Genomics
Why conserved genomic regions matter in molecular diagnostics
Conserved regions can provide more robust targets for diagnostic development, especially in the face of high pathogen mutation rates.
Read moreRESEARCH NOTESSmall Notes.
Small Notes.
Big Questions.
A collection of notes, thoughts, and resources from my research journey — from literature insights to technical workflows, and everything in between.
ALL NOTES (8)
Bioinformatics
Building a diagnostic primer design workflow: Clean architecture & thermodynamic fidelity
Practical considerations in building PrimerLab Genomic: automated oligo design, ViennaRNA hairpin evaluation, and test-driven domain boundaries.
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Environment
Understanding flood severity in Sumatra: Triangulating satellite alerts with public discourse
Empirical synthesis linking Global Forest Watch integrated alerts and NASA precipitation with 132k social media posts across 77 spatial units in northern Sumatra.
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Pharmacology
Molecular docking notes: Stereochemical refinement of Mitragyna alkaloids
Comparative docking notes analyzing mitragynine, rhynchophylline, and control opioids against crystallographic OPRD1 (6PT3) and KOR (4DJH) structures.
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Genomics
From FASTQ to insights: Practical transcriptomic pipelines & batch effect handling
A step-by-step summary of modern RNA-seq data pipelines: quality control, decoy-aware pseudoalignment, dispersion modeling with DESeq2, and pathway enrichment.
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Environment
Field notes: Environmental telemetry & ground truth in rural Sumatra
Practical takeaways from ground-truth hydrological verification across rural Sumatra: telemetry sensor deployment, SAR backscatter validation, and participatory mapping.
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AMR
Understanding antimicrobial resistance through comparative genomics and MGE co-localization
Comparative metagenomic notes exploring the decoupling between raw ARG abundance and mobile genetic element transfer potential across human gut cohorts.
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Bioinformatics
Notes from building a genomic analysis pipeline: Reproducibility, orchestration, and scale
Engineering takeaways from scaling pan-genome and metagenomic pipelines across HPC clusters: deterministic environments, profile configurations, and storage lifecycle management.
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