Microarray

Gerstein Lab Publications

Main • By Subject • Queries • Code • Other Writings

Assessing the need for sequence-based normalization in tiling microarray experiments.

TE Royce, JS Rozowsky, MB Gerstein (2007). Bioinformatics 23:988-97.

Global analysis of protein phosphorylation in yeast.

J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder (2005). Nature 438:679-84.

Global changes in STAT target selection and transcription regulation upon interferon treatments.

SE Hartman, P Bertone, AK Nath, TE Royce, M Gerstein, S Weissman, M Snyder (2005). Genes Dev 19:2953-68.

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

EJ White, O Emanuelsson, D Scalzo, T Royce, S Kosak, EJ Oakeley, S Weissman, M Gerstein, M Groudine, M Snyder, D Schübeler (2004). Proc Natl Acad Sci U S A 101:17771-6.

Fast optimal genome tiling with applications to microarray design and homology search.

P Berman, P Bertone, B Dasgupta, M Gerstein, MY Kao, M Snyder (2004). J Comput Biol 11:766-85.

Regulation of gene expression by a metabolic enzyme.

DA Hall, H Zhu, X Zhu, T Royce, M Gerstein, M Snyder (2004). Science 306:482-4.

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.

JL Rinn, JS Rozowsky, IJ Laurenzi, PH Petersen, K Zou, W Zhong, M Gerstein, M Snyder (2004). Dev Cell 6:791-800.

CREB binds to multiple loci on human chromosome 22.

G Euskirchen, TE Royce, P Bertone, R Martone, JL Rinn, FK Nelson, F Sayward, NM Luscombe, P Miller, M Gerstein, S Weissman, M Snyder (2004). Mol Cell Biol 24:3804-14.

A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development.

Y Jiao, H Yang, L Ma, N Sun, H Yu, T Liu, Y Gao, H Gu, Z Chen, M Wada, M Gerstein, H Zhao, LJ Qu, XW Deng (2003). Plant Physiol 133:1480-93.

A Bayesian networks approach for predicting protein-protein interactions from genomic data.

R Jansen, H Yu, D Greenbaum, Y Kluger, NJ Krogan, S Chung, A Emili, M Snyder, JF Greenblatt, M Gerstein (2003). Science 302:449-53.

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.

J Qian, J Lin, NM Luscombe, H Yu, M Gerstein (2003). Bioinformatics 19:1917-26.

Distribution of NF-kappaB-binding sites across human chromosome 22.

R Martone, G Euskirchen, P Bertone, S Hartman, TE Royce, NM Luscombe, JL Rinn, FK Nelson, P Miller, M Gerstein, S Weissman, M Snyder (2003). Proc Natl Acad Sci U S A 100:12247-52.

ExpressYourself: A modular platform for processing and visualizing microarray data.

NM Luscombe, TE Royce, P Bertone, N Echols, CE Horak, JT Chang, M Snyder, M Gerstein (2003). Nucleic Acids Res 31:3477-82.

Spectral biclustering of microarray data: coclustering genes and conditions.

Y Kluger, R Basri, JT Chang, M Gerstein (2003). Genome Res 13:703-16.

The transcriptional activity of human Chromosome 22.

JL Rinn, G Euskirchen, P Bertone, R Martone, NM Luscombe, S Hartman, PM Harrison, FK Nelson, P Miller, M Gerstein, S Weissman, M Snyder (2003). Genes Dev 17:529-40.

Fast optimal genome tiling with applications to microarray design and homology search.

P Berman, P Bertone, B DasGupta, M Gerstein, M-Y Kao, M Snyder (2002). Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics. Springer-Verlag LNCS 2452: 419-433

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.

CE Horak, NM Luscombe, J Qian, P Bertone, S Piccirrillo, M Gerstein, M Snyder (2002). Genes Dev 16:3017-33.

YMD: a microarray database for large-scale gene expression analysis.

KH Cheung, K White, J Hager, M Gerstein, V Reinke, K Nelson, P Masiar, R Srivastava, Y Li, J Li, H Zhao, J Li, DB Allison, M Snyder, P Miller, K Williams (2002). Proc AMIA Symp :140-4.

Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line.

Z Lian, Y Kluger, DS Greenbaum, D Tuck, M Gerstein, N Berliner, SM Weissman, PE Newburger (2002). Blood 100:3209-20.

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.

CE Horak, MC Mahajan, NM Luscombe, M Gerstein, SM Weissman, M Snyder (2002). Proc Natl Acad Sci U S A 99:2924-9.

Global analysis of protein activities using proteome chips.

H Zhu, M Bilgin, R Bangham, D Hall, A Casamayor, P Bertone, N Lan, R Jansen, S Bidlingmaier, T Houfek, T Mitchell, P Miller, RA Dean, M Gerstein, M Snyder (2001). Science 293:2101-5.

Genomic and proteomic analysis of the myeloid differentiation program.

Z Lian, L Wang, S Yamaga, W Bonds, Y Beazer-Barclay, Y Kluger, M Gerstein, PE Newburger, N Berliner, SM Weissman (2001). Blood 98:513-24.

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