{"id":31799511,"url":"https://github.com/mims-harvard/pathways","last_synced_at":"2025-10-10T22:02:33.807Z","repository":{"id":77398096,"uuid":"121286143","full_name":"mims-harvard/pathways","owner":"mims-harvard","description":"Disease pathways in the human interactome","archived":false,"fork":false,"pushed_at":"2018-03-20T16:55:12.000Z","size":1529,"stargazers_count":21,"open_issues_count":1,"forks_count":6,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-03-26T02:22:12.097Z","etag":null,"topics":["interactome","molecular-biology","network-analysis","network-science","pathway-analysis","pathway-prediction"],"latest_commit_sha":null,"homepage":"http://snap.stanford.edu/pathways","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mims-harvard.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-02-12T18:38:56.000Z","updated_at":"2023-11-07T03:35:13.000Z","dependencies_parsed_at":"2023-05-04T08:01:51.045Z","dependency_job_id":null,"html_url":"https://github.com/mims-harvard/pathways","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mims-harvard/pathways","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mims-harvard%2Fpathways","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mims-harvard%2Fpathways/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mims-harvard%2Fpathways/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mims-harvard%2Fpathways/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mims-harvard","download_url":"https://codeload.github.com/mims-harvard/pathways/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mims-harvard%2Fpathways/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005432,"owners_count":26083891,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-10T02:00:06.843Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["interactome","molecular-biology","network-analysis","network-science","pathway-analysis","pathway-prediction"],"created_at":"2025-10-10T22:02:23.042Z","updated_at":"2025-10-10T22:02:33.801Z","avatar_url":"https://github.com/mims-harvard.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Pathways\n\nWe perform a large-scale analysis of *disease pathways* in the human *interactome* to better understand connectivity and higher-order network structure of disease pathways.\n\nDiscovering disease pathways, which can be defined as sets of proteins associated with a given disease, is an important problem that has the potential to provide clinically actionable insights for disease diagnosis, prognosis, and treatment.\n\n![Examples of disease pathways](/images/disease-pathway-examples.png)\n\nHere we study the PPI network structure of disease pathways. We find that 90% of pathways do not correspond to single well-connected components in the PPI network. Instead, proteins associated with a single disease tend to form many separate connected components/regions in the network. We then evaluate state-of-the-art disease pathway discovery methods and show that their performance is especially poor on diseases with disconnected pathways.\n\n![Disease pathway discovery](/images/disease-pathway-discovery.png)\n\nWe conclude that network connectivity structure alone may not be sufficient for disease pathway discovery. However, we show that higher-order network structures, such as small subgraphs of the pathway, provide a promising direction for the development of new methods.\n\nPlease check the [project website](http://snap.stanford.edu/pathways/) for more details. \n  \n## Citing\n\nIf you find disease pathway analysis useful for your research, please consider citing:\n\n    @inproceedings{agrawal2018,\n      author={Agrawal, Monica and Zitnik, Marinka and Leskovec, Jure},\n      title = {Large-scale Analysis of Disease Pathways in the Human Interactome},\n      year = {2018},\n      booktitle = {Pacific Symposium on Biocomputing},\n      volume = {23},\n      pages = {111-122}\n    }\n\n## Miscellaneous\n\nPlease send any questions you might have about the code and/or the \nalgorithm to \u003cmarinka@cs.stanford.edu\u003e.\n\n## License\n\nDecagon is licensed under the MIT License.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmims-harvard%2Fpathways","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmims-harvard%2Fpathways","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmims-harvard%2Fpathways/lists"}