Curriculum Vitae

Madis Rumming, M.Sc.

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Madis Rumming

28 January 1984

Hannover, Germany

German

Married

Comparative Metagenomics, Data Mining, HPC, Visualization, Ontologies, Semantic Web, Databases, Cloud Computing, and Microbiology, Bacteria, Archaea, Viruses

Madis Rumming, M.Sc.

Education & Work Experience

I did my Bachelor studies in Bielefeld at the Faculty of Technology in Bioinformatics & Genome Research, followed by a Master of Science at the same faculty in Computer Science in the Natural Sciences including an Erasmus semester abroad in Tartu, Estonia.

After one year of practical work as a JavaEE web application developer, I moved back to science to work on the challenging problem of interpretation and understanding of metagenomes in the Computational Metagenomics Lab, headed by Dr. Alexander Sczyrba (Bielefeld University). I am a member of the DFG funded international graduate school Computational Methods for the Analysis of the Diversity and Dynamics of Genomes (GRK 1906). I had my PhD defense talk in September 2017. Publishing of my PhD thesis is scheduled for November 2017.

During my PhD studies I worked in 2015 as an intern in the R&D department of Illumina Inc. in Cambridge, UK, in the Computational Biology group to investigate the construction of gold standard variant call sets to evaluate whole-genome somatic variant callers using supervised learning techniques. In 2016 I was also a visiting researcher at the Joint Genome Institue DOE, Walnut Creek, California, United States of America, where I performed studies related to the collectiond and correction of (meta)genomic metadata.

Currently I am working as an informatician (postdoc position) in the SFB 1288 - Practices of Comparing - as a data analyst and infrastructure expert for the digital humanities.

Invited Talks

MADD-Gen & DiDy Workshop Rumming, M.. MeGeMeBase – Metagenome Metadata Data Warehouse. Joint Workshop. Vancouver, Canada, March 2014 & April 2016.
ISMB/ECCB Sczyrba, A., Krueger, J. and Rumming, M.. BiBiCloud: a Cloud-Based Server for Big Data Bioinformatics. Technology Track. Berlin, Germany, 23 July 2013.
EMBRACE Allbio Rumming, M.. CeBiTec - Present, Future and Past and BiBiServ2 - Built to persist. Amsterdam, Netherlands, 18-20 March 2013.

Publications

[1] Yvonne Stolze, Andreas Bremges, Madis Rumming, Christiane Henkel, Irena Maus, Alfred Pühler, Alexander Sczyrba, Andreas Schlüter. Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants. Biotechnology for Biofuels 9 (2016): 156.

[2] Birgit Henrich, Madis Rumming, Alexander Sczyrba, Eunike Velleuer, Ralf Dietrich, Wolfgang Gerlach, Michael Gombert, Sebastian Rahn, Jens Stoye, Arndt Borkhardt, and Ute Fischer. Mycoplasma salivarium as a dominant coloniser of fanconi anaemia associated oral carcinoma. PLoS ONE, 9(3), 2014.

[3] Madis Rumming. Megemebase - data warehouse for metadata-based analysis of bacterial and archaeal genomes in metagenome studies. Proceedings: BREW 2014 – The 12th Bioinformatics Research and Education Workshop, 2014.

[4] Björn Sommer, Jörn Künsemöller, Norbert Sand, Arne Husemann, Madis Rumming, and Benjamin Kormeier. Cellmicrocosmos 4.1 - an interactive approach to integrating spatially localized metabolic networks into a virtual 3d cell environment. In Ana L. N. Fred, Joaquim Filipe, and Hugo Gamboa, editors, BIOINFORMATICS, pages 90–95. INSTICC Press, 2010.

Posters

[P1] Rumming M, Krusche P, Tedder PM. Developing gold standard variant calls for whole-genome somatic variant calling using supervised learning. EMBL Conference: Cancer Genomics. Heidelberg, Germany, 1-4 November 2015.

[P2] Osterholz B, Pätzold W, Fust A, Rumming M, Schlüter A and Sczyrba A. A Bioinformatics Pipeline for the Detection of ß-lactamase Genes in Metagenome Sequence Data and its Application to Production-Scale Biogas Plants. 3rd International Symposium on the environmental Dimension of Antibiotic Resistance. Wernigerode, Germany, 17-21 May 2015. 

[P3] Krüger J, Gatter T, Henke C, Konermann S, Lückner A, Rumming M and Sczyrba A. BiBiCloud - a Cloud Computing Framework for Big Data Bioinformatics. GCB 2014, Bielefeld. 2014; ISSN 1617-5468.

[P4] Henrich B, Rumming M, Sczyrba A, Velleuer E, Dietrich R, Gombert M, Rahn S, Gerlach W, Stoye J, Borkhardt A and Fischer U. Mycoplasma salivarium-colonised oral squamos cell carcinoma. GCB 2014. 2014; ISSN 1617-5468.