Shmulevich I - Search Results

1

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.

Ramsey SA, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, Shmulevich I. Ramsey SA, et al. Among authors: shmulevich i. Bioinformatics. 2010 Sep 1;26(17):2071-5. doi: 10.1093/bioinformatics/btq405. Epub 2010 Jul 27. Bioinformatics. 2010. PMID: 20663846 Free PMC article.

2

ProbCD: enrichment analysis accounting for categorization uncertainty.

Vêncio RZ, Shmulevich I. Vêncio RZ, et al. Among authors: shmulevich i. BMC Bioinformatics. 2007 Oct 12;8:383. doi: 10.1186/1471-2105-8-383. BMC Bioinformatics. 2007. PMID: 17935624 Free PMC article.

3

The Innate Immune Database (IIDB).

Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H. Korb M, et al. Among authors: shmulevich i. BMC Immunol. 2008 Mar 5;9:7. doi: 10.1186/1471-2172-9-7. BMC Immunol. 2008. PMID: 18321385 Free PMC article.

4

Probabilistic inference of transcription factor binding from multiple data sources.

Lähdesmäki H, Rust AG, Shmulevich I. Lähdesmäki H, et al. Among authors: shmulevich i. PLoS One. 2008 Mar 26;3(3):e1820. doi: 10.1371/journal.pone.0001820. PLoS One. 2008. PMID: 18364997 Free PMC article.

5

Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.

Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I. Ramsey SA, et al. Among authors: shmulevich i. PLoS Comput Biol. 2008 Mar 21;4(3):e1000021. doi: 10.1371/journal.pcbi.1000021. PLoS Comput Biol. 2008. PMID: 18369420 Free PMC article.

6

Taming data.

Aderem A, Shmulevich I. Aderem A, et al. Among authors: shmulevich i. Cell Host Microbe. 2008 Oct 16;4(4):312-3. doi: 10.1016/j.chom.2008.09.011. Cell Host Microbe. 2008. PMID: 18854235 Free PMC article.

7

Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform.

Taylor RJ, Falconnet D, Niemistö A, Ramsey SA, Prinz S, Shmulevich I, Galitski T, Hansen CL. Taylor RJ, et al. Among authors: shmulevich i. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3758-63. doi: 10.1073/pnas.0813416106. Epub 2009 Feb 17. Proc Natl Acad Sci U S A. 2009. PMID: 19223588 Free PMC article.

8

Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals.

Litvak V, Ramsey SA, Rust AG, Zak DE, Kennedy KA, Lampano AE, Nykter M, Shmulevich I, Aderem A. Litvak V, et al. Among authors: shmulevich i. Nat Immunol. 2009 Apr;10(4):437-43. doi: 10.1038/ni.1721. Epub 2009 Mar 8. Nat Immunol. 2009. PMID: 19270711 Free PMC article.

9

A data integration framework for prediction of transcription factor targets.

Nykter M, Lähdesmäki H, Rust A, Thorsson V, Shmulevich I. Nykter M, et al. Among authors: shmulevich i. Ann N Y Acad Sci. 2009 Mar;1158:205-14. doi: 10.1111/j.1749-6632.2008.03758.x. Ann N Y Acad Sci. 2009. PMID: 19348642 Free PMC article.

10

Fewer permutations, more accurate P-values.

Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I. Knijnenburg TA, et al. Among authors: shmulevich i. Bioinformatics. 2009 Jun 15;25(12):i161-8. doi: 10.1093/bioinformatics/btp211. Bioinformatics. 2009. PMID: 19477983 Free PMC article.

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