My NCBISign In
A comprehensive transcript index of the human genome generated using microarrays and computational approaches
Eric E Schadt, Stephen W Edwards, Debraj GuhaThakurta, Dan Holder, Lisa Ying, Vladimir Svetnik, Amy Leonardson, Kyle W Hart, Archie Russell, Guoya Li, Guy Cavet, John Castle, Paul McDonagh, Zhengyan Kan, Ronghua Chen, Andrew Kasarskis, Mihai Margarint, Ramon M Caceres, Jason M Johnson, Christopher D Armour, Philip W Garrett-Engele, Nicholas F Tsinoremas, Daniel D Shoemaker
Genome Biol. 2004; 5(10): R73. Published online 2004 September 23. doi: 10.1186/gb-2004-5-10-r73
PMCID:
PMC545593
Abstract Full Text PDF–666K Supplementary Material

Is Cited by the Following 32 Articles in this Archive:

Most “Dark Matter” Transcripts Are Associated With Known Genes
Harm van Bakel, Corey Nislow, Benjamin J. Blencowe, Timothy R. Hughes
PLoS Biol. 2010 May; 8(5): e1000371. Published online 2010 May 18. doi: 10.1371/journal.pbio.1000371
PMCID:
PMC2872640
Abstract Full Text PDF–1.2M Supplementary Material
Comparison and consolidation of microarray data sets of human tissue expression
Jenny Russ, Matthias E Futschik
BMC Genomics. 2010; 11: 305. Published online 2010 May 14. doi: 10.1186/1471-2164-11-305
PMCID:
PMC2885367
Abstract Full Text PDF–1.8M Supplementary Material
A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data
Wen-Han Yu, Hedda Høvik, Tsute Chen
Bioinformatics. 2010 June 1; 26(11): 1423–1430. Published online 2010 April 15. doi: 10.1093/bioinformatics/btq162
PMCID:
PMC2913668
Abstract Full Text PDF–804K
Age-related molecular genetic changes of murine bone marrow mesenchymal stem cells
Amber Wilson, Lina A Shehadeh, Hong Yu, Keith A Webster
BMC Genomics. 2010; 11: 229. Published online 2010 April 7. doi: 10.1186/1471-2164-11-229
PMCID:
PMC2873471
Abstract Full Text PDF–1.7M Supplementary Material
High-resolution transcription atlas of the mitotic cell cycle in budding yeast
Marina V Granovskaia, Lars J Jensen, Matthew E Ritchie, Joern Toedling, Ye Ning, Peer Bork, Wolfgang Huber, Lars M Steinmetz
Genome Biol. 2010; 11(3): R24. Published online 2010 March 1. doi: 10.1186/gb-2010-11-3-r24
PMCID:
PMC2864564
Abstract Full Text PDF–3.4M Supplementary Material
An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome
Danny A. Bitton, Duncan L. Smith, Yvonne Connolly, Paul J. Scutt, Crispin J. Miller
PLoS One. 2010; 5(1): e8949. Published online 2010 January 28. doi: 10.1371/journal.pone.0008949
PMCID:
PMC2812506
Abstract Full Text PDF–378K Supplementary Material
Conservation of core gene expression in vertebrate tissues
Esther T Chan, Gerald T Quon, Gordon Chua, Tomas Babak, Miles Trochesset, Ralph A Zirngibl, Jane Aubin, Michael JH Ratcliffe, Andrew Wilde, Michael Brudno, Quaid D Morris, Timothy R Hughes
J Biol. 2009; 8(3): 33. Published online 2009 April 16. doi: 10.1186/jbiol130
PMCID:
PMC2689434
Abstract Full Text PDF–1.8M Supplementary Material
Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays
Samuel P Hazen, Felix Naef, Tom Quisel, Joshua M Gendron, Huaming Chen, Joseph R Ecker, Justin O Borevitz, Steve A Kay
Genome Biol. 2009; 10(2): R17. Published online 2009 February 11. doi: 10.1186/gb-2009-10-2-r17
PMCID:
PMC2688271
Abstract Full Text PDF–1.0M Supplementary Material
Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High–Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species
Albert Lee, Kasper Daniel Hansen, James Bullard, Sandrine Dudoit, Gavin Sherlock
PLoS Genet. 2008 December; 4(12): e1000299. Published online 2008 December 19. doi: 10.1371/journal.pgen.1000299
PMCID:
PMC2601015
Abstract Full Text PDF–2.8M Supplementary Material
Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
Vitalina M. Komashko, Luis G. Acevedo, Sharon L. Squazzo, Sushma S. Iyengar, Alina Rabinovich, Henriette O’Geen, Roland Green, Peggy J. Farnham
Genome Res. 2008 April; 18(4): 521–532. doi: 10.1101/gr.074609.107
PMCID:
PMC2279240
Abstract Full Text PDF–881K
Differential Screening of Phage-Ab Libraries by Oligonucleotide Microarray Technology
Paolo Monaci, Alessandra Luzzago, Claudia Santini, Alessandra De Pra, Mirko Arcuri, Francesca Magistri, Alessandro Bellini, Helenia Ansuini, Maria Ambrosio, Virginia Ammendola, Maria Giulia Bigotti, Agostino Cirillo, Maurizio Nuzzo, Annamaria Assunta Nasti, Philippe Neuner, Laura Orsatti, Monica Pezzanera, Andrea Sbardellati, Giuseppe Silvestre, Paolo Uva, Valentina Viti, Gaetano Barbato, Stefano Colloca, Anna Demartis, Emanuele De Rinaldis, Saverio Giampaoli, Armin Lahm, Fabio Palombo, Fabio Talamo, Alessandra Vitelli, Alfredo Nicosia, Riccardo Cortese
PLoS ONE. 2008; 3(1): e1508. Published online 2008 January 30. doi: 10.1371/journal.pone.0001508
PMCID:
PMC2204054
Abstract Full Text PDF–403K Supplementary Material
Deep analysis of cellular transcriptomes – LongSAGE versus classic MPSS
Lawrence Hene, Vattipally B Sreenu, Mai T Vuong, S Hussain I Abidi, Julian K Sutton, Sarah L Rowland-Jones, Simon J Davis, Edward J Evans
BMC Genomics. 2007; 8: 333. Published online 2007 September 24. doi: 10.1186/1471-2164-8-333
PMCID:
PMC2104538
Abstract Full Text PDF–508K Supplementary Material
A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences
Joseph C Lee, David Stiles, Jun Lu, Margaret C Cam
BMC Genomics. 2007; 8: 284. Published online 2007 August 20. doi: 10.1186/1471-2164-8-284
PMCID:
PMC2000902
Abstract Full Text PDF–1.0M Supplementary Material
Moving toward a system genetics view of disease
Solveig K. Sieberts, Eric E. Schadt
Mamm Genome. 2007 July; 18(6-7): 389–401. Published online 2007 July 26. doi: 10.1007/s00335-007-9040-6
PMCID:
PMC1998874
Abstract Full Text PDF–511K
An efficient pseudomedian filter for tiling microrrays
Thomas E Royce, Nicholas J Carriero, Mark B Gerstein
BMC Bioinformatics. 2007; 8: 186. Published online 2007 June 7. doi: 10.1186/1471-2105-8-186
PMCID:
PMC1913926
Abstract Full Text PDF–431K
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
Olof Emanuelsson, Ugrappa Nagalakshmi, Deyou Zheng, Joel S. Rozowsky, Alexander E. Urban, Jiang Du, Zheng Lian, Viktor Stolc, Sherman Weissman, Michael Snyder, Mark B. Gerstein
Genome Res. 2007 June; 17(6): 886–897. doi: 10.1101/gr.5014606
PMCID:
PMC1891347
Abstract Full Text PDF–654K
Discovery of tissue-specific exons using comprehensive human exon microarrays
Tyson A Clark, Anthony C Schweitzer, Tina X Chen, Michelle K Staples, Gang Lu, Hui Wang, Alan Williams, John E Blume
Genome Biol. 2007; 8(4): R64. Published online 2007 April 24. doi: 10.1186/gb-2007-8-4-r64
PMCID:
PMC1896007
Abstract Full Text PDF–565K Supplementary Material
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human
Zhaolei Zhang, Andy Wing Chun Pang, Mark Gerstein
BMC Evol Biol. 2007; 7(Suppl 1): S14. Published online 2007 February 8. doi: 10.1186/1471-2148-7-S1-S14
PMCID:
PMC1796608
Abstract Full Text PDF–493K Supplementary Material
Functionality of Intergenic Transcription: An Evolutionary Comparison
Philipp Khaitovich, Janet Kelso, Henriette Franz, Johann Visagie, Thomas Giger, Sabrina Joerchel, Ekkehard Petzold, Richard E Green, Michael Lachmann, Svante Pääbo
PLoS Genet. 2006 October; 2(10): e171. Prepublished online 2006 August 28. Published online 2006 October 13. doi: 10.1371/journal.pgen.0020171
PMCID:
PMC1599769
Abstract Full Text PDF–257K Supplementary Material
Cis-regulatory variations: A study of SNPs around genes showing cis-linkage in segregating mouse populations
Debraj GuhaThakurta, Tao Xie, Manish Anand, Stephen W Edwards, Guoya Li, Susanna S Wang, Eric E Schadt
BMC Genomics. 2006; 7: 235. Published online 2006 September 15. doi: 10.1186/1471-2164-7-235
PMCID:
PMC1618400
Abstract Full Text PDF–798K Supplementary Material
Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array
Frédéric Biemar, David A. Nix, Jessica Piel, Brant Peterson, Matthew Ronshaugen, Victor Sementchenko, Ian Bell, J. Robert Manak, Michael S. Levine
Proc Natl Acad Sci U S A. 2006 August 22; 103(34): 12763–12768. Published online 2006 August 14. doi: 10.1073/pnas.0604484103
PMCID:
PMC1636694
Abstract Full Text PDF–2.0M Supplementary Material
Detecting transcriptionally active regions using genomic tiling arrays
Gabor Halasz, Marinus F van Batenburg, Joelle Perusse, Sujun Hua, Xiang-Jun Lu, Kevin P White, Harmen J Bussemaker
Genome Biol. 2006; 7(7): R59. Published online 2006 July 19. doi: 10.1186/gb-2006-7-7-r59
PMCID:
PMC1779562
Abstract Full Text PDF–452K Supplementary Material
Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity
Miao Sun, Laurence D. Hurst, Gordon G. Carmichael, Jianjun Chen
Genome Res. 2006 July; 16(7): 922–933. doi: 10.1101/gr.5210006
PMCID:
PMC1484459
Abstract Full Text PDF–695K
Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae
Carrie Anne Davis, Manuel Ares, Jr.
Proc Natl Acad Sci U S A. 2006 February 28; 103(9): 3262–3267. Published online 2006 February 16. doi: 10.1073/pnas.0507783103
PMCID:
PMC1413877
Abstract Full Text PDF–808K Supplementary Material
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
Timothy Ravasi, Harukazu Suzuki, Ken C. Pang, Shintaro Katayama, Masaaki Furuno, Rie Okunishi, Shiro Fukuda, Kelin Ru, Martin C. Frith, M. Milena Gongora, Sean M. Grimmond, David A. Hume, Yoshihide Hayashizaki, John S. Mattick
Genome Res. 2006 January; 16(1): 11–19. doi: 10.1101/gr.4200206
PMCID:
PMC1356124
Abstract Full Text PDF–284K
Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2
Juan I. Young, Eugene P. Hong, John C. Castle, Juan Crespo-Barreto, Aaron B. Bowman, Matthew F. Rose, Dongcheul Kang, Ron Richman, Jason M. Johnson, Susan Berget, Huda Y. Zoghbi
Proc Natl Acad Sci U S A. 2005 December 6; 102(49): 17551–17558. Published online 2005 October 26. doi: 10.1073/pnas.0507856102
Correction in:
Proc Natl Acad Sci U S A. 2006 January 31; 103(5): 1656.
PMCID:
PMC1266160
Abstract Full Text PDF–604K Supplementary Material Correction
Identification of Histoplasma capsulatum Transcripts Induced in Response to Reactive Nitrogen Species
M. Paige Nittler, Davina Hocking-Murray, Catherine K. Foo, Anita Sil
Mol Biol Cell. 2005 October; 16(10): 4792–4813. doi: 10.1091/mbc.E05-05-0434
PMCID:
PMC1237084
Abstract Full Text PDF–1.4M Supplementary Material
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
Thomas E. Royce, Joel S. Rozowsky, Paul Bertone, Manoj Samanta, Viktor Stolc, Sherman Weissman, Michael Snyder, Mark Gerstein
Trends Genet. Author manuscript; available in PMC 2007 April 23.
Published in final edited form as: Trends Genet. 2005 August; 21(8): 466–475. doi: 10.1016/j.tig.2005.06.007
PMCID:
PMC1855044
Abstract Full Text PDF–1012K
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray
Mark G Carter, Alexei A Sharov, Vincent VanBuren, Dawood B Dudekula, Condie E Carmack, Charlie Nelson, Minoru SH Ko
Genome Biol. 2005; 6(7): R61. Published online 2005 June 30. doi: 10.1186/gb-2005-6-7-r61
PMCID:
PMC1175992
Abstract Full Text PDF–303K Supplementary Material
An integrative genomics approach to infer causal associations between gene expression and disease
Eric E Schadt, John Lamb, Xia Yang, Jun Zhu, Steve Edwards, Debraj GuhaThakurta, Solveig K Sieberts, Stephanie Monks, Marc Reitman, Chunsheng Zhang, Pek Yee Lum, Amy Leonardson, Rolf Thieringer, Joseph M Metzger, Liming Yang, John Castle, Haoyuan Zhu, Shera F Kash, Thomas A Drake, Alan Sachs, Aldons J Lusis
Nat Genet. Author manuscript; available in PMC 2010 March 18.
Published in final edited form as: Nat Genet. 2005 July; 37(7): 710–717. Published online 2005 June 19. doi: 10.1038/ng1589
PMCID:
PMC2841396
Abstract Full Text PDF–1.0M Supplementary Material
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