Shaurita's Computational Notebook
About
Introduction
Daily Entries
2025
May 8, 2025
2024
October 9, 2024
Projects
Pulmonary Arterial Hypertension
To-Do List
Completed Tasks
Current Status (as of May 08, 2025)
ME/CFS
To-Do List
Completed Tasks
Current Status (as of May 08, 2025)
CF
To-Do List
Completed Tasks
Current Status (as of May 08, 2025)
Specific Aims Tracker
Aim 1: To develop and refine algorithms that analyze and integrate transcriptomic and genomic sequencing data to identify genetic modifiers of the HPAH phenotype in our cohort.
Objective
Sub-Aim 1.1: To identify potential genetic modifiers for HPAH.
Sub-Aim 1.2: To extract protein-protein interactions (PPIs) networks.
Sub-Aim 1.3: To generate a network of hub genes.
Aim 2: To identify and validate candidate drug targets for PAH.
Objective
Sub-Aim 2.1: To obtain reversing gene expression signatures.
Sub-Aim 2.2: To implement knowledge graph-based drug repositioning methods.
Sub-Aim 2.3: To validate the efficacy of identified drug candidates in PAH models.
Professional Development
Skill Development
Technical Skills
Soft Skills
Networking & Collaborations
Conferences & Workshops
Collaborations
Publications & Presentations
Published Work
In-Progress Work
Peer Review & Editorial Experience
Peer Review
Editorial Roles
Career Planning
4.1 Short-Term Goals
4.2 Long-Term Goals
4.3 CV & Portfolio Development
Self-Reflection & Feedback
Reflective Journal
Feedback from Mentors & Peers
Appendices
Appendix A: Extended Methodologies
Automated Workflow for Extracting and Analyzing Gene-Disease Associations in Rare Diseases Using RENET2, Comparative Tools, and Advanced Functional Annotation
Automated Extraction of Gene-Disease Associations Using RENET2
Appendix B: Troubleshooting Guides
Appendix C: Glossary
Appendix D: Additional Resources
References
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Shaurita’s Computational Notebook
Appendix C: Glossary
Definitions of terms specific to computational biology and bioinformatics.