Publications

An up to date list of my publications:

Journal Articles

- 2024 -

Identification of additional body weight QTLs in the Berlin Fat Mouse BFMI861 lines using time series dataManuel Delpero, Paula Korkuć, Danny Arends, Gudrun A. Brockmann, Deike Hesse - Scientific Reports (2024)

- 2023 -

Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets: Anna C Salvador, M Nazmul Huda, Danny Arends, Ahmed M Elsaadi, Anthony C Gacasan, Gudrun A Brockmann, William Valdar, Brian J Bennett, David W Threadgill - Microbiome (2023)

A deleterious mutation in Acat2 promotes ectopic liver fat storage by disturbing cholesterol metabolism in adipose tissue of the Berlin Fat Mouse: Deike Hesse-Wilting, Maximilian Sprechert , Manuel Delpero, Aimée Freiberg, Paula Korkuc, Danny Arends, Gudrun A. Brockmann - Diabetologie und Stoffwechsel (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 originShijie 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 GoatsSiham 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 CowsRamona 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 MouseKourosh 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 cattleSalma 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 diseaseManuel 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)

- GeneNetwork: A 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 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, 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

The effectiveness of cruciate-retaining versus posterior-stabilized designs on extensor mechanism function and knee function in patients after simultaneous bilateral total knee arthroplasty: a two-year retrospective follow-up studySerkan Bakırhan, Ertan Şahinoğlu, Emre Uysal, Bayram Ünver, Vasfi Karatosun - Orthopaedics & Traumatology: Surgery & Research (2023)

Detecting epistatic selection with partially observed genotype data by using copula graphical modelsPariya 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: 18 Mar 2024, 16:53 | Edit