gene editing

Measurement reliability bounds functional benchmarks and relocates where variant effect prediction fails

Background Variant effect predictors are increasingly benchmarked against multiplexed assays of variant effect (MAVEs) rather than clinical labels, which removes label circularity but introduces a new problem: a correlation against a measurement cannot exceed the measurement’s own reproducibility, and precision varies...

Multiscale transcriptomic analysis separates epithelial identity loss from FN1-associated stromal remodeling in ulcerative colitis: reproducibility package

This repository contains the reproducibility materials supporting the manuscript “Multiscale transcriptomic analysis separates epithelial identity loss from FN1-associated stromal remodeling in ulcerative colitis.” The archive includes analysis and figure-generation scripts, frozen and processed source tables used for...

Integrated Phenomic and Transcriptomic Network Analysis Reveals Key Regulators of Drought Tolerance in OsC2H2-Edited Rice

Drought poses a major threat to rice ( Oryza sativa ) production, causing severe yield losses and jeopardizing yield stability. C2H2 Jumonji domain–containing zinc-finger proteins play diverse roles in plant growth, development, and abiotic-stress responses through regulation of gene expression and chromatin-associated...

Multiscale transcriptomic analysis separates epithelial identity loss from FN1-associated stromal remodeling in ulcerative colitis: reproducibility package

This repository contains the reproducibility materials supporting the manuscript “Multiscale transcriptomic analysis separates epithelial identity loss from FN1-associated stromal remodeling in ulcerative colitis.” The archive includes analysis and figure-generation scripts, frozen and processed source tables used for...

Advancing the sterile insect technique for the New World screwworm fly: the case for CRISPR-engineered genetic sexing strains.

The sterile insect technique (SIT) has long been a cornerstone of area-wide integrated pest management programs, and the eradication of the New World screwworm Cochliomyia hominivorax (Coquerel) from North and Central America is widely regarded as a landmark success. However, its resurgence underscores the need to mode...

Multiplex CRISPR/Cas12a editing of ROC5, GS3, GW2, and LARGE2 reveals effects on yield-related traits in rice cultivar Kasalath

'Epigenetic' editing is here: gene-tagging technique banishes hepatitis B virus.

Waterlogging and hypoxia in plant abiotic stress.

Waterlogging is a major abiotic stress affecting 12-27% of global cultivated land and causing average yield losses of 20-33% in cereals and legumes. This poses a serious threat to food security in flood-prone regions. Soil saturation reduces gas diffusion nearly 10,000-fold compared to air. This rapidly induces hypoxia...

Genomic insights into the mitochondrial architecture of Sarcandra glabra: structure, evolution, and functional implications

Sarcandra glabra , an early-diverging angiosperm of the family Chloranthaceae, is extensively used in traditional medicine and has taxonomic importance. However, the research on the structural information of the complete mitochondrial genome of S . glabra is limited, with no data available for SSR, Ka/Ks rat...

Molecular Targets and Trait Innovation in CRISPR-Edited Vegetable Crops: An Up-to-Date Review (2020–2026)

Vegetable crops are of fundamental nutritional and economic importance worldwide, yet their improvement through conventional breeding remains time consuming and constrained by genomic complexity. For that reason, over the period 2020–2026, CRISPR/Cas-mediated genome editing, a new genomic technique (NGT), has emerged a...

13. DIRECT CRISPR-EDITING OF RS4702 DECIPHERS CELL-TYPE SPECIFIC EPISTATIC INTERACTIONS WITH SCHIZOPHRENIA POLYGENIC RISK

Background Schizophrenia (SCZ) has a complex, heterogeneous, and highly polygenic genetic architecture. Polygenic risk scores (PRS) assume additive genetic effects and may not capture epistatic or gene-by-environment interactions. However, PRS analyzed in conjunction with functional genomic approaches using CRISPR edit...

Precision engineering of upstream open reading frames for translational regulation and crop improvement

Upstream open reading frames (uORFs) are pervasive cis-regulatory elements in the 5′untranslated regions (UTRs) of eukaryotic mRNAs that modulate translation of downstream main open reading frames (mORFs) by shaping ribosome scanning, initiation, and reinitiation. By operating downstream of transcription, uORFs enable...