Hi, I am Gurpreet Kaur, a Bioinformatics & Computational Genomics Scientist ๐งฌ with 14+ years of experience in the area of bioinformatics including leading, managing and analyzing bioinformatics and genomics/multi-omics projects, transforming complex datasets into actionable insights across academia and clinical research ๐ป.
- Omics data analysis and visualization: Upstream and Downstream
- Causal variant discovery (germline and somatic) and variant curation acc. to ACMG guidelines | Genetic modifiers identification | Case-by-case | Cohort
- Differential Gene Expression Analysis | Functional Enrichment Analysis | Network Analysis | RNA Splicing | RNA-Fusion Analysis
- Conceptualization and leading web application development
-
Cystic Fibrosis (Project lead)
- Presented at ACMG Annual Meeting 2023: Identification of molecular modifiers of disease in a group of systematically phenotyped patients with cystic fibrosis
- Mentored this project: Implementing polygenic score catalog calculator for identifying genetic modifiers in cystic fibrosis
- Unraveling the complexity of cystic fibrosis: genetic modifiers and their roles in cystic fibrosis pathogenesis
-
Muscular Dystrophies (Project lead)
- Abstract in Neuromuscular Disorders 2023: Generation and characterization of a novel XMEA mouse model and pharmacological evaluation of autophagy antagonists
- Presented at UAB Postdoc Research Day 2022: Computational workflow of RNA-Seq-based diagnostics for rare, undiagnosed and misdiagnosed diseases: A Case Study
- 2022 Human Mutation Manuscript: DOCKopathies: A systematic review of the clinical pathologies associated with human DOCK pathogenic variants
-
Pediatric Thyroid Cancer (Project lead)
- Presented at CSHL Biological Data Science Meeting 2024: Integrative genomic characterization of a rare pediatric differentiated thyroid cancer from FFPE samples using RNA sequencing and whole exome sequencing
- Investigating the oncogenic variation of pediatric differentiated thyroid cancer from FFPE samples using RNA sequencing and whole exome sequencing
-
Chorioangiomas (placenta tumor):
- 2021: Conceptulalize the project idea, approach, tools, analysis and also the material for the presentation Health Equity Award as a team "BirthSeq-AI" on โDevelopment of an AI-based approach to better understand chorangiomas by studying placental heterogeneityโ, AI against Cancer Data Science Hackathon, UAB
- Slides here: https://www.youtube.com/watch?v=qeVsJACDe88&t=6743s
- 2021: Conceptulalize the project idea, approach, tools, analysis and also the material for the presentation Health Equity Award as a team "BirthSeq-AI" on โDevelopment of an AI-based approach to better understand chorangiomas by studying placental heterogeneityโ, AI against Cancer Data Science Hackathon, UAB
-
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS):
- Led and mentored RNA-Seq analysis, created analysis workflow figure (Fig 1 in the manuscript), performed interpretation of RNA-Seq secondary results including QC, preparation of input metadata, provided my R code and consultation for RNA-Seq tertiary analysis and visulization methods.
-
Neurofibromatosis:
- DITTO4NF: In silico classification and prioritization of likely pathogenic variants for NF1 using explainable machine learning
- Won challenge#2 as a team "DITTO4NF" on "Prioritizing likely pathogenic NF1 germline variants for Neurofibromatosis" at Hack4NF Hackathon by Children's Tumor Foundation, USA. Also won two other prizes: best use of PMP platform and incubation prize
-
Hepatocellular Carcinoma:
-
Pediatric Cancer Cardiotoxicity
-
Amyotrophic Lateral Sclerosis (ALS)
-
Prader-Willi Syndrome (PWS)
- Workflow Manager & Pipelines: Nextflow-based pipelines on High-Performance Computing (HPC) cluster
- Statistics & Visualization: R packages - DESeq2 | limma | ggplot2 | ComplexHeatmap | EnhancedVolcano | UpsetR
- Interactive Visualization: R packages - InteractiveComplexHeatmap | Shiny
- Functional Enrichment Analysis: g:Profiler | Metascape | enrichR
- Network Analysis: Cytoscape | BioNERO R package | STRING
- Variant Analysis: Varsome | Genome Aggregation Database (gnomAD) | ClinVar | DISGENET