Muhammad
Elhossary.

~ $ whoami # about

~ $ git log --graph # career & education

* work* education

1. a0aecf0 2020-06..2026-11 (education)

   Doctorate (Dr. rer. nat.) in Bioinformatics

   Faculty of Technology, Bielefeld University

   Graduate School of Digital Infrastructure for the Life Sciences (DILS) at the Bielefeld Institute for Bioinformatics Infrastructure (BIBI). Dissertation: Regulatory Small RNAs in Gammaproteobacteria. Supervisor: Prof. Dr. Konrad Förstner.

2. 682b439 HEAD -> work 2018-09..now (work)

   Research Software Engineer & Bioinformatics Data Scientist

   ZB MED – Information Centre for Life Sciences, Cologne

   Lead of the technical implementation of measures in the NFDI4Microbiota consortium and the KGI4NFDI base service within the NFDI: multi-omics data analysis, knowledge graph development, full-stack web development, design, building, and maintenance of backend software infrastructure, and IT administration.

3. 9e48639 2018-02..2018-08 (work)

   Research Software Engineer (Bioinformatician)

   Institute for Molecular Infection Biology, University of Würzburg

   Knowledge graph modelling of small RNA interaction data in Wikidata.

4. 7588bb6 2017-01..2017-12 (work)

   Private Business Partner

   Elhossary Store

   Consumer electronics retail and technical services.

5. d663257 2016-08..2016-10 (education)

   Academic Internship, Bioinformatics

   Institute for Molecular Infection Biology, University of Würzburg

6. 2664f53 2016-01..2016-06 (work)

   Software Developer

   Freelance

   Oracle APEX development for a professional cleaning services company.

7. d4e4086 2015-03..2015-06 (work)

   Software Developer

   Engineering Systems Inc.

   .NET full-stack development for ERP systems and employee time tracking.

8. a726e3e 2014-01..2015-02 (work)

   Software Developer

   Etqan for Information Technology S.A.E.

   .NET full-stack and Oracle APEX development for SMS campaign tools and school management systems; Oracle Business Intelligence consulting.

9. ca0d933 2013..2014 (education)

   Postgraduate Diploma, Computer Sciences

   Arab Academy for Science, Technology and Maritime Transport (AASTMT), Egypt

10. e269b08 2013-06..2013-12 (work)

    Software Developer

    Freelance

    Technical requirements analysis for the digital automation of the Journal of the Egyptian Society of Radiation Research and Applied Sciences (ESRSA).

11. a0c8ba6 2012-09..2013-05 (work)

    Software Developer

    FodaDev LLC

    .NET / SQL Server full-stack development for recruitment and employment requisition automation.

12. d22081e 2011-06..2012-08 (work)

    Junior Software Developer

    Etqan for Information Technology S.A.E.

    .NET / SQL Server full-stack development for sales tracking.

13. 5b0856d 2008..2012 (education)

    BSc, Business Information Systems

    Canadian International College (CIC), Egypt

    Project: online education system.

~ $ cat publications.bib # papers

1. 2025

   Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene

   Jennifer A. F. Kothe, Till Sauerwein, Theresa Dietz, Robina Scheuer, Muhammad Elhossary, Susanne Barth-Weber, Jan Wähling, Konrad U. Förstner, Elena Evguenieva-Hackenberg

   RNA Biology 22(1), 1–16

   doi:10.1080/15476286.2025.2521887

   BibTeX

   @article{Kothe2025,
     title     = {Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene},
     author    = {Kothe, Jennifer A. F. and Sauerwein, Till and Dietz, Theresa and Scheuer, Robina and Elhossary, Muhammad and Barth-Weber, Susanne and W{\"a}hling, Jan and F{\"o}rstner, Konrad U. and Evguenieva-Hackenberg, Elena},
     journal   = {RNA Biology},
     volume    = {22},
     number    = {1},
     pages     = {1--16},
     year      = {2025},
     publisher = {Informa UK Limited},
     doi       = {10.1080/15476286.2025.2521887}
   }

2. 2024

   InteractOA: Showcasing the representation of knowledge from scientific literature in Wikidata

   Muhammad Elhossary, Konrad U. Förstner

   Semantic Web, 1–13

   doi:10.3233/SW-243685

   BibTeX

   @article{Elhossary2024,
     title     = {InteractOA: Showcasing the representation of knowledge from scientific literature in Wikidata},
     author    = {Elhossary, Muhammad and F{\"o}rstner, Konrad U.},
     journal   = {Semantic Web},
     pages     = {1--13},
     year      = {2024},
     publisher = {SAGE Publications},
     doi       = {10.3233/SW-243685}
   }

3. 2022

   A lesson for teaching fundamental Machine Learning concepts and skills to molecular biologists

   Rabea Müller, Akinyemi Mandela Fasemore, Muhammad Elhossary, Konrad U. Förstner

   Proceedings of Machine Learning Research 170, 68–72

   proceedings

   BibTeX

   @inproceedings{pmlr-v170-muller22a,
     title     = {A lesson for teaching fundamental Machine Learning concepts and skills to molecular biologists},
     author    = {M{\"u}ller, Rabea and Fasemore, Akinyemi Mandela and Elhossary, Muhammad and F{\"o}rstner, Konrad U.},
     booktitle = {Proceedings of the Second Teaching Machine Learning and Artificial Intelligence Workshop},
     series    = {Proceedings of Machine Learning Research},
     volume    = {170},
     pages     = {68--72},
     year      = {2022},
     publisher = {PMLR},
     url       = {https://proceedings.mlr.press/v170/muller22a.html}
   }

4. 2020

   The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes

   Hendrik Melior, Sandra Maaß, Siqi Li, Konrad U. Förstner, Saina Azarderakhsh, Adithi R. Varadarajan, Maximilian Stötzel, Muhammad Elhossary, Susanne Barth-Weber, Christian H. Ahrens, Dörte Becher, Elena Evguenieva-Hackenberg

   mBio 11(3)

   doi:10.1128/mbio.01027-20

   BibTeX

   @article{Melior2020,
     title     = {The Leader Peptide {peTrpL} Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes},
     author    = {Melior, Hendrik and Maa{\ss}, Sandra and Li, Siqi and F{\"o}rstner, Konrad U. and Azarderakhsh, Saina and Varadarajan, Adithi R. and St{\"o}tzel, Maximilian and Elhossary, Muhammad and Barth-Weber, Susanne and Ahrens, Christian H. and Becher, D{\"o}rte and Evguenieva-Hackenberg, Elena},
     journal   = {mBio},
     volume    = {11},
     number    = {3},
     year      = {2020},
     publisher = {American Society for Microbiology},
     doi       = {10.1128/mbio.01027-20}
   }

5. wip

   Web platform for comparative gene regulation information of Gammaproteobacteria based on multi-omics data

   Muhammad Elhossary, Lauren Walling, Kai Papenfort, Gisela Storz, Konrad U. Förstner

   in preparation

~ $ ls -R skills # tools & languages

~ $ history # conferences, teaching & more