Experimental

Global Changes in STAT Target Selection and Transcription Regulation Upon Interferon Treatments. S.E. Hartman, P. Bertone, A. Nath, T.E. Royce, M. Gerstein, S. Weissman, and M. Snyder (2005). Genes Devel. (in press).

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Y Gilad, SA Rifkin, P Bertone, M Gerstein, KP White (2005). Genome Res 15: 674-80.

The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. H Grosshans, T Johnson, KL Reinert, M Gerstein, FJ Slack (2005). Dev Cell 8: 321-30.

Global identification of human transcribed sequences with genome tiling arrays. P. Bertone, V. Stolc, T.E. Royce, J. Rozowsky, A.E. Urban, X. Zhu, J.L. Rinn, W. Tongprasit, M. Samanta, S. Weissman, M. Gerstein, M. Snyder (2004). Science 306:2242-2246.

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. E.J. White, O. Emanuelsson, D. Scalzo, T. Royce, S. Kosak, E.J. Oakeley, S. Weissman, M. Gerstein, M. Groudine, M. Snyder, D. Schübeler. (2004). Proc Natl Acad Sci. 101:17771-17776.

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. J.L. Rinn, J.S. Rozowsky, I.J. Laurenzi, P.H. 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, T.E. Royce, P. Bertone, R. Martone, J.L. Rinn, F.K. Nelson, F. Sayward, N.M. Luscombe, P. Miller, M. Gerstein, S. Weissman, M. Snyder (2004). Mol Cell Biol. 24:3804-3814.

Identification of novel functional elements in the human genome. Z. Lian, G. Euskirchen, J.L. Rinn, R. Martone, P. Bertone, S. Hartman, T.E. Royce, F.K. Nelson, F. Sayward, N.M. Luscombe, Y. Lang, J. Li, P. Miller, A.E. Urban, M. Gerstein, S. Weissman, M. Snyder (2003). Cold Spring Harb Symp Quant Biol. 68:317-322.

Distribution of NF-kappaB-binding sites across human chromosome 22. R. Martone, G. Euskirchen, P. Bertone, S. Hartman, T.E. Royce, N.M. Luscombe, J.L. Rinn, F.K. Nelson, P. Miller, M. Gerstein, S. Weissman, M. Snyder (2003). Proc Natl Acad Sci. 100:12247-12252.

The transcriptional activity of human chromosome 22. J.L. Rinn. G. Euskirchen, P. Bertone, R. Martone, N.M. Luscombe, S. Hartman, P.M. Harrison, F.K. Nelson, P. Miller, M. Gerstein, S. Weissman, M. Snyder (2003). Genes Dev. 17:529-540.

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. C.E. Horak, N.M. Luscombe, J. Qian, P. Bertone, S. Piccirrillo, M. Gerstein, M. Snyder (2002). Genes Dev. 16:3017-3033.

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, D.S. Greenbaum, D. Tuck, M. Gerstein, N. Berliner, S.M. Weissman, P.E. Newburger (2002). Blood 100: 3209-3220.

GATA-1 binding sites mapped in the b-globin locus by using mammalian chlp-chip analysis C.E. Horak, M. Mahajan, N.M. Luscombe, M. Gerstein, S. Weissman, M. Snyder (2002). Proc Natl Acad Sci. 99:2924-2929.

Bioinformatics

Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray Technologies. T. E. Royce, J. S. Rozowsky, N. M. Luscombe, O. Emanuelsson, H. Yu, X. Zhu, M. Snyder, M. Gerstein Methods Enzymol (in press).

Integrated pseudogene annotation for human chromosome 22: evidence for transcription. D. Zheng, Z. Zhang, P. M. Harrison, J. Karro, N. Carriero, M. Gerstein (2005) J Mol Biol 349: 27-45.

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. P. M. Harrison, D. Zheng, Z. Zhang, N. Carriero, M. Gerstein (2005) Nucleic Acids Res 33: 2374-83.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. T.E. Royce, J.S. Rozowsky, P. Bertone, M. Samanta, V. Stolc, S. Weissman, M. Snyder, M. Gerstein (2005) Trends Genet 21: 466-75.

Design optimization methods for genomic DNA tiling arrays. P. Bertone, F. Schubert, V. Trifonov, J. Rozowsky, O. Emanuelsson, J. Karro, M-Y Kao, M. Snyder, M. Gerstein (submitted).

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 (2004). J Comput Biol. 11:766-785.

Large scale analysis of pseudogenes in the human genome. Z. Zhang, M. Gerstein (2004). Curr Opin Genet Dev. 14:328-335.

Comparative analysis of processed pseudogenes in the mouse and human genomes. Z. Zhang, N. Carriero, M. Gerstein (2004). Trends Genet. 20:62-67.

Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Z. Zhang, P.M. Harrison, Y. Liu, M. Gerstein (2003). Genome Res. 13:2541-2558.

A “polyORFomic” analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs. P.M. Harrison, N. Carriero, Y. Liu, M. Gerstein (2003). J Mol Biol. 333:885-892.

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. J. Qian, J. Lin, N.M. Luscombe, H. Yu, M. Gerstein (2003). Bioinformatics 19:1917-1926.

Identification and correction of spurious spatial correlations in microarray data. J. Qian, Y. Kluger, H. Yu, M. Gerstein (2003). Biotechniques 35:42-4,46,48.

Relationship between gene co-expression and probe localization on microarray slides. Y Kluger, H Yu, J Qian, M Gerstein (2003) BMC Genomics 4:49.

ExpressYourself: A modular platform for processing and visualizing microarray data. N.M. Luscombe, T.E. Royce, P. Bertone, N. Echols, C.E. Horak, J.T. Chang, M. Snyder, M. Gerstein (2003). Nucleic Acids Res. 31:3477-3482.

Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. Z. Zhang, M. Gerstein (2003). J Biol. 2:11.

Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome. Z. Zhang, M. Gerstein (2003). Genomics 81:468-480.

Genomics. Defining genes in the genomics era. M. Snyder, M. Gerstein (2003). Science 300:258-260.

Spectral biclustering of microarray data: coclustering genes and conditions. K. Kluger, R. Basri, J.T. Chang, M. Gerstein (2003). Genome Res. 13:703-716.

Identification of pseudogenes in the Drosophila melanogaster genome. P.M. Harrison, D. Milburn, Z. Zhang, P. Bertone, M. Gerstein (2003). Nucleic Acids Res. 31:1033-1037.

Studying genomes through the aeons: protein families, pseudogenes and Proteome evolution. P.M. Harrison, M. Gerstein (2002). J Mol Biol. 318:1155-1174.

A question of size: the eukaryotic proteome and the problems in defining it. P.M. Harrison, A. Kumar, N. Lang, M. Snyder, M. Gerstein (2002). Nucleic Acids Res. 30:1083-1090.

Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Z. Zhang, P. Harrison, M. Gerstein (2002). Genome Res. 12:1466-1482.

SNPs on human chromosomes 21 and 22 - analysis in terms of protein features and pseudogenes. S. Balasubramanian, P.M. Harrison, P. Bertone, N. Echols, N. Luscombe, Z. Zhang, M. Gerstein (2002). Pharmacogenomics 3:393-402.

Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22. P.M. Harrison, H. Hegyi, S. Balasubramanian, N.M. Luscombe, P. Bertone, N. Echols, T. Johnson, M. Gerstein (2002). Genome Res. 12:272-280.

Medical Informatics

Network security and data integrity in academia: an assessment and a proposal for large-scale archiving. A. Smith, D. Greenbaum, S. M. Douglas, M. Long, M. Gerstein (2005). Genome Biol 6: 119.

A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies. Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. (2005). J Am Med Inform Assoc. 12:90-98.

YMD: a microarray database for large-scale gene expression analysis. K.H. Cheung, K. White, J. Hager, M. Gerstein, V. Reinke, K. Nelson, P. Masiar, R. Srivastava, Y. Li, J. Li, H. Zhao, J. Li, D.B. Allison, M. Snyder, P. Miller, K. Williams (2002). AMIA Symp. 140-144.

A Dynamic approach to mapping coordinates between microplates and microarrays. K.H. Cheung, J. Hager, K. Nelson, K. White, Y. Li, M. Snyder, K. Williams, P. Miller (2002). J Bioinformatics 35:306-312.

A Metadata framework for interoperating heterogeneous genome data using XML. K.H. Cheung, A.M. Deshpande, N. Tosches, S. Nath, A. Agrawal, P. Miller, A. Kumar, M. Snyder (2001). Proc. American Medical Informatics Assoc Annual Symp. 110-114.

An XML application for genomic data interoperation. K.H. Cheung, Y. Liu, K. Kumar, M. Snyder, M. Gerstein, P. Miller IEEE International Symposium on Bio-informatics and Biomedical Engineering 97-103.