SHANZIDA SIDDIQUE
Flowood,,Mississippi
Summary
Skilled Individual with experience using High Performance Computing, various bioinformatics softwares, and R programming to aid scientists in a highly collaborative research setting.
Overview
15
15
years of professional experience
Work History
Bioinformatician I
University of Mississippi Medical Center
Jackson, MS
07.2023 - Current
- Conduct NGS data analysis, developing pipelines for Bulk RNA-Seq (mRNA), Small RNA-Seq (miRNA), Whole Genome Sequencing (WGS), Differential Alternative Splicing (DAS), Gene Set Enrichment Analysis (GSEA) pipeline for the Genomics Core Facility
- Utilize genomic tools like STAR, SALMON, featureCounts, FASTQC, Bowtie, BWA, GATK
- Analyze Single-cell RNA-Seq using the R/Bioconductor package 'Seurat' and Bulk RNA-Seq data with DESeq2
- Create comprehensive HTML reports via R Markdown
- Write and maintain scripts in R/Python for data analysis, statistical analysis, and visualization
- Develop bash scripts and manage job submissions on HPC using SGE commands.
Research Associate (Data Science)
Lieber Institute for Brain Development
Baltimore, US
07.2022 - 07.2023
- Engaged in bioinformatics research to elucidate genetic and molecular mechanisms of schizophrenia and related brain disorders
- Integrated large-scale biomedical datasets, enhancing institute-wide projects
- Designed and executed pipelines, advancing research capabilities for genomics and RNAseq studies
- Conducted eQTL analysis by using R/Bioconductor package 'Matrix eQTL' and python package 'tensorQTL' to identify the cis-eQTLs and trans- eQTLs associated with Schizophrenia
- Prioritize causal risk variants within GWAS risk loci through colocalization and mendelian randomization.
Bioinformatics Analyst
School of Medicine, Johns Hopkins University
Baltimore, US
01.2021 - 07.2022
- Focused on identifying pancreatic cancer susceptibility genes through extensive GWAS data analysis
- Used GWAS data analysis tools such as PLINK, Michigan Imputation Server, SNPTEST, METAL, EPACTS etc
- Employed CYBERDUCK for secure file transfers and utilized BBEdit, Sublime text for script management
- Used R packages such as qqman (Manhatttan plots and QQ plots for GWAS data), ggplot2 (bar plots, density plot, etc), dplyr package (modify and summarize tabular data) for GWAS data analysis
- Used different command of BCF tools such as annotate, filter, index, tabix, etc to manipulate files in the Variant Call Format (vcf)
- Developed a pipeline use to infer local ancestry in admixed population by using LAMP-LD and made a R script to plot the output.
NIH Special Volunteer on Bioinformatics data analysis
Vaccine Research Center, NIAID/NIH
Bethesda, US
11.2020 - 01.2021
- Worked on variant calling by using QIAGEN CLC Genomic Workbench.
Graduate Research Assistant
Department of Bioinformatics, Hood College
Frederick, US
05.2019 - 05.2020
- Used large RNA seq data from human brain samples to decipher novel peptides expressed in the human brain by using PGA, a R/Bioconductor package
- Used High-Performance Cluster Computing system (Slurm) to store big proteomics data collected from PRIDE database and searched against peptide of interests
- Discovered novel exonized repetitive elements from human brain samples relevant to neuronal diseases
- Utilized MySQL workbench for creating and manipulating databases
- Used R/Bioconductor package 'airway' for analyzing RNA seq data.
Lab Assistant
Stamford University Bangladesh
Dhaka, Bangladesh
01.2011 - 07.2012
- Aided professor and tutored students to perform Microbiology laboratory courses.
Graduate Research Assistant
International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)
Dhaka, Bangladesh
01.2010 - 07.2011
- Used molecular biology-based detection system such as PCR and Genotyping to identify different cholera strains in estuarine ecosystem of Bangladesh.
Education
Bioinformatics MS -
Hood College
06.2020
Microbiology MS -
Stamford University
05.2012
Microbiology BS -
Stamford University
06.2010
Skills
- Proficient in scripting languages including R, Bioconductor Packages, and Python
- Extensive experience with Linux High Performance Computing (HPC) systems and scripting in Linux/Unix environments
- Skilled in NGS data analysis including RNA-seq, single-cell RNAseq,ChIP-Seq, and ATAC-seq
- Knowledgeable in GWAS data analysis using tools like PLINK, Michigan Imputation Server, SNPTEST, METAL, EPACTS
- Competent in statistical tests and methods such as hypothesis testing, regression modeling, and high-dimensional data analysis
- Familiar with biological databases like NCBI, ENSEMBL, and others
- Experienced in data visualization with tools like Cytoscape, ggplot2, Tableau
- Academic and laboratory experience in genomics/molecular biology
- GitHub: shanzida2014 (https://githubcom/shanzida2014?tab=repositories)
Publication
“Prevalence of Vibrio Cholerae in different food samples in the city of Dhaka, Bangladesh Mrityunjoy, A., Kaniz, F., Fahmida J., Shanzida, JS., Md. Aftab, U. and Rashed, N. International Food Research Journal 20(2): 1017-1022 (2013)
Conference Presentation
“Prevalence of V. Cholerae in Different Water Sources of Bangladesh” (Oral Presentation-26th Annual Conference of Bangladesh Society of Microbiologists, 2012)
Timeline
Bioinformatician I
University of Mississippi Medical Center
07.2023 - Current
Research Associate (Data Science)
Lieber Institute for Brain Development
07.2022 - 07.2023
Bioinformatics Analyst
School of Medicine, Johns Hopkins University
01.2021 - 07.2022
NIH Special Volunteer on Bioinformatics data analysis
Vaccine Research Center, NIAID/NIH
11.2020 - 01.2021
Graduate Research Assistant
Department of Bioinformatics, Hood College
05.2019 - 05.2020
Lab Assistant
Stamford University Bangladesh
01.2011 - 07.2012
Graduate Research Assistant
International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)
01.2010 - 07.2011
Bioinformatics MS -
Hood College
Microbiology MS -
Stamford University
Microbiology BS -
Stamford University
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