Analysis of Expression Datasets (including Tiling Arrays) [expression]
- An efficient pseudomedian filter for tiling microrrays.
- TE Royce, NJ Carriero, MB Gerstein (2007) BMC Bioinformatics 8: 186.
- Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.
- JO Korbel, AE Urban, F Grubert, J Du, TE Royce, P Starr, G Zhong, BS Emanuel, SM Weissman, M Snyder, MB Gerstein (2007) Proc Natl Acad Sci U S A 104: 10110-5.
- Tilescope: online analysis pipeline for high-density tiling microarray data.
- ZD Zhang, J Rozowsky, HY Lam, J Du, M Snyder, M Gerstein (2007) Genome Biol 8: R81.
- Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
- O Emanuelsson, U Nagalakshmi, D Zheng, JS Rozowsky, AE Urban, J Du, Z Lian, V Stolc, S Weissman, M Snyder, MB Gerstein (2007) Genome Res 17: 886-97.
- ProCAT: a data analysis approach for protein microarrays.
- X Zhu, M Gerstein, M Snyder (2006) Genome Biol 7: R110.
- A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
- J Du, JS Rozowsky, JO Korbel, ZD Zhang, TE Royce, MH Schultz, M Snyder, M Gerstein (2006) Bioinformatics 22: 3016-24.
- Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
- TE Royce, JS Rozowsky, NM Luscombe, O Emanuelsson, H Yu, X Zhu, M Snyder, MB Gerstein (2006) Methods Enzymol 411: 282-311.
- Design optimization methods for genomic DNA tiling arrays.
- P Bertone, V Trifonov, JS Rozowsky, F Schubert, O Emanuelsson, J Karro, MY Kao, M Snyder, M Gerstein (2006) Genome Res 16: 271-81.
- Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
- TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein (2005) Trends Genet 21: 466-75.
- Reconstructing genetic networks in yeast.
- Z Zhang, M Gerstein (2003) Nat Biotechnol 21: 1295-7.
- Genomic analysis of gene expression relationships in transcriptional regulatory networks.
- H Yu, NM Luscombe, J Qian, M Gerstein (2003) Trends Genet 19: 422-7.
- 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.
- 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.
- Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.
- R Jansen, HJ Bussemaker, M Gerstein (2003) Nucleic Acids Res 31: 2242-51.
- Relating whole-genome expression data with protein-protein interactions.
- R Jansen, D Greenbaum, M Gerstein (2002) Genome Res 12: 37-46.
- Proteomics. Integrating interactomes.
- M Gerstein, N Lan, R Jansen (2002) Science 295: 284-7.
- Integration of genomic datasets to predict protein complexes in yeast.
- R Jansen, N Lan, J Qian, M Gerstein (2002) J Struct Funct Genomics 2: 71-81.
- Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.
- J Qian, M Dolled-Filhart, J Lin, H Yu, M Gerstein (2001) J Mol Biol 314: 1053-66.
- Integrative data mining: the new direction in bioinformatics.
- P Bertone, M Gerstein (2001) IEEE Eng Med Biol Mag 20: 33-40.
- The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?
- M Gerstein, R Jansen (2000) Curr Opin Struct Biol 10: 574-84.
- A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome.
- A Drawid, M Gerstein (2000) J Mol Biol 301: 1059-75.
- Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins.
- R Jansen, M Gerstein (2000) Nucleic Acids Res 28: 1481-8.
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