Lucian P. Smith (24 publications)
  • Joseph L. Hellerstein (16 publications)
  • David Nickerson (14 publications)
  • Jonathan R. Karr (12 publications)
  • H Wiley (12 publications)

Herbert M. Sauro's publications commonly appear in the following venues:

  • arXiv (Cornell University) with 21 publications
  • bioRxiv (Cold Spring Harbor Laboratory) with 11 publications
  • Bioinformatics with 7 publications
  • Faculty Opinions - Post-Publication Peer Review of the Biomedical Literature with 7 publications
  • Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics with 6 publications

Herbert M. Sauro has contributed to book publications, including the title "Economic Principles in Cell Biology," published by the Centre National de la Recherche Scientifique, expected in 2025.

Award recognition includes being named Fellow of the Indian National Academy of Engineering (INAE) in 2020.

Best Publications

  • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

    M. Hucka;A. Finney;H. M. Sauro;H. Bolouri;H. Bolouri

  • The Systems Biology Graphical Notation

    Nicolas Le Novere;Michael Hucka;Huaiyu Mi;Stuart Moodie

  • BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

    Nicolas Le Novère;Benjamin J. Bornstein;Alexander Broicher;Mélanie Courtot

  • Minimum information requested in the annotation of biochemical models (MIRIAM)

    Nicolas Le Novère;Andrew Finney;Michael Hucka;Upinder S. Bhalla

  • Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration

    Herbert M. Sauro;Michael Hucka;Andrew Finney;Cameron Wellock

  • The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

    Michal Galdzicki;Kevin P. Clancy;Ernst Oberortner;Matthew Pocock

  • Transcriptional dynamics of the embryonic stem cell switch.

    Vijay Chickarmane;Carl Troein;Ulrike A Nuber;Herbert M Sauro

  • Quantitative analysis of signaling networks

    Herbert M. Sauro;Boris N. Kholodenko

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

    Sarah M. Keating;Sarah M. Keating;Dagmar Waltemath;Matthias König;Fengkai Zhang

  • TinkerCell: modular CAD tool for synthetic biology.

    Deepak Chandran;Frank T Bergmann;Frank T Bergmann;Herbert M Sauro

  • Designing and engineering evolutionary robust genetic circuits.

    Sean C Sleight;Bryan A Bartley;Jane A Lieviant;Herbert M Sauro

  • libRoadRunner: a high performance SBML simulation and analysis library

    Endre T. Somogyi;Jean-Marie Bouteiller;James A. Glazier;Matthias König

  • In-Fusion BioBrick assembly and re-engineering.

    Sean C. Sleight;Bryan A. Bartley;Jane A. Lieviant;Herbert M. Sauro

  • SCAMP: a general-purpose simulator and metabolic control analysis program

    Herbert M. Sauro

  • Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories

    Brian P. Ingalls;Herbert M. Sauro

  • Minimum Information About a Simulation Experiment (MIASE)

    Dagmar Waltemath;Richard R. Adams;Daniel A. Beard;Frank T. Bergmann;Frank T. Bergmann

  • 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

  • Tellurium: An extensible python-based modeling environment for systems and synthetic biology.

    Kiri Choi;J. Kyle Medley;Matthias König;Kaylene Stocking

  • Antimony: a modular model definition language

    Lucian P. Smith;Frank T. Bergmann;Deepak Chandran;Herbert M. Sauro

  • Standard Biological Parts Knowledgebase

    Michal Galdzicki;Cesar Rodriguez;Deepak Chandran;Herbert M. Sauro

  • The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology.

    Michael Hucka;Andrew Finney;Herbert M. Sauro;Hamid Bolouri

  • One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project

    Frank T. Bergmann;Richard Adams;Stuart Moodie;Jonathan Cooper

Frequent Co-Authors

Michael Hucka
Michael Hucka California Institute of Technology
Chris J. Myers
Chris J. Myers University of Colorado Boulder
Jacob Beal
Jacob Beal Raytheon (United States)
John H. Gennari
John H. Gennari University of Washington
Nicolas Le Novère
Nicolas Le Novère Babraham Institute
Guy-Bart Stan
Guy-Bart Stan Imperial College London
Jacky L. Snoep
Jacky L. Snoep Stellenbosch University
Hiroaki Kitano
Hiroaki Kitano Okinawa Institute of Science and Technology
Boris N. Kholodenko
Boris N. Kholodenko University College Dublin
David A. Fell
David A. Fell Oxford Brookes University

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