Genome Biology

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Variation in alternative splicing across human tissues

Gene Yeo, Dirk Holste, Gabriel Kreiman and Christopher B Burge*

  • * Corresponding author: Christopher B Burge cburge@mit.edu

  • † Equal contributors

Genome Biology 2004, 5:R74 doi:10.1186/gb-2004-5-10-r74

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The relationship between proteome size, structural disorder and organism complexity

Eva Schad, Peter Tompa, Hedi Hegyi Genome Biology 2011, 12:R120 (19 December 2011)

Complexity is a multi-parametric trait, determined by interaction potential, alternative splicing capacity, protein disorder and, above all, proteome size

Research article   Open Access

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site

Pingzhang Wang, Peng Yu, Peng Gao, Taiping Shi, Dalong Ma BMC Genomics 2009, 10:518 (12 November 2009)

Research   Open Access Highly Accessed

Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing

Xin Wang, Kejun Wang, Milan Radovich, Yue Wang, Guohua Wang, Weixing Feng, Jeremy R Sanford, Yunlong Liu BMC Genomics 2009, 10(Suppl 1):S4 (7 July 2009)

Methodology article   Open Access Highly Accessed

Differential splicing using whole-transcript microarrays

Mark D Robinson, Terence P Speed BMC Bioinformatics 2009, 10:156 (22 May 2009)

The Affymetrix GeneChip microarray platform, widely used to assay gene expression, can also detect differential splicing events with the help of a new statistical method called FIRMAGene that analyses information from poorly fitting adjacent probes.

Database   Open Access

GarlicESTdb: an online database and mining tool for garlic EST sequences

Dae-Won Kim, Tae-Sung Jung, Seong-Hyeuk Nam, Hyuk-Ryul Kwon, Aeri Kim, Sung-Hwa Chae, Sang-Haeng Choi, Dong-Wook Kim, Ryong Kim, Hong-Seog Park BMC Plant Biology 2009, 9:61 (18 May 2009)

Research article   Open Access

A family of splice variants of CstF-64 expressed in vertebrate nervous systems

Ganesh S Shankarling, Penelope W Coates, Brinda Dass, Clinton C MacDonald BMC Molecular Biology 2009, 10:22 (12 March 2009)

Methodology article   Open Access

Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays

Katerina Kechris, Yee Yang, Ru-Fang Yeh BMC Genomics 2008, 9:551 (20 November 2008)

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Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays

Hannah C Cheung, Keith A Baggerly, Spiridon Tsavachidis, Linda L Bachinski, Valerie L Neubauer, Tamara J Nixon, Kenneth D Aldape, Gilbert J Cote, Ralf Krahe BMC Genomics 2008, 9:216 (12 May 2008)

Research article   Open Access

Comparative analysis of sequence features involved in the recognition of tandem splice sites

Ralf Bortfeldt, Stefanie Schindler, Karol Szafranski, Stefan Schuster, Dirk Holste BMC Genomics 2008, 9:202 (30 April 2008)

Research article   Open Access

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 (20 August 2007)

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Functional coordination of alternative splicing in the mammalian central nervous system

Matthew Fagnani, Yoseph Barash, Joanna Y Ip, Christine Misquitta, Qun Pan, Arneet L Saltzman, Ofer Shai, Leo Lee, Aviad Rozenhek, Naveed Mohammad, Sandrine Willaime-Morawek, Tomas Babak, Wen Zhang, Timothy R Hughes, Derek van der Kooy, Brendan J Frey, Benjamin J Blencowe Genome Biology 2007, 8:R108 (12 June 2007)

A microarray analysis provides new evidence suggesting that specific cellular processes in the mammalian CNS are coordinated at the level of alternative splicing, and that a complex splicing code underlies CNS-specific alternative splicing regulation.

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A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants

Pierre de la Grange, Martin Dutertre, Margot Correa, Didier Auboeuf BMC Bioinformatics 2007, 8:180 (4 June 2007)

Research article   Open Access

Three novel ABCC5 splice variants in human retina and their role as regulators of ABCC5 gene expression

Jelena Stojic, Heidi Stöhr, Bernhard HF Weber BMC Molecular Biology 2007, 8:42 (23 May 2007)

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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 Biology 2007, 8:R64 (24 April 2007)

Comprehensive exon microarrays with a simple intra-gene normalization algorithm were used to detect human tissue-specific alternative splicing events, suggesting significant expression outside of known exons and well annotated genes and a high frequency of alternative splicing events.

Research article   Open Access Highly Accessed

Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis

Matthew A Campbell, Brian J Haas, John P Hamilton, Stephen M Mount, C Robin Buell BMC Genomics 2006, 7:327 (28 December 2006)

Research article   Open Access

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects

Patrizia Lastella, Nicoletta Surdo, Nicoletta Resta, Ginevra Guanti, Alessandro Stella BMC Genomics 2006, 7:243 (22 September 2006)

Methodology article   Open Access

The effects of multiple features of alternatively spliced exons on the KA/KS ratio test

Feng-Chi Chen, Trees-Juen Chuang BMC Bioinformatics 2006, 7:259 (19 May 2006)

Software   Open Access

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

Erdahl T Teber, Edward Crawford, Kent B Bolton, Derek Van Dyk, Peter R Schofield, Vimal Kapoor, W Bret Church BMC Bioinformatics 2006, 7:33 (23 January 2006)

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Biased alternative polyadenylation in human tissues

Haibo Zhang, Ju Lee, Bin Tian Genome Biology 2005, 6:R100 (28 November 2005)

Bioinformatic analyses of the occurrence and mechanism of alternative polyadenylation in different human tissues reveals systematic differences among tissues and suggests the involvement of both trans- and cis-regulatory elements.