James R. Faeder

Biochemistry, Genetics and Molecular BiologyPhysics and Astronomy

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 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 14 papers. Top paper: “Parallel Tempering with Lasso for model reduction in systems biology”.

Parallel Tempering with Lasso for model reduction in systems biology

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007669

N/A

1.2DataRank · unranked

33 citations

Robin Lee, James R. Faeder, Sanjana Gupta

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

A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]

Living Journal of Computational Molecular Science(2023)10.33011/livecoms.5.1.1655

N/A

0.664DataRank · unranked

15 citations

Jeremy M. G. Leung, John D. Russo, She Zhang, Jeffrey P. Thompson, Ali Sinan Saglam +17 more

Iterative community-driven development of a SARS-CoV-2 tissue simulator

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.02.019075

N/A

0.641DataRank · unranked

71 citations

Yafei Wang, Gary An, Maansi Asthana, Andrew Becker, Chase Cockrell +30 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

WEBNG: A templating tool for weighted ensemble sampling of rule-based models

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.28.514312

N/A

0.104DataRank · unranked

1 citations

James R. Faeder, Ali Sinan Saglam

MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface

PLoS Computational Biology(2024)10.1371/journal.pcbi.1011800

N/A

0DataRank · unranked

15 citations

Mariam Ordyan, Guadalupe C. García, Joel G. Yancey, Ali Sinan Saglam, James R. Faeder +4 more

A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.13.628424

N/A

0DataRank · unranked

0 citations

Matthew D. Dunn, Jason E. Shoemaker, William B. Klimstra, James R. Faeder, Caroline I. Larkin

Mathematical modeling predicts quantization of Ras activation in membrane corrals

Research Square(2025)10.21203/rs.3.rs-7889340/v1

N/A

0DataRank · unranked

0 citations

James R. Faeder, Katherine A. Yonosh

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics(2020)10.1515/jib-2020-0015

N/A

0DataRank · unranked

12 citations

Lucian P. Smith, Michael L Blinov, James R. Faeder, William S. Hlavacek, José Juan Tapia +9 more

The Roles of Space and Stochasticity in Computational Simulations of Cellular Biochemistry: Quantitative Analysis and Qualitative Insights

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.02.185595

N/A

0DataRank · unranked

1 citations

Athena Chen, James R. Faeder, Philipp Henning, Ion I Moraru, Martin Meier-Schellersheim +5 more

Combination treatment optimization using a pan-cancer pathway model

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009689

N/A

0DataRank · unranked

16 citations

Gabriele Farina, James R. Faeder, Fabian Fröhlich, Ali Sinan Saglam, Tüomas Sandholm +1 more

Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility

Frontiers in Systems Biology(2022)10.3389/fsysb.2022.822606

N/A

0DataRank · unranked

17 citations

Rahuman S. Malik‐Sheriff, James M. Osborne, Gilberto González‐Parra, Eric Forgoston, Ruth Bowness +13 more

A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v0.1]

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.04.510803

N/A

0DataRank · unranked

4 citations

Jeremy M. G. Leung, John D. Russo, She Zhang, Jeffrey P. Thompson, Ali Sinan Saglam +10 more