Khushbu Patel
Bioinformatics Scientist
About
Good to see you here 👋
I'm Khushbu Patel, a bioinformatics scientist based in Georgia, currently working at The Children's Hospital of Philadelphia.
What I do? (For technical folks)
The overarching goal is to build on my extensive experience with multi-omics data from pediatric cancers, applying statistical and computational methods, understanding genomic landscape to identify critical gene and protein targets and understand the underlying mechanisms of pediatric cancers in order to develop effective therapies and minimize long-term side effects.
Okay...for you non-technical amigos
I use cool computer algorithms and write code to make sense out of long strings of letters or large matrices containing thousands of rows and multiple columns with numbers (multi-omics data) to generate valuable insights and report scholarly findings, which are often a part of peer-reviewed manuscripts. These findings add to the knowledge base and can be a useful resource to build targeted therapies. Make sense?
Outside of work...
When I am not working, I love learning new things. I am a sucker for productivity apps (current favorite is notion!) I love to read and paint. I write to express. I read articles everyday to overcome my imposter syndrome and my instagram feed is filled with memes and dog videos. Sunny days make me happy and I am too attached to my roots.
Work
Top Skills
My top skills include analyzing multi-omics data (WGS, WES, RNA-Seq, ChIP-Seq, Microarray), applying statistical methods in hypothesis driven study, data wrangling using programming languages, data mining and data visualization.
Programming Languages
‣ R, Bash, Python, Perl
Tools & Softwares
‣ GATK, bcftools, samtools, STAR, StringTie, Kallisto, MACS2, Homer, RShiny, BBMap, MEME suite, VEP, snakemake, Docker
Methods & Concepts
- Gene set enrichment analysis (GSEA)
- Gene Ontology enrichment analysis (ToppGene, Enrichr)
- Differential Gene expression analysis (DESeq2, EdgeR)
- Dimensionality reduction methods (t-SNE, PCA, hierarchical clustering)
- Sequence Assembly & Alignment (BWA/STAR/BowTie)
- Gene abundance estimations (HTSeq-counts)
- Survival Analysis (survminer and survival R packages)
- Calling and Annotating mutations and genetic aberrations (VarScan2, CNVkit, ClinVar, COSMIC)
- Statistical Analysis (Pearson/Spearman correlation, student t-test, wilcox rank sum test, ANOVA, Kruskal-Wallis test)
Please click here to find my CV for more details.
Contact
If you want to reach out for collaborations, ideas or just to chat – you are very welcome to contact me.
The quickest way to reach me is via LinkedIn although email works too (I try to check my emails regularly).
Khushbu Patel
Bioinformatics Scientist
Shoot me a quick email!
