Welcome

In September 2019, I finished my PhD in Genetics under the Erasmus-Mundus Joint Doctorate Program EGS-ABG, jointly hosted by Aarhus University Center for Quantitative Genetics and Genomics (QGG) and AgroParisTech Génétique Animale et Biologie Intégrative (GABI). The focus of my PhD project was the use of whole-genome sequences to identify causal variants for recessive genetic defects in dairy cattle. The title of the PhD project: “Identification of Causal Factors for Recessive Lethals in Dairy Cattle with Special Focus on Large Chromosomal Deletions”

Ongoing Projects:

• Role of Clonal hematopoiesis in differential DNA methylation
• Genetic determinant of Clonal hematopoiesis

Recently finished Projects

• Genomic Prediction Prediction of genomic breeding values using imputed SNPs, indels and large chromosomal deletion
• GWAS and meta-analysis for female fertility using imputed whole-genome sequence variants and large deletions
• Deletion genotyping using Gaussian mixture model GMM
• Building haplotype reference for imputing chromosomal deletions ImputeDelPipeline

Research Interest

• I am interested in precision health care using genomics and machine learning appraoches:
  • Gene Mapping
  • Genomic prediction: using Frequentist, Bayesian and Deep Learning approaches

Publication

Published

1. Mesbah-Uddin, M., B. Guldbrandtsen, A. Capitan, M. S. Lund, D. Boichard and G. Sahana. Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in 3 Nordic dairy cattle breeds. **Journal of Dairy Science, 2021. **
2. C. Hoze, C. Escouflaire, M. Mesbah-Uddin, et al., Short Communication: A splice site mutation in CENPU is associated with recessive embryonic lethality in Holstein cattle. Journal of Dairy Science, 2020. 103(1): p. 607–612
3. M. Mesbah-Uddin, et al., Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. Journal of Dairy Science, 2019. 102(12): p. 11193–11206
4. Wu, X., M. Mesbah-Uddin, et al., Haplotypes responsible for early embryonic lethality detected in Nordic Holstein. Journal of Dairy Science, 2019. 102(12): p. 11116–11123
5. M. Mesbah-Uddin, et al., A missense mutation (p.Tyr452Cys) in the CAD gene compromises reproductive success in French Normande cattle. Journal of Dairy Science, 2019. 102(7): p. 6340–6356
6. M. Mesbah-Uddin, et al., Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. DNA Research, 2018. 25(1): p. 49-59
7. M. Mesbah-Uddin, et al., In-silico analysis of inflammatory bowel disease (IBD) GWAS loci to novel connections. PLoS One, 2015. 10(3): p. e0119420
8. M. Mesbah-Uddin, Prediction of deleterious nonsynonymous SNPs by integrating multiple classifiers – An application to neurodegenerative diseases. PeerJ PrePrints, 2015. 3: p. e994v1
9. Wu, X., M. Mesbah-Uddin, et al., Novel haplotypes responsible for prenatal death in Nordic Red and Danish Jersey cattle.

Conference

1. Mesbah-Uddin, M., et al. Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle. in Proceedings of the World Congress on Genetics Applied to Livestock Production. 2018. Auckland, New Zealand.Paper Poster
2. Mesbah-Uddin, M., et al., A population scale discovery of large deletions in Holstein, Jersey and Nordic Red Cattle genome, in 36th International Society for Animal Genetics Conference. 2017: Dublin, Ireland. Poster

Github repo:

• ImputeDelPipeline: Pipelines for read-depth genotyping, building haplotype reference panel and imputing large chromosomal deletions along with WGS SNPs and indels
• GWAS: collections of scripts I’m using for GWAS and Meta-analysis
• GenomicPrediction