Basil Khuder

People
Graduate Research Assistant, Ph.D., Rotation Student

Basil Khuder

Research Interests: Noncoding RNA, Genetics, Genomics and Epigenomics, Proteomics, Gene Regulation and Processing, Machine Learning and Artificial Intelligence.

Research:

Master's Thesis: Analysis of Ultra-Conserved Intronic Regions of Mammalian Fat-Mass and Obesity Gene (FTO)

 

  • Constructed a model to define expression levels of FTO intronic elements across multiple tissues, sequencing libraries, and species.
  • Used publicly available databases to analyze a wide variety of sequencing data including SRA, FASTQ, and SAM/BAM.
  • Created PERL Scripts to identify specific nucleotides of interest within sequencing files.

 

 

Project in Laboratory of Dr. Robert Blumenthal:  Investigation of Specific DNA-Methylation Sites.

 

  • Analysed RNA-Seq and WGBS data from the ENCODE project to investigate methylation sites across endodermal and ectodermal tissue.
  • Using the Genome Analysis Toolkit, SAMTools and Picard Tools, raw sequencing reads were mapped/aligned, and variant-calling was then conducted to produce VCF files.
  • Variant annotation using the Variant Effect Predictor was then completed, and variants of interest were studied further.

 

Publications

Intricacies in Arrangement of SNP Haplotypes Suggest "Great Admixture" That Created Modern Humans

BMC Genomics (Under Review) Authors: Rajib Dutta; Joseph Mainsah; Yuriy Yatskiv; Sharmistha Chakrabortty; Basil Khuder; Patrick Brennan; Shuhao Qiu; Larisa Fedorova; Alexei Fedorov

 

 

Organizations

Founder and Lead Director, YDSOA

--YDSOA is the online community for young data scientists and bioinformaticians

Area of Expertise: 
Noncoding RNA
Genetics
Genomics and Epigenomics
Education: 
B.A. in Psychology, Univ. of Toledo, 2015
Certificate in Biostatistics and Epidemiology, Univ. of Toledo, 2017
M.S. in Bioinformatics, Proteomics, and Genomics, Univ. of Toledo, 2017
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