Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

Alternative isoform regulation in human tissue transcriptomes

Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

Pan, Q., Shai, O., Lee, L. J., Frey, B. J., & Blencowe, B. J. (2008) · Nature Genetics · doi:10.1038/ng.259 · Cited by 3,951

Expansion of the eukaryotic proteome by alternative splicing

Nilsen, T. W., & Graveley, B. R. (2010) · Nature · doi:10.1038/nature08909 · Cited by 2,270

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

Chen, M., & Manley, J. L. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2777 · Cited by 1,284

A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

Jansen, R., Yu, H., Greenbaum, D. S., Kluger, Y., Krogan, N. J., Chung, S., Emili, A., Snyder, M. P., Greenblatt, J. F., & Gerstein, M. (2003) · Science · doi:10.1126/science.1087361 · Cited by 1,254

RNA and Disease

Cooper, T. A., Wan, L., & Dreyfuss, G. (2009) · Cell · doi:10.1016/j.cell.2009.02.011 · Cited by 1,198

Deciphering the splicing code

Barash, Y., Calarco, J. A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B. J., & Frey, B. J. (2010) · Nature · doi:10.1038/nature09000 · Cited by 925

RNA processing and its regulation: global insights into biological networks

Licatalosi, D. D., & Darnell, R. B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2673 · Cited by 777

A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons

Boutz, P. L., Stoilov, P., Li, Q., Lin, C.-H., Chawla, G., Ostrow, K., Shiue, L., Ares, M., & Black, D. L. (2007) · Genes & Development · doi:10.1101/gad.1558107 · Cited by 577

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

Zhang, Y., Chen, K., Sloan, S. A., Bennett, M. L., Scholze, A. R., O'Keeffe, S., Phatnani, H. P., Guarnieri, P., Caneda, C., Ruderisch, N., et al. (2014) · The Journal of Neuroscience · doi:10.1523/jneurosci.1860-14.2014 · Cited by 4,875

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

Tasic, B., Menon, V., Nguyen, T. N., Kim, T. K., Jarsky, T., Yao, Z., Levi, B., Gray, L. T., Sorensen, S. A., Dolbeare, T., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4216 · Cited by 1,714

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

Lee, Y., & Rio, D. C. (2015) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034316 · Cited by 1,291

The human splicing code reveals new insights into the genetic determinants of disease

Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K. C., Hua, Y., Gueroussov, S., Najafabadi, H. S., Hughes, T., et al. (2014) · Science · doi:10.1126/science.1254806 · Cited by 1,243

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

Sharon, G., Cruz, N. J., Kang, D.-W., Gandal, M. J., Wang, B., Kim, Y.-M., Zink, E. M., Casey, C. P., Taylor, B. C., Lane, C. J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.05.004 · Cited by 1,182

Context-dependent control of alternative splicing by RNA-binding proteins

Fu, X.-D., & Ares, M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3778 · Cited by 1,044

Complexity of the Alternative Splicing Landscape in Plants

Reddy, A. S. N., Márquez, Y., Kalyna, M., & Barta, A. (2013) · The Plant Cell · doi:10.1105/tpc.113.117523 · Cited by 867

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulationPreprint

Ke, S., Alemu, E. A., Mertens, C., Gantman, E. C., Fak, J. J., Mele, A., Haripal, B., Zucker-Scharff, I., Moore, M. J., Park, C. Y., et al. (2015) · Genes & Development · doi:10.1101/gad.269415.115 · Cited by 815

The ctenophore genome and the evolutionary origins of neural systems

Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., Grigorenko, A. P., Dailey, C., Berezikov, E., Buckley, K. M., et al. (2014) · Nature · doi:10.1038/nature13400 · Cited by 716

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

Lagier‐Tourenne, C., Polymenidou, M., Hutt, K. R., Vu, A. Q., Baughn, M. W., Huelga, S. C., Clutario, K. M., Ling, S., Liang, T. Y., Mazur, C., et al. (2012) · Nature Neuroscience · doi:10.1038/nn.3230 · Cited by 769

Functional consequences of developmentally regulated alternative splicing

Kalsotra, A., & Cooper, T. A. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3052 · Cited by 729

Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins

Wang, E. T., Cody, N. A. L., Jog, S., Biancolella, M., Wang, T. T., Treacy, D. J., Luo, S., Schroth, G. P., Housman, D. E., Reddy, S., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.041 · Cited by 490

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

Raj, B., & Blencowe, B. J. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.004 · Cited by 475

The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines

Eizirik, D. L., Sammeth, M., Bouckenooghe, T., Bottu, G., Sisino, G., Igoillo-Esteve, M., Ortis, F., Santin, I., Colli, M. L., Barthson, J., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002552 · Cited by 465

Tissue-specific alternative splicing remodels protein-protein interaction networks

Ellis, J. D., Barrios-Rodiles, M., Çolak, R., Irimia, M., Kim, T., Calarco, J. A., Wang, X., Pan, Q., O'Hanlon, D., Kim, P. M., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.037 · Cited by 431

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

Zhang, C., & Darnell, R. B. (2011) · Nature Biotechnology · doi:10.1038/nbt.1873 · Cited by 414

Dynamic integration of splicing within gene regulatory pathways

Braunschweig, U., Gueroussov, S., Plocik, A. M., Graveley, B. R., & Blencowe, B. J. (2013) · Cell · doi:10.1016/j.cell.2013.02.034 · Cited by 406

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

Darnell, R. B. (2010) · WIREs RNA · doi:10.1002/wrna.31 · Cited by 382

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism

Weyn-Vanhentenryck, S. M., Mele, A., Yan, Q., Sun, S., Farny, N., Zhang, Z., Xue, C., Herre, M., Silver, P. A., Zhang, M. Q., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.005 · Cited by 333

The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain

Gehman, L. T., Stoilov, P., Maguire, J., Damianov, A., Lin, C.-H., Shiue, L., Ares, M., Mody, I., & Black, D. L. (2011) · Nature Genetics · doi:10.1038/ng.841 · Cited by 331

miRNA–target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity

Moore, M. J., Scheel, T. K. H., Luna, J. M., Park, C. Y., Fak, J. J., Nishiuchi, E., Rice, C. M., & Darnell, R. B. (2015) · Nature Communications · doi:10.1038/ncomms9864 · Cited by 326

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

Ameur, A., Zaghlool, A., Halvardson, J., Wetterbom, A., Gyllensten, U., Cavelier, L., & Feuk, L. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2143 · Cited by 323

Site identification in high-throughput RNA–protein interaction data

Uren, P. J., Bahrami‐Samani, E., Burns, S. C., Qiao, M., Karginov, F. V., Hodges, E. C., Hannon, G. J., Sanford, J. R., Penalva, L. O. F., & Smith, A. D. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts569 · Cited by 316

Precise temporal regulation of alternative splicing during neural development

Weyn‐Vanhentenryck, S. M., Feng, H., Ustianenko, D., Duffié, R., Yan, Q., Jacko, M., Martinez, J. C., Goodwin, M., Zhang, X., Hengst, U., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04559-0 · Cited by 272

Understanding splicing regulation through RNA splicing maps

Witten, J. T., & Ule, J. (2011) · Trends in Genetics · doi:10.1016/j.tig.2010.12.001 · Cited by 289

Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain

Rogelj, B., Easton, L. E., Bogu, G. K., Stanton, L. W., Rot, G., Curk, T., Zupan, B., Sugimoto, Y., Modic, M., Haberman, N., et al. (2012) · Scientific Reports · doi:10.1038/srep00603 · Cited by 278

The human gene damage index as a gene-level approach to prioritizing exome variants

Itan, Y., Shang, L., Boisson, B., Patin, É., Bolze, A., Moncada‐Vélez, M., Scott, E., Ciancanelli, M. J., Lafaille, F. G., Markle, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518646112 · Cited by 271

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain

Tollervey, J. R., Wang, Z., Hortobágyi, T., Witten, J. T., Zarnack, K., Kayikci, M., Clark, T. A., Schweitzer, A. C., Rot, G., Curk, T., et al. (2011) · Genome Research · doi:10.1101/gr.122226.111 · Cited by 252

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Sugimoto, Y., König, J., Hussain, S., Zupan, B., Curk, T., Frye, M., & Ule, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-8-r67 · Cited by 234

Conservation of an RNA regulatory map between Drosophila and mammalsPreprint

Brooks, A. N., Yang, L. C., Duff, M. O., Hansen, K. D., Park, J. W., Dudoit, S., Brenner, S. E., & Graveley, B. R. (2010) · Genome Research · doi:10.1101/gr.108662.110 · Cited by 240

RBFOX1 regulates both splicing and transcriptional networks in human neuronal development

Fogel, B. L., Wexler, E., Wahnich, A., Friedrich, T., Vijayendran, C., Gao, F., Parikshak, N., Konopka, G., & Geschwind, D. H. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds240 · Cited by 216

Defective control of pre–messenger RNA splicing in human disease

Chabot, B., & Shkreta, L. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201510032 · Cited by 220

Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability

Ince-Dunn, G., Okano, H. J., Jensen, K. B., Park, W.-Y., Zhong, R., Ule, J., Mele, A., Fak, J. J., Yang, C., Zhang, C., et al. (2012) · Neuron · doi:10.1016/j.neuron.2012.07.009 · Cited by 212

Alternative polyadenylation: New insights from global analyses

Shi, Y. (2012) · RNA · doi:10.1261/rna.035899.112 · Cited by 212

Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR

Damianov, A., Yi, Y., Lin, C.-H., Lee, J.-A., Tran, D., Vashisht, A. A., Bahrami‐Samani, E., Xing, Y., Martin, K. C., Wohlschlegel, J. A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.03.040 · Cited by 210

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain

Licatalosi, D. D., Yano, M., Fak, J. J., Mele, A., Grabinski, S. E., Zhang, C., & Darnell, R. B. (2012) · Genes & Development · doi:10.1101/gad.191338.112 · Cited by 193

The changing paradigm of intron retention: regulation, ramifications and recipes

Monteuuis, G., Wong, J. J. L., Bailey, C. G., Schmitz, U., & Rasko, J. E. J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1068 · Cited by 191

RNA Protein Interaction in Neurons

Darnell, R. B. (2013) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-062912-114322 · Cited by 181

Alternative splicing: decoding an expansive regulatory layer

Irimia, M., & Blencowe, B. J. (2012) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2012.03.005 · Cited by 177

Regulation of Neuronal Differentiation, Function, and Plasticity by Alternative Splicing

Furlanis, E., & Scheiffele, P. (2018) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100617-062826 · Cited by 177

Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators

Yan, Q., Weyn‐Vanhentenryck, S. M., Wu, J., Sloan, S. A., Zhang, Y., Chen, K., Wu, J. Q., Barres, B. A., & Zhang, C. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1502849112 · Cited by 169

Cholinergic‐associated loss of hnRNP‐A/B in Alzheimer's disease impairs cortical splicing and cognitive function in mice

Berson, A., Barbash, S., Shaltiel, G., Goll, Y., Hanin, G., Greenberg, D., Ketzef, M., Becker, A. J., Friedman, A., & Soreq, H. (2012) · EMBO Molecular Medicine · doi:10.1002/emmm.201100995 · Cited by 166

Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional controlPreprint

Patel, V., Mitra, S., Harris, R., Buxbaum, A. R., Lionnet, T., Brenowitz, M. D., Girvin, M. E., Levy, M., Almo, S. C., Singer, R. H., et al. (2012) · Genes & Development · doi:10.1101/gad.177428.111 · Cited by 167

Methods for comprehensive experimental identification of RNA-protein interactions

McHugh, C. A., Russell, P. H., & Guttman, M. (2014) · Genome biology · doi:10.1186/gb4152 · Cited by 172

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticityPreprint

Márquez, Y., Höpfler, M., Ayatollahi, Z., Barta, A., & Kalyna, M. (2015) · Genome Research · doi:10.1101/gr.186585.114 · Cited by 172

Functional Splicing Network Reveals Extensive Regulatory Potential of the Core Spliceosomal Machinery

Papasaikas, P., Tejedor, J. R., Vigevani, L., & Valcárcel, J. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.10.030 · Cited by 172

Global target mRNA specification and regulation by the RNA-binding protein ZFP36

Mukherjee, N., Jacobs, N. C., Hafner, M., Kennington, E. A., Nusbaum, J. D., Tuschl, T., Blackshear, P. J., & Ohler, U. (2014) · Genome biology · doi:10.1186/gb-2014-15-1-r12 · Cited by 157

Global Profiling and Molecular Characterization of Alternative Splicing Events Misregulated in Lung Cancer

Misquitta-Ali, C. M., Cheng, E., O’Hanlon, D., Liu, G., McGlade, C. J., Tsao, M., & Blencowe, B. J. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.00709-10 · Cited by 162

Structure-based systems biology for analyzing off-target binding

Xie, L., Xie, L., & Bourne, P. E. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.01.004 · Cited by 155

Bayesian networks in neuroscience: a survey

Bielza, C., & Larrañaga, P. (2014) · Frontiers in Computational Neuroscience · doi:10.3389/fncom.2014.00131 · Cited by 152

RBFOX2 Is an Important Regulator of Mesenchymal Tissue-Specific Splicing in both Normal and Cancer Tissues

Venables, J. P., Brosseau, J., Gadéa, G., Klinck, R., Prinos, P., Beaulieu, J., Lapointe, E., Durand, M., Thibault, P., Tremblay, K., et al. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.01174-12 · Cited by 158

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

Wu, J., Anczuków, O., Krainer, A. R., Zhang, M. Q., & Zhang, C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt216 · Cited by 123

Building Robust Transcriptomes with Master Splicing Factors

Jangi, M., & Sharp, P. A. (2014) · Cell · doi:10.1016/j.cell.2014.09.054 · Cited by 141

RNA Editing: A Contributor to Neuronal Dynamics in the Mammalian Brain

Behm, M., & Öhman, M. (2016) · Trends in Genetics · doi:10.1016/j.tig.2015.12.005 · Cited by 139

Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

Dittmar, K. A., Jiang, P., Park, J. W., Amirikian, K., Wan, J., Shen, S., Xing, Y., & Carstens, R. P. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.06536-11 · Cited by 139

Developmental regulation of RNA processing by Rbfox proteins

Conboy, J. G. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1398 · Cited by 133

Rbfox3-regulated alternative splicing of Numb promotes neuronal differentiation during development

Kim, K. K., Nam, J., Mukouyama, Y.-S., & Kawamoto, S. (2013) · Journal of Cell Biology · doi:10.1083/jcb.201206146 · Cited by 120

Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly

Jacko, M., Weyn‐Vanhentenryck, S. M., Smerdon, J. W., Yan, R., Feng, H., Williams, D. J., Pai, J. A., Xu, K., Wichterle, H., & Zhang, C. (2018) · Neuron · doi:10.1016/j.neuron.2018.01.020 · Cited by 131

Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites

Feng, H., Bao, S., Rahman, M. A., Weyn‐Vanhentenryck, S. M., Khan, A., Wong, J., Shah, A., Flynn, E. D., Krainer, A. R., & Zhang, C. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.002 · Cited by 123

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

Stražar, M., Žitnik, M., Zupan, B., Ule, J., & Curk, T. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw003 · Cited by 119

NOVA2-mediated RNA regulation is required for axonal pathfinding during development

Saito, Y., Miranda‐Rottmann, S., Ruggiu, M., Park, C. Y., Fak, J. J., Ru, Z., Duncan, J. S., Fabella, B. A., Junge, H. J., Chen, Z., et al. (2016) · eLife · doi:10.7554/elife.14371 · Cited by 122

NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure

Eom, T., Zhang, C., Wang, H., Lay, K., Fak, J., Noebels, J. L., & Darnell, R. B. (2013) · eLife · doi:10.7554/elife.00178 · Cited by 118

Alternative pre-mRNA splicing in neurons: growing up and extending its reach

Zheng, S., & Black, D. L. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.04.003 · Cited by 115

Reflections on the history of pre-mRNA processing and highlights of current knowledge: A unified picture

Darnell, J. E., Jr. (2013) · RNA · doi:10.1261/rna.038596.113 · Cited by 109

RNA-binding proteins balance brain function in health and disease

Schieweck, R., Ninkovic, J., & Kiebler, M. A. (2020) · Physiological Reviews · doi:10.1152/physrev.00047.2019 · Cited by 111

Emerging Roles of Alternative Pre-mRNA Splicing Regulation in Neuronal Development and Function

Norris, A. D., & Calarco, J. A. (2012) · Frontiers in Neuroscience · doi:10.3389/fnins.2012.00122 · Cited by 100

Microexons: discovery, regulation, and function

Ustianenko, D., Weyn‐Vanhentenryck, S. M., & Zhang, C. (2017) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1418 · Cited by 104

PTEN expression is upregulated by a RNA-binding protein RBM38 via enhancing its mRNA stability in breast cancer

Zhou, S., Wu, J., Shi, L., Li, X., Zhu, L., Sun, X., Qian, J., Wang, Y., Wei, J., & Ding, Q. (2017) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-017-0620-3 · Cited by 98

Finding the target sites of RNA ‐binding proteins

Li, X., Kazan, H., Lipshitz, H. D., & Morris, Q. (2013) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1201 · Cited by 94

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context

Xiong, H. Y., Barash, Y., & Frey, B. J. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr444 · Cited by 98

Alternative RNA splicing and cancer

Liu, S., & Cheng, C. (2013) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1178 · Cited by 96

Control of neuronal voltage-gated calcium ion channels from RNA to protein

Lipscombe, D., Allen, S. E., & Toro, C. P. (2013) · Trends in Neurosciences · doi:10.1016/j.tins.2013.06.008 · Cited by 94

Predicting Long Noncoding RNA and Protein Interactions Using Heterogeneous Network Model

Li, A., Ge, M., Zhang, Y., Chen, P., & Wang, M. (2015) · BioMed Research International · doi:10.1155/2015/671950 · Cited by 89

Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing

Rambout, X., Dequiedt, F., & Maquat, L. E. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00470 · Cited by 89

Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization

Lu, Z., Huang, Q., Park, J. W., Shen, S., Lin, L., Tokheim, C. J., Henry, M. D., & Xing, Y. (2014) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-14-0366 · Cited by 81

NOVA1 regulates hTERT splicing and cell growth in non-small cell lung cancer

Ludlow, A. T., Wong, M. S., Robin, J. D., Batten, K. G., Yuan, L., Lai, T., Dahlson, N., Zhang, L., Mender, I., Tedone, E., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05582-x · Cited by 83

Alternative splicing takes shape during neuronal development

Grabowski, P. J. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.03.005 · Cited by 97

Nova1 is a master regulator of alternative splicing in pancreatic beta cells

Villate, O., Turatsinze, J., Mascali, L. G., Grieco, F. A., Nogueira, T. C., Cunha, D. A., Nardelli, T. R., Sammeth, M., Salunkhe, V. A., Esguerra, J. L. S., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku861 · Cited by 80

Neuron-specific alternative splicing of transcriptional machineries: Implications for neurodevelopmental disorders

Porter, R. S., Jaamour, F., & Iwase, S. (2017) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2017.10.006 · Cited by 82

Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder

Gonatopoulos-Pournatzis, T., & Blencowe, B. J. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.03.007 · Cited by 79

The Alternative Heart: Impact of Alternative Splicing in Heart Disease

Lara‐Pezzi, E., Gómez-Salinero, J. M., Gatto, A., & García‐Pavía, P. (2013) · Journal of Cardiovascular Translational Research · doi:10.1007/s12265-013-9482-z · Cited by 89

RNA-binding proteins in neurological diseases

Zhou, H.-L., Mangelsdorf, M., Liu, J., Zhu, L., & Wu, J. Y. (2014) · Science China Life Sciences · doi:10.1007/s11427-014-4647-9 · Cited by 82

ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism

Berto, S., Usui, N., Konopka, G., & Fogel, B. L. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw110 · Cited by 80

De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function

Han, A., Stoilov, P., Linares, A. J., Zhou, Y., Fu, X., & Black, D. L. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003442 · Cited by 84

“Seq-ing” Insights into the Epigenetics of Neuronal Gene Regulation

Telese, F., Gamliel, A., Skowronska‐Krawczyk, D., García-Bassets, I., & Rosenfeld, M. G. (2013) · Neuron · doi:10.1016/j.neuron.2013.01.034 · Cited by 81

Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function

Saito, Y., Yuan, Y., Zucker-Scharff, I., Fak, J. J., Jereb, S., Tajima, Y., Licatalosi, D. D., & Darnell, R. B. (2019) · Neuron · doi:10.1016/j.neuron.2018.12.019 · Cited by 77

A Pair of RNA-Binding Proteins Controls Networks of Splicing Events Contributing to Specialization of Neural Cell Types

Norris, A. D., Gao, S., Norris, M. L., Ray, D., Ramani, A. K., Fraser, A. G., Morris, Q., Hughes, T., Zhen, M., & Calarco, J. A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.004 · Cited by 78

MiR-181b-5p Downregulates NOVA1 to Suppress Proliferation, Migration and Invasion and Promote Apoptosis in Astrocytoma

Zhi, F., Wang, Q., Deng, D., Shao, N., Wang, R., Xue, L., Wang, S., Xia, X., & Yang, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0109124 · Cited by 76

cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation

Hwang, H.-W., Saito, Y., Park, C. Y., Blachère, N. E., Tajima, Y., Fak, J. J., Zucker-Scharff, I., & Darnell, R. B. (2017) · Neuron · doi:10.1016/j.neuron.2017.08.024 · Cited by 74

Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts

Calarco, J. A., Zhen, M., & Blencowe, B. J. (2011) · RNA · doi:10.1261/rna.2603911 · Cited by 72

Complexity and graded regulation of neuronal cell-type–specific alternative splicing revealed by single-cell RNA sequencing

Feng, H., Moakley, D. F., Chen, S., McKenzie, M. G., Menon, V., & Zhang, C. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013056118 · Cited by 76

Functional Analysis of Long Noncoding RNAs in Development and Disease

Chen, L., & Zhao, J. C. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-1-4939-1221-6_4 · Cited by 72

Neuron-enriched RNA-binding Proteins Regulate Pancreatic Beta Cell Function and Survival

Juan‐Mateu, J., Rech, T. H., Villate, O., Lizárraga-Mollinedo, E., Wendt, A., Turatsinze, J., Brondani, L. D. A., Nardelli, T. R., Nogueira, T. C., Esguerra, J. L. S., et al. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.748335 · Cited by 70

Protein-RNA and Protein-Protein Recognition by Dual KH1/2 Domains of the Neuronal Splicing Factor Nova-1

Teplova, M., Malinina, L. V., Darnell, J. C., Song, J., Lu, M., Abagyan, R. A., Musunuru, K., Теплов, А. А., Burley, S. K., Darnell, R. B., et al. (2011) · Structure · doi:10.1016/j.str.2011.05.002 · Cited by 71

An alternative splicing program promotes adipose tissue thermogenesis

Vernia, S., Edwards, Y. J. K., Han, M. S., Cavanagh, J., Barrett, T., Kim, J. K., & Davis, R. J. (2016) · eLife · doi:10.7554/elife.17672 · Cited by 71

Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing

Çolak, R., Kim, T. P., Michaut, M., Sun, M., Irimia, M., Bellay, J., Myers, C. L., Blencowe, B. J., & Kim, P. M. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003030 · Cited by 69

Prediction of clustered RNA-binding protein motif sites in the mammalian genome

Zhang, C., Lee, K., Swanson, M. S., & Darnell, R. B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt421 · Cited by 65

RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis

Chatterjee, B., Shen, C.-K. J., & Majumder, P. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222111870 · Cited by 68

NOVA regulates Dcc alternative splicing during neuronal migration and axon guidance in the spinal cord

Leggere, J. C., Saito, Y., Darnell, R. B., Tessier-Lavigne, M., Junge, H. J., & Chen, Z. (2016) · eLife · doi:10.7554/elife.14264 · Cited by 67

Functional coupling of transcription and splicing

Montes, M., Becerra, S., Sánchez‐Álvarez, M., & Suñé, C. (2012) · Gene · doi:10.1016/j.gene.2012.04.006 · Cited by 72

An RNA map predicting Nova-dependent splicing regulation

Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B. J., & Darnell, R. B. (2006) · Nature · doi:10.1038/nature05304 · Cited by 528

Functional and Mechanistic Insights From Genome-Wide Studies of Splicing Regulation in the Brain

Ule, J., & Darnell, R. B. (2007) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-77374-2_9 · Cited by 21

Networking in an Alternative Splicing World

Carstens, R. P. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.014 · Cited by 2

Nova regulates brain-specific splicing to shape the synapse

Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J.-S., Cline, M., Wang, H., Clark, T., Fraser, C., Ruggiu, M., et al. (2005) · Nature Genetics · doi:10.1038/ng1610 · Cited by 509

Splicing on the brain

Blencowe, B. J. (2005) · Nature Genetics · doi:10.1038/ng0805-796 · Cited by 7