Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses
Kapeli, Katannya, Pratt, Gabriel A., Vu, Anthony Q., Hutt, Kasey R., Martinez, Fernando J., Sundararaman, Balaji, Batra, Ranjan, Freese, Peter, Lambert, Nicole J., Huelga, Stephanie C., Chun, Seung J., Liang, Tiffany Y., Chang, Jeremy, Donohue, John P., Shiue, Lily, Zhang, Jiayu, Zhu, Haining, Cambi, Franca, Kasarskis, Edward, Hoon, Shawn, Ares Jr, Manuel, Burge, Christopher B., Ravits, John, Rigo, Frank, Yeo, Gene W.
Published in Nature communications (05.07.2016)
Published in Nature communications (05.07.2016)
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Sam68 Regulates a Set of Alternatively Spliced Exons during Neurogenesis
Chawla, Geetanjali, Lin, Chia-Ho, Han, Areum, Shiue, Lily, Ares, Manuel, Black, Douglas L.
Published in Molecular and Cellular Biology (01.01.2009)
Published in Molecular and Cellular Biology (01.01.2009)
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Correction: Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome
Talkish, Jason, Igel, Haller, Perriman, Rhonda J, Shiue, Lily, Katzman, Sol, Munding, Elizabeth M, Shelansky, Robert, Donohue, John Paul, Ares, Jr, Manuel
Published in PLoS genetics (27.05.2020)
Published in PLoS genetics (27.05.2020)
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Rbfox1 downregulation and altered calpain 3 splicing by FRG1 in a mouse model of Facioscapulohumeral muscular dystrophy (FSHD)
Pistoni, Mariaelena, Shiue, Lily, Cline, Melissa S, Bortolanza, Sergia, Neguembor, Maria Victoria, Xynos, Alexandros, Ares, Jr, Manuel, Gabellini, Davide
Published in PLoS genetics (01.01.2013)
Published in PLoS genetics (01.01.2013)
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Unusual intron conservation near tissue-regulated exons found by splicing microarrays
Sugnet, Charles W, Srinivasan, Karpagam, Clark, Tyson A, O'Brien, Georgeann, Cline, Melissa S, Wang, Hui, Williams, Alan, Kulp, David, Blume, John E, Haussler, David, Ares, Jr, Manuel
Published in PLoS computational biology (01.01.2006)
Published in PLoS computational biology (01.01.2006)
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The structure of a rigorously conserved RNA element within the SARS virus genome
Robertson, Michael P, Igel, Haller, Baertsch, Robert, Haussler, David, Ares, Jr, Manuel, Scott, William G
Published in PLoS biology (01.01.2005)
Published in PLoS biology (01.01.2005)
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Prp43p Is a DEAH-Box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis
Combs, D. Joshua, Nagel, Roland J., Ares, Manuel, Stevens, Scott W.
Published in Molecular and Cellular Biology (01.01.2006)
Published in Molecular and Cellular Biology (01.01.2006)
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Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays
CHUNXIA LI, KATO, Mitsuo, SHIUE, Lily, SHIVELY, John E, ARES, Manuel, LIN, Ren-Jang
Published in Cancer research (Chicago, Ill.) (15.02.2006)
Published in Cancer research (Chicago, Ill.) (15.02.2006)
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Intron lariat spliceosomes convert lariats to true circles: implications for intron transposition
Ares, Jr, Manuel, Igel, Haller, Katzman, Sol, Donohue, John P
Published in Genes & development (01.04.2024)
Published in Genes & development (01.04.2024)
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The UCSC SARS-CoV-2 Genome Browser
Fernandes, Jason D., Hinrichs, Angie S., Clawson, Hiram, Gonzalez, Jairo Navarro, Lee, Brian T., Nassar, Luis R., Raney, Brian J., Rosenbloom, Kate R., Nerli, Santrupti, Rao, Arjun A., Schmelter, Daniel, Fyfe, Alastair, Maulding, Nathan, Zweig, Ann S., Lowe, Todd M., Ares, Manuel, Corbet-Detig, Russ, Kent, W. James, Haussler, David, Haeussler, Maximilian
Published in Nature genetics (01.10.2020)
Published in Nature genetics (01.10.2020)
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Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers
Yao, Jun, Xu, Hengyi, Ferrick-Kiddie, Elizabeth A, Nottingham, Ryan M, Wu, Douglas C, Ares, Jr, Manuel, Lambowitz, Alan M
Published in PLoS genetics (26.09.2024)
Published in PLoS genetics (26.09.2024)
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The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain
Black, Douglas L, Gehman, Lauren T, Stoilov, Peter, Maguire, Jamie, Damianov, Andrey, Lin, Chia-Ho, Shiue, Lily, Ares, Manuel, Mody, Istvan
Published in Nature genetics (01.07.2011)
Published in Nature genetics (01.07.2011)
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Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay
Ni, Julie Z, Grate, Leslie, Donohue, John Paul, Preston, Christine, Nobida, Naomi, O'Brien, Georgeann, Shiue, Lily, Clark, Tyson A, Blume, John E, Ares, Jr, Manuel
Published in Genes & development (15.03.2007)
Published in Genes & development (15.03.2007)
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An RNA gene expressed during cortical development evolved rapidly in humans
Lambert, Nelle, Haussler, David, Coppens, Sandra, Katzman, Sol, Pollard, Katherine S, King, Bryan, Siepel, Adam, Kern, Andrew D, Onodera, Courtney, Ares, Manuel, Lambot, Marie-Alexandra, Dehay, Colette, Vanderhaeghen, Pierre, Pedersen, Jakob S, Igel, Haller, Salama, Sofie R
Published in Nature (14.09.2006)
Published in Nature (14.09.2006)
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Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain
Hunter, Oarteze, Talkish, Jr, Jason, Quick-Cleveland, Jen, Igel, Haller, Tan, Asako, Kuersten, Scott, Katzman, Sol, Donohue, John Paul, Jurica, Melissa S, Ares, Jr, Manuel
Published in RNA (Cambridge) (01.02.2024)
Published in RNA (Cambridge) (01.02.2024)
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Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins
Huelga, Stephanie C., Vu, Anthony Q., Arnold, Justin D., Liang, Tiffany Y., Liu, Patrick P., Yan, Bernice Y., Donohue, John Paul, Shiue, Lily, Hoon, Shawn, Brenner, Sydney, Ares, Manuel, Yeo, Gene W.
Published in Cell reports (Cambridge) (23.02.2012)
Published in Cell reports (Cambridge) (23.02.2012)
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A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons
Boutz, Paul L, Stoilov, Peter, Li, Qin, Lin, Chia-Ho, Chawla, Geetanjali, Ostrow, Kristin, Shiue, Lily, Ares, Jr, Manuel, Black, Douglas L
Published in Genes & development (01.07.2007)
Published in Genes & development (01.07.2007)
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Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy
Osborne, Robert J, Shiue, Lily, Swanson, Maurice S, Du, Hongqing, Cline, Melissa S, Tuttle, Daniel L, Clark, Tyson A, Donohue, John Paul, Thornton, Charles A, Hall, Megan P, Ares, Manuel
Published in Nature structural & molecular biology (01.02.2010)
Published in Nature structural & molecular biology (01.02.2010)
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