ArticleGenome biology2008
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Trial
- SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes.bioRxiv : the preprint server for biology · 2023Article
- Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient.Cell systems · 2023Article
- Review
- Annotating the Insect Regulatory Genome.Insects · 2021Review
- Deep Conservation ofThe Plant cell · 2019Article
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
- Computational enhancer prediction: evaluation and improvements.BMC bioinformatics · 2019Article
- REDfly: the transcriptional regulatory element database for Drosophila.Nucleic acids research · 2019Article
- Alignment-free sequence comparison: benefits, applications, and tools.Genome biology · 2017Review
- Simple Expression Domains Are Regulated by Discrete CRMs DuringG3 (Bethesda, Md.) · 2017Article
- A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model.BioMed research international · 2017Article
- Circular Helix-Like Curve: An Effective Tool of Biological Sequence Analysis and Comparison.Computational and mathematical methods in medicine · 2016Article
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning.BMC systems biology · 2013Article
- Alignment-free sequence comparison based on next-generation sequencing reads.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis.PLoS genetics · 2012Article
- Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.Nucleic acids research · 2011Article
- New powerful statistics for alignment-free sequence comparison under a pattern transfer model.Journal of theoretical biology · 2011Article
- Genome Surveyor 2.0: cis-regulatory analysis in Drosophila.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
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 new data sets, using Drosophila modules, to use as a 'benchmark'. We propose two new methods for the problem, and evaluate these, as well as two existing methods, on our benchmark. We find that the challenge of predicting cis-regulatory modules ab initio, without any input of relevant motifs, is a realizable goal.
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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.