Foundations

GUIDE-seq detects tagged double-strand-break locations by oligonucleotide integration and sequencing.

EmptyDrops tests barcode expression against an ambient-RNA null rather than relying solely on total-count thresholds.

UMIs help distinguish amplified reads from captured molecules, but barcode errors and finite capture affect estimated counts.

In Lecuit’s nondimensional two-cell example, the isolated reaction Jacobian has eigenvalues −1, whereas an antisymmetric spatial mode can become unstable after unequal diffusive coupling.

Dupont and colleagues altered substrate rigidity and cell geometry and tested actomyosin/Rho and YAP/TAZ responses in specified cultured mammalian cells.

Jinek and colleagues demonstrated RNA-programmable Cas9 double-stranded DNA cleavage in vitro and a fused guide-RNA architecture.

Cytidine base editors couple a deaminase with DNA-targeting Cas9 machinery; UGI and nicking modifications bias processing toward desired substitutions.

Prime editing combines a Cas9 nickase–reverse-transcriptase fusion with a pegRNA carrying the desired edit.

An intended amplicon edit fraction describes the assayed surviving population and locus.

WHO’s human-genome-editing framework distinguishes somatic, germline and heritable applications and calls for oversight, transparency and responsible governance.

MINFLUX uses spatially positioned excitation minima to infer a fluorescent emitter’s location from detected photons.

A fitted relation between metabolism and body mass depends on basal-state criteria, temperature, species sampling and regression treatment.

Mechanistic niche models combine microclimate with organismal heat, water and nutritional budgets across a life cycle.

Cells sampled from one animal or culture share experimental history.

CITE-seq joins antibody-derived epitope tags with transcriptome profiling in the same sampled cell.

Integration attempts to align datasets while preserving biological differences.

Spatial transcriptomics retains coordinates but its observable depends on platform: capture-based spots can mix cells, while imaging-based panels sample selected transcripts.

Ordering cells along a transcriptional trajectory describes similarities among sampled states.

RNA velocity uses spliced/unspliced RNA relationships to estimate a local expression-change direction under a transcription/splicing/degradation model.

Spatial Perturb-Seq combines AAV-delivered genetic perturbation barcodes with spatial transcriptomic readouts in the studied Cas9 mouse hippocampus.

Whether a perturbation-derived regulatory edge persists across tissue, developmental stage or environment is a separate question from detecting a response in one experiment.

Conformational selection and induced fit describe competing temporal paths between conformation change and ligand binding.

AlphaFold 3 predicts biomolecular complex structures but reports limitations including clashes, stereochemistry errors and hallucinated regions.

RFdiffusion generates proposed protein backbones and constrained designs.

In the EX2 opening model, exchange rates constrain approximate opening free energies.

Ferrari and colleagues profile 5,778 small domains with multiplexed HDX-MS and compare 13 domains with site-resolved HDX NMR.

Turing proposed that reacting and diffusing morphogens can destabilize an initially homogeneous equilibrium and generate patterned states.

Traction microscopy infers forces from cell-induced substrate displacements using a substrate mechanics model.

Predicting conformational free energies, kinetics and function from sequence/static structures remains an open research challenge.