Dr. Martin Hölzer

Martin Hölzer

E-Mail: martin.hoelzer*
Room: 08N09
Phone: +49-3641-9-46485
ORCID: 0000-0001-7090-8717


Maximilian Collatz
PhD Student
Room 08N09
Sebastian Krautwurst
PHD Student
Room 08S01
Lisa-Marie Barf
Master Student
Room 08N09
Former members

Ruman Gerst, master thesis

Research Interests

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.

Next-Generation Sequencing, Viruses, Assembly, Transcriptomic, Differential Gene Expression, Positive Selection
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!).



D, Steinbach; M, Hölzer; M, Marz; M, Gajda; FC, Von Rundstedt; MO, Grimm

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.

(Links | BibTeX)


Hölzer, Martin; Marz, Manja

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” (Book Chapter)

Academic Press, 2017, ISSN: 0065-3527.

(Abstract | Links | BibTeX)

P, Möbius; G, Nordsiek; M, Hölzer; M, Jarek; M, Marz; H, Köhler

Complete Genome sequence of JII-1961, a bovine Mycobacterium avium subsp. paratuberculosis field isolate from Germany (Journal Article)

Genome Announcements, 2017.

(Abstract | Links | BibTeX)

J, Fuchs; M, Hölzer; M, Schilling; C, Patzina; A, Schoen; T, Hoenen; G, Zimmer; M, Marz; F, Weber; M, Müller; G, Kochs

Evolution and antiviral specificity of interferon-induced Mx proteins of bats against Ebola-, Influenza-, and other RNA viruses. (Journal Article)

Journal of Virology, pp. JVI.00361-17, 2017.

(Abstract | Links | BibTeX)

P, Möbius; E, Liebler-Tenorio; M, Hölzer; H, Köhler

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.

(Abstract | Links | BibTeX)

K, Riege; M, Hölzer; E., Klassert; E, Barth; J, Bräuer; M, Collatz; F, Hufsky; N, Mostajo; M, Stock; B, Vogel; H, Slevogt; M, Marz

Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D (Journal Article)

Scientific Reports (Nature PG), 7 (40598 ), 2017.

(Abstract | Links | BibTeX)

E., Klassert; J, Bräuer; M, Hölzer; M, Stock; K, Riege; C, Zubiria-Barrera; M., Müller; S, Rummler; C, Skerka; M, Marz; H, Slevogt

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.

(Abstract | Links | BibTeX)


M, Hölzer; V, Krähling; F, Amman; E, Barth; H, Bernhart; O, Carmelo; M, Collatz; G, Doose; F, Eggenhofer; J, Ewald; J, Fallmann; M, Feldhahn; M, Fricke; J, Gebauer; J, Gruber; F, Hufsky; H, Indrischek; S, Kanton; J, Linde; N, Mostajo; R, Ochsenreiter; K, Riege; L, Rivarola-Duarte; H, Sahyoun; J, Saunders; E, Seemann; A, Tanzer; B, Vogel; S, Wehner; T, Wolfinger; R, Backofen; J, Gorodkin; I, Grosse; I, Hofacker; S, Hoffmann; C, Kaleta; F, Stadler; S, Becker; M, Marz

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells (Journal Article)

Scientific Reports (Nature PG), 6 (34589 ), 2016.

(Abstract | Links | BibTeX)

M, Hölzer; K, Laroucau; HH, Creasy; S, Ott; F, Vorimore; PM, Bavoil; M, Marz; K, Sachse

Whole-genome sequence of Chlamydia gallinacea type strain 08-1274/3 (Journal Article)

Genome Announcements, 2016.

(Abstract | Links | BibTeX)


P, Möbius; M, Hölzer; M, Felder; G, Nordsiek; M, Groth; H, Köhler; K, Reichwald; M, Platzer; M, Marz

Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany (Journal Article)

Genome Biol Evol, 2015.

(Abstract | Links | BibTeX)

H, Sahyoun; M, Hölzer; F, Jühling; zu C, Höner Siederdissen; M, Al-Arab; K, Tout; M, Marz; M, Middendorf; F, Stadler; M, Bernt

Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes (Journal Article)

Nucleic Acids Res, 43 (16), pp. 8044-8056, 2015.

(Abstract | Links | BibTeX)


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)

Curriculum Vitae

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


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