On the public citation graph

A large-scale analysis of bioinformatics code on GitHub

https://doi.org/10.1101/321919
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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/10.1002/j.1538-7305.1948.tb01338.xopenalex-snapshot
A Mathematical Theory of Communication
inferredcites →https://doi.org/10.1016/j.csbj.2017.07.002openalex-snapshot
Scalability and Validation of Big Data Bioinformatics Software
inferredcites →https://doi.org/10.1016/j.infsof.2015.10.002openalex-snapshot
Understanding the popular users: Following, affiliation influence and leadership on GitHub
inferredcites →https://doi.org/10.1038/35042090openalex-snapshot
The origins of bioinformatics
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1073/pnas.1700616114openalex-snapshot
Gender diversity leads to better science
inferredcites →https://doi.org/10.1093/bib/bbq084openalex-snapshot
Case studies in reproducibility
inferredcites →https://doi.org/10.1093/bioinformatics/btn397openalex-snapshot
BioJava: an open-source framework for bioinformatics
inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot
Biopython: freely available Python tools for computational molecular biology and bioinformatics
inferredcites →https://doi.org/10.1093/bioinformatics/bts494openalex-snapshot
BioJava: an open-source framework for bioinformatics in 2012
inferredcites →https://doi.org/10.1109/icsme.2016.31openalex-snapshot
Understanding the Factors That Impact the Popularity of GitHub Repositories
inferredcites →https://doi.org/10.1109/qsic.2013.57openalex-snapshot
An Empirical Study of Adoption of Software Testing in Open Source Projects
inferredcites →https://doi.org/10.1109/tsa.2016.23openalex-snapshot
What Are the Dominant Projects in the GitHub Python Ecosystem?
inferredcites →https://doi.org/10.1145/2133806.2133826openalex-snapshot
Probabilistic topic models
inferredcites →https://doi.org/10.1145/2635868.2635922openalex-snapshot
A large scale study of programming languages and code quality in github
inferredcites →https://doi.org/10.1162/jmlr.2003.3.4-5.993openalex-snapshot
10.1162/jmlr.2003.3.4-5.993
inferredcites →https://doi.org/10.1186/1471-2105-10-24openalex-snapshot
An innovative approach for testing bioinformatics programs using metamorphic testing
inferredcites →https://doi.org/10.1186/2047-217x-2-15openalex-snapshot
Ten recommendations for creating usable bioinformatics command line software
inferredcites →https://doi.org/10.1186/gb-2004-5-10-r80openalex-snapshot
Bioconductor: open software development for computational biology and bioinformatics
inferredcites →https://doi.org/10.1186/s40064-016-2897-7openalex-snapshot
Influence analysis of Github repositories
inferredcites →https://doi.org/10.1186/s40411-017-0044-yopenalex-snapshot
How diverse is your team? Investigating gender and nationality diversity in GitHub teams
inferredcites →https://doi.org/10.12688/f1000research.3-62.v1openalex-snapshot
Software Carpentry: lessons learned
inferredcites →https://doi.org/10.1371/journal.pbio.1001745openalex-snapshot
Best Practices for Scientific Computing
inferredcites →https://doi.org/10.1371/journal.pcbi.1000809openalex-snapshot
The Roots of Bioinformatics
inferredcites →https://doi.org/10.1371/journal.pcbi.1002216openalex-snapshot
BioStar: An Online Question & Answer Resource for the Bioinformatics Community
inferredcites →https://doi.org/10.1371/journal.pcbi.1003285openalex-snapshot
Ten Simple Rules for Reproducible Computational Research
inferredcites →https://doi.org/10.1371/journal.pcbi.1004668openalex-snapshot
A Quick Introduction to Version Control with Git and GitHub
inferredcites →https://doi.org/10.1371/journal.pcbi.1005134openalex-snapshot
Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology
inferredcites →https://doi.org/10.1371/journal.pone.0157989openalex-snapshot
A Survey of Bioinformatics Database and Software Usage through Mining the Literature
inferredcites →https://doi.org/10.3389/fgene.2014.00199openalex-snapshot
On best practices in the development of bioinformatics software
inferredcites →https://doi.org/10.5334/jors.35openalex-snapshot
Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab
inferredcites →https://doi.org/10.5555/944919.944937openalex-snapshot
Latent dirichlet allocation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/gigascience/giz109openalex-snapshot
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software
inferred← citeshttps://doi.org/10.1109/tse.2021.3092813openalex-snapshot
Including Everyone, Everywhere: Understanding Opportunities and Challenges of Geographic Gender-Inclusion in OSS
inferred← citeshttps://doi.org/10.1142/s0218194022500358openalex-snapshot
Automatic Analysis of Available Source Code of Top Artificial Intelligence Conference Papers
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2399015/v1openalex-snapshot
The rworkflows suite: automated continuous integration for quality checking, documentation website creation, and containerised deployment of R packages
inferred← citeshttps://doi.org/10.3390/app9010150openalex-snapshot
A Systematic Review of Open Source Clinical Software on GitHub for Improving Software Reuse in Smart Healthcare
inferred← citeshttps://doi.org/10.3390/metabo10050202openalex-snapshot
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources
inferred← citeshttps://doi.org/10.3390/sym18091559openalex-snapshot
Computational Performance of Programming Languages in Mathematical Biology: A Ten-Language Evaluation Across Six Modeling Regimes
inferred← citeshttps://doi.org/10.34719/rjbz6161openalex-snapshot
The Role Of Software Engineering In Bioinformatics
inferred← citeshttps://doi.org/10.7287/peerj-cs.835v0.2/reviews/2openalex-snapshot
Peer Review #2 of "The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central (v0.2)"
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