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Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome
Noa Sela, Britta Mersch, Nurit Gal-Mark, Galit Lev-Maor, Agnes Hotz-Wagenblatt, Gil Ast
Genome Biol. 2007; 8(6): R127. Published online 2007 June 27. doi: 10.1186/gb-2007-8-6-r127
PMCID:
PMC2394776
Abstract Full Text PDF–776K Supplementary Material

Is Cited by the Following 37 Articles in this Archive:

Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism
Rajesh Pandey, Amit K Mandal, Vineet Jha, Mitali Mukerji
Genome Biol. 2011; 12(11): R117. Published online 2011 November 23. doi: 10.1186/gb-2011-12-11-r117
PMCID:
PMC3334603
Abstract Full Text PDF–1.2M Supplementary Material
The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates
Jonathan M. Mudge, Adam Frankish, Julio Fernandez-Banet, Tyler Alioto, Thomas Derrien, Cédric Howald, Alexandre Reymond, Roderic Guigó, Tim Hubbard, Jennifer Harrow
Mol Biol Evol. 2011 October; 28(10): 2949–2959. Published online 2011 May 6. doi: 10.1093/molbev/msr127
PMCID:
PMC3176834
Abstract Full Text PDF–645K Supplementary Material
Alu distribution and mutation types of cancer genes
Wensheng Zhang, Andrea Edwards, Wei Fan, Prescott Deininger, Kun Zhang
BMC Genomics. 2011; 12: 157. Published online 2011 March 23. doi: 10.1186/1471-2164-12-157
PMCID:
PMC3074553
Abstract Full Text PDF–725K Supplementary Material
Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads
Schraga Schwartz, Ram Oren, Gil Ast
PLoS One. 2011; 6(1): e16685. Published online 2011 January 31. doi: 10.1371/journal.pone.0016685
PMCID:
PMC3031631
Abstract Full Text PDF–982K Supplementary Material
Genomic signatures of germline gene expression
Graham McVicker, Phil Green
Genome Res. 2010 November; 20(11): 1503–1511. doi: 10.1101/gr.106666.110
PMCID:
PMC2963814
Abstract Full Text PDF–551K
Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants
Michał W Szcześniak, Joanna Ciomborowska, Witold Nowak, Igor B Rogozin, Izabela Makałowska
Mol Biol Evol. 2011 January; 28(1): 33–37. Published online 2010 October 1. doi: 10.1093/molbev/msq260
PMCID:
PMC3002245
Abstract Full Text PDF–381K Supplementary Material
Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales
Robert W. Meredith, John Gatesy, Joyce Cheng, Mark S. Springer
Proc Biol Sci. 2011 April 7; 278(1708): 993–1002. Published online 2010 September 22. doi: 10.1098/rspb.2010.1280
PMCID:
PMC3049022
Abstract Full Text PDF–2.1M
Long-range function of an intergenic retrotransposon
Wenhu Pi, Xingguo Zhu, Min Wu, Yongchao Wang, Sadanand Fulzele, Ali Eroglu, Jianhua Ling, Dorothy Tuan
Proc Natl Acad Sci U S A. 2010 July 20; 107(29): 12992–12997. Published online 2010 July 6. doi: 10.1073/pnas.1004139107
PMCID:
PMC2919959
Abstract Full Text PDF–665K Supplementary Material
The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates
Noa Sela, Eddo Kim, Gil Ast
Genome Biol. 2010; 11(6): R59. Published online 2010 June 2. doi: 10.1186/gb-2010-11-6-r59
PMCID:
PMC2911107
Abstract Full Text PDF–1.6M Supplementary Material
Characteristics of Transposable Element Exonization within Human and Mouse
Noa Sela, Britta Mersch, Agnes Hotz-Wagenblatt, Gil Ast
PLoS One. 2010; 5(6): e10907. Published online 2010 June 1. doi: 10.1371/journal.pone.0010907
PMCID:
PMC2879366
Abstract Full Text PDF–521K Supplementary Material
PDZD7 is a modifier of retinal disease and a contributor to digenic Usher syndrome
Inga Ebermann, Jennifer B. Phillips, Max C. Liebau, Robert K. Koenekoop, Bernhard Schermer, Irma Lopez, Ellen Schäfer, Anne-Francoise Roux, Claudia Dafinger, Antje Bernd, Eberhart Zrenner, Mireille Claustres, Bernardo Blanco, Gudrun Nürnberg, Peter Nürnberg, Rebecca Ruland, Monte Westerfield, Thomas Benzing, Hanno J. Bolz
J Clin Invest. 2010 June 1; 120(6): 1812–1823. Published online 2010 May 3. doi: 10.1172/JCI39715
PMCID:
PMC2877930
Abstract Full Text PDF–3.3M Supplementary Material
Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements
Asaf Levy, Schraga Schwartz, Gil Ast
Nucleic Acids Res. 2010 March; 38(5): 1515–1530. Published online 2010 March. doi: 10.1093/nar/gkp1134
PMCID:
PMC2836564
Abstract Full Text PDF–4.6M Supplementary Material
Genomic gems: SINE RNAs regulate mRNA production
Steven L. Ponicsan, Jennifer F. Kugel, James A. Goodrich
Curr Opin Genet Dev. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Curr Opin Genet Dev. 2010 April; 20(2): 149–155. Published online 2010 February 20. doi: 10.1016/j.gde.2010.01.004
PMCID:
PMC2859989
Abstract Full Text PDF–957K
Ubiquitous internal gene duplication and intron creation in eukaryotes
Xiang Gao, Michael Lynch
Proc Natl Acad Sci U S A. 2009 December 8; 106(49): 20818–20823. Published online 2009 November 19. doi: 10.1073/pnas.0911093106
PMCID:
PMC2791625
Abstract Full Text PDF–929K Supplementary Material
The Pivotal Roles of TIA Proteins in 5′ Splice-Site Selection of Alu Exons and Across Evolution
Nurit Gal-Mark, Schraga Schwartz, Oren Ram, Eduardo Eyras, Gil Ast
PLoS Genet. 2009 November; 5(11): e1000717. Published online 2009 November 13. doi: 10.1371/journal.pgen.1000717
PMCID:
PMC2766253
Abstract Full Text PDF–764K Supplementary Material
An Alu-derived intronic splicing enhancer facilitates intronic processing and modulates aberrant splicing in ATM
Tibor Pastor, Gabriele Talotti, Marzena Anna Lewandowska, Franco Pagani
Nucleic Acids Res. 2009 November; 37(21): 7258–7267. Published online 2009 November. doi: 10.1093/nar/gkp778
PMCID:
PMC2790898
Abstract Full Text PDF–4.4M Supplementary Material
TEs or not TEs? That is the evolutionary question
Keren Vaknin, Amir Goren, Gil Ast
J Biol. 2009; 8(9): 83. Published online 2009 October 23. doi: 10.1186/jbiol188
PMCID:
PMC2776909
Abstract Full Text PDF–96K
Endogenous Mechanisms for the Origins of Spliceosomal Introns
Francesco Catania, Xiang Gao, Douglas G. Scofield
J Hered. 2009 Sep-Oct; 100(5): 591–596. Published online 2009 July 27. doi: 10.1093/jhered/esp062
PMCID:
PMC2877546
Abstract Full Text PDF–101K
Transcription of the rat testis-specific Rtdpoz-T1 and -T2 retrogenes during embryo development: co-transcription and frequent exonisation of transposable element sequences
Chiu-Jung Huang, Wan-Yi Lin, Che-Ming Chang, Kong-Bung Choo
BMC Mol Biol. 2009; 10: 74. Published online 2009 July 25. doi: 10.1186/1471-2199-10-74
PMCID:
PMC2724483
Abstract Full Text PDF–535K Supplementary Material
Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes
Lan Lin, Peng Jiang, Shihao Shen, Seiko Sato, Beverly L. Davidson, Yi Xing
Hum Mol Genet. 2009 June 15; 18(12): 2204–2214. Published online 2009 March 26. doi: 10.1093/hmg/ddp152
PMCID:
PMC2685757
Abstract Full Text PDF–229K Supplementary Material
Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery
Schraga Schwartz, Nurit Gal-Mark, Nir Kfir, Ram Oren, Eddo Kim, Gil Ast
PLoS Comput Biol. 2009 March; 5(3): e1000300. Published online 2009 March 6. doi: 10.1371/journal.pcbi.1000300
PMCID:
PMC2639721
Abstract Full Text PDF–844K Supplementary Material
L1 recombination-associated deletions generate human genomic variation
Kyudong Han, Jungnam Lee, Thomas J. Meyer, Paul Remedios, Lindsey Goodwin, Mark A. Batzer
Proc Natl Acad Sci U S A. 2008 December 9; 105(49): 19366–19371. Published online 2008 November 26. doi: 10.1073/pnas.0807866105
PMCID:
PMC2614767
Abstract Full Text PDF–555K Supplementary Material
Where Do Introns Come From?
Francesco Catania, Michael Lynch
PLoS Biol. 2008 November; 6(11): e283. Published online 2008 November 25. doi: 10.1371/journal.pbio.0060283
PMCID:
PMC2586383
Full Text PDF–455K
Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues
Lan Lin, Shihao Shen, Anne Tye, James J. Cai, Peng Jiang, Beverly L. Davidson, Yi Xing
PLoS Genet. 2008 October; 4(10): e1000225. Published online 2008 October 17. doi: 10.1371/journal.pgen.1000225
PMCID:
PMC2562518
Abstract Full Text PDF–390K Supplementary Material
Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans
Noa Sela, Adi Stern, Wojciech Makalowski, Tal Pupko, Gil Ast
Biol Direct. 2008; 3: 41. Published online 2008 October 8. doi: 10.1186/1745-6150-3-41
PMCID:
PMC2572040
Abstract Full Text PDF–2.2M
Retrocopy contributions to the evolution of the human genome
Robert Baertsch, Mark Diekhans, W James Kent, David Haussler, Jürgen Brosius
BMC Genomics. 2008; 9: 466. Published online 2008 October 8. doi: 10.1186/1471-2164-9-466
PMCID:
PMC2584115
Abstract Full Text PDF–1.0M Supplementary Material
Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes
Ju Youn Lee, Zhe Ji, Bin Tian
Nucleic Acids Res. 2008 October; 36(17): 5581–5590. Published online 2008 October. doi: 10.1093/nar/gkn540
PMCID:
PMC2553571
Abstract Full Text PDF–1.1M Supplementary Material
Intronic Alus Influence Alternative Splicing
Galit Lev-Maor, Oren Ram, Eddo Kim, Noa Sela, Amir Goren, Erez Y. Levanon, Gil Ast
PLoS Genet. 2008 September; 4(9): e1000204. Published online 2008 September 26. doi: 10.1371/journal.pgen.1000204
PMCID:
PMC2533698
Abstract Full Text PDF–451K Supplementary Material
Exon creation and establishment in human genes
André Corvelo, Eduardo Eyras
Genome Biol. 2008; 9(9): R141. Published online 2008 September 23. doi: 10.1186/gb-2008-9-9-r141
PMCID:
PMC2592719
Abstract Full Text PDF–544K Supplementary Material
Cis- and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells
Gianfranco Di Segni, Serena Gastaldi, Glauco P. Tocchini-Valentini
Proc Natl Acad Sci U S A. 2008 May 13; 105(19): 6864–6869. Published online 2008 May 5. doi: 10.1073/pnas.0800420105
PMCID:
PMC2383978
Abstract Full Text PDF–1.0M Supplementary Material
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