AIMC Topic: Histones

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Automated machine learning based on radiomics features predicts H3 K27M mutation in midline gliomas of the brain.

Neuro-oncology Mar 5, 2020
BACKGROUND: Conventional MRI cannot be used to identify H3 K27M mutation status. This study aimed to investigate the feasibility of predicting H3 K27M mutation status by applying an automated machine learning (autoML) approach to the MR radiomics fea...
Male Middle Aged Adolescent Adult Brain Neoplasms Magnetic Resonance Imaging Mutation Histones Child, Preschool Child Glioma Humans Machine Learning Retrospective Studies Female Young Adult
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HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.

Nucleic acids research Sep 19, 2019
ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragm...
DNA Supervised Machine Learning High-Throughput Nucleotide Sequencing Humans Software Sequence Analysis, DNA Transposases Genome, Human Markov Chains Histones Datasets as Topic Nucleosomes
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Deep repeat resolution-the assembly of the Drosophila Histone Complex.

Nucleic acids research Feb 20, 2019
Though the advent of long-read sequencing technologies has led to a leap in contiguity of de novo genome assemblies, current reference genomes of higher organisms still do not provide unbroken sequences of complete chromosomes. Despite reads in exces...
Computer Heuristics Tandem Repeat Sequences Consensus Sequence Histones Sequence Alignment Machine Learning Animals Sequence Analysis, DNA Genetic Variation Base Sequence Drosophila melanogaster Neural Networks, Computer
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DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications.

Bioinformatics (Oxford, England) Sep 1, 2018
MOTIVATION: Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing different...
Histones Histone Code Protein Processing, Post-Translational Gene Expression Humans Machine Learning Software
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Investigating the Generalizability of the MultiFlow ® DNA Damage Assay and Several Companion Machine Learning Models With a Set of 103 Diverse Test Chemicals.

Toxicological sciences : an official journal of the Society of Toxicology Mar 1, 2018
The in vitro MultiFlow DNA Damage assay multiplexes p53, γH2AX, phospho-histone H3, and polyploidization biomarkers into 1 flow cytometric analysis (Bryce, S. M., Bernacki, D. T., Bemis, J. C., and Dertinger, S. D. (2016). Genotoxic mode of action pr...
Humans Mutagens Cell Line, Tumor Machine Learning Mutagenicity Tests DNA Damage Histones Flow Cytometry Biomarkers
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HIPred: an integrative approach to predicting haploinsufficient genes.

Bioinformatics (Oxford, England) Jun 15, 2017
MOTIVATION: A major cause of autosomal dominant disease is haploinsufficiency, whereby a single copy of a gene is not sufficient to maintain the normal function of the gene. A large proportion of existing methods for predicting haploinsufficiency inc...
Sequence Analysis, DNA Genome, Human Histones Chromatin Haploinsufficiency Humans Machine Learning Protein Interaction Maps Genomics Sequence Analysis, RNA Epigenesis, Genetic
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LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.

Oncotarget Nov 24, 2015
Accumulating evidences suggest that long non-coding RNAs (lncRNAs) perform important functions. Genome-wide chromatin-states area rich source of information about cellular state, yielding insights beyond what is typically obtained by transcriptome pr...
Methylation Promoter Regions, Genetic Lysine RNA, Long Noncoding HeLa Cells Chromatin Cell Line, Tumor K562 Cells Transcription Initiation Site Cells, Cultured Gene Regulatory Networks Histones Humans Models, Genetic Neoplasms RNA, Messenger Gene Ontology Algorithms Hep G2 Cells Gene Expression Profiling Cell Line
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