Genome-wide prediction of transcription factor binding sites using an integrated model

By Kyoung-Jae Won, Bing Ren, Wei Wang. Genome Biology, 2010

360 citations recorded by the source corpus.

We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bdd21a9233c75aa26188bf09019d793092e61450

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 (2018, background): “…assembly errors are crucial for the generation of accurate assemblies (Salzberg and Yorke 2005; Phillippy, Schatz, and Pop 2008; Gnerre et al. 2009; Tsai, Otto, and Berriman 2010; Salzberg et al. 2012; Hunt et al. 2013; Gurevich et al. 2013; Bradnam et al. 2013; Simão et al. 2015; Fierst 2015;…”
Sequence and chromatin determinants of cell-type–specific transcription factor binding (2012, methodology): “combined PSSMs and chromatin data in probabilistic models (Ernst et al. 2010; Won et al. 2010; Pique-Regi et al. 2011) or”
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach (2013, methodology): “We demonstrate how MITObim is capable of assembling mitochondrial genomes without the need of a reference genome of the targeted species by relying solely on mitochondrial genome information of more distantly related taxa as a starting point, and compare its performance to the previously published t”
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement (2014, methodology): “We benchmarked Pilon ' s ability to close gaps in the draft bacterial assemblies against two tools built for this purpose , IMAGE v2 .”
RATT: Rapid Annotation Transfer Tool (2011, background): “Genome builds are frequently corrected by gap closing/contig reorienting (3), or SNP calling and consensus correction (19).”
Sequence-specific error profile of Illumina sequencers (2011, background): “Even with bacterial sequencing, state-of-the-art assemblers still provide a mere collection of hundreds of contigs, and are unable to produce a single cyclic genome sequence without gaps (33,34).”