On the public citation graph
Notions of similarity for computational biology models
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Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/978-1-4419-1428-6_5195openalex-snapshot
Pattern Classification
inferredcites →https://doi.org/10.1007/978-3-642-41281-3_3openalex-snapshot
Information Retrieval in Life Sciences: A Programmatic Survey
inferredcites →https://doi.org/10.1007/978-94-007-6803-1_10openalex-snapshot
Reproducibility of Model-Based Results in Systems Biology
inferredcites →https://doi.org/10.1016/b978-0-12-385118-5.00019-0openalex-snapshot
Sustainable Model Building
inferredcites →https://doi.org/10.1016/j.bpj.2015.12.012openalex-snapshot
The Cardiac Electrophysiology Web Lab
inferredcites →https://doi.org/10.1016/j.pbiomolbio.2011.06.003openalex-snapshot
High-throughput functional curation of cellular electrophysiology models
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/msb.2011.41openalex-snapshot
Retrieval, alignment, and clustering of computational models based on semantic annotations
inferredcites →https://doi.org/10.1038/msb.2011.77openalex-snapshot
Controlled vocabularies and semantics in systems biology
inferredcites →https://doi.org/10.1038/nbt.1558openalex-snapshot
The Systems Biology Graphical Notation
inferredcites →https://doi.org/10.1038/nbt.2488openalex-snapshot
A community-driven global reconstruction of human metabolism
inferredcites →https://doi.org/10.1038/nrg3885openalex-snapshot
Quantitative and logic modelling of molecular and gene networks
inferredcites →https://doi.org/10.1073/pnas.0305199101openalex-snapshot
Local graph alignment and motif search in biological networks
inferredcites →https://doi.org/10.1073/pnas.88.16.7328openalex-snapshot
Modeling the cell division cycle: cdc2 and cyclin interactions.
inferredcites →https://doi.org/10.1088/1478-3975/9/5/055001openalex-snapshot
Boolean modeling in systems biology: an overview of methodology and applications
inferredcites →https://doi.org/10.1093/bioinformatics/btg015openalex-snapshot
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
inferredcites →https://doi.org/10.1093/bioinformatics/btn319openalex-snapshot
Comparing simulation results of SBML capable simulators
inferredcites →https://doi.org/10.1093/bioinformatics/btp642openalex-snapshot
Annotation and merging of SBML models with semanticSBML
inferredcites →https://doi.org/10.1093/bioinformatics/btq388openalex-snapshot
A graphical method for reducing and relating models in systems biology
inferredcites →https://doi.org/10.1093/bioinformatics/btq723openalex-snapshot
The Physiome Model Repository 2
inferredcites →https://doi.org/10.1093/bioinformatics/btt018openalex-snapshot
Improving the reuse of computational models through version control
inferredcites →https://doi.org/10.1093/bioinformatics/btt765openalex-snapshot
The EBI RDF platform: linked open data for the life sciences
inferredcites →https://doi.org/10.1093/bioinformatics/btu307openalex-snapshot
A comparison of algorithms for the pairwise alignment of biological networks
inferredcites →https://doi.org/10.1093/bioinformatics/btv484openalex-snapshot
An algorithm to detect and communicate the differences in computational models describing biological systems
inferredcites →https://doi.org/10.1093/database/bau130openalex-snapshot
Combining computational models, semantic annotations and simulation experiments in a graph database
inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot
UniProt: the Universal Protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkh151openalex-snapshot
The major role of human AP-endonuclease homolog Apn2 in repair of abasic sites in Schizosaccharomyces pombe
inferredcites →https://doi.org/10.1093/nar/gkm791openalex-snapshot
ChEBI: a database and ontology for chemical entities of biological interest
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1109/esciencew.2011.28openalex-snapshot
A Profile of Today's SBML-Compatible Software
inferredcites →https://doi.org/10.1109/icdm.2002.1184038openalex-snapshot
gSpan: graph-based substructure pattern mining
inferredcites →https://doi.org/10.1109/tbme.2016.2555481openalex-snapshot
How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine
inferredcites →https://doi.org/10.1126/science.1089072openalex-snapshot
Biological Networks: The Tinkerer as an Engineer
inferredcites →https://doi.org/10.1126/science.298.5594.824openalex-snapshot
Network Motifs: Simple Building Blocks of Complex Networks
inferredcites →https://doi.org/10.1146/annurev.physchem.012809.103457openalex-snapshot
Functional Motifs in Biochemical Reaction Networks
inferredcites →https://doi.org/10.1177/0037549703040939openalex-snapshot
An Overview of CellML 1.1, a Biological Model Description Language
inferredcites →https://doi.org/10.1186/1471-2105-11-423openalex-snapshot
Ranked retrieval of Computational Biology models
inferredcites →https://doi.org/10.1186/1471-2105-12-22openalex-snapshot
Revision history aware repositories of computational models of biological systems
inferredcites →https://doi.org/10.1186/1471-2105-13-18openalex-snapshot
Propagating semantic information in biochemical network models
inferredcites →https://doi.org/10.1186/1752-0509-3-34openalex-snapshot
Version control of pathway models using XML patches
inferredcites →https://doi.org/10.1186/1752-0509-5-198openalex-snapshot
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
inferredcites →https://doi.org/10.1186/s13326-015-0014-4openalex-snapshot
Annotation-based feature extraction from sets of SBML models
inferredcites →https://doi.org/10.1186/s13326-016-0080-2openalex-snapshot
COMODI: an ontology to characterise differences in versions of computational models in biology
inferredcites →https://doi.org/10.1201/9781420011432openalex-snapshot
An Introduction to Systems Biology
inferredcites →https://doi.org/10.1371/journal.pcbi.1000443openalex-snapshot
Semantic Similarity in Biomedical Ontologies
inferredcites →https://doi.org/10.1371/journal.pone.0054201openalex-snapshot
A Method for Comparing Multivariate Time Series with Different Dimensions
inferredcites →https://doi.org/10.7287/peerj.preprints.1479v1openalex-snapshot
Finding pattern in biochemical reaction networks - a sub-graph mining approach
inferredcites →https://doi.org/10.7287/peerj.preprints.640v1openalex-snapshot
An algorithm to detect and communicate the differences in computational models describing biological systems
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1101/2021.03.04.433874openalex-snapshot
Linguistic Analysis of the bioRxiv Preprint Landscape
inferred← citeshttps://doi.org/10.7287/peerj.preprints.1479v2openalex-snapshot
Finding patterns in biochemical reaction networks
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