Survey on time series motif discovery
Sign Up to like & getrecommendations! Published in 2017 at "Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery"
DOI: 10.1002/widm.1199
Abstract: Last decades witness a huge growth in medical applications, genetic analysis, and in performance of manufacturing technologies and automatised production systems. A challenging task is to identify and diagnose the behavior of such systems, which… read more here.
Keywords: discovery; series motif; time series; motif discovery ... See more keywords
Motif Discovery from CLIP Experiments.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1307-8_3
Abstract: RNA primary and secondary motif discovery is an important step in the annotation and characterization of unknown interaction dynamics between RNAs and RNA-Binding Proteins, and several methods have been developed to meet the need of… read more here.
Keywords: discovery clip; motif discovery; discovery; biology ... See more keywords
A modified Henry gas solubility optimization for solving motif discovery problem
Sign Up to like & getrecommendations! Published in 2019 at "Neural Computing and Applications"
DOI: 10.1007/s00521-019-04611-0
Abstract: The DNA motif discovery (MD) problem is the main challenge of genome biology, and its importance is directly proportional to increasing sequencing technologies. MD plays a vital role in the identification of transcription factor binding… read more here.
Keywords: henry gas; motif discovery; modified henry; discovery ... See more keywords
FSM: Fast and Scalable Network Motif Discovery for Exploring Higher-order Network Organizations.
Sign Up to like & getrecommendations! Published in 2019 at "Methods"
DOI: 10.1016/j.ymeth.2019.07.008
Abstract: Networks exhibit rich and diverse higher-order organizational structures. Network motifs, which are recurring significant patterns of inter-connections, are recognized as fundamental units to study the higher-order organizations of networks. However, the principle of selecting representative… read more here.
Keywords: order; network motif; network; motif discovery ... See more keywords
AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX.
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa054
Abstract: SUMMARY High-Throughput Sequencing can enhance the analysis of aptamer libraries generated by the Systematic Evolution of Ligands by EXponential enrichment (HTS-SELEX). Robust analysis of the resulting sequenced rounds is best implemented by determining a ranked… read more here.
Keywords: hts selex; aptcompare; aptcompare optimized; optimized novo ... See more keywords
IndeCut evaluates performance of network motif discovery algorithms
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx798
Abstract: Motivation Genomic networks represent a complex map of molecular interactions which are descriptive of the biological processes occurring in living cells. Identifying the small over-represented circuitry patterns in these networks helps generate hypotheses about the… read more here.
Keywords: indecut; network motif; network; motif discovery ... See more keywords
Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example.
Sign Up to like & getrecommendations! Published in 2021 at "Plant physiology"
DOI: 10.1093/plphys/kiaa091
Abstract: The identification of functional elements encoded in plant genomes is necessary to understand gene regulation. Although much attention has been paid to model species like Arabidopsis (Arabidopsis thaliana), little is known about regulatory motifs in… read more here.
Keywords: promoter boundaries; motif discovery; example; discovery ... See more keywords
A Graph-Theoretical Approach for Motif Discovery in Protein Sequences
Sign Up to like & getrecommendations! Published in 2017 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2015.2511750
Abstract: Motif recognition is a challenging problem in bioinformatics due to the diversity of protein motifs. Many existing algorithms identify motifs of a given length, thus being either not applicable or not efficient when searching simultaneously… read more here.
Keywords: motif; approach motif; motif discovery; approach ... See more keywords
Matrix Profile IX: Admissible Time Series Motif Discovery With Missing Data
Sign Up to like & getrecommendations! Published in 2021 at "IEEE Transactions on Knowledge and Data Engineering"
DOI: 10.1109/tkde.2019.2950623
Abstract: The discovery of time series motifs has emerged as one of the most useful primitives in time series data mining. Researchers have shown its utility for exploratory data mining, summarization, visualization, segmentation, classification, clustering, and… read more here.
Keywords: missing data; motif discovery; discovery; time series ... See more keywords
Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets
Sign Up to like & getrecommendations! Published in 2018 at "Journal of bioinformatics and computational biology"
DOI: 10.1142/s0219720017400121
Abstract: The development of chromatin immunoprecipitation sequencing (ChIP-seq) technology has revolutionized the genetic analysis of the basic mechanisms underlying transcription regulation and led to accumulation of information about a huge amount of DNA sequences. There are… read more here.
Keywords: dna; motif discovery; argo cuda; discovery ... See more keywords
Greedy de novo motif discovery to construct motif repositories for bacterial proteomes
Sign Up to like & getrecommendations! Published in 2019 at "BMC Bioinformatics"
DOI: 10.1186/s12859-019-2686-8
Abstract: BackgroundBacterial surfaces are complex systems, constructed from membranes, peptidoglycan and, importantly, proteins. The proteins play crucial roles as critical regulators of how the bacterium interacts with and survive in its environment. A full catalog of… read more here.
Keywords: motif; motif discovery; discovery construct; plasma proteins ... See more keywords