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688
M (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817–825
"... A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation, and the onset of disease. While some modifications have been linked with activity levels of different functional elements, their combinatorial ..."
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Cited by 172 (12 self)
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distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, large-scale repressed and repeat-associated states. Each chromatin state shows specific functional, experimental, conservation, annotation, and sequence-motif enrichments, revealing their distinct
Modeling within-motif dependence for transcription factor binding site predictions
- Bioinformatics
, 2004
"... Motivation: The position-specific weight matrix (PWM) model, which assumes that each position in the DNA site contributes independently to the overall protein–DNA inter-action, has been the primary means to describe transcrip-tion factor binding site motifs. Recent biological experiments, however, s ..."
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Cited by 70 (6 self)
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Motivation: The position-specific weight matrix (PWM) model, which assumes that each position in the DNA site contributes independently to the overall protein–DNA inter-action, has been the primary means to describe transcrip-tion factor binding site motifs. Recent biological experiments, however
Heparan Sulfate Motifs†,‡
, 2001
"... ABSTRACT: Stromal cell-derived FGF-7 binds and activates only the resident FGFR2IIIb in epithelial cells while FGF-1 and FGF-2 exhibit a broader interaction with multiple isoforms of FGFR. Here we report the structure of FGF-7 that has been solved to 3.1 Å resolution by molecular replacement with th ..."
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with the structure of a dual function chimera of FGF-7 and FGF-1 (FGF-7/1) which was resolved to 2.3 Å. Comparison of the FGF-7 structure to that of FGF-1 and FGF-2 revealed the strongly conserved CR backbone among the three FGF polypeptides and the surface hydrophobic patch that forms the primary receptor
Finding Motifs in miRNA Sequences
"... Recently, the emergence of non-coding miRNA has attracted biology and computer researchers. miRNA plays an important role in regulation of genes. Finding motifs in RNA is one of important topics. In our work, we attempt to find motifs in mature miRNA from combinations ranging from two to ten nucleot ..."
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nucleotides. Interestingly, we have found several motifs only appear in mature miRNA but not appear in other regions of primary miRNA sequences taken from latest miRNA datasets. The findings of our investigation may help in the building model to predict all possible miRNAs in genomes 1.
On motifs and functional blocks in technological networks
- in ECCS 2007: Proc. 2007 European Conference on Complex Systems
, 2007
"... One primary focus of complex systems research has been the topological analysis of the network underlying a complex system. One key question is the size and structure/function of the underlying building blocks. Two proposed building blocks are called motif and functional module. A motif has been def ..."
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Cited by 1 (1 self)
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One primary focus of complex systems research has been the topological analysis of the network underlying a complex system. One key question is the size and structure/function of the underlying building blocks. Two proposed building blocks are called motif and functional module. A motif has been
Quadrant Motif Approach for Image Retrieval
"... In this paper, we propose an image retrieval approach based on Quadrant Motif Scan (QMS). Motif scans from segmented blocks inside an image are the primary notion to extract image features. We exploit recursive quadrant segmentation in images and stratify hierarchical regions for matching comparison ..."
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Cited by 1 (0 self)
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In this paper, we propose an image retrieval approach based on Quadrant Motif Scan (QMS). Motif scans from segmented blocks inside an image are the primary notion to extract image features. We exploit recursive quadrant segmentation in images and stratify hierarchical regions for matching
Analysis of the DDE Motif in the Mutator Superfamily
"... Abstract The eukaryotic Mutator family of transposable elements is widespread in plants. Active or potentially active copies are also found in fungi and protozoans, and sequences related to this family have been detected in metazoans as well. Members of this family are called Mutator-like elements ..."
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(MULEs). They encode transposases, which contain a region conserved with transposases of the IS256 prokaryotic family, known to harbor a DDE catalytic domain. Different DDE or D34E motifs have been proposed in some groups of eukaryotic MULEs based on primary sequence conservation. On a large number
Conserved helicase motifs in the PIF protein
, 1990
"... Recently, Hodgman (1) and Gorbalenya et al. (2) observed the presence of several conserved motifs in a subset of cellular and viral proteins. Seraphin et al. subsequently identified a second set of motifs (3), related to the first one, which is present in a novel series of proteins (3—5). Based on t ..."
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super-family. Interestingly, both the primary sequence and the location of the new motif V, suggest a stronger similarity between the PIF protein and putative helicases from herpesviruses.
Exon silencing by UAGG motifs in response to neuronal excitation
- PLoS Biol
, 2007
"... Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse. The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response t ..."
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Cited by 12 (1 self)
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to cell excitation, but the molecular nature of this splicing responsiveness is not yet understood. Here we investigate the molecular basis for the induced changes in splicing of the CI cassette exon in primary rat cortical cultures in response to KCl-induced depolarization using an expression assay
Clustering of Time Series Subsequences is Meaningless: Implications for Past and Future Research
- In Proc. of the 3rd IEEE International Conference on Data Mining
, 2003
"... Time series data is perhaps the most frequently encountered type of data examined by the data mining community. Clustering is perhaps the most frequently used data mining algorithm, being useful in it’s own right as an exploratory technique, and also as a subroutine in more complex data mining algor ..."
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Cited by 117 (18 self)
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, and a comprehensive set of experiments on reimplementations of previous work. Although the primary contribution of our work is to draw attention to the fact that an apparent solution to an important problem is incorrect and should no longer be used, we also introduce a novel method which, based
Results 1 - 10
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688
