Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space
Authors
Keywords
-
Journal
PLoS One
Volume 10, Issue 10, Pages e0140557
Publisher
Public Library of Science (PLoS)
Online
2015-10-15
DOI
10.1371/journal.pone.0140557
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- A method to predict the impact of regulatory variants from DNA sequence
- (2015) Dongwon Lee et al. NATURE GENETICS
- Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
- (2015) Dmitri D. Pervouchine et al. Nature Communications
- A comparative encyclopedia of DNA elements in the mouse genome
- (2014) Feng Yue et al. NATURE
- Comparison of the transcriptional landscapes between human and mouse tissues
- (2014) Shin Lin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
- (2014) Mahmoud Ghandi et al. PLoS Computational Biology
- Discriminative motif optimization based on perceptron training
- (2013) Ronak Y. Patel et al. BIOINFORMATICS
- Discriminative motif analysis of high-throughput dataset
- (2013) Zizhen Yao et al. BIOINFORMATICS
- A general approach for discriminative de novo motif discovery from high-throughput data
- (2013) Jan Grau et al. NUCLEIC ACIDS RESEARCH
- kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets
- (2013) Christopher Fletez-Brant et al. NUCLEIC ACIDS RESEARCH
- Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
- (2012) D. U. Gorkin et al. GENOME RESEARCH
- The Limits of De Novo DNA Motif Discovery
- (2012) David Simcha et al. PLoS One
- DECOD: fast and accurate discriminative DNA motif finding
- (2011) Peter Huggins et al. BIOINFORMATICS
- DREME: motif discovery in transcription factor ChIP-seq data
- (2011) Timothy L. Bailey BIOINFORMATICS
- A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans
- (2011) C. Linhart et al. GENOME RESEARCH
- Discriminative prediction of mammalian enhancers from DNA sequence
- (2011) D. Lee et al. GENOME RESEARCH
- Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- (2011) L. Song et al. GENOME RESEARCH
- A cis-regulatory map of the Drosophila genome
- (2011) Nicolas Nègre et al. NATURE
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
- (2010) Sven Heinz et al. MOLECULAR CELL
- Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
- (2010) M. B. Gerstein et al. SCIENCE
- ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands
- (2009) Willem-Jan Welboren et al. EMBO JOURNAL
- WormBase: a comprehensive resource for nematode research
- (2009) Todd W. Harris et al. NUCLEIC ACIDS RESEARCH
- Seeder: discriminative seeding DNA motif discovery
- (2008) François Fauteux et al. BIOINFORMATICS
- Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
- (2008) Xi Chen et al. CELL
- Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
- (2008) C. Linhart et al. GENOME RESEARCH
- UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
- (2008) D. E. Newburger et al. NUCLEIC ACIDS RESEARCH
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
- Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast
- (2007) Matthew J. Brauer et al. MOLECULAR BIOLOGY OF THE CELL
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now