Related papers: Template-based eukaryotic genome editing directed …
Type I CRISPR-Cas systems are the most common among six types of CRISPR-Cas systems, however, non-self-targeting genome editing based on a single Cas3 of type I CRISPR-Cas systems has not been reported. Here, we present the subtype I-B-Svi…
Gene and RNA editing methods, technologies, and applications are emerging as innovative forms of therapy and medicine, offering more efficient implementation compared to traditional pharmaceutical treatments. Current trends emphasize the…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…
CRISPR-Cas13 is a system that utilizes single stranded RNAs for RNA editing. Prediction of on-target and off-target effects for the CRISPR-Cas13d dependency enables us to design specific single guide RNAs (sgRNAs) that help locate the…
CRISPR-Cas systems are an adaptive immunity that protects prokaryotes against foreign genetic elements. Genetic templates acquired during past infection events enable DNA-interacting enzymes to recognize foreign DNA for destruction. Due to…
The need for diverse chromosomal modifications in biotechnology, synthetic biology and basic research requires the development of new technologies. With CRISPR SWAPnDROP, we extend the limits of genome editing to large-scale in-vivo DNA…
Protein tagging with CRISPR-Cas9 enables the investigation of protein function in its native environment but is limited by low homology-directed repair (HDR) efficiency causing low knock-in rates. We present a detailed pipeline using HDR…
Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…
Since the advent of CRISPR-Cas9, a groundbreaking gene-editing technology that enables precise genomic modifications via a short RNA guide sequence, there has been a marked increase in the accessibility and application of this technology…
Genetic screens mediated via CRISPR-Cas9 combined with high-content readouts have emerged as powerful tools for biological discovery. However, computational analyses of these screens come with additional challenges beyond those found with…
Predicting guide RNA (gRNA) activity is critical for effective CRISPR-Cas12 genome editing but remains challenging due to limited data, variation across protospacer adjacent motifs (PAMs-short sequence requirements for Cas binding), and…
Designing regulatory DNA sequences that achieve precise cell-type-specific gene expression is crucial for advancements in synthetic biology, gene therapy and precision medicine. Although transformer-based language models (LMs) can…
CRISPR systems experience off-target effects that interfere with the ability to accurately perform genetic edits. While empirical models predict off-target effects in specific platforms, there is a gap for a wide-ranging mechanistic model…
Annotating the structure of protein-coding genes represents a major challenge in the analysis of eukaryotic genomes. This task sets the groundwork for subsequent genomic studies aimed at understanding the functions of individual genes.…
We previously proposed the existence of DNA to DNA transcription in eukaryotic cells, but the mechanism by which single-stranded DNA (ssDNA) transcript is produced and released from the genome remains unknown. We once speculated that the…
Motivation: Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expression from histone modification signals are highly desirable for understanding their…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
Background: Single-stranded whole-genome bisulfite sequencing (ssWGBS) enables DNA methylation profiling in low-input and highly fragmented material, including cell-free DNA. In widely used post-bisulfite protocols, Adaptase-mediated…
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…