Gero Doose

 

phd

Gero Doose

Junior Research Group

Transcriptome Bioinformatics

LIFE - Leipzig Research Center

for Civilization Diseases

University Leipzig

Haertelstrasse 16-18

04107 Leipzig


E-mail: gero@bioinf.uni-leipzig.de

Phone: +49 341 97 16 693

Background:

I studied bioinformatics and genome research at the university of Bielefeld. As part of Jens Stoye's group I wrote my bachelor thesis in the field of genome informatics. Afterwards I obtained a master's degree in bioinformatics at the Ludwig-Maximilians-Universität and the Technische Universität München. During my studies I participated in a research project in Dmitrij Frishman's group concerning a machine-learning approach for predicting protein solubility. In the statistical genetics group I worked on RNA structure prediction algorithms and wrote my master thesis under the supervision of Dirk Metzler.


I received my Ph.D. (Dr. rer. nat.) with the predicate 'magna cum laude' from the University of Leipzig, where I worked at the Interdisciplinary Center for Bioinformatics in the group of Peter Stadler and Steve Hoffmann's junior research group which belongs to the LIFE research cluster. My research focused on the computational analysis of high-throughput sequencing data.

Publications:


Rituparno Sen, Gero Doose, Peter F. Stadler: Rare Splice Variants in Long Non-Coding RNAs. Non-Coding RNA 2017


Stephan H. Bernhart, Helene Kretzmer, Lesca M. Holdt, Frank Jühling, Ole Ammerpohl, Anke K. Bergmann, Bernd Northoff, Gero Doose, Reiner Siebert, Peter F. Stadler, Steve Hoffmann: Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. Sci. Rep. 2016


Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Sci. Rep. 2016


Shostak A, Ruppert B, Ha N, Bruns P, Toprak UH; ICGC MMML-Seq Project., Eils R, Schlesner M, Diernfellner A, Brunner M: MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation. Nat Commun. 2016


Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Hummel M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenze D, Loeffler M, Lopez C, MacLeod RA, Martens JH, Kulis M, Martin-Subero JI, Möller P, Nagel I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG; ICGC MMML-Seq project; BLUEPRINT project, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B: DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat. Genet. 2015


Doose G, Haake A, Bernhart SH, Lopez C, Duggimpudi S, Wojciech F, Bergmann AK, Borkhardt A, Burkhardt B, Claviez A, Dimitrova L, Haas S, Hoell JI, Hummel M, Karsch D, Klapper W, Kleo K, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Lenze D, Loeffler M, Mantovani-Löffler L, Möller P, Ott G, Richter J, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schneider M, Scholz I, Stilgenbauer S, Stunnenberg HG, Szczepanowski M, Trümper L, Weniger MA; ICGC MMML-Seq Consortium, Hoffmann S, Siebert R, Iaccarino I: MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells. PNAS 2015


Wagener R, Aukema SM, Schlesner M, Haake A, Burkhardt B, Claviez A, Drexler HG, Hummel M, Kreuz M, Loeffler M, Rosolowski M, López C, Möller P, Richter J, Rohde M, Betts MJ, Russell RB, Bernhart SH, Hoffmann S, Rosenstiel P, Schilhabel M, Szczepanowski M, Trümper L, Klapper W, Siebert R; ICGC MMML-Seq-Project.; "Molecular Mechanisms in Malignant Lymphomas" Network Project of the Deutsche Krebshilfe: The PCBP1 gene encoding poly(rC) binding protein I is recurrently mutated in Burkitt lymphoma. Genes Chromosomes Cancer. 2015


Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermüller J, Stadler PF:  A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection. Genome Biol. 2014


Schneider H, Bartschat S, Doose G, Maciel L, Pizani E, Bassani M, Torres FA, Will S, Raiol T, Brigido M, Walter ME, Stadler PF: Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115. Advances in Bioinformatics and Computational Biology 2014


Nitsche A*, Doose G*, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF: Atypical RNAs in the coelacanth transcriptome. J Exp Zool Mol Dev Evol. 2014 (* authors contributed equally)


Amman F, Bernhart SH, Doose G, Hofacker IL, Qin J, Stadler PF, Will S: The Trouble with Long-Range Base Pairs in RNA Folding. Advances in Bioinformatics and Computational Biology 2013


Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machne R, Mörl M, Hoffmann S, Stadler PF: Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biol. 2013


Doose G, Metzler D: Bayesian Sampling of evolutionarily conserved RNA secondary structures with pseudoknots. Bioinformatics 2013


Smialowski P, Doose G, Torkler P, Kaufmann S, Frishman D: PROSO II - a new method for protein solubility prediction. FEBS J. 2012