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Dolle Dirk-D.

Dirk-D. Dolle

PostDoc - Laboratoire AMIS CNRS UMR 5288

Contact : dirk-dominik.dolle@univ-tlse3.fr

Research Interests :
In the past I have worked on various different research/development topics including medical database development, miRNA/gene expression analysis, ChIP-chip & ChIP-seq analysis, enhancer prediction & testing, genome annotation & assembly, variant calling, and sequence data storage. I am interested in anything « omics » related, especially when it helps to get a better understanding of what one could call « the source code of life ». Biological organisms are the most complicated and intricate machines known to us and exists in a staggering variety. Yet, all of them start as single cells with a highly compressed instruction set stored in DNA and a set of tools in the shape of proteins and chemical compounds. Understanding how the complexity and variety of life is generated from such a tiny origin will keep the (bio)sciences busy for generations to come and I am happy that I have the opportunity to help shedding light on some of the mechanisms involved.

Current/Ongoing Research :
I have recently switched to the field of ancient DNA and now work on methods to increase the amount of information that can be extracted from samples that are thousands of years old. DNA has proven that it can reliably preserve information in ancient samples across such time scales yet in the majority of cases this information drowns in the noise generated by more recent contamination. This contamination mainly stems from microbes and fungi that have colonised the ancient material over time. Methods for the separation of endogenous (ancient) DNA from the exogenous contamination on the one hand enable researchers to gain more information from a single sample at reduced cost while on the other allow them to analyse more samples for the price of a single (contaminated) sample. In addition, they make samples accessible for research which are too contaminated for direct analysis and hence help to provide a broader picture of the sequence variation that existed thousands of years ago.

Academic background and research experiences :
-  09/2017 - present : PostDoc in the group of Prof. Ludovic Orlando, Laboratoire AMIS CNRS UMR 5288, Faculté de Médecine de Purpan, Université Paul Sabatier, Toulouse, France
-  08/2014 – 08/2017 : Senior Bioinformatician at the Wellcome Trust Sanger Institute, Hinxton, United Kingdom
-  08/2013 – 07/2014 : PostDoc in the group of Dr. Ewan Birney, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
-  12/2012 – 07/2013 : PostDoc in the group of Prof. Dr. Joachim Wittbrodt, Centre for Organismal Studies (COS), Heidelberg, Germany
-  03/2009 – 11/2012 : Ph.D. in the group of Prof. Dr. Joachim Wittbrodt, EMBL/University of Heidelberg, Germany
-  05/2008 - 10/2008 : Diploma thesis at the EMBL Genetics Core Facility, Heidelberg, Germany

Bibliography :
-  Dolle D, Liu Z, Cotten M, Simpson JT, Iqbal Z, Durbin R, McCarthy S, Keane TM. 2017.
Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.
Genome Research. 2017 ;27(2):300-309. doi:10.1101/gr.211748.116.
-  Dolle D, Mateo J, Eichenlaub MP, Sinn R, Reinhardt R, Höckendorf B, Inoue D, Centanin L, Ettwiller L, Wittbrodt J. 2015.
Handling Permutation in Sequence Comparison : Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle.
PLoS ONE 10(10) : e0141487. https://doi.org/10.1371/journal.pone.0141487
-  Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J. 2014.
Genomic and phenotypic characterization of a wild medaka population : Towards the establishment of an isogenic population genetic resource in fish.
G3 : Genes, Genomes, Genetics, vol. 4 no. 3 433-445. https://doi.org/10.1534/g3.113.008722