Gerstein Lab Publications

Main  •  By Subject  •  Queries  •  Code  •  Other Writings


2007 snippet describing some of the lab's work in designing expression analysis tools [html] [doc]

Early 2009 blurb on Lab's Transcriptome Experience [html] [doc]


An efficient pseudomedian filter for tiling microrrays.
TE Royce, NJ Carriero, MB Gerstein (2007). BMC Bioinformatics 8:186.
website
preprint
medline

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.
website
preprint
medline

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.
website
preprint
medline

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.
website
preprint
medline

ProCAT: a data analysis approach for protein microarrays.
X Zhu, M Gerstein, M Snyder (2007). Genome Biol 7:R110.
website
preprint
medline

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.
website
preprint
medline

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.
 
preprint
medline

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.
website
preprint
medline

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.
 
preprint
medline

Reconstructing genetic networks in yeast.
Z Zhang, M Gerstein (2003). Nat Biotechnol 21:1295-7.
 
preprint
medline

Genomic analysis of gene expression relationships in transcriptional regulatory networks.
H Yu, NM Luscombe, J Qian, M Gerstein (2003). Trends Genet 19:422-7.
website
preprint
medline

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.
 
preprint
medline

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.
website
preprint
medline

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.
website
preprint
medline

Relating whole-genome expression data with protein-protein interactions.
R Jansen, D Greenbaum, M Gerstein (2002). Genome Res 12:37-46.
website
preprint
medline

Proteomics. Integrating interactomes.
M Gerstein, N Lan, R Jansen (2002). Science 295:284-7.
website
preprint
medline

Integration of genomic datasets to predict protein complexes in yeast.
R Jansen, N Lan, J Qian, M Gerstein (2003). J Struct Funct Genomics 2:71-81.
website
preprint
medline

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.
website
preprint
medline

Integrative data mining: the new direction in bioinformatics.
P Bertone, M Gerstein (2001). IEEE Eng Med Biol Mag 20:33-40.
 
preprint
medline

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.
website
preprint
medline

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.
website
preprint
medline

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.
website
preprint
medline


Return to front page