Muhammad Arshad Email & Phone Number

Abu Dhabi, United Arab Emirates

Abu Dhabi, United Arab Emirates

• Deployed metaWRAP pipeline for whole-metagenome shotgun sequencing data analysis for microbiome studies
• Leading a human metagenome research to study infant gut microbial community dynamics in two health contexts: a). infants born from normal-weight healthy mothers, b). infants born from obese but otherwise healthy mothers
• Leading an environmental metagenome project to identify microbial communities from the extreme (hot) environment within the UAE including Eastern mangroves, Saadiyat channels and Cyanobacterial mats.
• Set up a workflow for small RNA (microRNA) data analysis locally using shell script environment
• Integrated the phylogenetic analysis pipeline for SARS-CoV-2 (COVID-19) research at New York University, Abu Dhabi, UAE
• Contributed to other projects such as a) single cell RNA data analysis with monocle, b) running CellRanger count on 10x data, and c) identification of antibiotic resistance genes

Calgary, Canada Area

• Took a lead role on the biological data analysis team; developing, implementing "omics" data analysis plan, and supervised the implementation
• Analyzed whole genome sequencing data for genome-wide association study (GWAS) in children exposed to natural adversities
• Analyzed mental health research and clinical trial data using longitudinal and predictive modelling
• Presented results in collaborative meetings and integrated new data analysis techniques, tools and workflow into the project
• Supervised Masters and PhD students and research staff for analysis design, development and training

Calgary, Canada Area

• Identified SNPs that showed association with child resilience to natural adversities
• Using high throughput mRNA sequencing data, I identified differentially expressed genes in resilient verses non-resilient children
• Analyzed metabolite data on cortisol stress hormone and predicted child resilience to natural disaster using cortisol and other child and family variables
• Built predictive models using a data set of >15,000 subjects, and identified predictors of maternaldepression and anxiety and how they impacts child development

London, Canada Area

• Through transcriptomics approach, I identified differentially expressed genes and metabolic pathway under heat stress in alfalfa
• Conducted LC-MS/MS experiments to identify miR156-regulated proteins in response to heat stress in alfalfa
• Carried out deep sequencing of small RNA to discover alfalfa microRNA in response to heat stress, using suitable bioinformatics tools

Faisalabad, Punjab, Pakistan

• Taught plant biotechnology and bioinformatics courses to Undergraduate, MPhil and PhD students
• Supervised MPhil and PhD students on their thesis projects specifically on NGS work
• Prepared and submitted research grant proposals for external funding
• Performed other departmental duties related to research and student management

London, Canada Area

• I generated transgenic alfalfa with improved drought, salt and heat stress tolerance
• Performed RNA-seq assembly and analysis of alfalfa root transcriptome (de novo and reference) in UNIX shell scripting environment
• Through NGS approaches, I identified differentially expressed genes targeted by microRNA156 under drought stress
• Using various molecular techniques (5‘ RACE, ChIP-qPCR etc.), I investigated miR156/SPL network and explored mechanisms how microRNA156 regulates transcription factors and downstream effector genes
• Conducted physiological and molecular analysis on alfalfa plants overexpressing miR156 under mild, moderate and severe salinity stress
• Planned CRISPR/Cas9 experiments to downregulate protein phosphatase 2C and improve drought stress tolerance in alfalfa

Vancouver, Canada Area

• Assisted in developing protocol for RNA extraction and purification from Western Redcedar heartwood; the most difficult portion to get RNA
• Used heartwood RNA to Synthesize cDNA libraries for RNA-seq (NGS)
• Performed sequencing reactions in MiSeq Sequencing System (Illumina)

Vancouver, Canada Area

• Conducted group tutorials related to class lectures
• Engaged students in discussion on various topics of plant biology research
• Supervised students experiments in the teaching laboratory
• Delivered guest lectures to the Biology class at Simon Fraser University BC

Burnaby, BC, Canada

• Organised social events including movies nights, fundraising and cultural shows
• Managed executive team and looked over their duties
• Public speaking

Vancouver, Canada Area

• Established a collaborative research project between Simon Fraser University BC and University of California, Davis.
• Serve as a bridge to bring together Simon Fraser University BC and Monsanto Canada to jointly work on a project bearing a commercial value.
• Successfully developed relationship between Simon Fraser University BC and Syngenta Canada for joint investment in the future projects. Graduate Student Mentor
• Guided new comers and get them familiarized with the university facilities
• Touched-based with them regarding questions and concerns
• Led a small group of new students for a campus tourStudent Fundraiser