dannyarends.nl

Publications

An up to date list of my publications:

Journal Articles

- 2016 -

Milk protein polymorphisms and casein haplotypes in Butana cattle: A. Said Ahmed, S. Rahmatalla, R. Bortfeldt, D. Arends, M. Reissmann, G. A. Brockmann - J Appl Genetics (2016)

Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype: Danny Arends, Yang Li, Gudrun A. Brockmann, Ritsert C. Jansen, Robert W. Williams, Pjotr Prins - Journal of open source software (2016)

Fine mapping a major obesity locus (jObes1) using a Berlin Fat Mouse x B6N advanced intercross population: Danny Arends, Sebastian Heise, Stefan Kärst, Jan Trost, Gudrun A. Brockmann - Int J Obes (Lond) (2016)

High Variability of Insulin Sensitivity in Closely Related Obese Mouse Inbred Strains: Sebastian Heise, Jan Trost, Danny Arends, E.K. Wirth, N Schäfer, J. Köhrle, A. Schürmann, Gudrun A. Brockmann - Exp Clin Endocrinol Diabetes (2016)

- GenetNetwork: framework for web-based genetics: Z. Sloan, Danny Arends , Karl W. Broman, A. Centeno, N. Furlotte, H. Nijveen, L. Yan, X. Zhou, Rob W. Williams, Pjotr Prins - The Journal of Open Source Software (2016)

- Systems genetics of obesity: Sebastian Heise, Danny Arends, A. Dogan, Gudrun A. Brockmann - Book Chapter (2016)

- Feeding of Enterococcus faecium NCIMB 10415 leads to intestinal miRNA-423-5p induced regulation of immune-relevant genesSusanne Kreuzer-Redmer, Jennifer C. Bekurtz, Danny Arends, ..., Ralf Einspanier, Gudrun A. Brockmann  - Applied and Environmental Microbiology (2016)

- 2015 -

- The direction of cross obesity after puberty in male but not female offspring: Stefan Kärst*, Danny Arends*, Sebastian Heise*, Jan Trost, ... , Hans Lehrach and Gudrun A. Brockmann - BMC Genomics  (2015)
- Identification of a quantitative trait locus effecting liver fat content and blood glucose in an NZOxB6 backcross: Anne Kamitz, N. Hallahan, ... , Danny Arends, R. Kluge, H.G. Joost and A. Schürmann - Diabetologie und Stoffwechsel  (2015)
- Cell specific eQTL analysis without sorting cells: Harm-Jan Westra*, Danny Arends*, Tõnu Esko, ... , Cisca Wijmenga, Ritsert C Jansen and Lude Franke - PLoS genetics  (2015)
- Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains: Konrad Zych, Yang Li, Joeri K van der Velde, ... , Ritsert C Jansen and Danny Arends  - BMC bioinformatics  (2015)

- 2014 -

- Regulatory Network of Secondary Metabolism in Brassica rapa: Insight into the Glucosinolate Pathway: Dunia Pino Del Carpio, Ram Kumar Basnet, Danny Arends, Ke Lin,  ... , Xiaowu Wang, Ritsert Jansen and Guusje Bonnema  - PLoS one  (2014)
- An Integrative Genomic Approach Identifies Multiple Genes Involved in Cardiac Collagen Deposition: Elisabeth M Lodder, Brendon P Scicluna, Leander Beekman, Danny Arends,  ... , Michiel E Adriaens and Connie R Bezzina  - Circulation: Cardiovascular Genetics  (2014)

- 2013 -

- WormQTLHD - a web database for linking human disease to natural variation data in C. elegans: K Joeri van der Velde*, Mark de Haan*, Konrad Zych, Danny Arends, ... , Ritsert C Jansen, Morris A Swertz and Yang Li - Nucleic Acids Research  (2013)
- Multiple QTL mapping of cardiac collagen deposition in an F2 population of Scn5a mutant mice reveals interaction between Fgf1 and Pdlim3, Gpr158 & Itga6: Elisabeth M Lodder, Leander Beekman, Danny Arends, Michiel E Adriaens, ..., Ritsert C Jansen, Connie R Bezzina - European Heart Journal  (2013)
- Identifying genotype-by-environment interactions in the metabolism of germinating Arabidopsis seeds using Generalized Genetical Genomics: Ronny V L Joosen*, Danny Arends*, Yang Li*,  ... , Ritsert C Jansen and Henk W M  Hilhorst - Plant Physiology (2013)

- 2012 -

WormQTL: Public archive and analysis web portal for natural variation data in Caenorhabditis spp: L. Basten Snoek*, Joeri Van der Velde*, Danny Arends*, Yang Li*, Antje Beyer, ... , Ritsert C. Jansen, Jan E. Kammenga1 and Morris A. Swertz - Nucleic Acids Research (2012)
- xQTL workbench: a scalable web environment for multi-level QTL analysis: Danny Arends*, K Joeri van der Velde*, Pjotr Prins, Karl W Broman, Steffen Moller, Ritsert C Jansen, Morris A Swertz - Bioinformatics (2012)

- 2011 -

- Visualizing the genetic landscape of Arabidopsis seed performance: Ronny V L Joosen*, Danny Arends*, Leo Willems, Wilco Ligterink, Henk Hilhorst, Ritsert C Jansen - Plant Physiology (2011)
- Trans-eQTLs Reveal that Independent Genetic Variants Associated With a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA: Rudolf S N Fehrmann, Ritsert C Jansen, Jan H Veldink, Harm-Jan Westra, Danny Arends , ... , Gerard J te Meerman, Lude Franke - Plos Genetics (2011)
- Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs: Caroline Durrant, Morris A Swertz, Rudi Alberts, Danny Arends, Steffen Möller, ... , Ritsert C Jansen and Klaus Schughart - Briefings in Bioinformatics (2011)

- 2010 -

- R/qtl: high throughput Multiple QTL mapping: Danny Arends, Pjotr Prins, Ritsert C Jansen and Karl W Broman - Bioinformatics (2010)
- XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments: Morris A Swertz, K Joeri van der Velde, Bruno M Tesson, Danny Arends, Ritsert C Jansen, et al. - Genome Biology (2010)
- The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button: Morris A Swertz, Martijn Dijkstra, Tomasz Adamusiak, ... , Danny Arends, Ritsert C Jansen, Helen Parkinson, et al. - BMC Bioinformatics (2010)

Conference Proceedings and Meeting Reports

- Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs: Caroline Durrant, Morris A Swertz, Rudi Alberts, Danny Arends, ... , Ritsert C Jansen, Klaus Schughart - Briefings in Bioinformatic (2011)
- SYSGENET: a meeting report from a new European network for systems genetics: Klaus Schughart, Danny Arends, P Andreux, R Balling, Pjotr Prins - Mammalian Genome 21 (7-8). - p. 331 - 336. (2010)

Thesis

- High-throughput computational methods and software for quantitative trait locus (QTL) mapping: PhD Thesis
- Adding multiple QTL mapping to R/qtl: Master Thesis II
- Machine learning to predict transcriptional regulation: Master Thesis I
- Using Genetical genomics in mouse heamopoietic development: Bachelor Thesis

Tutorials and cheat sheets

- Introduction into R Danny Arends (2011)
- MQM for R/qtl tutorial Danny Arends, Pjotr Prins and Karl W. Broman (2010)
- R cheat sheet Danny Arends (2009-2010)

Acknowledged in

- DesignGG: an R-package and web tool for the optimal design of genetical genomics experiments: Yang Li, Morris A Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling and Ritsert C Jansen - BMC Bioinformatics, 10:188 (2009)
- Generalizing genetical genomics: getting added value from environmental perturbation: Yang Li, Rainer Breitling and Ritsert C. Jansen - Trends in Genetics, 24:518-524 (2008)

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Last modified: 09 Dec 2016, 09:24 | Edit

Contact

Dr. Danny Arends
Lebenswissenschaftliche Fakultät
Albrecht Daniel Thaer-Institut
Humboldt-Universität zu Berlin

Invalidenstraße 42
10115 Berlin
Germany

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Tel: +49 30 2093 6086
Email: Danny.Arends@Gmail.com


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