Publications

An up to date list of my publications:

Journal Articles

- 2023 -

- Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN): Paula Korkuc, Guilherme B. Neumann, Deike Hesse, Danny Arends, Monika Reißmann, Siham Rahmatalla, Katharina May, Manuel J. Wolf, Sven König, Gudrun A. Brockmann - Genes (2023)

- Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing: Guilherme B Neumann, Paula Korkuc, Danny Arends, Manuel J Wolf, Katharina May, Sven König, Gudrun A Brockmann - Frontiers in Genetics (2023)

- High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin: Shijie Lyu*, Danny Arends*, Mostafa K. Nassar, A. Weigend, S. Weigend, E. Wang, Gudrun A Brockmann - Poultry Science (2023)

- 2022 -

- MiRNA profiling in intrauterine exosomes of pregnant cattle on day 7: Shijie Lyu, Yaying Zhai, Shi Qiaoting, Qiuxia Chu, Fuying Chen, Xinglei Qi, Danny Arends, Gudrun A Brockmann, Eryao Wang, Yajie Feng, Zijing Zhang - Frontiers in Veterinary Science (2022)

- Review: Genetic and Protein Variants of Milk Caseins in Goats: Siham A Rahmatalla, Danny Arends, Gudrun A Brockmann - Frontiers in Genetics (2022)

- Association between Fatty Acid Composition in Hair and Energy Availability during Early Lactation in Simmental and German Holstein Cows: Ramona Wulf, Danny Arends, Dirk Dannenberger, Thomas Ettle, Ulrich Meyer, Uwe Mohr, Gudrun A Brockmann - Metabolites (2022)

- A 5′ UTR Mutation Contributes to Down-Regulation of Bbs7 in the Berlin Fat Mouse: Kourosh Mohebian, Deike Hesse, Danny Arends, Gudrun A Brockmann - International Journal of Molecular Sciences (2022)

- Effects of DGAT1 on milk performance in Sudanese Butana × Holstein crossbred cattle: Salma Elzaki, Paula Korkuc, Danny Arends, Monika Reißmann, Siham A Rahmatalla, Gudrun A Brockmann - Tropical Animal Health and Production (2022)

- QTL-mapping in the obese Berlin Fat Mouse identifies additional candidate genes for obesity and fatty liver disease: Manuel Delpero, Danny Arends, Aimée Freiberg, Gudrun A Brockmann, Deike Hesse - Scientific Reports (2022)

- Validation of somatic cell score-associated SNPs from Holstein cattle in Sudanese Butana and Butana × Holstein crossbred cattle: Salma Elzaki, Paula Korkuc, Danny Arends, Monika Reißmann, Siham A. Rahmatalla, Gudrun A Brockmann - Tropical Animal Health and Production (2022)

- Variation in Blood Lead (Pb) Accumulation Is Strongly Influenced by Genetics: Danila Cuomo, Danny Arends, David Threadgill - Environmental and Molecular Mutagenesis (2022)

- Identification of four novel QTL linked to the metabolic syndrome in the Berlin Fat Mouse: Manuel Delpero, Danny Arends, Maximilian Sprechert, Florian Krause, Oliver Kluth, Annette Schürmann, Gudrun A Brockmann, Deike Hesse - International Journal of Obesity (2022)

- A deletion containing a CTCF-element in intron 8 of the Bbs7 gene is partially responsible for juvenile obesity in the Berlin Fat Mouse: Florian Krause, Kourosh Mohebian, Manuel Delpero, Deike Hesse, Ralf Kühn, Danny Arends, Gudrun A Brockmann - Mammalian Genome (2022)

- Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line: Danny Arends, Stefan Kärst, Sebastian Heise, Paula Korkuc, Deike Hesse, Gudrun A Brockmann - Genetics (2022)

- 2021 -

- Design and performance of a bovine 200k SNP chip developed for endangered German Black Pied cattle (DSN): Guilherme B Neumann, Paula Korkuc, Danny Arends, Manuel J Wolf, Katharina May, Monika Reißmann, Salma Elzaki, Sven König, Gudrun A Brockmann - BMC Genomics (2021)

- Sex-specific genetic architecture in response to American and ketogenic diets: Anna Salvador, Danny Arends, William Barrington, Ahmed Elsaadi, Gudrun A Brockmann, David Threadgill - International Journal of Obesity (2021)

- Genomic loci affecting milk production in German Black Pied cattle (DSN): Paula Korkuc, Danny Arends, Katharina May, Sven König, Gudrun A Brockmann - Frontiers in Genetics (2021)

- Capture Sequencing to Explore and Map Rare Casein Variants in Goats: Siham A Rahmatalla, Danny Arends, Ammar Said Ahmed, Lubna M Hassan, Stefan Krebs, Monika Reissmann, Gudrun A Brockmann - Frontiers in Genetics (2021)

- A Platform for Experimental Precision Medicine: The Extended BXD Mouse Family: David G Ashbrook*, Danny Arends*, Pjotr Prins, Megan K Mulligan, ..., Lu Lu, Robert W Williams - Cell Systems (2021)

- Implementation of an Economic Lifetime Net Merit for the Dual-Purpose German Black Pied Cattle Breed: Saskia Meier, Danny Arends, Paula Korkuc, Sandra Kipp, Dierck Segelke, Günther Filler, Gudrun A Brockmann - Agriculture (2021)

- 2020 -

- Identification of novel potential type 2 diabetes genes mediating β-cell loss and hyperglycemia using positional cloning: Heja Aga, Nicole Hallahan, Pascal Gottmann, Markus Jähnert, Sophie Osburg, Gunnar Schulze, Anne Kamitz, Danny Arends, ..., Annette Schürmann, Heike Vogel - Frontiers in Genetics (2020)

- A genome-wide association study for clinical mastitis in the dual-purpose German Black Pied cattle breed: Saskia Meier, Danny Arends, Paula Korkuc, Guilherme B Neumann, Gudrun A Brockmann - Journal of Dairy Science (2020)

- Strain, Sex, and Diet Dependent Responses to American and Ketogenic Diets in Mice: Anna Salvador, Danny Arends, Gudrun A Brockmann, David Threadgill - Current Developments in Nutrition (2020)

- Whey protein polymorphisms in Sudanese goat breeds: Siham A Rahmatalla, Danny Arends, Ammar Said Ahmed, Monika Reissmann, Gudrun A Brockmann - Tropical Animal Health and Production (2020)

- Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation: Kristin Schwerbel, Anne Kamitz, Natalie Krahmer, Nicole Hallahan, Markus Jähnert, Pascal Gottmann, Sandra Lebek, Tanja Schallschmidt, Danny Arends, ..., Annette Schürmann - Journal of Hepatology (2020)

- 2019 -

- DNA sequence variants and protein haplotypes of casein genes in German Black Pied cattle (DSN): Saskia Meier, Paula Korkuc, Danny Arends, Gudrun A Brockmann - Frontiers in Genetics (2019)

- Weed Suppression in Only-Legume Cover Crop Mixtures: Heba Elsalahy, Thomas Döring, Sonoko Bellingrath-Kimura, Danny Arends - Agronomy (2019)

- Systems Genetics for Evolutionary Studies: Pjotr Prins, Geert Smant, Danny Arends, Megan K Mulligan, Rob W Williams, Ritsert C. Jansen - Evolutionary Genomics (2019)

- Unterschiedliche Fettspeicherung in verschiedenen Linien der Berliner Fettmaus assoziiert mit einer Varianz in der Insulinresistenz: Deike Hesse-Wilting, Aimee Freiberg, Max Sprechert, Manuel Delpero, Florian Krause, Annette Schürmann, Danny Arends, Gudrun A Brockmann - Diabetologie und Stoffwechsel (2019)

- Finding the optimal imputation strategy for small cattle populations: Paula Korkuc, Danny Arends, Gudrun A Brockmann - Frontiers in Genetics (2019)

- Genetic dissection of femoral and tibial microarchitecture: Lu Lu, Jinsong Huang, Fuyi Xu, Zhousheng Xiao, Jing Wang, Bing Zhang, Nicolae Valentin David, Danny Arends, ... , Charles R. Farber, Leigh Darryl Quarles, Robert W Williams - JBMR Plus (2019)

- 2018 -

- High dosage of zinc modulates T-cells in a time-dependent manner within porcine gut-associated lymphatic tissue: Susanne Kreuzer-Redmer, Danny Arends, Jasper N Schulte, Diana Karweina, Paula Korkuc, ..., Francois Meurens, Gudrun A Brockmann - British Journal of Nutrition (2018)

- Genetic diversity of Nubian ibex in comparison to other ibex and domesticated goat species: Lubna M. A. Hassan, Danny Arends, Siham A. Rahmatalla, Monika Reissmann, Henry Reyer, Klaus Wimmers, Sumaia M. A. Abukashawa, Gudrun A Brockmann - European Journal of Wildlife Research (2018)

- 1-step versus 2-step imputation: a case study in German Black Pied cattle: Paula Korkuc, Danny Arends, Carsten Scheper, Katharina May, Sven König, Gudrun A Brockmann - European Journal of Wildlife Research (2018)

- Genetic Contribution to Initial and Progressive Alcohol Intake Among Recombinant Inbred Strains of Mice: Megan K Mulligan, Wenyuan Zhao, Morgan Dickerson, Danny Arends, ..., Lu Lu, Byron C Jones - Frontiers in Genetics (2018)

- Genome-wide association study of body morphological traits in Sudanese goats: Siham A Rahmatalla, Danny Arends, Monika Reissmann, Klaus Wimmers, Henry Reyer, Gudrun A Brockmann - Animal Genetics (2018)

- Reducing the interval of a growth QTL on chromosome 4 in laying hens: Shijie Lyu, Danny Arends, Mostafa K Nassar, A. Weigend, S. Weigend, R. Preisinger, Gudrun A Brockmann - Animal Genetics (2018)

- netgwas: An R Package for Network-Based Genome-Wide Association Studies: Pariya Behrouzi, Danny Arends, Ernst C. Wit - arxiv.org (2018)

- Invited review: Genetic and genomic mouse models for livestock research: Danny Arends, Deike Hesse, Gudrun A Brockmann - Archiv für Tierzucht (2018)

- An Integrated Systems Genetics and Omics Toolkit to Probe Gene Function: Hao Li, Xu Wang, Daria Rukina, ..., Danny Arends, ... , Robert W Williams, Johan Auwerx - Cell Systems (2018)

- 2017 -

- Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits: Siham A Rahmatalla, Danny Arends, Monika Reissmann, Ammar Said Ahmed, Klaus Wimmers, Henry Reyer, Gudrun A Brockmann - BMC Genetics (2017)

- Milk protein polymorphisms and casein haplotypes in Butana cattle: Ammar Said Ahmed, Siham Rahmatalla, Ralf Bortfeldt, Danny Arends, Monika Reissmann, Gudrun A Brockmann - J Appl Genetics (2017)

- Systems Genetics of Obesity: Gudrun A Brockmann, Danny Arends, Sebastian Heise, Ayca Dogan - Systems Genetics: Methods and Protocols (2017)

- Genetic diversity of Syrian Arabian horses: Saria Almarzook, Monika Reissmann, Danny Arends, Gudrun A Brockmann - Animal Genetics (2017)

- Fine mapping of a distal chromosome 4 QTL affecting growth and muscle mass in a chicken advanced intercross line: Shijie Lyu, Danny Arends, Mostafa K Nassar, Gudrun A Brockmann - Animal Genetics (2017)

- reGenotyper: Detecting mislabeled samples in genetic data: Konrad Zych, Basten L Snoek, Mark Elvin, Miriam Rodriguez, K Joeri van der Velde, Danny Arends, ... , Ritsert C. Jansen, Yang Li - PLoS ONE (2017)

- 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)

- Feeding of Enterococcus faecium NCIMB 10415 leads to intestinal miRNA-423-5p induced regulation of immune-relevant genes: Susanne 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, 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, 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, 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, K Joeri van der Velde, ... , Ritsert C Jansen, 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, 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, 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, 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, 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*, K Joeri Van der Velde*, Danny Arends*, Yang Li*, Antje Beyer, ... , Ritsert C. Jansen, Jan E. Kammenga, 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, Klaus Schughart - Briefings in Bioinformatics (2011)

- 2010 -

- R/qtl: high throughput Multiple QTL mapping: Danny Arends, Pjotr Prins, Ritsert C Jansen, 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 (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

- Workshop CTL mapping Danny Arends (2018)
- Introduction into R Danny Arends (2011)
- MQM for R/qtl tutorial Danny Arends, Pjotr Prins, Karl W Broman (2010)
- R cheat sheet Danny Arends (2009-2010)

Acknowledged in

- Detecting epistatic selection with partially observed genotype data by using copula graphical models: Pariya Behrouzi, Ernst C. Wit - Journal of the Royal Statistical Society (2018)

- RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection: Esther Wilk, Ashutosh K. Pandey, Sarah Rebecca Leist, Bastian Hatesuer, Matthias Preusse, Claudia Pommerenke, Junxi Wang, Klaus Schughart - BMC Genomics (2015)

- Probability genotype imputation method and integrated weighted lasso for QTL identification: Nino Demetrashvili, Edwin R. Van den Heuvel, Ernst C. Wit - BMC Genetics (2013)

- Introducing Data Provenance and Error Handling for NGS Workflows within the MOLGENIS Computational Framework: Heorhiy Byelas, Martijn Dijkstra, Morris A. Swertz - Bioinformatics (2012)

- 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, Ritsert C Jansen - BMC Bioinformatics (2009)

- Generalizing genetical genomics: getting added value from environmental perturbation: Yang Li, Rainer Breitling, Ritsert C. Jansen - Trends in Genetics (2008)

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Last modified: 02 Mar 2023, 12:47 | Edit