Zhang ZD - Search Results

1

Modeling ChIP sequencing in silico with applications.

Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M. Zhang ZD, et al. PLoS Comput Biol. 2008 Aug 22;4(8):e1000158. doi: 10.1371/journal.pcbi.1000158. PLoS Comput Biol. 2008. PMID: 18725927 Free PMC article.

2

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.

Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M. Du J, et al. Among authors: zhang zd. Bioinformatics. 2006 Dec 15;22(24):3016-24. doi: 10.1093/bioinformatics/btl515. Epub 2006 Oct 12. Bioinformatics. 2006. PMID: 17038339

3

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.

Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Zhang ZD, et al. Genome Res. 2007 Jun;17(6):787-97. doi: 10.1101/gr.5573107. Genome Res. 2007. PMID: 17567997 Free PMC article.

4

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.

Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M. Euskirchen GM, et al. Among authors: zhang zd. Genome Res. 2007 Jun;17(6):898-909. doi: 10.1101/gr.5583007. Genome Res. 2007. PMID: 17568005 Free PMC article.

5

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.

Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M. Borneman AR, et al. Among authors: zhang zd. Funct Integr Genomics. 2007 Oct;7(4):335-45. doi: 10.1007/s10142-007-0054-7. Epub 2007 Jul 19. Funct Integr Genomics. 2007. PMID: 17638031

6

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. Rozowsky J, et al. Among authors: zhang zd. Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4. Nat Biotechnol. 2009. PMID: 19122651 Free PMC article.

7

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Du J, et al. Among authors: zhang zd. PLoS Comput Biol. 2009 Jul;5(7):e1000432. doi: 10.1371/journal.pcbi.1000432. Epub 2009 Jul 10. PLoS Comput Biol. 2009. PMID: 19593373 Free PMC article.

8

Tilescope: online analysis pipeline for high-density tiling microarray data.

Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M. Zhang ZD, et al. Genome Biol. 2007;8(5):R81. doi: 10.1186/gb-2007-8-5-r81. Genome Biol. 2007. PMID: 17501994 Free PMC article.

9

Divergence of transcription factor binding sites across related yeast species.

Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. Borneman AR, et al. Among authors: zhang zd. Science. 2007 Aug 10;317(5839):815-9. doi: 10.1126/science.1140748. Science. 2007. PMID: 17690298

10

Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.

Zhang ZD, Cayting P, Weinstock G, Gerstein M. Zhang ZD, et al. Mol Biol Evol. 2008 Jan;25(1):131-43. doi: 10.1093/molbev/msm251. Epub 2007 Dec 7. Mol Biol Evol. 2008. PMID: 18065488

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