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Gene Knockout Techniques

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[Role of interleukin-17 in alveolar fluid clearance in mice with acute lung injury].

Nan fang yi ke da xue xue bao = Journal of Southern Medical University
OBJECTIVE: To investigate the role of interleukin-17 (IL-17) in alveolar fluid clearance in mice with acute lung injury (ALI) and explore the possible mechanism.

A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.

PLoS computational biology
O-linked glycosylation is an important post-translational modification of mucin-type protein, changes to which are important biomarkers of cancer. For this study of the enzymes of O-glycosylation, we developed a shorthand notation for representing Ga...

High-throughput transformation of Saccharomyces cerevisiae using liquid handling robots.

PloS one
Saccharomyces cerevisiae (budding yeast) is a powerful eukaryotic model organism ideally suited to high-throughput genetic analyses, which time and again has yielded insights that further our understanding of cell biology processes conserved in human...

Min3: Predict microRNA target gene using an improved binding-site representation method and support vector machine.

Journal of bioinformatics and computational biology
MicroRNAs are single-stranded noncoding RNAs known to down-regulate target genes at the protein or mRNA level. Computational prediction of targets is essential for elucidating the detailed functions of microRNA. However, prediction specificity and se...

Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping.

Nature communications
Predicting effects of gene regulatory elements (GREs) is a longstanding challenge in biology. Machine learning may address this, but requires large datasets linking GREs to their quantitative function. However, experimental methods to generate such d...

Mini-batch optimization enables training of ODE models on large-scale datasets.

Nature communications
Quantitative dynamic models are widely used to study cellular signal processing. A critical step in modelling is the estimation of unknown model parameters from experimental data. As model sizes and datasets are steadily growing, established paramete...

A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments.

Nature communications
A genetic knockout can be lethal to one human cell type while increasing growth rate in another. This context specificity confounds genetic analysis and prevents reproducible genome engineering. Genome-wide CRISPR compendia across most common human c...

Understanding TCR T cell knockout behavior using interpretable machine learning.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Genetic perturbation of T cell receptor (TCR) T cells is a promising method to unlock better TCR T cell performance to create more powerful cancer immunotherapies, but understanding the changes to T cell behavior induced by genetic perturbations rema...