Defining control and function of alternative splicing during tumorigenesis

Number of publications: 21
Israeli Partner: G. Ast, Tel Aviv University
German Partner: A. Hotz-Wagenblatt, DKFZ

Publications

Publication
Publication
Amit, M., Donyo, M., Hollander, D., Goren, A., Kim, E., Gelfman, S., Lev-Maor, G., Burstein, D., Schwartz, S., Postolsky, B., Pupko, T., Ast, G.

Differential GC content between exons and introns establishes distinct strategies of splice-site recognition 1 (5), Cell Rep, 543-56, 2012

Amit, M., Sela, N., Keren, H., Melamed, Z., Muler, I., Shomron, N., Izraeli, S., Ast, G.

Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene 8, BMC Mol Biol, 109, 2007

Aschoff, M., Hotz-Wagenblatt, A., Glatting, K. H., Fischer, M., Eils, R., Konig, R.

SplicingCompass: differential splicing detection using RNA-seq data 29 (9), Bioinformatics, 1141-8, 2013

Gal-Mark, N., Schwartz, S., Ram, O., Eyras, E., Ast, G.

The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution 5 (11), PLoS Genet, e1000717, 2009

Gelfman, S., Burstein, D., Penn, O., Savchenko, A., Amit, M., Schwartz, S., Pupko, T., Ast, G.

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons 22 (1), Genome Res, 35-50, 2012

Goren, A., Kim, E., Amit, M., Bochner, R., Lev-Maor, G., Ahituv, N., Ast, G.

Alternative approach to a heavy weight problem 18 (2), Genome Res, 214-20, 2008

Goren, A., Kim, E., Amit, M., Vaknin, K., Kfir, N., Ram, O., Ast, G.

Overlapping splicing regulatory motifs--combinatorial effects on splicing 38 (10), Nucleic Acids Res, 3318-27, 2010

Keren-Shaul, H., Lev-Maor, G., Ast, G.

Pre-mRNA splicing is a determinant of nucleosome organization 8 (1), PLoS One, e53506, 2013

Levy, A., Schwartz, S., Ast, G.

Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements 38 (5), Nucleic Acids Res, 1515-30, 2010

Levy, A., Sela, N., Ast, G.

TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates 36, Nucleic Acids Res, D47-52, 2008

Llorian, M., Schwartz, S., Clark, T. A., Hollander, D., Tan, L. Y., Spellman, R., Gordon, A., Schweitzer, A. C., de la Grange, P., Ast, G., Smith, C. W.

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB 17 (9), Nat Struct Mol Biol, 1114-23, 2010

Mersch, B., Sela, N., Ast, G., Suhai, S., Hotz-Wagenblatt, A.

SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements 8, BMC Genet, 78, 2007

Schwartz, S., Ast, G.

Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing 29 (10), Embo j, 1629-36, 2010

Schwartz, S., Gal-Mark, N., Kfir, N., Oren, R., Kim, E., Ast, G.

Alu exonization events reveal features required for precise recognition of exons by the splicing machinery 5 (3), PLoS Comput Biol, e1000300, 2009

Schwartz, S., Hall, E., Ast, G.

SROOGLE: webserver for integrative, user-friendly visualization of splicing signals 37, Nucleic Acids Res, W189-92, 2009

Schwartz, S., Meshorer, E., Ast, G.

Chromatin organization marks exon-intron structure 16 (9), Nat Struct Mol Biol, 990-5, 2009

Schwartz, S., Oren, R., Ast, G.

Detection and removal of biases in the analysis of next-generation sequencing reads 6 (1), PLoS One, e16685, 2011

Sela, N., Kim, E., Ast, G.

The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates 11 (6), Genome Biol, R59, 2010

Sela, N., Mersch, B., Gal-Mark, N., Lev-Maor, G., Hotz-Wagenblatt, A., Ast, G.

Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome 8 (6), Genome Biol, R127, 2007

Sela, N., Mersch, B., Hotz-Wagenblatt, A., Ast, G.

Characteristics of transposable element exonization within human and mouse 5 (6), PLoS One, e10907, 2010

Sela, N., Stern, A., Makalowski, W., Pupko, T., Ast, G.

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans 3, Biol Direct, 41, 2008

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