AIMC Topic: DNA

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iDHS-DT: Identifying DNase I hypersensitive sites by integrating DNA dinucleotide and trinucleotide information.

Biophysical chemistry Nov 14, 2021
DNase I hypersensitive sites (DHSs) is important for identifying the location of gene regulatory elements, such as promoters, enhancers, silencers, and so on. Thus, it is crucial for discriminating DHSs from non-DHSs. Although some traditional method...
Support Vector Machine DNA Deoxyribonuclease I Algorithms
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Machine Learning Approach to Calculate Electronic Couplings between Quasi-diabatic Molecular Orbitals: The Case of DNA.

The journal of physical chemistry letters Oct 21, 2021
Diabatization of one-electron states in flexible molecular aggregates is a great challenge due to the presence of surface crossings between molecular orbital (MO) levels and the complex interaction between MOs of neighboring molecules. In this work, ...
Machine Learning Electrons Electron Transport DNA Quantum Theory
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A GO catalogue of human DNA-binding transcription factors.

Biochimica et biophysica acta. Gene regulatory mechanisms Oct 18, 2021
To control gene transcription, DNA-binding transcription factors recognise specific sequence motifs in gene regulatory regions. A complete and reliable GO annotation of all DNA-binding transcription factors is key to investigating the delicate balanc...
Gene Ontology DNA Molecular Sequence Annotation Humans Transcription Factors Databases, Genetic
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Using a multi-head, convolutional neural network with data augmentation to improve electropherogram classification performance.

Forensic science international. Genetics Oct 13, 2021
DNA profiles are generated in forensic biology laboratories around the world. It is possible that these profiles are assessed by two independent people in order for the profiles to be 'read'. Recent work has been carried out to develop a neural netwo...
Laboratories Australia DNA Neural Networks, Computer Software Humans
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Predicting TF-DNA Binding Motifs from ChIP-seq Datasets Using the Bag-Based Classifier Combined With a Multi-Fold Learning Scheme.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
The rapid development of high-throughput sequencing technology provides unique opportunities for studying of transcription factor binding sites, but also brings new computational challenges. Recently, a series of discriminative motif discovery (DMD) ...
Humans DNA Binding Sites Computational Biology Machine Learning Chromatin Immunoprecipitation Sequencing Transcription Factors Algorithms
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Effective gene expression prediction from sequence by integrating long-range interactions.

Nature methods Oct 4, 2021
How noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human genetics depend on improved solutions. Here, we report substantially improved gene expression prediction a...
Nerve Net Genome DNA Gene Expression Regulation Quantitative Trait Loci Genomics Epigenesis, Genetic Animals Databases, Genetic Humans Mice Cell Line Machine Learning
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Evaluation of deep learning approaches for modeling transcription factor sequence specificity.

Genomics Sep 14, 2021
As a key component of gene regulation, transcription factors (TFs) play an important role in a number of biological processes. To fully understand the underlying mechanism of TF-mediated gene regulation, it is therefore critical to accurately identif...
DNA Binding Sites Humans Neural Networks, Computer Deep Learning Transcription Factors
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RF-SVM: Identification of DNA-binding proteins based on comprehensive feature representation methods and support vector machine.

Proteins Sep 9, 2021
Protein-DNA interactions play an important role in biological progress, such as DNA replication, repair, and modification processes. In order to have a better understanding of its functions, the one of the most important steps is the identification o...
Databases, Protein DNA DNA-Binding Proteins Computational Biology Support Vector Machine
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Easy-Prime: a machine learning-based prime editor design tool.

Genome biology Aug 19, 2021
Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime, a machine learning-based program traine...
HEK293 Cells Gene Editing DNA RNA, Guide, CRISPR-Cas Systems Humans CRISPR-Cas Systems Machine Learning
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iPromoter-ET: Identifying promoters and their strength by extremely randomized trees-based feature selection.

Analytical biochemistry Aug 10, 2021
Promoter is a region of DNA that determines the transcription of a particular gene. There are several σ factors in the RNA polymerase, which has the function of identifying the promoter and facilitating the binding of the RNA polymerase to the promot...
Nucleotides Promoter Regions, Genetic Sequence Analysis, DNA DNA Support Vector Machine
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