An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

By X. S. Liu, Douglas L. Brutlag, J. Liu. Nature Biotechnology, 2002

733 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ca6077253dd62c1d98994e02f8e406251b7dd16c

How researchers see this paper

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

In Genetics

1. Guo-li Ming
2. Hongjun Song
3. B. van Steensel
4. Peter Buhlmann
5. Christina S. Leslie
6. Modan K. Das
7. Ho-Kwok Dai
8. William Stafford Noble

In Molecular Biology

1. Christina S. Leslie
2. Peter Buhlmann
3. William Stafford Noble
4. B. van Steensel
5. Timothy L. Bailey
6. Sara A. van de Geer
7. X. S. Liu
8. Yong Zhang

Citations in the corpus

• Genome-Wide Mapping of the Cohesin Complex in the Yeast Saccharomyces cerevisiae (2004, unknown): “Attempts to identify a genome-wide linear consensus binding site for cohesin using BioProspector (Liu et al. 2002), MobyDick (Bussemaker et al.”
• High-dimensional additive modeling (2008, methodology): “The candidate list of motifs and their corresponding scores were created with a variant of the MDScan algorithm [ 20 ].”
• Discovering Motifs in Ranked Lists of DNA Sequences (2007, methodology): “One exception is a recent work in which a CACACACACAC sequence was found to be enriched in Rap1 experiments [33].”
• CEAS: cis-regulatory element annotation system (2006, methodology): “The current best de novo motif finding methods for ChIP–chip includes MEME (11), AlignACE (12), Mascan (13) and their combinations (14).”
• DNA methylation presents distinct binding sites for human transcription factors (2013, methodology): “The known consensus for KLF4 shown in Figure 2A was created based on the dataset from in vitro oligonucleotide library using MDscan (Liu et al., 2002).”
• FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. (2008, unknown): “, unpublished data), a modified MDscan (Liu et al., 2002) with ninth-order Markov dependency for the genome background.”
• Discovering Sequence Motifs with Arbitrary Insertions and Deletions (2008, methodology): “These include A-GLAM [1], AlignACE [2], BioProspector [3], MDscan [4], RSA Tools [5,6], Weeder [7] and YMF [8].”
• Densely interconnected transcriptional circuits control cell states in human hematopoiesis (2011, unknown): “The motifs were discovered using 6 different algorithms: AlignAce (Hughes et al., 2000), MEME (Bailey and Elkan, 1995) and MDScan (Liu et al., 2002) (managed with TAMO software (Gordon et al., 2005)), FIRE (Elemento et al., 2007), Amadeus (Linhart et al., 2008) and SeedSearcher (Barash et al., 2002)”
• Cistrome: an integrative platform for transcriptional regulation studies (2011, methodology): “SeqPos can also find de novo motifs using the MDscan algorithm [30].”