Reviews of cool things
Sequencing
How modern sequencing platforms read DNA: Illumina’s sequencing by synthesis, Element’s avidity chemistry, and Ultima’s flow sequencing. Covers library prep, cluster generation, optics, error profiles, and practical tradeoffs.
Lentivirus
How HIV-1 was domesticated into a gene delivery vector, and why reverse transcription generates recombination in pooled screens: template switching during minus-strand elongation, intra-molecular repeat deletion, and the design rules that follow.
Transposons
Transposable elements from first principles: DNA transposons and retrotransposons, the piRNA ping-pong cycle that keeps them in check, how CRISPR-Cas systems evolved from mobile elements, and what transposon reactivation means for aging.
miRNAs
The miR-E/miR-30 scaffold traced step by step: Pol II transcription, Drosha cleavage at the CNNC motif, Dicer processing, and RISC loading, with actual sequences and intermediates at each stage.
Perturbations
The molecular toolkit for breaking genes on purpose: CRISPR-Cas nucleases and base editors, TALENs and zinc fingers, and RNA interference from siRNAs to shRNAs.
AAV
Adeno-associated virus as a gene therapy vector: serotype tropism, capsid engineering, ITR biology, manufacturing, and the immunology that limits redosing.
Assembly
Genome and transcriptome assembly from short and long reads: de Bruijn graphs, overlap-layout-consensus, scaffolding, polishing, and how T2T finally closed the human genome.
Replication
How cells copy their DNA: origin licensing, the replisome, Okazaki fragment processing, fork stalling and restart, and the basics of RNA-dependent RNA replication in viruses.
Transcription
Gene expression from chromatin to mature mRNA: promoter architecture, Pol II initiation and elongation, co-transcriptional splicing, and the regulatory logic of enhancers.
Translation
From mRNA to protein: ribosome structure, cap-dependent initiation, elongation and wobble decoding, co-translational folding, and how cells regulate translational output.
Division
The cell cycle end to end: CDK oscillations, DNA damage checkpoints, mitotic spindle assembly, chromosome segregation, and what goes wrong in aneuploidy.