AIMC Topic: Gene Library

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Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning.

Cell Jun 12, 2020
Although base editors are widely used to install targeted point mutations, the factors that determine base editing outcomes are not well understood. We characterized sequence-activity relationships of 11 cytosine and adenine base editors (CBEs and AB...
Gene Editing Gene Library Mouse Embryonic Stem Cells Point Mutation Humans Machine Learning Animals Mice RNA, Guide, CRISPR-Cas Systems
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PiNN: A Python Library for Building Atomic Neural Networks of Molecules and Materials.

Journal of chemical information and modeling Jan 29, 2020
Atomic neural networks (ANNs) constitute a class of machine learning methods for predicting potential energy surfaces and physicochemical properties of molecules and materials. Despite many successes, developing interpretable ANN architectures and im...
Neural Networks, Computer Machine Learning Software Computer Simulation Gene Library
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A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS).

Nature communications Jun 28, 2019
Cell state-specific promoters constitute essential tools for basic research and biotechnology because they activate gene expression only under certain biological conditions. Synthetic Promoters with Enhanced Cell-State Specificity (SPECS) can be supe...
Machine Learning Software Female Breast Neoplasms Humans Regulatory Elements, Transcriptional Induced Pluripotent Stem Cells Promoter Regions, Genetic Organoids Lentivirus Cell Separation Cell Line, Tumor Gene Library Neoplastic Stem Cells Glioblastoma Gene Expression Regulation
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Selene: a PyTorch-based deep learning library for sequence data.

Nature methods Mar 28, 2019
To enable the application of deep learning in biology, we present Selene (https://selene.flatironinstitute.org/), a PyTorch-based deep learning library for fast and easy development, training, and application of deep learning model architectures for ...
Area Under Curve Mutation Alzheimer Disease Programming Languages Genomics Computational Biology Sequence Analysis, DNA Models, Statistical Mutagenesis Normal Distribution Gene Library Humans Neural Networks, Computer Software Algorithms Deep Learning
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Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.

PLoS computational biology Nov 20, 2018
Multiplexing, the simultaneous sequencing of multiple barcoded DNA samples on a single flow cell, has made Oxford Nanopore sequencing cost-effective for small genomes. However, it depends on the ability to sort the resulting sequencing reads by barco...
Gene Library Genome Nanopores Nanotechnology Neural Networks, Computer High-Throughput Nucleotide Sequencing Reproducibility of Results Software DNA Barcoding, Taxonomic Bacteria Algorithms Electronic Data Processing Computational Biology DNA
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A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters.

Nature chemical biology Feb 26, 2018
We developed a new way to engineer complex proteins toward multidimensional specifications using a simple, yet scalable, directed evolution strategy. By robotically picking mammalian cells that were identified, under a microscope, as expressing prote...
Brain Female Animals Male Fluorescence Mice Robotics Flow Cytometry Humans Gene Library Caenorhabditis elegans HEK293 Cells Microscopy, Fluorescence Luminescent Proteins Genes, Reporter Directed Molecular Evolution Optogenetics Neurons Protein Engineering Zebrafish Cell Separation Hippocampus
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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.

Nucleic acids research May 3, 2016
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gen...
Molecular Sequence Annotation Gene Ontology Gene Library Databases, Genetic Humans Internet Gene Expression Profiling Benchmarking User-Computer Interface Genome, Human Computational Biology
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TRAL: tandem repeat annotation library.

Bioinformatics (Oxford, England) May 18, 2015
MOTIVATION: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.
Databases, Protein Amino Acid Sequence Knowledge Bases Documentation Humans Molecular Sequence Annotation Software Gene Library Cluster Analysis Molecular Sequence Data Tandem Repeat Sequences
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De novo transcriptome assembly of pummelo and molecular marker development.

PloS one Mar 23, 2015
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...
High-Throughput Nucleotide Sequencing Physical Chromosome Mapping Gene Frequency Citrus Transcriptome Molecular Sequence Annotation Phenotype Gene Ontology Polymorphism, Single Nucleotide Reproducibility of Results Nucleotide Motifs Cluster Analysis Phylogeny Gene Library Genetic Markers Gene Expression Profiling Microsatellite Repeats
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High throughput variant libraries and machine learning yield design rules for retron gene editors.

Nucleic acids research Jan 11, 2025
The bacterial retron reverse transcriptase system has served as an intracellular factory for single-stranded DNA in many biotechnological applications. In these technologies, a natural retron non-coding RNA (ncRNA) is modified to encode a template fo...
Saccharomyces cerevisiae RNA, Untranslated Gene Library RNA, Guide, CRISPR-Cas Systems Machine Learning CRISPR-Cas Systems Gene Editing
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