ArticleBioinformatics (Oxford, England)2008
Seeder: discriminative seeding DNA motif discovery.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 48 citations in OpenAlex.
- The chloroplast redox-responsive transcriptome of solanaceous plants reveals significant nuclear gene regulatory motifs associated to stress acclimation.Plant molecular biology · 2022Article
- SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.Bioinformatics (Oxford, England) · 2019Article
- Towards a map of cis-regulatory sequences in the human genome.Nucleic acids research · 2018Article
- WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data.Scientific reports · 2017Article
- De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome.Scientific reports · 2017Article
- The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs.Scientific reports · 2016Article
- De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes.PloS one · 2015Article
- Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space.PloS one · 2015Article
- De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.BMC genomics · 2014Article
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- Discriminative motif optimization based on perceptron training.Bioinformatics (Oxford, England) · 2014Article
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- Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.BMC systems biology · 2013Article
- Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics.Plant physiology · 2012Article
- The limits of de novo DNA motif discovery.PloS one · 2012Article
- DECOD: fast and accurate discriminative DNA motif finding.Bioinformatics (Oxford, England) · 2011Article
- MotifClick: prediction of cis-regulatory binding sites via merging cliques.BMC bioinformatics · 2011Article
- WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures.BMC bioinformatics · 2010Article
- Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae.BMC plant biology · 2009Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches.
resultsWe describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters. The algorithm is tested on biological benchmark data and shown to perform equally or better than other motif discovery tools. The algorithm is applied to the analysis of plant tissue-specific promoter sequences and successfully identifies key regulatory elements.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.