Journal Article (222)
121.
Journal Article
17 (12), pp. 1591 - 1606 (2010)
Studying the evolution of promoter sequences: a waiting time problem. Journal Computational Biology 122.
Journal Article
38 (18), pp. 6112 - 6123 (2010)
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Research 123.
Journal Article
467 (7314), pp. 460 - 464 (2010)
A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature 124.
Journal Article
17 (8), pp. 953 - 967 (2010)
Introducing knowledge into differential expression analysis. Journal of Computational Biology 125.
Journal Article
38 Suppl, pp. W275 - W280 (2010)
TransFind--predicting transcriptional regulators for gene sets. Nucleic Acids Research 126.
Journal Article
38 (10), p. e112 - e112 (2010)
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Research 127.
Journal Article
31 (4), pp. 477 - 483 (2010)
Quantifying the effect of sequence variation on regulatory interactions. Hum Mutation 128.
Journal Article
38 (4), p. e23 - e23 (2010)
A calibrated diversity assay for nucleic acid libraries using DiStRO-a Diversity Standard of Random Oligonucleotides. Nucleic Acids Research 129.
Journal Article
107 (7), pp. 2926 - 2931 (2010)
Histone modification levels are predictive for gene expression. Proceedings of the National Academy of Sciences USA 130.
Journal Article
11, p. 11:267 - 11:267 (2010)
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. BMC Bioinformatics 131.
Journal Article
19, pp. 2036 - 2051 (2009)
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Genome Resaerch 132.
Journal Article
37 (19), pp. 6305 - 6315 (2009)
CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses. Nucleic Acids Research 133.
Journal Article
10, p. 314 - 314 (2009)
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. BMC Genomics 134.
Journal Article
16 (7), pp. 887 - 896 (2009)
Maximum Similarity: A New Formulation of Phylogenetic Reconstruction. Journal of Computational Biology 135.
Journal Article
5, 2009.45 (2009)
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments. Molecular Systems Biology 136.
Journal Article
10, p. 204 - 204 (2009)
Comparison of sequence-dependent tiling array normalization approaches. BMC Bioinformatics 137.
Journal Article
25 (4), pp. 435 - 442 (2009)
PASTAA: identifying transcription factors associated with sets of co-regulated genes. Bioinformatics 138.
Journal Article
10, p. e144 - e144 (2009)
Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse. BMC Genomics 139.
Journal Article
386 (5), pp. 1411 - 1422 (2009)
Sequence-dependent Nucleosome Positioning. Journal of Molecular Biology 140.
Journal Article
25 (16), pp. 2103 - 2109 (2009)
Statistical detection of cooperative transcription factors with similarity adjustment. Bioinformatics