AIMC Topic: Gene Knockout Techniques

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Intersecting impact of CAG repeat and huntingtin knockout in stem cell-derived cortical neurons.

Neurobiology of disease Apr 19, 2025
Huntington's Disease (HD) is caused by a CAG repeat expansion in the gene encoding huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are u...
Humans Gene Knockout Techniques Huntington Disease Huntingtin Protein Trinucleotide Repeat Expansion Cell Differentiation Neurons Cerebral Cortex
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A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments.

Nature communications Feb 2, 2022
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...
Humans Gene Knockout Techniques Genetic Engineering Synthetic Lethal Mutations Cell Line CRISPR-Cas Systems Clustered Regularly Interspaced Short Palindromic Repeats Machine Learning Animals Genomics
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Mini-batch optimization enables training of ODE models on large-scale datasets.

Nature communications Jan 10, 2022
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...
Software Algorithms Neoplasms Humans Machine Learning Benchmarking Models, Biological Gene Knockout Techniques Cell Line, Tumor Computational Biology Signal Transduction
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Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping.

Nature communications Jul 15, 2020
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...
Regulatory Sequences, Nucleic Acid High-Throughput Nucleotide Sequencing Datasets as Topic Molecular Sequence Annotation Genome, Bacterial Ribosomes Binding Sites Gene Knockout Techniques Computational Biology Escherichia coli Sequence Analysis, DNA Phenotype Deep Learning
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High-throughput transformation of Saccharomyces cerevisiae using liquid handling robots.

PloS one Mar 20, 2017
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...
Culture Media Transformation, Genetic Canavanine Saccharomyces cerevisiae Automation, Laboratory Genomic Library Gene Knockout Techniques Time Factors Robotics Hot Temperature
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A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.

PLoS computational biology Apr 7, 2016
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...
Computational Biology Glycosylation Protein Processing, Post-Translational Humans Genetic Engineering Models, Biological Computer Simulation Polysaccharides Animals Terminology as Topic CHO Cells Gene Knockout Techniques Cricetulus Knowledge Bases Glycosyltransferases Metabolic Networks and Pathways Mucins
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Understanding TCR T cell knockout behavior using interpretable machine learning.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2025
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...
CRISPR-Cas Systems Gene Knockout Techniques Neoplasms Receptors, Antigen, T-Cell Machine Learning Humans Computational Biology T-Lymphocytes Neural Networks, Computer
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Min3: Predict microRNA target gene using an improved binding-site representation method and support vector machine.

Journal of bioinformatics and computational biology Oct 1, 2019
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...
3' Untranslated Regions Support Vector Machine Databases, Genetic MicroRNAs Binding Sites Gene Knockout Techniques HeLa Cells Computational Biology Gene Knockdown Techniques Humans RNA, Messenger Software Models, Genetic
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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 Apr 20, 2016
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.
Interleukin-8 Acute Lung Injury AMP-Activated Protein Kinases Mice Epithelial Sodium Channels Animals Bronchoalveolar Lavage Fluid Lipopolysaccharides Gene Knockout Techniques Lung Protein Serine-Threonine Kinases Interleukin-17
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