gene editing

Independent evaluation of the AlphaGenome Variant Impact (AVI) score: Step 1 pre-registration, frozen (feasibility count, design decision rule, development-material exclusions)

Second version of the study record: the frozen Step 1 pre-registration, deposited before any ClinVar data row has been counted and before any score has been retrieved. It adds to version 1: - the result of the registered feasibility look (bins of upper bounds only; `results/feasibility_look.json`); - the clarifications...

Analysis code and amplicon sequencing data for "Contact-dependent intercellular dTMP transfer sustains tumor cell proliferation"

This archive provides analysis code and raw mouse Kras/Trp53 amplicon sequencing data accompanying Contact-dependent intercellular dTMP transfer sustains tumor cell proliferation. Analyses include bulk RNA-seq differential expression (GSE271721), single-cell classification (GSE148071), Visium spatial neighborhood analy...

Overexpressing FLP Recombinase Can Cause Synaptic Trafficking Defects in C. elegans

Site-specific recombinases, such as Cre recombinase (Cre) and FLP recombinase (FLPase), are popular tools that enable precise spatiotemporal control over fluorescent reporter genes. However, studies show that increased Cre expression can lead to cytotoxic phenotypes including DNA damage, cell cycle arrest, cell death,...

Agrobacterium-mediated genetic transformation studies in soybean (Glycine max (L.) Merrill) for sustainable food and nutritional security: A Review

Soybean (Glycine max (L.) Merrill), is a major legume crop in the family Fabaceae. It is significant source of plant-based protein and oil, which is important determinant in the food and nutritional security of the world. However, its productivity is progressively being limited by the abiotic stresses (drought and sali...

Prime editing enables high-throughput identification and characterization of selective MutSβ inhibitors

DNA mismatch repair (MMR) maintains genome stability but paradoxically drives expansion of pathogenic repeats responsible for trinucleotide repeat disorders. Attenuating repeat instability through targeted inhibition of MMR is therefore a therapeutic strategy of interest; however, progress is constrained by a lack of r...

Pre-specification analysis plan: two-sample Mendelian randomization of whole-blood cis-eQTLs for ESR1 and three neighbouring skeletal genes against fracture risk

This record is the pre-specification analysis plan for a two-sample Mendelian randomization (MR) study of fracture risk, submitted to the Journal of Bone and Mineral Research (JBMR). Scope. Two-sample MR of four pre-specified cis-eQTL instruments from whole blood (eQTLGen Phase-I, N = 31,684) -- ESR1 and its neighbours...

Editing the rulebook: building the policy environment for children to access gene therapy.

Kabuki syndrome type 1 and type 2 converge on a shared chromatin and transcriptional state in hiPSC-derived neuroectoderm

Genetic dissection of DNA damage response pathways reveals divergent modulation of PD-1 blockade response in colorectal cancer

Although MSI-H/dMMR colorectal cancers and the rarer subset with pathogenic POLE exonuclease domain mutations can benefit from immune checkpoint blockade, MSS colorectal cancer remains largely refractory, raising the question of whether other DNA damage response defects may also confer sensitivity to immunotherapy. Her...

Characterization and comparative analysis of the complete mitochondrial genomes of two Amorphophallus species (Araceae)

Amorphophallus muelleri and Amorphophallus krausei are perennial herbaceous plants of the genus Amorphophallus (family Araceae). Their tubers can be processed into food and possess medicinal and economic value. However, their mitochondrial genomes have not yet been reported. Therefore, this study sequenced, assembled,...

The Genomic Equity Accessibility Framework (GEAF): A dimensionally consistent framework for modeling affordability and equity in genomic and regenerative therapies

Background Advances in CRISPR-based gene editing and stem cell-derived embryo models have created substantial biomedical opportunity alongside significant ethical and distributive concerns. Personalized genomic and regenerative therapies approved in the United States as of this writing carry list prices spanning approx...

Analysis codes for "CRISPR Engineering of Photoperiod Response Genes for Rapid Adaptation of Tropical Maize"

"Photoperiod_Editing_GH24-25_Analysis.Rmd" is an R markdown file with R script to analyze trait data from greenhouse trial."qRT-PCR_Chapter2.Rmd" is an R markdown file with R script to analyze gene expression data."Photoperiod Editing Field 2025 Analysis NatComms.Rmd" is an R markdown file with R script to analyze trai...