- Research Group
- Research Interests
- Conferences, talks and posters
- Short Curriculum Vitae (Full scientific; PDF)
Ruman Gerst, master thesis
Hi, I am Martin and I am a bioinformatician and Post-Doc at the research group of Prof. Dr. Manja Marz. I’m interested in a broad variety of bioinformatical topics, predominantly related to the fast-emerging field of Next-Generation Sequencing (NGS). I am experienced in designing new NGS studies from scratch and in analyzing this kind of data to answer versatile biological questions. My research is further focused on the assembly of smaller and larger genomes, especially by combining short-read data from well established NGS techniques like Illumina with data derived from novel long-read technologies like PacBio and Nanopore. Another big piece of my research is focused on the evaluation of RNA-Seq data, comprising de novo transcriptome assembly, annotation of protein- and non-coding genes, transcript abundance estimation and quantification, and the identification of significant differential expressed genes. I also like viruses. And positive selection. And building up pipelines. It is always important for me to combine different tools, approaches, parameter settings and experiments and to visualize all results in a comprehensive and handsome way to allow other researchers to understand, interpret and dilate the data.
Figure: Summary of my skills and research interests – from a broad overview with NGS (A) to taking a closer look, e.g. with positive selection detection (K) or SNP calling (L). At the end of the day, visualization of the results is the key (M). Click to enlarge (8.4MB!).
Analysis of molecular mechanism of progression of non-muscle- invasive bladder cancer (NMIBC) by genome-wide exome and UTR mutation analysis (Journal Article)
Eur Urol Suppl., 17 (2), pp. e1523, 2018.
Academic Press, 2017, ISSN: 0065-3527.
Complete Genome sequence of JII-1961, a bovine Mycobacterium avium subsp. paratuberculosis field isolate from Germany (Journal Article)
Genome Announcements, 2017.
Journal of Virology, pp. JVI.00361-17, 2017.
Evaluation of associations between genotypes of Mycobacterium avium subsp. paratuberculosis and presence of intestinal lesions characteristic of paratuberculosis (Journal Article)
Veterinary Microbiology, 201 , pp. 188-194, 2017.
Scientific Reports (Nature PG), 7 (40598 ), 2017.
Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection (Journal Article)
Scientific Reports (Nature PG), 7 (40599), 2017.
Scientific Reports (Nature PG), 6 (34589 ), 2016.
Whole-genome sequence of Chlamydia gallinacea type strain 08-1274/3 (Journal Article)
Genome Announcements, 2016.
Genome Biol Evol, 2015.
Nucleic Acids Res, 43 (16), pp. 8044-8056, 2015.
|03/2018||28th Annual Meeting of the Society for Virology, Würzburg (poster, ~1MB)|
|02/2018||33rd Winterseminar der Bioinformatik, Bled, (talk, ~20MB)|
|10/2017||15th Herbstseminar der Bioinformatik, Doubice (Karaoke about pseudoknots in cat tails and the taxonomy of Pokemon)|
|08/2017||AquaDiva Recruitment Symposium, (talk, ~28MB)|
|05/2017||Bioinformatics Mittelerde Meeting, Leipzig (poster, ~1MB)|
|04/2017||Hacken: “Stay Young or Die Trying” – Hackathon on aging, Jena (F.U.N. Coordinator)|
|03/2017||27th Annual Meeting of the Society for Virology, Marburg (poster, ~1MB)|
|03/2017||1st European Virus Bioinformatics Center (EVBC) Meeting, Jena, (Facilitator)|
|02/2017||32nd Winterseminar der Bioinformatik, Bled, (talk, ~17MB)|
|10/2016||14th Herbstseminar der Bioinformatik, Doubice, (talk, ~20MB)|
|04/2016||26th Annual Meeting of the Society for Virology, Münster (poster, ~2MB)|
|02/2016||31th Winterseminar der Bioinformatik, Bled, (talk, ~8MB)|
|10/2015||13th Herbstseminar der Bioinformatik, Doubice|
|09/2015||Elixir Hackathon: RNA tools registry, Copenhagen|
|04/2015||SPP Meeting on “Ecology and Species Barriers in Emerging Viral Diseases”, Bonn|
|03/2015||25th Annual Meeting of the Society for Virology, Bochum (talk, ~34MB)|
|02/2015||30th TBI Winterseminar, Bled (talk, ~71MB)|
|12/2014||SPP Meeting on “Ecology and Species Barriers in Emerging Viral Diseases”, Bonn|
|11/2014||Fight against Ebola – in silico Meeting, Jena, (Coordinator)|
|10/2014||12th Herbstseminar der Bioinformatik, Doubice (talk, ~19MB)|
|02/2014||29th TBI Winterseminar, Bled (talk, ~1MB)|
|10/2013||11th Herbstseminar der Bioinformatik, Doubice (talk, ~6MB)|
Download full CV: PDF
|since 01/2018||PostDoc at Friedrich Schiller University, Jena, RNA Bioinformatics and High-Throughput Analysis|
|01/2018||Doctorate degree: Dr. rer. nat.
Thesis: „The Dark Art of Next-Generation Sequencing: Fundamental approaches for genomics, transcriptomics, and differential gene expression“, Friedrich Schiller University, supervisor: Prof. Dr. Manja Marz
|07/2013 – 01/2018||PhD. Student at Friedrich Schiller University, Jena RNA Bioinformatics and High-Throughput Analysis|
|09/2009 – 05/2012||Student Research Assistent at Friedrich Schiller University, Jena|
|10/2007 – 12/2012||Study of Bioinformatics at Friedrich Schiller University, Jena|