{"id":24529900,"url":"https://github.com/mschubert/mschubert","last_synced_at":"2026-02-10T17:31:28.931Z","repository":{"id":142445535,"uuid":"424197257","full_name":"mschubert/mschubert","owner":"mschubert","description":null,"archived":false,"fork":false,"pushed_at":"2025-02-11T09:02:37.000Z","size":69,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-15T18:22:37.437Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mschubert.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-11-03T11:30:37.000Z","updated_at":"2025-02-11T09:02:41.000Z","dependencies_parsed_at":"2025-01-28T14:28:00.131Z","dependency_job_id":"fb489350-584a-487c-980d-ff47da2da9f3","html_url":"https://github.com/mschubert/mschubert","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mschubert/mschubert","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fmschubert","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fmschubert/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fmschubert/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fmschubert/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mschubert","download_url":"https://codeload.github.com/mschubert/mschubert/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mschubert%2Fmschubert/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268448362,"owners_count":24252019,"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":"2025-08-02T02:00:12.353Z","response_time":74,"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":[],"created_at":"2025-01-22T07:53:01.863Z","updated_at":"2026-02-10T17:31:28.914Z","avatar_url":"https://github.com/mschubert.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"### Hi there 👋\n\nI'm Michael, a computational biologist. This means that I'm using computers and code to analyze biological data, often in collaboration with experimental scientists. I'm working on how cancer cells overcome their growth limitations and how we can use that to help patients. Here you can find some of the work I did, and more general purpose tools I wrote for anyone to use. Please reach out if you want to collaborate!\n    \n\u003cdetails open\u003e\u003csummary\u003e\u003cb\u003eThis is what I do for research 👨‍🔬 (\u003ca href=https://scholar.google.com/citations?user=z6mKdjAAAAAJ\u0026hl=en\u003efull list 🔗\u003c/a\u003e)\u003c/b\u003e\u003c/summary\u003e\n\n| | \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;article\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; | \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;code\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; |\n:- | :-: | :-:\n| Developed a reliable method for estimating cell signaling pathways from gene expression | [![Cell](https://img.shields.io/badge/Cell-2016-blue.svg)](https://www.cell.com/cell/fulltext/S0092-8674(16)30746-2)\u003cbr/\u003e[![Nat Comm](https://img.shields.io/badge/Nat%20Comm-2018-blue.svg)](https://www.nature.com/articles/s41467-017-02391-6) | [github :octocat:](https://github.com/saezlab/footprints)\u003cbr/\u003e[bioc 📦](http://bioconductor.org/packages/release/bioc/html/progeny.html)\n| Showed how gene coexpression networks often reflect cell mixtures instead of regulation | [![BBA-GRM](https://img.shields.io/badge/BBA--GRM-2020-blue.svg)](https://eriba.umcg.nl/wp-content/uploads/2021/07/Foijer-2019-10-23-Biochim-Biophys-Acta-Gene-Regul-Mech.pdf) | [github :octocat:](https://github.com/mschubert/GRN-aneup-purity)\n| Found a way how cancer cells can tolerate abnormal DNA content (aneuploidy, ***c***hromosomal ***in***stability) and potential treatments, in collaboration with experimental scientists | [![bioRxiv](https://img.shields.io/badge/bioRxiv-2021-yellow.svg)](https://www.biorxiv.org/content/10.1101/2021.12.03.471107v2)\u003cbr/\u003e[![Nature](https://img.shields.io/badge/Nature-2022-blue.svg)](https://www.nature.com/articles/s41586-022-04847-2)\u003cbr/\u003e[![Nat Comm](https://img.shields.io/badge/Nat%20Comm-2025-blue.svg)](https://www.nature.com/articles/s41467-025-56301-2) | [transposon :octocat:](https://github.com/mschubert/mad2-transposon)\u003cbr/\u003e[cgas_ko :octocat:](https://github.com/mschubert/cgas_ko)\u003cbr/\u003e[ToxicGenes :octocat:](https://github.com/mschubert/ToxicGenes) \n| Working on estimating DNA copy number of single-cell RNA sequencing | \u003csup\u003e\u003csub\u003ecoming soon\u003c/sub\u003e\u003c/sup\u003e |\n  \n\u003c/details\u003e\n\n\u003cdetails open\u003e\u003csummary\u003e\u003cb\u003eHere are some of my open source contributions 👨‍💻 (\u003ca href=https://github.com/mschubert?tab=repositories\u003efull list 🔗\u003c/a\u003e)\u003c/b\u003e\u003c/summary\u003e\n\n| | | \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;status\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; | \u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;code\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp;\u0026nbsp; |\n:-: | :- | :-: | :-:\n| *clustermq* | R package for efficient high performance computing\u003cbr/\u003e[![Bioinformatics](https://img.shields.io/badge/Bioinformatics-2019-blue.svg)](https://academic.oup.com/bioinformatics/article/35/21/4493/5499081) [![downloads](https://cranlogs.r-pkg.org/badges/grand-total/clustermq)](https://github.com/mschubert/clustermq) | [![CRAN version](https://www.r-pkg.org/badges/version/clustermq)](https://cran.r-project.org/package=clustermq)\u003cbr/\u003e[![Build Status](https://github.com/mschubert/clustermq/actions/workflows/check-standard.yaml/badge.svg?branch=master)](https://github.com/mschubert/clustermq/actions) | [github :octocat:](https://github.com/mschubert/clustermq)\u003cbr/\u003e[cran 📦](https://cran.r-project.org/package=clustermq)\u003cbr/\u003e[testing :gear:](https://github.com/mschubert/clustermq-performance) \n| *narray* | R package for simplifying array operations\u003cbr/\u003e[![downloads](https://cranlogs.r-pkg.org/badges/grand-total/narray)](https://github.com/mschubert/narray) | [![CRAN version](https://www.r-pkg.org/badges/version/narray)](https://cran.r-project.org/package=narray)\u003cbr/\u003e[![Build Status](https://github.com/mschubert/narray/actions/workflows/check-standard.yaml/badge.svg?branch=master)](https://github.com/mschubert/narray/actions) | [github :octocat:](https://github.com/mschubert/narray)\u003cbr/\u003e[cran 📦](https://cran.r-project.org/package=narray)\n| *ebits* | R bioinformatics toolkit incubator and data API | [![Build Status](https://github.com/mschubert/ebits/actions/workflows/check-standard.yaml/badge.svg?branch=master)](https://github.com/mschubert/ebits/actions) | [ebits :octocat:](https://github.com/mschubert/ebits)\u003cbr/\u003e[data :octocat:](https://github.com/mschubert/data)\n| | Software build scripts for the [ArchLinux User Repository 🔗](https://aur.archlinux.org/packages/?K=mschu\u0026SeB=m) and as [Gentoo overlay 🔗](https://en.wikipedia.org/wiki/Portage_(software)#ebuild) | [![pkgcheck](https://github.com/mschubert/overlay/actions/workflows/pkgcheck.yml/badge.svg)](https://github.com/mschubert/overlay/actions) | [pkgbuilds :octocat:](https://github.com/mschubert/PKGBUILDs)\u003cbr/\u003e[overlay :octocat:](https://github.com/mschubert/overlay)\n  \n\u003c/details\u003e\n  \n\u003c!--\n**mschubert/mschubert** is a ✨ _special_ ✨ repository because its `README.md` (this file) appears on your GitHub profile.\n\nHere are some ideas to get you started:\n\n- 🔭 I’m currently working on ...\n- 🌱 I’m currently learning ...\n- 👯 I’m looking to collaborate on ...\n- 🤔 I’m looking for help with ...\n- 💬 Ask me about ...\n- 📫 How to reach me: ...\n- 😄 Pronouns: ...\n- ⚡ Fun fact: ...\n--\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmschubert%2Fmschubert","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmschubert%2Fmschubert","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmschubert%2Fmschubert/lists"}