Herbert M Sauro

Also affiliated with Weizmann Institute of Science

Biochemistry, Genetics and Molecular BiologyDecision Sciences

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 5%percentile

0.571Author DataRank

Indexed papers

5in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 5 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Cesium: A public database of evolved oscillatory reaction networks

Biosystems(2023)10.1016/j.biosystems.2023.104836

Top 52%

0.330DataRank

Top 52%8 citations

Wesley Luk, Timothy C. Elston, Joseph L. Hellerstein, Herbert M Sauro, Lillian T. Tatka

Papers

Driven by 42 papers — median percentile 19. Top paper: “SBML Level 3: an extensible format for the exchange and reuse of biological models”.

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

Molecular Systems Biology(2020)10.15252/msb.20199110

N/A

0.861DataRank · unranked

311 citations

Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya +95 more

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Nucleic Acids Research(2022)10.1093/nar/gkac331

N/A

0.489DataRank · unranked

25 citations

Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon +71 more

SimpleSBML: A Python package for creating and editing SBML models

10.1101/030312

N/A

0.409DataRank · unranked

8 citations

Kyle Medley, Herbert M Sauro, Caroline Cannistra

Cesium: A public database of evolved oscillatory reaction networks

Biosystems(2023)10.1016/j.biosystems.2023.104836

Top 52%

0.330DataRank

Top 52%8 citations

Wesley Luk, Timothy C. Elston, Joseph L. Hellerstein, Herbert M Sauro, Lillian T. Tatka

A Phosphoproteomics Data Resource for Systems-level Modeling of Kinase Signaling Networks

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.03.551714

Top 61%

0.241DataRank

Top 61%4 citations

James Sanford, Thomas J. Weber, Chelsea Hutchinson-Bunch, Panshak Dakup, Vanessa Paurus +5 more

SBbadger: biochemical reaction networks with definable degree distributions

Bioinformatics(2022)10.1093/bioinformatics/btac630

N/A

0.208DataRank · unranked

3 citations

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

An automated model annotation system (AMAS) for SBML models

Bioinformatics(2023)10.1093/bioinformatics/btad658

N/A

0.165DataRank · unranked

2 citations

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

Adapting Modeling and Simulation Credibility Standards to Computational Systems Biology

arXiv (Cornell University)(2023)10.48550/arxiv.2301.06007

N/A

0.104DataRank · unranked

1 citations

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

SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.09.463757

N/A

0DataRank · unranked

2 citations

Joseph L. Hellerstein, Yuda Munarko, Maxwell L. Neal, David P Nickerson, Anand K Rampadarath +3 more

Dynamics and Sensitivity of Signaling Pathways

Current Pathobiology Reports(2022)10.1007/s40139-022-00230-y

N/A

0DataRank · unranked

10 citations

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

Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology

Current Opinion in Systems Biology(2021)10.1016/j.coisb.2021.06.001

N/A

0DataRank · unranked

2 citations

John H. Gennari, Jonathan R Karr, Ion I Moraru, David P Nickerson, Herbert M Sauro +1 more

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

Bioinformatics(2022)10.1093/bioinformatics/btac730

N/A

0DataRank · unranked

3 citations

Jessie Jiang, Herbert M Sauro, Jin Xu

Tissue Forge: Interactive Biological and Biophysics Simulation Environment

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.28.518300

N/A

0DataRank · unranked

3 citations

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

Adapting modeling and simulation credibility standards to computational systems biology

Journal of Translational Medicine(2023)10.1186/s12967-023-04290-5

N/A

0DataRank · unranked

22 citations

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

Tissue Forge: Interactive biological and biophysics simulation environment

PLoS Computational Biology(2023)10.1371/journal.pcbi.1010768

N/A

0DataRank · unranked

20 citations

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

Standards, dissemination, and best practices in systems biology

Current Opinion in Biotechnology(2023)10.1016/j.copbio.2023.102922

N/A

0DataRank · unranked

11 citations

Veronica L. Porubsky, James M. Carothers, Herbert M Sauro, Janis Shin

libOmexMeta: enabling semantic annotation of models to support FAIR principles

Bioinformatics(2021)10.1093/bioinformatics/btab445

N/A

0DataRank · unranked

11 citations

David P Nickerson, Anand K Rampadarath, Maxwell L. Neal, Herbert M Sauro, John H. Gennari +1 more

SBcoyote: An extensible Python-based reaction editor and viewer

Biosystems(2023)10.1016/j.biosystems.2023.105001

N/A

0DataRank · unranked

3 citations

Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes, Claire Samuels, Herbert M Sauro +1 more

libsbmljs—Enabling web-based SBML tools

Biosystems(2020)10.1016/j.biosystems.2020.104150

N/A

0DataRank · unranked

3 citations

Joseph L. Hellerstein, Herbert M Sauro, Kyle Medley

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

Bioinformatics(2023)10.1093/bioinformatics/btad753

N/A

0DataRank · unranked

1 citations

Longxuan Fan, Sai Anish Konanki, Eva Salazar Liu, John H. Gennari, Lucian P. Smith +3 more

A compiler for biological networks on silicon chips

PLoS Computational Biology(2020)10.1371/journal.pcbi.1008063

N/A

0DataRank · unranked

6 citations

Jonathan J. Y. Teo, Sung Sik Woo, Joseph L. Hellerstein, Rahul Sarpeshkar, Herbert M Sauro +1 more

Publishing reproducible dynamic kinetic models

Briefings in Bioinformatics(2020)10.1093/bib/bbaa152

N/A

0DataRank · unranked

11 citations

Lucian P. Smith, Herbert M Sauro, Veronica L. Porubsky

SBcoyote: An Extensible Python-Based Reaction Editor and Viewer

arXiv (Cornell University)(2023)10.48550/arxiv.2302.09151

N/A

0DataRank · unranked

0 citations

Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes, Claire Samuels, Herbert M Sauro +1 more

An Automated Model Annotation System (AMAS) for SBML Models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.19.549722

N/A

0DataRank · unranked

0 citations

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

MakeSBML: A tool for converting between Antimony and SBML

arXiv (Cornell University)(2023)10.48550/arxiv.2309.03344

N/A

0DataRank · unranked

0 citations

Lucian P. Smith, Herbert M Sauro, Bartholomew Jardine

Sensitivity and Frequency Response of Biochemical Cascades

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.14.557821

N/A

0DataRank · unranked

0 citations

Joseph L. Hellerstein, Herbert M Sauro, Michael A. Kochen

Design patterns of biological cells

BioEssays(2024)10.1002/bies.202300188

N/A

0DataRank · unranked

12 citations

H Wiley, Herbert M Sauro, Steven S. Andrews

Generating synthetic signaling networks for in silico modeling studies

Journal of Theoretical Biology(2024)10.1016/j.jtbi.2024.111901

N/A

0DataRank · unranked

5 citations

H Wiley, Herbert M Sauro, Jin Xu

MakeSBML: a tool for converting between Antimony and SBML

Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics(2024)10.1515/jib-2024-0002

N/A

0DataRank · unranked

3 citations

Lucian P. Smith, Herbert M Sauro, Bartholomew Jardine

First-order ultrasensitivity in phosphorylation cycles

Interface Focus(2024)10.1098/rsfs.2023.0045

N/A

0DataRank · unranked

1 citations

Joseph L. Hellerstein, Herbert M Sauro, Michael A. Kochen

Use of interactive mathematical simulations in Fundamentals of Biochemistry, a LibreText online educational resource, to promote understanding of dynamic reactions

Biochemistry and Molecular Biology Education(2024)10.1002/bmb.21830

N/A

0DataRank · unranked

0 citations

Henry Agnew, Bartholomew Jardine, Herbert M Sauro, Henry V. Jakubowski

An Update to the SBML Human-Readable Antimony Language

PubMed(2024)10.48550/arxiv.2405.15109

N/A

0DataRank · unranked

0 citations

Herbert M Sauro, Lucian P. Smith

Computing the Frequency Response of Biochemical Networks: A Python module

PubMed(2024)10.48550/arxiv.2406.11140

N/A

0DataRank · unranked

0 citations

Herbert M Sauro

EFECT: A Method to Quantify the Reproducibility of Stochastic Simulations

arXiv (Cornell University)(2024)10.48550/arxiv.2406.16820

N/A

0DataRank · unranked

0 citations

Matthias König, Luís L. Fonseca, Pathirana, Dilan, Bergmann, Frank T., Grecco, Hernán E. +11 more

A Roadmap for the Future of Systems Biology in Cancer Research

Cancer Research(2025)10.1158/0008-5472.can-25-0700

N/A

0DataRank · unranked

2 citations

Carlos F. Lopez, Andréi S. Rodin, Russell C. Rockne, Thomas E. Yankeelov, Herbert M Sauro +23 more

SBMLNetwork: A framework for standards-based visualization of biochemical models

PLoS Computational Biology(2025)10.1371/journal.pcbi.1013128

N/A

0DataRank · unranked

1 citations

Lucian P. Smith, Joseph L. Hellerstein, Herbert M Sauro, Adel Heydarabadipour

Verification and reproducible curation of the BioModels repository

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.16.633337

Top 100%

0DataRank

Top 100%0 citations

Rahuman S. Malik‐Sheriff, Tung V. N. Nguyen, Henning Hermjakob, Jonathan R Karr, Bilal Shaikh +12 more

Speciated evolution of oscillatory mass-action chemical reaction networks

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.10.648132

N/A

0DataRank · unranked

0 citations

Lucian P. Smith, Herbert M Sauro, Lillian T. Tatka

SBMLNetwork: a framework for standards-based visualization of biochemical models

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.09.653024

N/A

0DataRank · unranked

0 citations

Lucian P. Smith, Joseph L. Hellerstein, Herbert M Sauro, Adel Heydarabadipour

Discovering subnetworks in SBML models

Bioinformatics(2025)10.1093/bioinformatics/btaf482

N/A

0DataRank · unranked

0 citations

Lucian P. Smith, Lillian T. Tatka, Steven S. Andrews, Michael A. Kochen, Herbert M Sauro +1 more

Verification and reproducible curation of the BioModels repository

PLoS Computational Biology(2025)10.1371/journal.pcbi.1013239

Top 100%

0DataRank

Top 100%0 citations

Rahuman S. Malik‐Sheriff, Tung V. N. Nguyen, Henning Hermjakob, Jonathan R Karr, Bilal Shaikh +12 more

Best Practices for Making Reproducible Biochemical Models

Cell Systems(2020)10.1016/j.cels.2020.06.012

N/A

0DataRank · unranked

49 citations

Arthur P. Goldberg, Anand K Rampadarath, David P Nickerson, Jonathan R Karr, Herbert M Sauro +1 more

Herbert M Sauro

Indexed papers

Top data-sharing exemplar

Papers