AIMC Topic: Gene Expression Regulation, Plant

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Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function.

Proceedings of the National Academy of Sciences of the United States of America Aug 10, 2021
The circadian clock is an important adaptation to life on Earth. Here, we use machine learning to predict complex, temporal, and circadian gene expression patterns in Most significantly, we classify circadian genes using DNA sequence features genera...
Phytochrome Circadian Clocks Gene Expression Regulation, Plant Models, Biological Circadian Rhythm Ecotype Apoproteins Phytochrome A Arabidopsis Proteins Arabidopsis Regulatory Sequences, Nucleic Acid Machine Learning Gene Expression Profiling
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Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
As the interest in genetic resequencing increases, so does the need for effective mathematical, computational, and statistical approaches. One of the difficult problems in genome annotation is determination of precise positions of transcription start...
Transcription, Genetic Oryza Transcription Initiation Site Machine Learning Genome, Plant Plant Proteins Software Promoter Regions, Genetic Gene Expression Regulation, Plant
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Prediction of condition-specific regulatory genes using machine learning.

Nucleic acids research Jun 19, 2020
Recent advances in genomic technologies have generated data on large-scale protein-DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has bec...
Transcription Factors Datasets as Topic Stress, Physiological RNA-Seq Gene Regulatory Networks Arabidopsis Proteins Arabidopsis Genes, Regulator Promoter Regions, Genetic Gene Expression Regulation, Plant Genes, Plant Machine Learning Gene Expression Profiling Deep Learning Single-Cell Analysis
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An Overview on Predicting Protein Subchloroplast Localization by using Machine Learning Methods.

Current protein & peptide science Jan 1, 2020
The chloroplast is a type of subcellular organelle of green plants and eukaryotic algae, which plays an important role in the photosynthesis process. Since the function of a protein correlates with its location, knowing its subchloroplast localizatio...
Chloroplasts Protein Transport Machine Learning Amino Acid Sequence Computational Biology Datasets as Topic Gene Expression Regulation, Plant Proteome Chloroplast Proteins Models, Statistical Plants
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High-throughput phenotyping with deep learning gives insight into the genetic architecture of flowering time in wheat.

GigaScience Nov 1, 2019
BACKGROUND: Measurement of plant traits with precision and speed on large populations has emerged as a critical bottleneck in connecting genotype to phenotype in genetics and breeding. This bottleneck limits advancements in understanding plant genome...
Gene Expression Regulation, Plant Triticum Flowers Deep Learning Databases, Nucleic Acid Genotype Genetic Association Studies
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Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Nucleic acids research Jan 4, 2018
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,...
Molecular Sequence Annotation Genomics Gene Ontology Epigenesis, Genetic Databases, Genetic Genetic Research Genome, Plant Software Knowledge Bases Metabolic Networks and Pathways Gene Expression Regulation, Plant User-Computer Interface Genetic Variation Plants
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Design of Knowledge Bases for Plant Gene Regulatory Networks.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2017
Developing a knowledge base that contains all the information necessary for the researcher studying gene regulation in a particular organism can be accomplished in four stages. This begins with defining the data scope. We describe here the necessary ...
Database Management Systems Transcription Factors Chromosome Mapping Gene Regulatory Networks Plants Transcription Initiation Site Software Protein Binding User-Computer Interface Databases, Genetic Computational Biology Gene Expression Regulation, Plant Knowledge Bases Web Browser Search Engine Binding Sites
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