Skills
🖥️ Programming Languages
- R
- Python (Beginner)
- SQL (Beginner)
- Command Line Tools (Beginner)
🧬 Bioinformatic Data Analysis
High-Throughput Data Processing
- NanoString nCounter Gene Expression
- Microarray
- Bulk RNA-Sequencing
Data Repositories and Data Acquisition
- NCBI GEO
- R Bioconductor Package: GEOQuery
Differential Expression and Functional Enrichment Analysis
- R Bioconductor Packages: DESeq2, limma, clusterProfiler
- gProfiler (also R package gprofiler2 )
- GSEA
- Metascape
- NIH Database for Annotation, Visualization, and Integrated Discovery (DAVID)
- iDEP
- Qiagen Ingenity Pathway Analysis (IPA)
Network Analysis
- StringDB
- Weighted Gene Correlation Network Analysis (WGCNA)
- Cytoscape
Variant Analysis and Genome Annotation
- VCFtools
- R Package: VcfR
- bedTools
- samTools
- bcfTools
- UCSC Genome Browser
- Intergrative Genomics Viewer (IGV)
📊 Data Visualization and Scientific Illustration
- R package: ggplot2
- R Bioconductor Packages: EnhancedVolcano, ComplexHeatmap
- Python libraries: Seaborn, Matplotlib
- Tableau
- BioRender
- Inkscape
📉 Statistical Analysis
- R
- GraphPad Prism
- SPSS
🧪 Molecular and Cell Biology
- Isolation of Nucleic Acids (DNA/RNA)
- Polymerase Chain Reaction (PCR) Amplification and Quantification of DNA/RNA
- Reverse Transcription PCR (RT-PCR)
- Quantitative or Real-time PCR (qPCR)
- Cell Viability Assessment via MTT Assay
- Enzyme-linked Immunosorbent Assay (ELISA)
🧫 Histology and Immunostaining
Tissue Preparation Techniques
- Formalin Fixed Paraffin-Embedded (FFPE) Tissue Fixation, Processing, and Embedding
- Frozen Tissue Sample Fixation, Processing, and Optimal Cutting Temperature (OCT) Compound Embedding
Histological Staining Methods
- Hematoxylin and Eosin stain (H&E)
- Alcian Blue/ Periodic Acid Schiff (AB/PAS)
- Masson’s Trichrome
Immunostaining
- Immunofluorescence (IF)
- Immunohistochemistry (IHC)
🔬 Microscopy and Digital Pathology/Image Analysis
Imaging Techniques
- Brightfield Microscopy
- Fluorescent Microscopy
- Confocal Microscopy
- Scanning Electron Microscopy (SEM)
Image Processing Tools
- ImageJ/Fiji
- QuPath
- CellProfiler
- Aperio Imagescope
- Zen Lite
🐭 In Vivo Research and Handling
Experimental Model Development
- In Vivo Injury Model Development (Tobacco exposure and bacterial inoculation models)
Animal Care
- Husbandry and Colony Management
Compound Administration
- Intraperitoneal (IP)
- Oral Gavage
Tissue Collection
- Tissue Harvesting and Processing
🦠 Microbiology
Culture Techniques
- Establishing Aerobic and Anaerobic Bacterial Cell Cultures
Specialized Assays
- Isolation and Growing Bacteriophages
- Time-Kill Assays with Antibiotics
- Minimum Inhibitory Concentration (MIC) assessments
📋 Laboratory Management
Operational Skills
- Inventory Management (Quartzy)
- Equipment Troubleshooting
- Media and Buffer Preparation
Documentation and Training
- Standard Operating Procedures (SOP) Documentation
- Training and Mentoring Laboratory Personnel
📄 Office and Productivity
Microsoft Office Suite
- Microsoft Word
- Microsoft Excel
- Microsoft PowerPoint
- Microsoft OneDrive
Google Workspace
- Google Docs
- Google Sheets
- Google Slides
- Google Drive