Professional Preparation

 

Researcher. UPSC (Umeå Plant Science Center), Umeå, Sweden. 2015-present

 

Post-doc. UPSC (Umeå Plant Science Center), Umeå, Sweden. 2012-2015

 

Technical Officer. EMBL (European Molecular Biology Laboratory), Heidelberg, Germany. 2008-2011

 

PhD student. German Cancer Research Centre (DKFZ), Germany. 2004-2008

 

Project leader. LION bioscience AG, Heidelberg, Germany. 2001-2004

 

Master of Bioinformatics, University Bordeaux I, France.  2000-2001

 

Bachelor of cellular and molecular biology, University Bordeaux II, France. 1997-1999

 

 

Selected Publications

David Sundell et al., AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula, Plant Cell (2017)

 

Teresa Laitinen*, Kris Morreel*, Nicolas Delhomme*, et al., A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism, Plant Physiology  (2017)

 

Bastian Schiffthaler, Myrto Kostadima, NGS Trainer Consortium and Gabriella Rustici* and Nicolas Delhomme*, Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability, PLOS Computational Biology (2016)

 

Delhomme N, Sundström G, Zamani N, Lantz H, Lin Y-C, Hvidsten TR, et al. Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). PLoS ONE (2015)

 

D. Sundell*, C. Mannapperuma*, S. Netotea*, N. Delhomme, Y-C. Lin, A. Sjödin, Y. Van de Peer, S. Jansson, T. Hvidsten and N.R. Street, The Plant Genome Integrative Explorer Resource: PlantGenIE.org, New Phytologist (2015)

 

Nicolas Delhomme*, Robinson KM*, Mähler N, Schiffthaler B, Onskog J, Albrectsen BR, Ingvarsson PK, Hvidsten TR, Jansson S, Street NR. Populus tremula (European aspen) shows no evidence of sexual dimorphism. BMC Plant Biol. (2014)

 

Björn Nystedt. Nathaniel R. Street, Anna Wetterbom, Andrea Zuccolo, Yao-Cheng Lin, Douglas G. Scofield, Francesco Vezzi, Nicolas Delhomme et al. The Norway spruce genome sequence and conifer genome evolution. Nature (2013)

 

Jonathan Landry et al., The Genomic and Transcriptomic Landscape of a HeLa Cell Line. G3 (Bethesda) (2013)

 

 Nicolas Delhomme, Ismaël Padioleau and Eileen E. M. Furlong and Lars M. Steinmetz, easyRNASeq: a bioconductor package for processing RNA-Seq data, Bioinformatics (2012).

 

Daniel Haag, Petra Zipper, Viola Westrich, Daniela Karra, Karin Pfleger, Grischa Toedt, Frederic Blond, Nicolas Delhomme, Meinhard Hahn, Julia Reifenberger, Guido Reifenberger and Peter Lichter, Nos2 Inactivation Promotes the Development of Medulloblastoma in Ptch1+/- Mice by Deregulation of Gap43-Dependent Granule Cell Precursor Migration, PLoS Genet (2012)

 

Stefan Bonn et al., Tissue specific analysis of chromatin state reveals temporal signatures of enhancer activity during embryonic development, Nature Genetics (2012)

 

Anton Khmelinskii, Matthias Meurer, Nurlanbek Duishoev, Nicolas Delhomme, Michael Knop, Seamless Gene Tagging by Endonuclease-Driven Homologous Recombination. PLoS ONE (2011)

 

Sebastian Barbus et al., Differential retinoic acid signaling in tumors of long- and short-term glioblastoma survivors. J Natl Cancer Inst (2011)

 

 K T Nishant et al., The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. PLoS Genet (2010)

 

 Daniel Stange et al., Expression of an ASCL2 related stem cell signature and IGF2 in colorectal cancer liver metastases with 11p15.5 gain. Gut (2010)

 

Felix Kokocinski, Nicolas Delhomme, Gunnar Wrobel, Lars Hummerich, Grischa Toedt and Pete Lichter, FACT--a framework for the functional interpretation of high-throughput experiments. BMC Bioinformatics (2005)

 

 

Software and resources

 

Bioconductor packages:

 

▪ easyRNASeq: RNA-Seq data pre-processing

 

▪ genomeIntervals: definition and manipulation of genomic ranges

 

 

Web-resources:

 

▪ PlantGenIE: The Plant Genome Integrative Explorer for arabidopsis, conifers and poplars

 

▪ Complex: Comparative analysis of Plant co-EXpression networks

 

▪ Galaxy: Public plant RNA-Seq data analysis

 

▪ EpiGeneSys Bioinformatics Protocol: Guidelines for RNA-Seq data analysis

 

▪ UPSC bioinformatics: UPSC bioinformatics facility public repository and resources

 

▪ HTS training material repository: High-throughput sequencing training material repository

 

▪ Docker HTS containers: docker containers for HTS data analysis and training

 

▪ UPSC Bioinformatics Facility Git repository: UPSC Git repository