TY - JOUR AU - Black, D. L. PY - 2003 DA - 2003// TI - Mechanisms of alternative pre-messenger RNA splicing JO - Annu Rev Biochem VL - 72 UR - https://doi.org/10.1146/annurev.biochem.72.121801.161720 DO - 10.1146/annurev.biochem.72.121801.161720 ID - Black2003 ER - TY - JOUR AU - Pan, Q. AU - Shai, O. AU - Lee, L. AU - Frey, B. AU - Blencowe, B. J. PY - 2008 DA - 2008// TI - Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing JO - Nat Genet VL - 40 UR - https://doi.org/10.1038/ng.259 DO - 10.1038/ng.259 ID - Pan2008 ER - TY - JOUR AU - Wang, E. AU - Sandberg, R. AU - Luo, S. AU - Khrebtukova, I. AU - Zhang, L. AU - Mayr, C. AU - Kingsmore, S. AU - Schroth, G. AU - Burge, C. B. PY - 2008 DA - 2008// TI - Alternative isoform regulation in human tissue transcriptomes JO - Nature VL - 456 UR - https://doi.org/10.1038/nature07509 DO - 10.1038/nature07509 ID - Wang2008 ER - TY - JOUR AU - Lewis, B. P. AU - Green, R. E. AU - Brenner, S. E. PY - 2003 DA - 2003// TI - Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.0136770100 DO - 10.1073/pnas.0136770100 ID - Lewis2003 ER - TY - JOUR AU - Rehwinkel, J. AU - Letunic, I. AU - Raes, J. AU - Bork, P. AU - Izaurralde, E. PY - 2005 DA - 2005// TI - Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets JO - RNA VL - 11 UR - https://doi.org/10.1261/rna.2160905 DO - 10.1261/rna.2160905 ID - Rehwinkel2005 ER - TY - JOUR AU - Wittmann, J. AU - Hol, E. M. AU - Jäck, H. -. M. PY - 2006 DA - 2006// TI - hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay JO - Mol Cell Biol VL - 26 UR - https://doi.org/10.1128/MCB.26.4.1272-1287.2006 DO - 10.1128/MCB.26.4.1272-1287.2006 ID - Wittmann2006 ER - TY - JOUR AU - Weischenfeldt, J. AU - Damgaard, I. AU - Bryder, D. AU - Theilgaard-Mönch, K. AU - Thoren, L. A. AU - Nielsen, F. C. AU - Jacobsen, S. E. W. AU - Nerlov, C. AU - Porse, B. T. PY - 2008 DA - 2008// TI - NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements JO - Genes Dev VL - 22 UR - https://doi.org/10.1101/gad.468808 DO - 10.1101/gad.468808 ID - Weischenfeldt2008 ER - TY - JOUR AU - Gardner, L. B. PY - 2010 DA - 2010// TI - Nonsense-mediated RNA decay regulation by cellular stress: implications for tumorigenesis JO - Mol Cancer Res VL - 8 UR - https://doi.org/10.1158/1541-7786.MCR-09-0502 DO - 10.1158/1541-7786.MCR-09-0502 ID - Gardner2010 ER - TY - JOUR AU - Perlick, H. A. AU - Medghalchi, S. M. AU - Spencer, F. A. AU - Kendzior, R. J. AU - Dietz, H. C. PY - 1996 DA - 1996// TI - Mammalian orthologues of a yeast regulator of nonsense transcript stability JO - Proc Natl Acad Sci USA VL - 93 UR - https://doi.org/10.1073/pnas.93.20.10928 DO - 10.1073/pnas.93.20.10928 ID - Perlick1996 ER - TY - JOUR AU - Lykke-Andersen, J. AU - Shu, M. D. AU - Steitz, J. A. PY - 2000 DA - 2000// TI - Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon JO - Cell VL - 103 UR - https://doi.org/10.1016/S0092-8674(00)00214-2 DO - 10.1016/S0092-8674(00)00214-2 ID - Lykke-Andersen2000 ER - TY - JOUR AU - Le Hir, H. AU - Gatfield, D. AU - Izaurralde, E. AU - Moore, M. J. PY - 2001 DA - 2001// TI - The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay JO - EMBO J VL - 20 UR - https://doi.org/10.1093/emboj/20.17.4987 DO - 10.1093/emboj/20.17.4987 ID - Le Hir2001 ER - TY - JOUR AU - Nagy, E. AU - Maquat, L. E. PY - 1998 DA - 1998// TI - A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance JO - Trends Biochem Sci VL - 23 UR - https://doi.org/10.1016/S0968-0004(98)01208-0 DO - 10.1016/S0968-0004(98)01208-0 ID - Nagy1998 ER - TY - JOUR AU - Behm-Ansmant, I. AU - Gatfield, D. AU - Rehwinkel, J. AU - Hilgers, V. AU - Izaurralde, E. PY - 2007 DA - 2007// TI - A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay JO - EMBO J VL - 26 UR - https://doi.org/10.1038/sj.emboj.7601588 DO - 10.1038/sj.emboj.7601588 ID - Behm-Ansmant2007 ER - TY - JOUR AU - Eberle, A. B. AU - Stalder, L. AU - Mathys, H. AU - Orozco, R. Z. AU - Mühlemann, O. PY - 2008 DA - 2008// TI - Posttranscriptional gene regulation by spatial rearrangement of the 3' untranslated region JO - PloS Biol VL - 6 UR - https://doi.org/10.1371/journal.pbio.0060092 DO - 10.1371/journal.pbio.0060092 ID - Eberle2008 ER - TY - JOUR AU - Wang, J. AU - Gudikote, J. P. AU - Olivas, O. R. AU - Wilkinson, M. F. PY - 2002 DA - 2002// TI - Boundary-independent polar nonsense-mediated decay JO - EMBO Rep VL - 3 UR - https://doi.org/10.1093/embo-reports/kvf036 DO - 10.1093/embo-reports/kvf036 ID - Wang2002 ER - TY - JOUR AU - Bühler, M. AU - Steiner, S. AU - Mohn, F. AU - Paillusson, A. AU - Mühlemann, O. PY - 2006 DA - 2006// TI - EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3' UTR length JO - Nat Struct Mol Biol VL - 13 UR - https://doi.org/10.1038/nsmb1081 DO - 10.1038/nsmb1081 ID - Bühler2006 ER - TY - JOUR AU - Morrison, M. AU - Harris, K. S. AU - Roth, M. B. PY - 1997 DA - 1997// TI - smg mutants affect the expression of alternatively spliced SR protein mRNAs in Caenorhabditis elegans JO - Proc Natl Acad Sci USA VL - 94 UR - https://doi.org/10.1073/pnas.94.18.9782 DO - 10.1073/pnas.94.18.9782 ID - Morrison1997 ER - TY - JOUR AU - Ni, J. Z. AU - Grate, L. AU - Donohue, J. P. AU - Preston, C. AU - Nobida, N. AU - O'Brien, G. AU - Shiue, L. AU - Clark, T. A. AU - Blume, J. E. AU - Ares, M. PY - 2007 DA - 2007// TI - Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay JO - Genes Dev VL - 21 UR - https://doi.org/10.1101/gad.1525507 DO - 10.1101/gad.1525507 ID - Ni2007 ER - TY - JOUR AU - Saltzman, A. L. AU - Kim, Y. K. AU - Pan, Q. AU - Fagnani, M. M. AU - Maquat, L. E. AU - Blencowe, B. J. PY - 2008 DA - 2008// TI - Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay JO - Mol Cell Biol VL - 28 UR - https://doi.org/10.1128/MCB.00361-08 DO - 10.1128/MCB.00361-08 ID - Saltzman2008 ER - TY - JOUR AU - Lareau, L. F. AU - Inada, M. AU - Green, R. E. AU - Wengrod, J. C. AU - Brenner, S. E. PY - 2007 DA - 2007// TI - Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements JO - Nature VL - 446 UR - https://doi.org/10.1038/nature05676 DO - 10.1038/nature05676 ID - Lareau2007 ER - TY - JOUR AU - Saltzman, A. L. AU - Pan, Q. AU - Blencowe, B. J. PY - 2011 DA - 2011// TI - Regulation of alternative splicing by the core spliceosomal machinery JO - Genes Dev VL - 25 UR - https://doi.org/10.1101/gad.2004811 DO - 10.1101/gad.2004811 ID - Saltzman2011 ER - TY - JOUR AU - Pinol-Roma, S. AU - Choi, Y. D. AU - Matunis, M. J. AU - Dreyfuss, G. PY - 1988 DA - 1988// TI - Immunopurification of heterogeneous nuclear ribonucleoprotein particles reveals an assortment of RNA-binding proteins JO - Genes Dev VL - 2 UR - https://doi.org/10.1101/gad.2.2.215 DO - 10.1101/gad.2.2.215 ID - Pinol-Roma1988 ER - TY - JOUR AU - Han, S. P. AU - Tang, Y. H. AU - Smith, R. PY - 2010 DA - 2010// TI - Functional diversity of the hnRNPs: past, present and perspectives JO - Biochem J VL - 430 UR - https://doi.org/10.1042/BJ20100396 DO - 10.1042/BJ20100396 ID - Han2010 ER - TY - JOUR AU - Boutz, P. L. AU - Stoilov, P. AU - Li, Q. AU - Lin, C. H. AU - Chawla, G. AU - Ostrow, K. AU - Shiue, L. AU - Ares, M. AU - Black, D. L. PY - 2007 DA - 2007// TI - A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons JO - Genes Dev VL - 21 UR - https://doi.org/10.1101/gad.1558107 DO - 10.1101/gad.1558107 ID - Boutz2007 ER - TY - JOUR AU - Hanamura, A. AU - Caceres, J. F. AU - Mayeda, A. AU - Franza, B. R. AU - Krainer, A. R. PY - 1998 DA - 1998// TI - Regulated tissue-specific expression of antagonistic pre-mRNA splicing factors JO - RNA VL - 4 ID - Hanamura1998 ER - TY - JOUR AU - Bai, Y. AU - Lee, D. AU - Yu, T. AU - Chasin, L. A. PY - 1999 DA - 1999// TI - Control of 3' splice site choice in vivo by ASF/SF2 and hnRNP A1 JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.4.1126 DO - 10.1093/nar/27.4.1126 ID - Bai1999 ER - TY - JOUR AU - Chen, M. AU - Manley, J. L. PY - 2009 DA - 2009// TI - Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches JO - Nat Rev Mol Cell Biol VL - 10 ID - Chen2009 ER - TY - JOUR AU - Pan, Q. AU - Saltzman, A. L. AU - Kim, Y. K. AU - Misquitta, C. AU - Shai, O. AU - Maquat, L. E. AU - Frey, B. J. AU - Blencowe, B. J. PY - 2006 DA - 2006// TI - Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression JO - Genes Dev VL - 20 UR - https://doi.org/10.1101/gad.1382806 DO - 10.1101/gad.1382806 ID - Pan2006 ER - TY - JOUR AU - Ramani, A. K. AU - Nelson, A. C. AU - Kapranov, P. AU - Bell, I. AU - Gingeras, T. R. AU - Fraser, A. G. PY - 2009 DA - 2009// TI - High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-9-r101 DO - 10.1186/gb-2009-10-9-r101 ID - Ramani2009 ER - TY - JOUR AU - Thoren, L. A. AU - Nørgaard, G. A. AU - Weischenfeldt, J. AU - Waage, J. AU - Jakobsen, J. S. AU - Damgaard, I. AU - Bergström, F. C. AU - Blom, A. M. AU - Borup, R. AU - Bisgaard, H. C. AU - Porse, B. T. PY - 2010 DA - 2010// TI - UPF2 Is a Critical Regulator of Liver Development, Function and Regeneration JO - PLoS ONE VL - 5 UR - https://doi.org/10.1371/journal.pone.0011650 DO - 10.1371/journal.pone.0011650 ID - Thoren2010 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. PY - 2009 DA - 2009// TI - TopHat: discovering splice junctions with RNA-Seq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - JOUR AU - McIlwain, D. R. AU - Pan, Q. AU - Reilly, P. T. AU - Elia, A. J. AU - McCracken, S. AU - Wakeham, A. C. AU - Itie-Youten, A. AU - Blencowe, B. J. AU - Mak, T. W. PY - 2010 DA - 2010// TI - Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay JO - Proc Natl Acad Sci USA VL - 107 UR - https://doi.org/10.1073/pnas.1007336107 DO - 10.1073/pnas.1007336107 ID - McIlwain2010 ER - TY - JOUR AU - Christofk, H. R. AU - Vander Heiden, M. G. AU - Harris, M. H. AU - Ramanathan, A. AU - Gerszten, R. E. AU - Wei, R. AU - Fleming, M. D. AU - Schreiber, S. L. AU - Cantley, L. C. PY - 2008 DA - 2008// TI - The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth JO - Nature VL - 452 UR - https://doi.org/10.1038/nature06734 DO - 10.1038/nature06734 ID - Christofk2008 ER - TY - JOUR AU - Yeo, G. AU - Holste, D. AU - Kreiman, G. AU - Burge, C. B. PY - 2004 DA - 2004// TI - Variation in alternative splicing across human tissues JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-10-r74 DO - 10.1186/gb-2004-5-10-r74 ID - Yeo2004 ER - TY - JOUR AU - Kim, E. AU - Goren, A. AU - Ast, G. PY - 2008 DA - 2008// TI - Alternative splicing: current perspectives JO - Bioessays VL - 30 UR - https://doi.org/10.1002/bies.20692 DO - 10.1002/bies.20692 ID - Kim2008 ER - TY - JOUR AU - Mitrovich, Q. M. AU - Anderson, P. PY - 2005 DA - 2005// TI - mRNA surveillance of expressed pseudogenes in C. elegans JO - Curr Biol VL - 15 UR - https://doi.org/10.1016/j.cub.2005.04.055 DO - 10.1016/j.cub.2005.04.055 ID - Mitrovich2005 ER - TY - JOUR AU - Mendell, J. T. AU - Sharifi, N. A. AU - Meyers, J. L. AU - Martinez-Murillo, F. AU - Dietz, H. C. PY - 2004 DA - 2004// TI - Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise JO - Nat Genet VL - 36 UR - https://doi.org/10.1038/ng1429 DO - 10.1038/ng1429 ID - Mendell2004 ER - TY - JOUR AU - Sayani, S. AU - Janis, M. AU - Lee, C. Y. AU - Toesca, I. AU - Chanfreau, G. F. PY - 2008 DA - 2008// TI - Widespread impact of nonsense-mediated mRNA decay on the yeast intronome JO - Mol Cell VL - 31 UR - https://doi.org/10.1016/j.molcel.2008.07.005 DO - 10.1016/j.molcel.2008.07.005 ID - Sayani2008 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Hillman, R. T. AU - Green, R. E. AU - Brenner, S. E. PY - 2004 DA - 2004// TI - An unappreciated role for RNA surveillance JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-2-r8 DO - 10.1186/gb-2004-5-2-r8 ID - Hillman2004 ER - TY - JOUR AU - Cases, S. PY - 1998 DA - 1998// TI - ACAT-2, A second mammalian Acyl-CoA:cholesterol acyltransferase. Its cloning, expression, and characterization JO - J Biol Chem VL - 273 UR - https://doi.org/10.1074/jbc.273.41.26755 DO - 10.1074/jbc.273.41.26755 ID - Cases1998 ER - TY - JOUR AU - Simons-Evelyn, M. AU - Young, H. A. AU - Anderson, S. K. PY - 1997 DA - 1997// TI - Characterization of the mouse Nktr gene and promoter JO - Genomics VL - 40 UR - https://doi.org/10.1006/geno.1996.4562 DO - 10.1006/geno.1996.4562 ID - Simons-Evelyn1997 ER - TY - JOUR AU - Weischenfeldt, J. AU - Damgaard, I. AU - Bryder, D. AU - Theilgaard-Mönch, K. AU - Thoren, L. A. AU - Nielsen, F. C. AU - Jacobsen, S. E. AU - Nerlov, C. AU - Porse, B. T. PY - 2008 DA - 2008// TI - NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements JO - Genes Dev VL - 22 UR - https://doi.org/10.1101/gad.468808 DO - 10.1101/gad.468808 ID - Weischenfeldt2008 ER - TY - JOUR AU - Hogg, J. R. AU - Goff, S. P. PY - 2010 DA - 2010// TI - Upf1 Senses 3'UTR Length to Potentiate mRNA Decay JO - Cell VL - 143 UR - https://doi.org/10.1016/j.cell.2010.10.005 DO - 10.1016/j.cell.2010.10.005 ID - Hogg2010 ER - TY - JOUR AU - Trapnell, C. AU - Roberts, A. AU - Goff, L. AU - Pertea, G. AU - Kim, D. AU - Kelley, D. R. AU - Pimentel, H. AU - Salzberg, S. L. AU - Rinn, J. L. AU - Pachter, L. PY - 2012 DA - 2012// TI - Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2012.016 DO - 10.1038/nprot.2012.016 ID - Trapnell2012 ER - TY - JOUR AU - Robinson, M. D. AU - Oshlack, A. PY - 2010 DA - 2010// TI - A scaling normalization method for differential expression analysis of RNA-seq data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-3-r25 DO - 10.1186/gb-2010-11-3-r25 ID - Robinson2010 ER - TY - STD TI - RAINMAN (RnAseq-based Isoform detection and NMd ANalysis pipeline). [http://people.binf.ku.dk/jwaage/RAINMAN/] UR - http://people.binf.ku.dk/jwaage/RAINMAN/ ID - ref47 ER -