ArticleNucleic acids research2013
DRIMust: a web server for discovering rank imbalanced motifs using suffix trees.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 61 citations in OpenAlex.
- Protocol for massively parallel RNA assay combined with immunoprecipitation for high-throughput analysis of RNA-protein interactions in cells.STAR protocols · 2026Article
- Inferring single-cell and spatial microRNA activity from transcriptomics data.Communications biology · 2025Article
- CRMnet: A deep learning model for predicting gene expression from large regulatory sequence datasets.Frontiers in big data · 2023Article
- miRNA activity inferred from single cell mRNA expression.Scientific reports · 2021Article
- MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates.BMC bioinformatics · 2020Article
- Pum2 Shapes the Transcriptome in Developing Axons through Retention of Target mRNAs in the Cell Body.Neuron · 2019Article
- Regulatory motifs found in the small heat shock protein (sHSP) gene family in tomato.BMC genomics · 2018Article
- Genome-wide analysis of fitness data and its application to improve metabolic models.BMC bioinformatics · 2018Article
- SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.Nucleic acids research · 2018Article
- Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments.Algorithms for molecular biology : AMB · 2018Article
- Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks.Nucleic acids research · 2017Article
- Identification and characterization of roles for Puf1 and Puf2 proteins in the yeast response to high calcium.Scientific reports · 2017Article
- Exhaustive search of linear information encoding protein-peptide recognition.PLoS computational biology · 2017Article
- Dysregulated IER3 Expression is Associated with Enhanced Apoptosis in Titin-Based Dilated Cardiomyopathy.International journal of molecular sciences · 2017Article
- RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.BMC bioinformatics · 2017Article
- A Comparative Analysis Between k-Mers and Community Detection-Based Features for the Task of Protein Classification.IEEE transactions on nanobioscience · 2016Article
- ATtRACT-a database of RNA-binding proteins and associated motifs.Database : the journal of biological databases and curation · 2016Article
- Regulation of alternative splicing at the single-cell level.Molecular systems biology · 2015Article
- RBPmap: a web server for mapping binding sites of RNA-binding proteins.Nucleic acids research · 2014Article
- DMINDA: an integrated web server for DNA motif identification and analyses.Nucleic acids research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cellular regulation mechanisms that involve proteins and other active molecules interacting with specific targets often involve the recognition of sequence patterns. Short sequence elements on DNA, RNA and proteins play a central role in mediating such molecular recognition events. Studies that focus on measuring and investigating sequence-based recognition processes make use of statistical and computational tools that support the identification and understanding of sequence motifs. We present a new web application, named DRIMust, freely accessible through the website http://drimust.technion.ac.il for de novo motif discovery services. The DRIMust algorithm is based on the minimum hypergeometric statistical framework and uses suffix trees for an efficient enumeration of motif candidates. DRIMust takes as input ranked lists of sequences in FASTA format and returns motifs that are over-represented at the top of the list, where the determination of the threshold that defines top is data driven. The resulting motifs are presented individually with an accurate P-value indication and as a Position Specific Scoring Matrix. Comparing DRIMust with other state-of-the-art tools demonstrated significant advantage to DRIMust, both in result accuracy and in short running times. Overall, DRIMust is unique in combining efficient search on large ranked lists with rigorous P-value assessment for the detected motifs.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.