Technologies for the global discovery and analysis of alternative splicing.

[1]  Yi Xing,et al.  Global analysis of alternative splicing differences between humans and chimpanzees. , 2007, Genes & development.

[2]  Qun Pan,et al.  Global analysis of alternative splicing during T-cell activation. , 2007, RNA.

[3]  B. Frey,et al.  Functional coordination of alternative splicing in the mammalian central nervous system , 2007, Genome Biology.

[4]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[5]  S. Sudarsanam,et al.  Profiling human phosphodiesterase genes and splice isoforms. , 2006, Biochemical and biophysical research communications.

[6]  Nabil Belacel,et al.  Data analysis of alternative splicing microarrays. , 2006, Drug discovery today.

[7]  Steven J. M. Jones,et al.  BMC Genomics BioMed Central Methodology article , 2006 .

[8]  R. Fluhr,et al.  Whole-genome microarray in Arabidopsis facilitates global analysis of retained introns. , 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.

[9]  S. Nuzhdin,et al.  Sex-specific expression of alternative transcripts in Drosophila , 2006, Genome Biology.

[10]  Y. Hayashizaki,et al.  A RecA-mediated exon profiling method , 2006, Nucleic acids research.

[11]  B. Blencowe.  Alternative Splicing: New Insights from Global Analyses , 2006, Cell.

[12]  Mihaela Zavolan,et al.  The types and prevalence of alternative splice forms. , 2006, Current opinion in structural biology.

[13]  J. Weissenbach,et al.  ASEtrap: a biological method for speeding up the exploration of spliceomes. , 2006, Genome research.

[14]  Gary D. Stormo,et al.  Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans , 2006, Bioinform..

[15]  Christina L. Zheng,et al.  Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. , 2006, Cancer research.

[16]  Brendan J. Frey,et al.  Inferring global levels of alternative splicing isoforms using a generative model of microarray data , 2006, Bioinform..

[17]  Mitsuo Kato,et al.  Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays. , 2006, Cancer research.

[18]  L. Milani,et al.  Detection of alternatively spliced transcripts in leukemia cell lines by minisequencing on microarrays. , 2006, Clinical chemistry.

[19]  B. Frey,et al.  Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. , 2006, Genes & development.

[20]  Christopher B. Burge,et al.  Hollywood: a comparative relational database of alternative splicing , 2005, Nucleic Acids Res..

[21]  David Haussler,et al.  Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays , 2005, PLoS Comput. Biol..

[22]  Michael Q. Zhang,et al.  Profiling alternatively spliced mRNA isoforms for prostate cancer classification , 2006, BMC Bioinformatics.

[23]  Trees-Juen Chuang,et al.  Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat , 2006, BMC Bioinformatics.

[24]  Ying Xu,et al.  Structural genomics analysis of alternative splicing and application to isoform structure modeling. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[25]  K. Greulich.  Single-molecule studies on DNA and RNA. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[26]  M. Metzker.  Emerging technologies in DNA sequencing. , 2005, Genome research.

[27]  Toshiyuki Miyashita,et al.  Detecting tissue-specific alternative splicing and disease-associated aberrant splicing of the PTCH gene with exon junction microarrays. , 2005, Human molecular genetics.

[28]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[29]  J. Shendure,et al.  Materials and Methods Som Text Figs. S1 and S2 Tables S1 to S4 References Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2022 .

[30]  Christopher J. Lee,et al.  Protein Modularity of Alternatively Spliced Exons Is Associated with Tissue-Specific Regulation of Alternative Splicing , 2005, PLoS genetics.

[31]  Tyson A. Clark,et al.  Nova regulates brain-specific splicing to shape the synapse , 2005, Nature Genetics.

[32]  Christopher B. Burge,et al.  Recognition of Unknown Conserved Alternatively Spliced Exons , 2005, PLoS Comput. Biol..

[33]  C. Ding,et al.  High-throughput alternative splicing quantification by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry , 2005, Nucleic acids research.

[34]  Eugene Y Chan,et al.  Advances in sequencing technology. , 2005, Mutation research.

[35]  L. Maquat,et al.  Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. , 2005, Current opinion in cell biology.

[36]  S. Brenner,et al.  Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. , 2005, Genes & development.

[37]  P. Fehlbaum,et al.  A microarray configuration to quantify expression levels and relative abundance of splice variants , 2005, Nucleic acids research.

[38]  Zuo-min Zhou,et al.  Novel development-related alternative splices in human testis identified by cDNA microarrays. , 2005, Journal of andrology.

[39]  Tomaso Poggio,et al.  Identification and analysis of alternative splicing events conserved in human and mouse. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[41]  V. Beneš,et al.  Alternative Splicing Microarrays Reveal Functional Expression of Neuron-specific Regulators in Hodgkin Lymphoma Cells* , 2005, Journal of Biological Chemistry.

[42]  B. Frey,et al.  Alternative splicing of conserved exons is frequently species-specific in human and mouse. , 2005, Trends in genetics : TIG.

[43]  S. Stamm,et al.  Function of Alternative Splicing , 2004 .

[44]  Jack D. Keene,et al.  Post-transcriptional operons and regulons co-ordinating gene expression , 2005, Chromosome Research.

[45]  B. Frey,et al.  Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. , 2004, Molecular cell.

[46]  B. Frey,et al.  The functional landscape of mouse gene expression , 2004, Journal of biology.

[47]  Brenton R Graveley,et al.  A computational and experimental approach toward a priori identification of alternatively spliced exons. , 2004, RNA.

[48]  J. Kawai,et al.  Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas , 2004, Nature Methods.

[49]  Brenton R Graveley,et al.  Identification of alternative splicing regulators by RNA interference in Drosophila. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[50]  Scott A. Rifkin,et al.  A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster , 2004, Science.

[51]  O. Griffith,et al.  Systematic recovery and analysis of full-ORF human cDNA clones. , 2004, Genome research.

[52]  M. Vidal,et al.  C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. , 2004, Genome research.

[53]  Ron Shamir,et al.  A non-EST-based method for exon-skipping prediction. , 2004, Genome research.

[54]  S. Brenner,et al.  The evolving roles of alternative splicing. , 2004, Current opinion in structural biology.

[55]  J. Shendure,et al.  Advanced sequencing technologies: methods and goals , 2004, Nature Reviews Genetics.

[56]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[57]  S. Cawley,et al.  Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. , 2004, Genome research.

[58]  J. Edwards,et al.  Detecting Changes in the Relative Expression of KRAS2 Splice Variants Using Polymerase Colonies , 2004, Biotechnology progress.

[59]  Christopher J. Lee,et al.  Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. , 2004, Nucleic acids research.

[60]  Ryan D. Morin,et al.  The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). , 2004, Genome research.

[61]  J. Castle,et al.  Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays , 2003, Science.

[62]  Eric E Schadt,et al.  Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing , 2003, Genome Biology.

[63]  Jay Shendure,et al.  Fluorescent in situ sequencing on polymerase colonies. , 2003, Analytical biochemistry.

[64]  J. Shendure,et al.  Single Molecule Profiling of Alternative Pre-mRNA Splicing , 2003, Science.

[65]  L. Bracco,et al.  The relevance of alternative RNA splicing to pharmacogenomics. , 2003, Trends in biotechnology.

[66]  D. Dressman,et al.  Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Steven E. Brenner,et al.  Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes , 2003, ISMB.

[68]  David Haussler,et al.  Gene structure-based splice variant deconvolution using a microarry platform , 2003, ISMB.

[69]  Christopher J. Lee,et al.  Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss , 2003, Nature Genetics.

[70]  David E. Housman,et al.  Digital genotyping and haplotyping with polymerase colonies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[71]  J. Hudson,et al.  C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression , 2003, Nature Genetics.

[72]  P. Dear.  One by one: Single molecule tools for genomics. , 2003, Briefings in functional genomics & proteomics.

[73]  J. Valcárcel,et al.  Splicing regulation in Drosophila sex determination. , 2003, Progress in molecular and subcellular biology.

[74]  S. Brenner,et al.  Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[75]  S. P. Fodor,et al.  Large-Scale Transcriptional Activity in Chromosomes 21 and 22 , 2002, Science.

[76]  Tyson A. Clark,et al.  Genomewide Analysis of mRNA Processing in Yeast Using Splicing-Specific Microarrays , 2002, Science.

[77]  M. Pirrung,et al.  Arrayed primer extension computing with variant mRNA splice forms. Multiple isoforms of CD44 in a human breast tumor. , 2002, Journal of the American Chemical Society.

[78]  A. Kornblihtt,et al.  Alternative splicing: multiple control mechanisms and involvement in human disease. , 2002, Trends in genetics : TIG.

[79]  Xiang-Dong Fu,et al.  Profiling alternative splicing on fiber-optic arrays , 2002, Nature Biotechnology.

[80]  A. Krainer,et al.  Listening to silence and understanding nonsense: exonic mutations that affect splicing , 2002, Nature Reviews Genetics.

[81]  Christopher J. Lee,et al.  A genomic view of alternative splicing , 2002, Nature Genetics.

[82]  T. Jatkoe,et al.  Predicting splice variant from DNA chip expression data. , 2001, Genome research.

[83]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[84]  R. Stoughton,et al.  Experimental annotation of the human genome using microarray technology , 2001, Nature.

[85]  Rithy K. Roth,et al.  Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays , 2000, Nature Biotechnology.

[86]  L. Bracco,et al.  Qualitative gene profiling: a novel tool in genomics and in pharmacogenomics that deciphers messenger RNA isoforms diversity. , 2000, Pharmacogenomics.

[87]  G. Church,et al.  In situ localized amplification and contact replication of many individual DNA molecules. , 1999, Nucleic acids research.

[88]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[89]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[90]  M. Bownes,et al.  The developmental consequences of alternate splicing in sex determination and differentiation in Drosophila. , 1995, Developmental biology.