Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

[1]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[2]  J. Thierry-Mieg,et al.  AceView: a comprehensive cDNA-supported gene and transcripts annotation , 2006, Genome Biology.

[3]  Michal J. Okoniewski,et al.  Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations , 2006, BMC Bioinformatics.

[4]  Rafael A. Irizarry,et al.  Comparison of Affymetrix GeneChip expression measures , 2006, Bioinform..

[5]  Z. Szallasi,et al.  Reliability and reproducibility issues in DNA microarray measurements. , 2006, Trends in genetics : TIG.

[6]  R. Myers,et al.  Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data , 2005, Nucleic acids research.

[7]  Ramil N. Nurtdinov,et al.  Alternative splicing and protein function , 2005, BMC Bioinformatics.

[8]  Lei Zhou,et al.  An expression index for Affymetrix GeneChips based on the generalized logarithm , 2005, Bioinform..

[9]  Miguel A. Andrade-Navarro,et al.  Inconsistencies over time in 5% of NetAffx probe-to-gene annotations , 2005, BMC Bioinformatics.

[10]  John Quackenbush,et al.  Multiple-laboratory comparison of microarray platforms , 2005, Nature Methods.

[11]  Isaac S. Kohane,et al.  Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements , 2005, BMC Bioinformatics.

[12]  Kenneth H Buetow,et al.  Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach. , 2005, Genomics.

[13]  Steen Knudsen,et al.  Implementation of a gene expression index calculation method based on the PDNN model , 2005, Bioinform..

[14]  S. Enkemann,et al.  A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array , 2005, Nucleic acids research.

[15]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[16]  Paul T. Groth,et al.  The ENCODE (ENCyclopedia Of DNA Elements) Project , 2004, Science.

[17]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[18]  Steen Knudsen,et al.  Alternative mapping of probes to genes for Affymetrix chips , 2004, BMC Bioinformatics.

[19]  Z. Szallasi,et al.  Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. , 2004, Nucleic acids research.

[20]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[21]  Terence P. Speed,et al.  A benchmark for Affymetrix GeneChip expression measures , 2004, Bioinform..

[22]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[23]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[24]  R. Lempicki,et al.  Evaluation of gene expression measurements from commercial microarray platforms. , 2003, Nucleic acids research.

[25]  K. Aldape,et al.  A model of molecular interactions on short oligonucleotide microarrays , 2003, Nature Biotechnology.

[26]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[27]  T. Speed,et al.  Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.

[28]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology , 2003, Nucleic Acids Res..

[29]  G. Pertea,et al.  RESOURCERER: a database for annotating and linking microarray resources within and across species , 2001, Genome Biology.

[30]  C. Li,et al.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  K. Katz,et al.  Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. , 2000, Trends in genetics : TIG.

[32]  L. Wodicka,et al.  Genome-wide expression monitoring in Saccharomyces cerevisiae , 1997, Nature Biotechnology.

[33]  D. Stern,et al.  Thermodynamics of Duplex Formation and Mismatch Discrimination on Photolithographically Synthesized Oligonucleotide Arrays , 1997 .

[34]  Neocles B. Leontis,et al.  Molecular modeling of nucleic acids , 1997 .

[35]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.