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BMC BIOINFORMATICS, ISSN 1471-2105, 04/2019, Volume 20
Background: Bacterial surfaces are complex systems, constructed from membranes, peptidoglycan and, importantly, proteins. The proteins play crucial roles as... 
Infectious diseases | PROTEIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | De novo motif discovery | Group A streptococcus | MODEL
Journal Article
Journal Article
Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, 02/2013, Volume 11, Issue 1
DNA-binding proteins are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in target regions... 
de-novo motif discovery | Transcription factor binding sites | statistical models | ACTIVATION | PROTEIN-DNA INTERACTIONS | SEQUENCES | TRANSCRIPTION | FACTOR-BINDING SITES | ACID RESPONSE ELEMENT | ABI3 | PROMOTERS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENE-EXPRESSION | ARABIDOPSIS
Journal Article
Journal Article
Cell Systems, ISSN 2405-4712, 01/2019, Volume 8, Issue 1, pp. 27 - 42.e6
DNA shape adds specificity to sequence motifs but has not been explored systematically outside this context. We hypothesized that DNA-binding proteins (DBPs)... 
transcription factor | DNA shape | DNA binding protein | de novo shape motif discovery | Gibbs sampling | sequence motif | HT-SELEX | shape-specific binding | shape-only binding | shape motif | shape specificity | ChIP-Seq | algorithm | FACTOR-BINDING | CHROMATIN-STRUCTURE | RECOGNITION | SPECIFICITY | ANNOTATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | MOUSE | REGIONS | REPRESSOR | OPERATORS | FEATURES | CELL BIOLOGY
Journal Article
2017 24th National and 2nd International Iranian Conference on Biomedical Engineering (ICBME), 11/2017, pp. 1 - 6
Motif discovery is a challenging problem in molecular biology and has been attracting researcher's attention for years. Different kind of data and... 
Clustering methods | Clustering algorithms | Transcription factor binding site (TFBS) | Biomedical measurement | Pulse width modulation | Position measurement | De novo motif prediction | Clustering | Anomaly detection | Biomedical engineering
Conference Proceeding
OpenAccess Series in Informatics, ISSN 2190-6807, 2013, Volume 34, pp. 101 - 109
Conference Proceeding
The Annals of Applied Statistics, ISSN 1932-6157, 6/2007, Volume 1, Issue 1, pp. 36 - 65
Journal Article
Genome Biology, ISSN 1474-7596, 01/2008, Volume 9, Issue 1, pp. R22 - R22
We consider the problem of predicting cis-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting, and create over 30... 
TARGET GENES | EMBRYO | SEQUENCES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DE-NOVO DISCOVERY | TRANSCRIPTION | GENETICS & HEREDITY | GENE-REGULATION | FACTOR-BINDING SITES | IDENTIFICATION | MELANOGASTER | GENOME | Genes, Insect | Computational Biology - methods | Animals | Enhancer Elements, Genetic | Drosophila - genetics | Index Medicus | Method
Journal Article
BMC Genomics, ISSN 1471-2164, 06/2015, Volume 16, Issue 7, pp. S13 - S13
Motifs are regulatory elements that will activate or inhibit the expression of related genes when proteins (such as transcription factors, TFs) bind to them.... 
ChIP-seq | Epigenetics | Suffix tree | De novo Motif finding | DNase I hypersensitivity sites | Computational Biology - methods | Algorithms | Animals | Regulatory Elements, Transcriptional | Epigenesis, Genetic | Humans | Gene Expression Regulation | Databases, Genetic | Mice | Genome | Index Medicus
Journal Article
Journal Article