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Showing 1 to 20 of 26 for “"Motif discovery"”.
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A Combined Motif Discovery Method
… is to find the binding sites for regulatory motifs. This is a challenging problem that leads us to a platform to apply a variety of data mining methods. In the efforts described here, a combined motif discovery method that uses mutual information and Gibbs sampling was developed. A new …
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Multi-syllabic DNA motif discovery
… describes a method for finding multi-syllabic motifs in a genome. It expands on the algorithm developed by Takusagawa, et al[1, 2] that uses data from Chromatin Immuno-Precipitation (ChIP) experiments to isolate regions that have a given motif. The Takusagawa method uses an enumeration method …
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Negative information for motif discovery
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.
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Motif discovery in sequential data
… and development of methods for the automated discovery of motifs in sequential data. These data include DNA sequences, protein sequences, and real-valued sequential data such as protein structures and timeseries of arbitrary dimension. As more genomes are sequenced and annotated, the need for …
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Applications of motif discovery in biological data
Sequential motif discovery, the ability to identify conserved patterns in ordered datasets without a priori knowledge of exactly what those patterns will be, is a frequently encountered and difficult problem in computational biology and biochemical engineering. The most prevalent example of such a …
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Integrating genomic conservation data with motif discovery
… model of inter-species sequence conservation for motif discovery, and demonstrate that adding large-scale genomic conservation data to an existing motif discovery procedure improves the quality of that procedure's results. Existing motif discovery algorithms reveal binding motifs that are …
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A bioinformatics framework for RNA structure mining, motif discovery and polyadenylation analysis
The RNA molecules play various important roles in the cell and their functionality depends not only on the sequence information but to a large extent on their structure. The development of computational and predictive approaches to study RNA molecules is extremely valuable. In this research, a tool …
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Towards a Complete Transcriptional Regulatory Code: Improved Motif Discovery Using Informative Priors
… of DNA binding specificities, represented as motifs, for all TFs. In spite of an explosion of TF binding data from high-throughput technologies, the problem of motif discovery remains unsolved, due to the short length and degeneracy of binding sites. </p><p>We introduce PRIORITY, a Gibbs …
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A Multi-Objective Genetic Algorithm with Side Effect Machines for Motif Discovery
… version of side effect machines for degenerate motif discovery. We compare some suggested objectives for the motifs they find, test different multi-objective scoring schemes and probabilistic models for the background sequence models and report our results on a synthetic dataset and some …
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Algoritmi avanzati per il Subgraph Isomorphism, Motif Discovery, e Graph Embedding su reti complesse
I grafi sono strumenti potenti nelle scienze computazionali, in grado di modellare relazioni complesse in ambiti come la bioinformatica, l'analisi delle reti sociali e la chimica computazionale. Questa tesi affronta sfide fondamentali nell'analisi dei grafi, con particolare riferimento al problema …
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MCAT: Motif Combining and Association Tool
De novo motif discovery in biological sequences is an important and computationally challenging problem. A myriad of algorithms have been developed to solve this problem with varying success, but it can be difficult for even a small number of these tools to reach a consensus. Because individual …
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Protein-DNA Binding: Discovering Motifs and Distinguishing Direct from Indirect Interactions
… and replication, the specific DNA binding motifs of many regulatory proteins and complexes are still to be determined. For this purpose, many computational tools for DNA motif discovery have been developed in the last two decades. These tools employ a variety of strategies, from exhaustive …
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Motif Mining On Structured And Semi-structured Biological Data
Motif discovery in biological data is very important to biologists becausethey are conjectured to have biological significance. Despite the considerateeffort put in this topic, it remains a challenging and difficult problem.There are several advances in biology such that the data is structured …
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Simultaneous computational discovery of DNA regulatory motifs and transcription factor binding constraints at high spatial resolution
… methods. Second, I present the k-mer set motif (KSM) representation and the k-mer motif alignment and clustering (KMAC) method which discovers DNA-binding motifs from ChIP-Seq derived sequences. I demonstrate that the KSM model is more predictive than the widely used position weight matrix …
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Using machine learning to predict gene expression and discover sequence motifs
… a novel algorithm to discover gene sequence motifs associated with temporal expression patterns of genes. Our algorithm, which is based on partial least squares (PLS) regression, is able to directly model the flow of information, from gene sequence to gene expression, to learn cis regulatory …
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Unsupervised discovery of activity primitives from multivariate sensor data
… addresses the problem of temporal pattern discovery in real-valued, multivariate sensor data. Several algorithms were developed, and subsequent evaluation demonstrates that they can efficiently and accurately discover unknown recurring patterns in time series data taken from many different …
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Topics in Genomic Signal Processing
… in DNA sequences. Moreover, the problem of motif discovery in DNA sequences is presented, where a set of sequences is observed and it is needed to determine which sequences contain instances (if any) of an unknown motif and estimate their positions. A statistical description of the problem …
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An In Vivo Functional Genomics Screen Identifies New Regulators of Tumorigenesis in Non-Small Cell Lung Cancer
… independent of NKX2-1, and combing de novo motif discovery with expression analyses has identified several other putative FOXA1 coregulators. Our findings provide new insight into the functional consequences of 14q amplification in lung adenocarcinomas and suggest exploration of new …
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Decoding Human T Cell Immunity With Single-Cell Multi-Omics
… clonal selection after infection through the discovery and characterisation of TCR motifs. Next, I link TCR motifs to antigen specificity using experimental T cell specificity databases and validate the findings with in-house data in the context of several viral infections, by integration with …
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Computational methodologies and resources for discovery of phosphorylation regulation and function in cellular networks
… of signaling molecules. The rate of discovery of PTM sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. The ten-fold increase in known phosphorylation sites over a five year time span can …
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