AIMC Topic: Gene Library

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Denoising DNA Encoded Library Screens with Sparse Learning.

ACS combinatorial science Jun 26, 2020
DNA-encoded libraries (DELs) are large, pooled collections of compounds in which every library member is attached to a stretch of DNA encoding its complete synthetic history. DEL-based hit discovery involves affinity selection of the library against ...
Machine Learning DNA 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...
Humans Machine Learning Animals Mice RNA, Guide, CRISPR-Cas Systems Gene Editing Gene Library Mouse Embryonic Stem Cells Point Mutation
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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...
Machine Learning Software Computer Simulation Gene Library Neural Networks, Computer
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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...
Humans Machine Learning Promoter Regions, Genetic Lentivirus Cell Separation Gene Library Regulatory Elements, Transcriptional Induced Pluripotent Stem Cells Organoids Software Female Cell Line, Tumor Breast Neoplasms 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 ...
Computational Biology Sequence Analysis, DNA Models, Statistical Area Under Curve Software Algorithms Deep Learning Genomics Normal Distribution Gene Library Mutation Alzheimer Disease Programming Languages Mutagenesis Humans Neural Networks, Computer
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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...
High-Throughput Nucleotide Sequencing DNA Barcoding, Taxonomic Electronic Data Processing Gene Library Genome Nanopores Bacteria Computational Biology DNA Nanotechnology Software Algorithms Reproducibility of Results Neural Networks, Computer
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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...
Humans Brain Female Animals Male Fluorescence Mice Protein Engineering Cell Separation Gene Library Robotics Zebrafish Genes, Reporter Caenorhabditis elegans Flow Cytometry Optogenetics Microscopy, Fluorescence Luminescent Proteins Hippocampus Neurons HEK293 Cells Directed Molecular Evolution
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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...
Gene Library Benchmarking Genome, Human Molecular Sequence Annotation Gene Ontology Computational Biology Databases, Genetic Internet Humans Gene Expression Profiling User-Computer Interface
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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.
Cluster Analysis Databases, Protein Amino Acid Sequence Tandem Repeat Sequences Knowledge Bases Documentation Humans Molecular Sequence Annotation Software Gene Library Molecular Sequence Data
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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...
Microsatellite Repeats Genetic Markers Physical Chromosome Mapping Gene Expression Profiling High-Throughput Nucleotide Sequencing Phenotype Transcriptome Gene Frequency Molecular Sequence Annotation Reproducibility of Results Polymorphism, Single Nucleotide Citrus Cluster Analysis Gene Ontology Phylogeny Nucleotide Motifs Gene Library
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