List of publications
Journal Article (15)
1.
Journal Article
19, pp. 2036 - 2051 (2009)
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Genome Resaerch 2.
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 3.
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 4.
Journal Article
16 (7), pp. 887 - 896 (2009)
Maximum Similarity: A New Formulation of Phylogenetic Reconstruction. Journal of Computational Biology 5.
Journal Article
5, 2009.45 (2009)
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments. Molecular Systems Biology 6.
Journal Article
10, p. 204 - 204 (2009)
Comparison of sequence-dependent tiling array normalization approaches. BMC Bioinformatics 7.
Journal Article
25 (4), pp. 435 - 442 (2009)
PASTAA: identifying transcription factors associated with sets of co-regulated genes. Bioinformatics 8.
Journal Article
10, p. e144 - e144 (2009)
Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse. BMC Genomics 9.
Journal Article
386 (5), pp. 1411 - 1422 (2009)
Sequence-dependent Nucleosome Positioning. Journal of Molecular Biology 10.
Journal Article
25 (16), pp. 2103 - 2109 (2009)
Statistical detection of cooperative transcription factors with similarity adjustment. Bioinformatics 11.
Journal Article
12 (4), pp. 418 - 427 (2009)
Paracrine control of oligodendrocyte differentiation by SRF-directed neuronal gene expression. Nature Neuroscience 12.
Journal Article
5 (2), p. e1000282 - e1000282 (2009)
Evidence for Gene-Specific Rather Than Transcription Rate–Dependent Histone H3 Exchange in Yeast Coding Regions. PLoS Computational Biology 13.
Journal Article
25 (2), pp. 63 - 66 (2009)
Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends in Genetics 14.
Journal Article
10 (1), p. 202 - 202 (2009)
Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biology 15.
Journal Article
9 (9), 1471-2148-9-9 (2009)
Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC Evolutionary Biology Book Chapter (1)
16.
Book Chapter
Exact Score Distribution Computation for Similarity Searches in Ontologies. In: Algorithms in Bioinformatics, pp. 298 - 309 (Eds. Salzberg, S. L.; Warnow, T.). Springer, New York [et al] (2009)