Dr. Manuel Allhoff

Dr. Manuel Allhoff

Advisor / Co. Advisor

Dr. Costa/ Prof. Berlage


Efficient Algorithms for Motif Discovery on Genomic Signals


AICES Graduate School
RWTH Aachen University
Schinkelstr. 2
D-52062 Aachen, Germany

Phone: +49 (0) 241 80 99 137

Computational Biology Group
Helmholtz Institute for Biomedical Engineering
Centre of Medical Technology (MTZ)
Pauwelsstr. 19
D-52074 Aachen

Phone: +49 (0) 241 80 80 271
Email: allhoff@aices.rwth-aachen.de

Here is my PGP public key.

Research Interests

Next Generation Sequencing, Histone Modification, Hidden Markov Models
Supervisors: Dr. Ivan G. Costa and Prof. Dr. Thomas Berlage


Eduardo G Gusmao, Manuel Allhoff, Martin Zenke and Ivan G. Costa. Analysis of computational footprinting methods for DNase sequencing experiments. Nature Methods, 2016, DOI: 10.1038/nmeth.3772

Manuel Allhoff, Kristin Seré, Heike Chauvistré, Qiong Lin, Martin Zenke and Ivan G. Costa. Detecting differential peaks in ChIP-seq signals with ODIN. Bioinformatics, 2014, DOI: 10.1093/bioinformatics/btu722

Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann and Tobias Marschall. Discovering motifs that induce sequencing errors. BMC Bioinformatics, 2013, 14(Suppl 5):S1, DOI: 10.1186/1471-2105-14-S5-S1

Research Reports

Modeling Sequence-Specific Errors in Second-Generation Sequencing Reads, 2012, Master's Thesis [pdf]


THOR Find differential peaks in ChIP-seq signals with replicates
ODIN Find differential peaks in ChIP-seq signals
Dis-CSE Discover sequence contexts that induce errors in next-generation sequencing reads


Detecting differential peaks in ChIP-seq signals with ODIN, HitSeq, Boston, MA, USA, 2014 [pdf]
Discovering Motifs that Induce Sequencing Errors, RECOMB-seq, Tsinghua University, Beijing, China, 2013 [pdf]


11/2012 - present Doctoral student at AICES Graduate School, RWTH Aachen University, Germany
04/2012 - 10/2012 Member of the Life Science Group at Centrum Wiskunde & Informatica (CWI) Amsterdam, The Netherlands
10/2007 - 10/2012 Studies of Computer Science at Technical University of Dortmund, Germany

Employment History

01/2010 - 03/2012 Research Assistant of the Bioinformatics Group headed by Prof. Dr. Sven Rahmann at Technical University of Dortmund