Blog
Notes and essays on computational biology, bioinformatics, and research methods. Shared as PDFs and viewable directly on-site.
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Isoform Complexity Analysis: Structural Resolution Beyond Gene-Level Expression
A concise conceptual insight into isoform complexity analysis, highlighting transcript-level resolution, alternative splicing architecture, long-read reconstruction, and the biological importance of isoform switching in disease. Emphasizes structural diversity as a functional determinant beyond aggregate gene expression.
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2026
12 postsIsoform Complexity Analysis: Structural Resolution Beyond Gene-Level Expression
A concise conceptual insight into isoform complexity analysis, highlighting transcript-level resolution, alternative splicing architecture, long-read reconstruction, and the biological importance of isoform switching in disease. Emphasizes structural diversity as a functional determinant beyond aggregate gene expression.
Isoform Complexity Analysis: Structural Resolution Beyond Gene-Level Expression
A concise conceptual insight into isoform complexity analysis, highlighting transcript-level resolution, alternative splicing architecture, long-read reconstruction, and the biological importance of isoform switching in disease. Emphasizes structural diversity as a functional determinant beyond aggregate gene expression.
Metatranscriptomics: Listening to the Active Functional State of Microbial Communities
A deep computational and conceptual guide to metatranscriptomics, covering RNA capture, host removal, functional quantification, normalization, pathway interpretation, and systems-level integration. Includes practical pitfalls, expert insight boxes, and translational perspectives for disease and microbiome research.
Normalization Across Omics: From RNA-seq and Proteomics to Statistical Validity
A detailed, concept-driven guide to normalization in RNA sequencing and proteomics, explaining FPKM, TPM, TMM, DESeq2, iBAQ, RIBAQ, and LFQ through worked examples, reviewer insights, and multi-omics integration principles.
The Soul of Code: Philosophy and Design of Programming Languages
A deep dive into the design motivations and tradeoffs behind major programming languages, highlighting how abstraction, control, and community shape modern software systems.
The Structured Dialogue: How Markdown Elevates LLM Outputs
Master the art of structured prompting by using Markdown to transform generic AI responses into precise, high-quality outputs for complex fields like bioinformatics.
Notes on Machine Learning: From Linear Models to Multimodal Transformers
Personal yet rigorous notes tracing the evolution of machine learning from linear and tree-based models to Transformers, language models, and vision–language systems. Written as a structured synthesis for learning and reflection, rather than a definitive textbook.
Demystifying Git: The Content-Addressable Filesystem
A technical synthesis of Git's inner architecture, framing version control as a navigable manifold. This guide integrates the mechanics of SHA-1 hashing, directed acyclic graphs (DAG), and content-addressable storage to explain how Git manages project entropy.
Navigating Spreading-out Graphs: Efficient Search in Biological Networks
A deep dive into the NSG paper, exploring how l2 norm proximity graphs and out-degree reduction enable fast complex detection and drug-response mapping in LINCS L1000.
The Geometry of Interaction: Proximity Graphs in Modern Network Biology
An expert-level exploration of how k-NN, RNG, and NSG frameworks transform topological 'hairballs' into precise geometric manifolds for drug discovery and spatial transcriptomics.
The Information Bottleneck of Life: Geometry, Entropy, and Topology in Biological Systems
A masterclass-style synthesis arguing that biological function and disease emerge from geometric constraints on information flow. Integrates spectral graph theory, curvature, entropy, graph signal processing, and persistent homology to frame life as a navigable manifold shaped by evolution and thermodynamics.
Scale-Free Networks in Biology: Power, Pitfalls, and the Seduction of Universality
A critical essay on scale-free networks in biology, examining why the concept became dominant, where it provides insight, and where it can mislead biological interpretation.
2025
4 postsThe Illusion in the Lab Coat: How Computational Biology Can Deceive Itself
A critical essay on self-deception, statistical illusion, and methodological fragility in computational biology.
Vivo-seq: A New Era of Single-Cell Biology Beyond Transcriptomics
An overview of Vivo-seq and why integrating phospho-signaling with transcriptomics changes how we interpret cell states.
Lenvatinib Resistance and the Role of Autophagy in Hepatocellular Carcinoma
Mechanistic insights into drug resistance in HCC, focusing on autophagy and therapeutic implications.
FDA-Approved Lung Cancer Drugs (2024–March 2025): Targets and Mechanisms
A concise review of recently approved lung cancer drugs, their molecular targets, and mechanisms.