ArticlePloS one2011
AMD, an automated motif discovery tool using stepwise refinement of gapped consensuses.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- BML: a versatile web server for bipartite motif discovery.Briefings in bioinformatics · 2022Article
- Article
- Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes inPlants (Basel, Switzerland) · 2020Article
- The C. elegans GATA transcription factor elt-2 mediates distinct transcriptional responses and opposite infection outcomes towards different Bacillus thuringiensis strains.PLoS pathogens · 2020Article
- Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting.PLoS neglected tropical diseases · 2020Article
- Sex chromosome evolution in parasitic nematodes of humans.Nature communications · 2020Article
- Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice.Scientific reports · 2019Article
- The Inducible Response of the NematodeFrontiers in microbiology · 2019Article
- DIpartite: A tool for detecting bipartite motifs by considering base interdependencies.PloS one · 2019Article
- TSS-Seq analysis of low pH-induced gene expression in intercalated cells in the renal collecting duct.PloS one · 2017Article
- Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1.BMC genomics · 2016Article
- Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury.BMC genomics · 2014Article
- Digital expression profiling of the compartmentalized translatome of Purkinje neurons.Genome research · 2014Article
- Discriminative motif optimization based on perceptron training.Bioinformatics (Oxford, England) · 2014Article
- Structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia.Journal of hematology & oncology · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motif discovery is essential for deciphering regulatory codes from high throughput genomic data, such as those from ChIP-chip/seq experiments. However, there remains a lack of effective and efficient methods for the identification of long and gapped motifs in many relevant tools reported to date. We describe here an automated tool that allows for de novo discovery of transcription factor binding sites, regardless of whether the motifs are long or short, gapped or contiguous.
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