Author

Bilal Shaikh

Icahn School of Medicine at Mount SinaiORCID 0000-0001-5801-5510Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Systems Biology· 3

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1 Assay:metabolomics· 1 Organism:multiple species· 1 Assay:proteomics· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Jonathan R. KarriD· 3 shared Ion I. MoraruiD· 2 shared Michael L. BlinoviD· 2 shared Alexander A. PatrieiD· 1 shared David Phillip NickersoniD· 1 shared Elebeoba E. May· 1 shared Eran AgmoniD· 1 shared Gnaneswara MarupillaiD· 1 shared

Activity by Year

2020-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersSystems Biology

Jonathan R. KarrORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Systems BiologyPLoS Computational BiologyPeer-reviewedDec 4, 2025

Verification and reproducible curation of the BioModels repository

Lucian P. Smith, Rahuman S. Malik‐Sheriff, Tung V. N. Nguyen…·Herbert M. Sauro

The paper updates and corrects SED-ML files for 1055 models in BioModels to improve reproducibility and verification across simulation engines.

3 citations

statistical modelbenchmarking

𝕏 PostBluesky

Systems BiologyNucleic Acids ResearchPeer-reviewedApr 30, 2021

runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Bilal Shaikh, Gnaneswara Marupilla, Michael Wilson…·Jonathan R. Karr

runBioSimulations provides a web platform to execute diverse computational models, enabling easier access to simulation tools and promoting reproducibility in modeling.

21 citations

experimental assaysoftware / tool

𝕏 PostBluesky

Systems BiologyNucleic Acids ResearchPeer-reviewedOct 22, 2020

Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior

Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju…·Jonathan R. Karr

Datanator is a database that integrates molecular data for modeling cellular behavior, providing tools to access and analyze diverse biochemical data across organisms and environments.

15 citations

multiple speciesmetabolomics

𝕏 PostBluesky