Functional coordination of alternative splicing in the mammalian central nervous system

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works

Modern Applied Statistics with S

Venables, W., & Ripley, B. (2010) · Statisctics and computing/Statistics and computing · doi:10.1007/978-0-387-21706-2 · Cited by 16,188 · see citing works

Bioconductor: open software development for computational biology and bioinformatics

Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 13,133 · see citing works

Gentleman R: R: A language for data analysis and graphics

Ihaka, R., & Gentleman, R. (1996) · Journal of Computational and Graphical Statistics · doi:10.1080/10618600.1996.10474713 · Cited by 11,747 · see citing works

Database resources of the National Center for Biotechnology Information: update

Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works

The control of the false discovery rate in multiple testing under dependency

Benjamini, Y., & Yekutieli, D. (2001) · The Annals of Statistics · doi:10.1214/aos/1013699998 · Cited by 10,490 · see citing works

Divergence measures based on the Shannon entropy

Lin, J.-H. (1991) · IEEE Transactions on Information Theory · doi:10.1109/18.61115 · Cited by 5,877 · see citing works

Bootstrap Methods and Their Application

Loughin, T. M., Davison, A. C., & HINKLEY, D. V. (1999) · Journal of the American Statistical Association · doi:10.2307/2669707 · Cited by 5,478 · see citing works

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · see citing works

Procedures for Detecting Outlying Observations in Samples

Grubbs, F. E. (1969) · Technometrics · doi:10.1080/00401706.1969.10490657 · Cited by 4,105 · see citing works

Mechanisms of Alternative Pre-Messenger RNA Splicing

Black, D. L. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161720 · Cited by 2,704 · see citing works

Mitofusins Mfn1 and Mfn2 coordinately regulate mitochondrial fusion and are essential for embryonic development

Chen, H., Detmer, S. A., Ewald, A. J., Griffin, E. E., Fraser, S. E., & Chan, D. C. (2003) · The Journal of Cell Biology · doi:10.1083/jcb.200211046 · Cited by 2,601 · see citing works

Modern Applied Statistics with S Fourth edition

Venables, W. N., & Ripley, B. D. (2002) · Cited by 2,538 · see citing works

Galaxy: a platform for interactive large-scale genome analysis.Preprint

Giardine, B., Riemer, C., Hardison, R., Burhans, R. C., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., et al. (2005) · Genome Research · doi:10.1101/gr.4086505 · Cited by 2,217 · see citing works

Entrez Gene: gene-centered information at NCBI

Maglott, D. R., Ostell, J., Pruitt, K. D., & Tatusova, T. A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1237 · Cited by 2,117 · see citing works

The UCSC Genome Browser Database: update 2006

Hinrichs, A. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj144 · Cited by 1,646 · see citing works

Sample criteria for testing outlying observations

Grubbs, F. E. (1950) · The Annals of Mathematical Statistics · doi:10.1214/aoms/1177729885 · Cited by 1,631 · see citing works

ESEfinder: a web resource to identify exonic splicing enhancers

Cartegni, L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg616 · Cited by 1,593 · see citing works

Calmodulin-dependent protein kinase kinase-β is an alternative upstream kinase for AMP-activated protein kinase

Hawley, S. A., Pan, D. A., Mustard, K. J., Ross, L., Bain, J., Edelman, A. M., Frenguelli, B. G., & Hardie, D. G. (2005) · Cell Metabolism · doi:10.1016/j.cmet.2005.05.009 · Cited by 1,589 · see citing works

P2X4 receptors induced in spinal microglia gate tactile allodynia after nerve injury

Tsuda, M., Shigemoto‐Mogami, Y., Koizumi, S., Mizokoshi, A., Kohsaka, S., Salter, M. W., & Inoue, K. (2003) · Nature · doi:10.1038/nature01786 · Cited by 1,567 · see citing works

PDZ domain proteins of synapses

Kim, E., & Sheng, M. (2004) · Nature reviews. Neuroscience · doi:10.1038/nrn1517 · Cited by 1,565 · see citing works

Nuclear gene OPA1, encoding a mitochondrial dynamin-related protein, is mutated in dominant optic atrophy

Delettre, C., Lenaers, G., Griffoin, J.-M., Gigarel, N., Lorenzo, C., Belenguer, P., Pelloquin, L., Grosgeorge, J., Turc-Carel, C., Perret, E., et al. (2000) · Nature Genetics · doi:10.1038/79936 · Cited by 1,446 · see citing works

Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

Johnson, J. M., Castle, J. C., Garrett-Engele, P. W., Kan, Z., Loerch, P., Armour, C. D., Santos, R., Schadt, E. E., Stoughton, R. B., & Shoemaker, D. D. (2003) · Science · doi:10.1126/science.1090100 · Cited by 1,418 · see citing works

OPA1, encoding a dynamin-related GTPase, is mutated in autosomal dominant optic atrophy linked to chromosome 3q28

Alexander, C., Votruba, M., Pesch, U. E. A., Thiselton, D. L., Mayer, S., Moore, A., Rodriguez, M., Kellner, U., Leo-Kottler, B., Auburger, G., et al. (2000) · Nature Genetics · doi:10.1038/79944 · Cited by 1,330 · see citing works

OPA1 requires mitofusin 1 to promote mitochondrial fusion

Cipolat, S., de Brito, O. M., Dal Zilio, B., & Scorrano, L. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407043101 · Cited by 1,300 · see citing works

Understanding alternative splicing: towards a cellular code

Matlin, A. J., Clark, F., & Smith, C. W. J. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1645 · Cited by 1,299 · see citing works

GOstat: find statistically overrepresented Gene Ontologies within a group of genes

Beißbarth, T., & Speed, T. P. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth088 · Cited by 1,256 · see citing works

Alternative splicing: increasing diversity in the proteomic world

Graveley, B. R. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(00)02176-4 · Cited by 1,228 · see citing works

A Transcriptively Active Complex of APP with Fe65 and Histone Acetyltransferase Tip60

Cao, X., & Südhof, T. C. (2001) · Science · doi:10.1126/science.1058783 · Cited by 1,202 · see citing works

Alternative Splicing: New Insights from Global Analyses

Blencowe, B. J. (2006) · Cell · doi:10.1016/j.cell.2006.06.023 · Cited by 1,122 · see citing works

CLIP Identifies Nova-Regulated RNA Networks in the Brain

Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A., & Darnell, R. B. (2003) · Science · doi:10.1126/science.1090095 · Cited by 1,120 · see citing works

Moderate expansion of a normally biallelic trinucleotide repeat in spinocerebellar ataxia type 2

Pulst, S.-M., Nechiporuk, A. V., Nechiporuk, T., Gispert, S., Chen, X., Lopes‐Cendes, Í., Pearlman, S., Starkman, S., Díaz, G. O., Lunkes, A., et al. (1996) · Nature Genetics · doi:10.1038/ng1196-269 · Cited by 1,113 · see citing works

Predictive Identification of Exonic Splicing Enhancers in Human Genes

Fairbrother, W. G., Yeh, R., Sharp, P. A., & Burge, C. B. (2002) · Science · doi:10.1126/science.1073774 · Cited by 1,019 · see citing works

Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2

Higuchi, M., Maas, S., Single, F. N., Hartner, J., Rozov, A., Burnashev, N., Feldmeyer, D., Sprengel, R., & Seeburg, P. H. (2000) · Nature · doi:10.1038/35017558 · Cited by 967 · see citing works

Alternative pre-mRNA splicing: the logic of combinatorial control

Smith, C. W. J., & Valcárcel, J. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01604-2 · Cited by 901 · see citing works

Rap1 mediates sustained MAP kinase activation induced by nerve growth factor

York, R. D., Yao, H. W., Dillon, T. J., Ellig, C. L., Eckert, S. P., McCleskey, E. W., & Stork, P. A. (1998) · Nature · doi:10.1038/33451 · Cited by 858 · see citing works

Cloning of the gene for spinocerebellar ataxia 2 reveals a locus with high sensitivity to expanded CAG/glutamine repeats

Imbert, G., Saudou, F., Yvert, G., Devys, D., Trottier, Y., Garnier, J., Weber, C., Mandel, J., Cancel‐Tassin, G., Abbas, N., et al. (1996) · Nature Genetics · doi:10.1038/ng1196-285 · Cited by 848 · see citing works

Mitofusin-2 Determines Mitochondrial Network Architecture and Mitochondrial Metabolism

Bach, D., Pich, S., Soriano, F. X., Vega, N., Baumgartner, B., Oriola, J., Daugaard, J. R., Lloberas, J., Camps, M., Zierath, J. R., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m212754200 · Cited by 832 · see citing works

Molecular motors and mechanisms of directional transport in neurons

Hirokawa, N., & Takemura, R. (2005) · Nature reviews. Neuroscience · doi:10.1038/nrn1624 · Cited by 830 · see citing works

Review of An R and S-PLUS companion to applied regression by J. Fox, Sage Publications, Thousand Oaks, California 2002

Ligges, U. (2003) · Computational Statistics & Data Analysis · Cited by 795 · see citing works

Identification of the spinocerebellar ataxia type 2 gene using a direct identification of repeat expansion and cloning technique, DIRECT

Sanpei, K., Takano, H., Igarashi, S., Sato, T., Oyake, M., Sasaki, H., Wakisaka, A., Tashiro, K., Ishida, Y., Ikeuchi, T., et al. (1996) · Nature Genetics · doi:10.1038/ng1196-277 · Cited by 763 · see citing works

Systematic Identification and Analysis of Exonic Splicing Silencers

Wang, Z., Rolish, M. E., Yeo, G. W.-M., Tung, V., Mawson, M., & Burge, C. B. (2004) · Cell · doi:10.1016/j.cell.2004.11.010 · Cited by 694 · see citing works

Genome-wide detection of alternative splicing in expressed sequences of human genes

Modrek, B. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.13.2850 · Cited by 681 · see citing works

An R and S-Plus Companion to Applied Regression

Millar, P., & Fox, J. P. (2003) · The Canadian Journal of Sociology · doi:10.2307/3341881 · Cited by 637 · see citing works

Regulation of alternative splicing by RNA editing

Rueter, S. M., Dawson, T. R., & Emeson, R. B. (1999) · Nature · doi:10.1038/19992 · Cited by 637 · see citing works

Online Predicted Human Interaction Database

Brown, K. R., & Jurišica, I. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti273 · Cited by 601 · see citing works

Rac1 and Cdc42 Capture Microtubules through IQGAP1 and CLIP-170

Fukata, M., Watanabe, T., Noritake, J., Nakagawa, M., Yamaga, M., Kuroda, S., Matsuura, Y., Iwamatsu, A., Perez, F., & Kaibuchi, K. (2002) · Cell · doi:10.1016/s0092-8674(02)00800-0 · Cited by 600 · see citing works

Variation in alternative splicing across human tissues

Yeo, G., Holste, D., Kreiman, G., & Burge, C. B. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r74 · Cited by 584 · see citing works

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 · see citing works

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 · see citing works

Resampling-based multiple testing for microarray data analysis

Ge, Y., Dudoit, S., & Speed, T. P. (2003) · Test · doi:10.1007/bf02595811 · Cited by 506 · see citing works

Multiple links between transcription and splicing

Kornblihtt, A. R., de la Mata, M., Fededa, J. P., Muñoz, M. J., & Nogués, G. (2004) · RNA · doi:10.1261/rna.7100104 · Cited by 492 · see citing works

RNA binding specificity of hnRNP A1: significance of hnRNP A1 high‐affinity binding sites in pre‐mRNA splicing.

Burd, C. G., & Dreyfuss, G. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06369.x · Cited by 488 · see citing works

Interaction with IQGAP1 links APC to Rac1, Cdc42, and actin filaments during cell polarization and migration

Watanabe, T., Wang, S., Noritake, J., Sato, K., Fukata, M., Takefuji, M., Nakagawa, M., Izumi, N., Akiyama, T., & Kaibuchi, K. (2004) · Developmental Cell · doi:10.1016/j.devcel.2004.10.017 · Cited by 480 · see citing works

Osprey: a network visualization system

Breitkreutz, B., Stark, C., & Tyers, M. (2003) · Genome biology · doi:10.1186/gb-2003-4-3-r22 · Cited by 472 · see citing works

Loss of the Intermembrane Space Protein Mgm1/OPA1 Induces Swelling and Localized Constrictions along the Lengths of Mitochondria

Griparić, L., van der Wel, N. N., Orozco, I. J., Peters, P. J., & van der Bliek, A. M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m400920200 · Cited by 468 · see citing works

Gene targeting of BPAG1: Abnormalities in mechanical strength and cell migration in stratified epithelia and neurologic degeneration

Guo, L., Degenstein, L., Dowling, J. J., Yu, Q., Wollmann, R. L., Perman, B., & Fuchs, E. V. (1995) · Cell · doi:10.1016/0092-8674(95)90333-x · Cited by 440 · see citing works

daughterless, a Drosophila gene essential for both neurogenesis and sex determination, has sequence similarities to myc and the achaete-scute complex

Caudy, M. A., Vaessin, H., Brand, M., Tuma, R. S., Jan, L. Y., & Jan, Y. N. (1988) · Cell · doi:10.1016/0092-8674(88)90250-4 · Cited by 433 · see citing works

Computational definition of sequence motifs governing constitutive exon splicingPreprint

Zhang, X. H.-F., & Chasin, L. A. (2004) · Genes & Development · doi:10.1101/gad.1195304 · Cited by 420 · see citing works

Identification of an evolutionarily conserved superfamily of DOCK180-related proteins with guanine nucleotide exchange activity

Côté, J., & Vuori, K. (2002) · Journal of Cell Science · doi:10.1242/jcs.00219 · Cited by 412 · see citing works

Mitofusins 1/2 and ERRα expression are increased in human skeletal muscle after physical exercise

Cartoni, R., Léger, B., Hock, M. B., Praz, M., Crettenand, A., Pich, S., Ziltener, J., Luthi, F., Dériaz, O., Zorzano, A., et al. (2005) · The Journal of Physiology · doi:10.1113/jphysiol.2005.092031 · Cited by 406 · see citing works

Differential Distribution of Dynamin Isoforms in Mammalian Cells

Cao, H., Garcı́a, F., & McNiven, M. A. (1998) · Molecular Biology of the Cell · doi:10.1091/mbc.9.9.2595 · Cited by 402 · see citing works

ASF/SF2-Regulated CaMKIIδ Alternative Splicing Temporally Reprograms Excitation-Contraction Coupling in Cardiac Muscle

Xu, X., Yang, D., Ding, J.-H., Wang, W., Chu, P., Dalton, N. D., Wang, H., Bermingham, J. R., Ye, Z., Liu, F. C., et al. (2005) · Cell · doi:10.1016/j.cell.2004.11.036 · Cited by 391 · see citing works

Neurotrophins and Netrins Require Calcineurin/NFAT Signaling to Stimulate Outgrowth of Embryonic Axons

Graef, I. A., Wang, F., Charron, F., Chen, L., Neilson, J., Tessier-Lavigne, M., & Crabtree, G. R. (2003) · Cell · doi:10.1016/s0092-8674(03)00390-8 · Cited by 379 · see citing works

A GIT1/PIX/Rac/PAK Signaling Module Regulates Spine Morphogenesis and Synapse Formation through MLC

Zhang, H., Webb, D. J., Asmussen, H., Niu, S., & Horwitz, A. F. (2005) · Journal of Neuroscience · doi:10.1523/jneurosci.3553-04.2005 · Cited by 354 · see citing works

Content-rich biological network constructed by mining PubMed abstracts

Chen, H., & Sharp, B. M. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-147 · Cited by 345 · see citing works

Essential Roles in Synaptic Plasticity for Synaptogyrin I and Synaptophysin I

Janz, R., Südhof, T. C., Hammer, R. E., Unni, V. K., Siegelbaum, S. A., & Bolshakov, V. Y. (1999) · Neuron · doi:10.1016/s0896-6273(00)81122-8 · Cited by 342 · see citing works

New insights into the roles of agrin

Bezáková, G., & Rüegg, M. A. (2003) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1074 · Cited by 341 · see citing works

Nuclear localization or inclusion body formation of ataxin-2 are not necessary for SCA2 pathogenesis in mouse or human

Huynh, D. P., Figueroa, K. P., Hoang, N., & Pulst, S.-M. (2000) · Nature Genetics · doi:10.1038/79162 · Cited by 330 · see citing works

IQGAP proteins are integral components of cytoskeletal regulation

Briggs, M. W., & Sacks, D. B. (2003) · EMBO Reports · doi:10.1038/sj.embor.embor867 · Cited by 329 · see citing works

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform

Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A. L., Mohammad, N., Babak, T., Siu, H., Hughes, T. R., Morris, Q. D., et al. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.12.004 · Cited by 323 · see citing works

The evolving roles of alternative splicing

Lareau, L. F., Green, R. E., Bhatnagar, R. S., & Brenner, S. E. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.05.002 · Cited by 315 · see citing works

Htra2-β 1 stimulates an exonic splicing enhancer and can restore full-length SMN expression to survival motor neuron 2 ( SMN2 )

Hofmann, Y., Lorson, C. L., Stamm, S., Androphy, E. J., & Wirth, B. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.160181697 · Cited by 314 · see citing works

Syndapin Isoforms Participate in Receptor-Mediated Endocytosis and Actin Organization

Qualmann, B., & Kelly, R. B. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.148.5.1047 · Cited by 313 · see citing works

The functional landscape of mouse gene expression

Zhang, W., Morris, Q., Chang, R., Shai, O., Bakowski, M. A., Mitsakakis, N., Mohammad, N., Robinson, M. D., Zirngibl, R. A., Somogyi, E., et al. (2004) · Journal of Biology · doi:10.1186/jbiol16 · Cited by 312 · see citing works

Cooperative Assembly of an hnRNP Complex Induced by a Tissue-Specific Homolog of Polypyrimidine Tract Binding Protein

Markovtsov, V. V., Nikolic, J. M., Goldman, J. A., Turck, C. W., Chou, M., & Black, D. L. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.20.7463-7479.2000 · Cited by 311 · see citing works

A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG

Jin, Y., Suzuki, H., Maegawa, S., Endo, H., Sugano, S., Hashimoto, K., Yasuda, K., & Inoue, K. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg089 · Cited by 311 · see citing works

Activated Mitofusin 2 Signals Mitochondrial Fusion, Interferes with Bax Activation, and Reduces Susceptibility to Radical Induced Depolarization

Neuspiel, M., Zunino, R., Gangaraju, S., Rippstein, P. U., & McBride, H. M. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m501599200 · Cited by 308 · see citing works

Disruption of scribble (Scrb1) causes severe neural tube defects in the circletail mouse

Murdoch, J. N. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg014 · Cited by 308 · see citing works

Calcium/calmodulin-dependent protein kinase II and synaptic plasticity

Colbran, R. J., & Brown, A. M. (2004) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2004.05.008 · Cited by 307 · see citing works

A Novel Protein Complex Linking the δ2 Glutamate Receptor and Autophagy

Yue, Z., Horton, A., Bravin, M., DeJager, P. L., Selimi, F., & Heintz, N. (2002) · Neuron · doi:10.1016/s0896-6273(02)00861-9 · Cited by 306 · see citing works

Phospholipase C isozymes selectively couple to specific neurotransmitter receptors

Kim, D., Jun, K. S., Lee, S. B., Kang, N.-G., Min, D. S., Kim, Y.-H., Ryu, S. H., Suh, P.-G., & Shin, H.-S. (1997) · Nature · doi:10.1038/38508 · Cited by 305 · see citing works

An Essential Cytoskeletal Linker Protein Connecting Actin Microfilaments to Intermediate Filaments

Yang, Y., Dowling, J. J., Yu, Q., Kouklis, P. D., Cleveland, D. W., & Fuchs, E. V. (1996) · Cell · doi:10.1016/s0092-8674(00)80138-5 · Cited by 305 · see citing works

Deficiency of a protein-repair enzyme results in the accumulation of altered proteins, retardation of growth, and fatal seizures in mice

Kim, E., Lowenson, J. D., MacLaren, D. C., Clarke, S. G., & Young, S. G. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.12.6132 · Cited by 293 · see citing works

N‐methyl‐D‐aspartate receptor signaling results in Aurora kinase‐catalyzed CPEB phosphorylation and αCaMKII mRNA polyadenylation at synapses

Huang, Y.-S., Jung, M.-Y., Sarkissian, M., & Richter, J. (2002) · EMBO Journal · doi:10.1093/emboj/21.9.2139 · Cited by 290 · see citing works

Neogenin mediates the action of repulsive guidance molecule

Rajagopalan, S., Deitinghoff, L., Davis, D., Conrad, S., Skutella, T., Chédotal, A., Mueller, B. K., & Strittmatter, S. M. (2004) · Nature Cell Biology · doi:10.1038/ncb1156 · Cited by 276 · see citing works

CZH proteins: a new family of Rho-GEFs

Meller, N., Merlot, S., & Guda, C. (2005) · Journal of Cell Science · doi:10.1242/jcs.02671 · Cited by 273 · see citing works

Homologues of the <i>Caenorhabditis elegans</i> Fox-1 Protein Are Neuronal Splicing Regulators in Mammals

Underwood, J. G., Boutz, P. L., Dougherty, J. D., Stoilov, P., & Black, D. L. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.22.10005-10016.2005 · Cited by 272 · see citing works

Calcium triggers calcineurin-dependent synaptic vesicle recycling in mammalian nerve terminals

Marks, B., & McMahon, H. T. (1998) · Current Biology · doi:10.1016/s0960-9822(98)70297-0 · Cited by 271 · see citing works

The mouse dystonia musculorum gene is a neural isoform of bullous pemphigoid antigen 1

Brown, A., Bernier, G., Mathieu, M., Rossant, J., & Kothary, R. (1995) · Nature Genetics · doi:10.1038/ng0795-301 · Cited by 268 · see citing works

RGM and its receptor neogenin regulate neuronal survival

Matsunaga, E., Tauszig-Delamasure, S., Monnier, P. P., Mueller, B. K., Strittmatter, S. M., Mehlen, P., & Chédotal, A. (2004) · Nature Cell Biology · doi:10.1038/ncb1157 · Cited by 267 · see citing works

Interaction of the Tumor Suppressor PTEN/MMAC with a PDZ Domain of MAGI3, a Novel Membrane-associated Guanylate Kinase

Wu, Y. L., Dowbenko, D. J., Spencer, S. D., Laura, R. P., Lee, J., Gu, Q., & Lasky, L. A. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m909741199 · Cited by 267 · see citing works

Syne-1, A Dystrophin- and Klarsicht-related Protein Associated with Synaptic Nuclei at the Neuromuscular Junction

Apel, E. D., Lewis, R. M., Grady, R. M., & Sanes, J. R. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m004775200 · Cited by 263 · see citing works

The MAP kinase kinase kinase MLK2 co‐localizes with activated JNK along microtubules and associates with kinesin superfamily motor KIF3

Nagata, K., Puls, A., Futter, C. E., Aspenstrom, P., Schaefer, E., Nakata, T., Hirokawa, N., & Hall, A. (1998) · The EMBO Journal · doi:10.1093/emboj/17.1.149 · Cited by 263 · see citing works

Interaction of the Postsynaptic Density-95/Guanylate Kinase Domain-Associated Protein Complex with a Light Chain of Myosin-V and Dynein

Naisbitt, S. R., Valtschanoff, J. G., Allison, D. W., Sala, C., Kim, E., Craig, A. M., Weinberg, R. J., & Sheng, M. (2000) · Journal of Neuroscience · doi:10.1523/jneurosci.20-12-04524.2000 · Cited by 259 · see citing works

A family of RIM-binding proteins regulated by alternative splicing: Implications for the genesis of synaptic active zones

Wang, Y., Liu, X., Biederer, T., & Südhof, T. C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.182532999 · Cited by 256 · see citing works

Amphiphysin II (SH3P9; BIN1), a Member of the Amphiphysin/Rvs Family, Is Concentrated in the Cortical Cytomatrix of Axon Initial Segments and Nodes of Ranvier in Brain and around T Tubules in Skeletal Muscle

Butler, M. H., David, C., Ochoa, G.-C., Freyberg, Z., Daniell, L., Grabs, D., Cremona, O., & Camilli, P. D. (1997) · The Journal of Cell Biology · doi:10.1083/jcb.137.6.1355 · Cited by 256 · see citing works

Nerve Growth Factor Activates Persistent Rap1 Signaling in Endosomes

Wu, C., Lai, C.-F., & Mobley, W. C. (2001) · Journal of Neuroscience · doi:10.1523/jneurosci.21-15-05406.2001 · Cited by 250 · see citing works

Use of minigene systems to dissect alternative splicing elements

Cooper, T. A. (2005) · Methods · doi:10.1016/j.ymeth.2005.07.015 · Cited by 248 · see citing works

Vav family GEFs link activated ephs to endocytosis and axon guidance

Cowan, C. W., Shao, Y. R., Sahin, M., Shamah, S. M., Lin, M. Z., Greer, P. L., Gao, S., Griffith, E. C., Brugge, J. S., & Greenberg, M. E. (2005) · Neuron · doi:10.1016/j.neuron.2005.03.019 · Cited by 246 · see citing works

The Muscleblind family of proteins: an emerging class of regulators of developmentally programmed alternative splicing

Pascual, M., Vicente-Crespo, M., Monferrer, L., & Artero, R. D. (2006) · Differentiation · doi:10.1111/j.1432-0436.2006.00060.x · Cited by 246 · see citing works

Brain Myosin V Is a Synaptic Vesicle-associated Motor Protein: Evidence for a Ca2+-dependent Interaction with the Synaptobrevin–Synaptophysin Complex

Prekeris, R., & Terrian, D. M. (1997) · The Journal of Cell Biology · doi:10.1083/jcb.137.7.1589 · Cited by 245 · see citing works

LAR receptor protein tyrosine phosphatases in the development and maintenance of excitatory synapses

Dunah, A. W., Hueske, E., Wyszynski, M. W., Hoogenraad, C. C., Jaworski, J., Pak, D. T. S., Simonetta, A., Liu, G., & Sheng, M. (2005) · Nature Neuroscience · doi:10.1038/nn1416 · Cited by 244 · see citing works

Cloning of a Novel Mitogen-activated Protein Kinase Kinase Kinase, MEKK4, That Selectively Regulates the c-Jun Amino Terminal Kinase Pathway

Gerwins, P., Jonathan, L., & Johnson, G. L. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.13.8288 · Cited by 242 · see citing works

Dynamin at the actin–membrane interface

Orth, J. D., & McNiven, M. A. (2003) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(02)00010-8 · Cited by 239 · see citing works

Intronic Binding Sites for hnRNP A/B and hnRNP F/H Proteins Stimulate Pre-mRNA Splicing

Martínez-Contreras, R. D., Fisette, J., Nasim, F., Madden, R., Cordeau, M., & Chabot, B. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040021 · Cited by 226 · see citing works

Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expressionPreprint

Pan, Q., Saltzman, A. L., Kim, Y. K., Misquitta, C., Ofer Shai, A., Maquat, L. E., Frey, B. J., & Blencowe, B. J. (2006) · Genes & Development · doi:10.1101/gad.1382806 · Cited by 226 · see citing works

A role for myosin VI in postsynaptic structure and glutamate receptor endocytosis

Osterweil, E. K., Wells, D. G., & Mooseker, M. S. (2005) · The Journal of Cell Biology · doi:10.1083/jcb.200410091 · Cited by 226 · see citing works

ASD: a bioinformatics resource on alternative splicing

Stamm, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj031 · Cited by 223 · see citing works

Calcineurin/NFAT-induced up-regulation of the Fas ligand/Fas death pathway is involved in methamphetamine-induced neuronal apoptosis

Jayanthi, S., Deng, X., Ladenheim, B., McCoy, M. T., Cluster, A. S., Cai, N.-S., & Cadet, J. L. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404990102 · Cited by 223 · see citing works

Finding signals that regulate alternative splicing in the post-genomic era.

Ladd, A. N., & Cooper, T. A. (2002) · Genome biology · doi:10.1186/gb-2002-3-11-reviews0008 · Cited by 221 · see citing works

A neuron-specific splicing switch mediated by an array of pre-mRNA repressor sites: evidence of a regulatory role for the polypyrimidine tract binding protein and a brain-specific PTB counterpart.

Ashiya, M., & Grabowski, P. J. (1997) · PubMed · Cited by 220 · see citing works

IQGAP1 Binds Rap1 and Modulates Its Activity

Jeong, H., Li, Z., Brown, M. P., & Sacks, D. B. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m700487200 · Cited by 218 · see citing works

Mammalian Scribble Forms a Tight Complex with the βPIX Exchange Factor

Audebert, S., Navarro, C., Nourry, C., Chasserot-Golaz, S., Lécine, P., Bellaiche, Y., Dupont, J.-L., Premont, R. T., Sempéré, C., Strub, J.-M., et al. (2004) · Current Biology · doi:10.1016/j.cub.2004.05.051 · Cited by 218 · see citing works

Syne proteins anchor muscle nuclei at the neuromuscular junction

Grady, R. M., Starr, D. A., Ackerman, G. L., Sanes, J. R., & Han, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500711102 · Cited by 218 · see citing works

The Polypyrimidine Tract Binding Protein Binds Upstream of Neural Cell-Specific c- src Exon N1 To Repress the Splicing of the Intron Downstream

Chan, R. C., & Black, D. L. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.8.4667 · Cited by 216 · see citing works

Four proline-rich sequences of the guanine-nucleotide exchange factor C3G bind with unique specificity to the first Src homology 3 domain of Crk

Knudsen, B. S., Feller, S. M., & Hanafusa, H. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(20)30059-4 · Cited by 215 · see citing works

Syndapins integrate N‐WASP in receptor‐mediated endocytosis

Kessels, M. M., & Qualmann, B. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf604 · Cited by 210 · see citing works

The Nesprins Are Giant Actin-Binding Proteins, Orthologous to Drosophila melanogaster Muscle Protein MSP-300

Zhang, Q., Ragnauth, C. D., Greener, M., Shanahan, C. M., & Roberts, R. G. (2002) · Genomics · doi:10.1006/geno.2002.6859 · Cited by 209 · see citing works

Kinesin Superfamily Protein 3 (Kif3) Motor Transports Fodrin-Associating Vesicles Important for Neurite Building

Takeda, S., Yamazaki, H., Seog, D., Kanai, Y., Terada, S., & Hirokawa, N. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.148.6.1255 · Cited by 209 · see citing works

Activation of a Dab1/CrkL/C3G/Rap1 Pathway in Reelin-Stimulated Neurons

Ballif, B. A., Arnaud, L., Arthur, W. T., Guris, D. L., Imamoto, A., & Cooper, J. A. (2004) · Current Biology · doi:10.1016/j.cub.2004.03.038 · Cited by 208 · see citing works

Natural variation and genetic covariance in adult hippocampal neurogenesis

Kempermann, G., Chesler, E. J., Lu, L., Williams, R. W., & Gage, F. H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510291103 · Cited by 205 · see citing works

A Rab8-specific GDP/GTP Exchange Factor Is Involved in Actin Remodeling and Polarized Membrane Transport

Hattula, K., Furuhjelm, J., Arffman, A., & Peränen, J. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-03-0143 · Cited by 205 · see citing works

All three PACSIN isoforms bind to endocytic proteins and inhibit endocytosis

Modregger, J., Ritter, B., Witter, B., Paulsson, M., & Plomann, M. (2000) · Journal of Cell Science · doi:10.1242/jcs.113.24.4511 · Cited by 202 · see citing works

A stimulatory GDP/GTP exchange protein for smg p21 is active on the post-translationally processed form of c-Ki-ras p21 and rhoA p21.

Mizuno, T., Kaibuchi, K., Yamamoto, T., Kawamura, M., Sakoda, T., Fujioka, H., Matsuura, Y., & Takai, Y. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.15.6442 · Cited by 199 · see citing works

The complexity of PDZ domain-mediated interactions at glutamatergic synapses: a case study on neuroligin

Meyer, G. R. Y. D., Varoqueaux, F., Neeb, A., Oschlies, M., & Brose, N. (2004) · Neuropharmacology · doi:10.1016/j.neuropharm.2004.06.023 · Cited by 199 · see citing works

Multisite RNA Binding and Release of Polypyrimidine Tract Binding Protein during the Regulation of c-src Neural-Specific Splicing

Chou, M., Underwood, J. G., Nikolic, J. M., Luu, M. H. T., & Black, D. L. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)80260-9 · Cited by 198 · see citing works

Cloning and characterization of KAP3: a novel kinesin superfamily-associated protein of KIF3A/3B.

Yamazaki, H., Nakata, T., Okada, Y., & Hirokawa, N. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.16.8443 · Cited by 197 · see citing works

Mechanism for elimination of a tumor suppressor: Aberrant splicing of a brain-specific exon causes loss of function of Bin1 in melanoma

Ge, K., DuHadaway, J. B., Du, W., Herlyn, M., Rodeck, U., & Prendergast, G. C. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.17.9689 · Cited by 196 · see citing works

MAGI-1, a Membrane-associated Guanylate Kinase with a Unique Arrangement of Protein-Protein Interaction Domains

Dobrosotskaya, I. Y., Guy, R. K., & James, G. L. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.50.31589 · Cited by 194 · see citing works

Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays

Sugnet, C. W., Srinivasan, K., Clark, T. A., O’Brien, G. S., Cline, M., Wang, H., Williams, A., Kulp, D., Blume, J. E., Haussler, D. H., et al. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020004 · Cited by 194 · see citing works

Identification and Characterization of a Nerve Terminal-enriched Amphiphysin Isoform

Ramjaun, A. R., Micheva, K. D., Bouchelet, I., & McPherson, P. S. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.26.16700 · Cited by 192 · see citing works

The KIF3 motor transports N-cadherin and organizes the developing neuroepithelium

Teng, J., Rai, T., Tanaka, Y., Takei, Y., Nakata, T., Hirasawa, M., Kulkarni, A. B., & Hirokawa, N. (2005) · Nature Cell Biology · doi:10.1038/ncb1249 · Cited by 192 · see citing works

Subunit structure of the mammalian exocyst complex

Kee, Y., Yoo, J.-S., Hazuka, C. D., Peterson, K. E., Hsu, S.-C., & Scheller, R. H. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.26.14438 · Cited by 189 · see citing works

Editing of Glutamate Receptor B Subunit Ion Channel RNAs by Four Alternatively Spliced DRADA2 Double-Stranded RNA Adenosine Deaminases

Lai, F., Chen, C., Carter, K. C., & Nishikura, K. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.5.2413 · Cited by 189 · see citing works

IQGAP1 Integrates Ca2+/Calmodulin and B-Raf Signaling

Ren, J.-G., Li, Z., & Sacks, D. B. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m804626200 · Cited by 188 · see citing works

The Amyloid Precursor Protein and Its Regulatory Protein, FE65, in Growth Cones and Synapses<i>In Vitro</i>and<i>In Vivo</i>

Sabo, S. L., Ikin, A. F., Buxbaum, J. D., & Greengard, P. (2003) · The Journal of Neuroscience · doi:10.1523/jneurosci.23-13-05407.2003 · Cited by 187 · see citing works

Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities

Nakahata, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki338 · Cited by 184 · see citing works

Multiple Amphiphysin II Splice Variants Display Differential Clathrin Binding: Identification of Two Distinct Clathrin‐Binding Sites

Ramjaun, A. R., & McPherson, P. S. (1998) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.1998.70062369.x · Cited by 183 · see citing works

Calcium-dependent interaction of Lis1 with IQGAP1 and Cdc42 promotes neuronal motility

Kholmanskikh, S., Koeller, H. B., Wynshaw-Boris, A., Gómez, T. M., Letourneau, P. C., & Ross, M. (2006) · Nature Neuroscience · doi:10.1038/nn1619 · Cited by 182 · see citing works

Vesicle Endocytosis Requires Dynamin-Dependent GTP Hydrolysis at a Fast CNS Synapse

Yamashita, T., Hige, T., & Takahashi, T. (2005) · Science · doi:10.1126/science.1103631 · Cited by 178 · see citing works

Expression of nitric oxide synthase-2 (NOS-2) in reactive astrocytes of the human glaucomatous optic nerve head

Liu, B., & Neufeld, A. H. (2000) · Glia · doi:10.1002/(sici)1098-1136(200004)30:2 · Cited by 177 · see citing works

The BPAG1 locus

Leung, C. L., Zheng, M. H., Prater, S. M., & Liem, R. K. H. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.200012098 · Cited by 177 · see citing works

Integrators of the Cytoskeleton that Stabilize Microtubules

Yang, Y., Bauer, C. R., Strasser, G. A., Wollman, R. L., Julien, J., & Fuchs, E. V. (1999) · Cell · doi:10.1016/s0092-8674(00)81017-x · Cited by 175 · see citing works

Synaptic multiprotein complexes associated with 5‐HT2C receptors: a proteomic approach

Bécamel, C., Alonso, G., Galéotti, N., Demey, E., Jouin, P., Ullmer, C., Dumuis, A., Bockaert, J., & Marin, P. (2002) · The EMBO Journal · doi:10.1093/emboj/21.10.2332 · Cited by 173 · see citing works

The Microtubule Plus End Tracking Protein Orbit/MAST/CLASP Acts Downstream of the Tyrosine Kinase Abl in Mediating Axon Guidance

Lee, H., Engel, U., Rusch, J., Scherrer, S., Sheard, K., & Vactor, D. V. (2004) · Neuron · doi:10.1016/j.neuron.2004.05.020 · Cited by 173 · see citing works

Zizimin1, a novel Cdc42 activator, reveals a new GEF domain for Rho proteins

Meller, N., Irani-Tehrani, M., Kiosses, W. B., Del Pozo, M. A., & Schwartz, M. A. (2002) · Nature Cell Biology · doi:10.1038/ncb835 · Cited by 171 · see citing works

The syndapin protein family: linking membrane trafficking with the cytoskeleton

Kessels, M. M., & Qualmann, B. (2004) · Journal of Cell Science · doi:10.1242/jcs.01290 · Cited by 171 · see citing works

Cycling of NMDA Receptors during Trafficking in Neurons before Synapse Formation

Washbourne, P., Liu, X.-B., Jones, E. G., & McAllister, A. K. (2004) · Journal of Neuroscience · doi:10.1523/jneurosci.2555-04.2004 · Cited by 170 · see citing works

Characterization of novel Rab6-interacting proteins involved in endosome-to-TGN transport

Monier, S., Jollivet, F., Janoueix‐Lerosey, I., Johannes, L., & Goud, B. (2002) · Traffic · doi:10.1034/j.1600-0854.2002.030406.x · Cited by 170 · see citing works

Neogenin, an avian cell surface protein expressed during terminal neuronal differentiation, is closely related to the human tumor suppressor molecule deleted in colorectal cancer.

Vielmetter, J., Kayyem, J. F., Roman, J. M., & Dreyer, W. J. (1994) · The Journal of Cell Biology · doi:10.1083/jcb.127.6.2009 · Cited by 165 · see citing works

An Evolutionarily Conserved Transmembrane Protein That Is a Novel Downstream Target of Neurotrophin and Ephrin Receptors

Kong, H., Boulter, J., Weber, J. L., Lai, C., & Chao, M. V. (2001) · Journal of Neuroscience · doi:10.1523/jneurosci.21-01-00176.2001 · Cited by 164 · see citing works

Identification of Guanine Nucleotide Exchange Factors (GEFs) for the Rap1 GTPase

Rebhun, J. F., Castro, A. F., & Quilliam, L. A. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m005327200 · Cited by 164 · see citing works

P2X Receptor Trafficking in Neurons Is Subunit Specific

Bobanović, L. K., Royle, S., & Murrell‐Lagnado, R. D. (2002) · Journal of Neuroscience · doi:10.1523/jneurosci.22-12-04814.2002 · Cited by 164 · see citing works

Mammalian CELF/Bruno-like RNA-binding proteins: molecular characteristics and biological functions

Barreau, C., Paillard, L., Méreau, A., & Osborne, H. B. (2005) · Biochimie · doi:10.1016/j.biochi.2005.10.011 · Cited by 156 · see citing works

Deficiency in Protein l-Isoaspartyl Methyltransferase Results in a Fatal Progressive Epilepsy

Yamamoto, A., Takagi, H., Kitamura, D., Tatsuoka, H., Nakano, H., Kawano, H., Kuroyanagi, H., Yahagi, Y., Kobayashi, S., Koizumi, K.-I., et al. (1998) · Journal of Neuroscience · doi:10.1523/jneurosci.18-06-02063.1998 · Cited by 154 · see citing works

Identification and Cloning of Kidins220, a Novel Neuronal Substrate of Protein Kinase D

Iglesias, T., Cabrera-Poch, N., Mitchell, M., Naven, T. J. P., Rozengurt, E., & Schiavo, G. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m005261200 · Cited by 153 · see citing works

Primary Structure of a Dynamin-related Mouse Mitochondrial GTPase and Its Distribution in Brain, Subcellular Localization, and Effect on Mitochondrial Morphology

Misaka, T., Miyashita, T., & Kubo, Y. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m109260200 · Cited by 153 · see citing works

MAGI-1 Is Required for Rap1 Activation upon Cell-Cell Contact and for Enhancement of Vascular Endothelial Cadherin-mediated Cell Adhesion

Sakurai, A., Fukuhara, S., Yamagishi, A., Sako, K., Kamioka, Y., Masuda, M., Nakaoka, Y., & Mochizuki, N. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e05-07-0647 · Cited by 152 · see citing works

Myosin VA Movements in Normal and Dilute-Lethal Axons Provide Support for a Dual Filament Motor Complex

Bridgman, P. C. (1999) · The Journal of Cell Biology · doi:10.1083/jcb.146.5.1045 · Cited by 151 · see citing works

Regulating Actin Dynamics at Membranes: A Focus on Dynamin

Schafer, D. A. (2004) · Traffic · doi:10.1111/j.1600-0854.2004.00199.x · Cited by 150 · see citing works

A POU Domain Transcription Factor–Dependent Program Regulates Axon Pathfinding in the Vertebrate Visual System

Erkman, L., Yates, P. A., McLaughlin, T., McEvilly, R. J., Whisenhunt, T. R., O’Connell, S. M., Krones, A., Kirby, M. A., Rapaport, D. H., Bermingham, J. R., et al. (2000) · Neuron · doi:10.1016/s0896-6273(00)00153-7 · Cited by 150 · see citing works

Alternative splicing of conserved exons is frequently species-specific in human and mouse

Pan, Q., Bakowski, M. A., Morris, Q., Zhang, W., Frey, B. J., Hughes, T. R., & Blencowe, B. J. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.12.004 · Cited by 149 · see citing works

Interaction of SAP97 with Minus-end-directed Actin Motor Myosin VI

Wu, H., Nash, J. E., Zamorano, P. L., & Garner, C. C. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m203735200 · Cited by 148 · see citing works

Dual role of the exocyst in AMPA receptor targeting and insertion into the postsynaptic membrane

Gerges, N. Z., Backos, D. S., Rupasinghe, C. N., Spaller, M. R., & Esteban, J. A. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601065 · Cited by 147 · see citing works

The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain

Jensen, K. B., Musunuru, K., Lewis, H. A., Burley, S. K., & Darnell, R. B. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.090553997 · Cited by 144 · see citing works

Local Phosphatidylinositol 3,4,5-Trisphosphate Accumulation Recruits Vav2 and Vav3 to Activate Rac1/Cdc42 and Initiate Neurite Outgrowth in Nerve Growth Factor-stimulated PC12 Cells

Aoki, K., Nakamura, T., Fujikawa, K., & Matsuda, M. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-10-0904 · Cited by 144 · see citing works

Structural Analysis of the Human BIN1 Gene

Wechsler-Reya, R., Sakamuro, D., Zhang, J., Duhadaway, J., & Prendergast, G. C. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.50.31453 · Cited by 142 · see citing works

A unique pathway for sustained neurotrophin signaling through an ankyrin‐rich membrane‐spanning protein

Arévalo, J. C., Yano, H., Teng, K. K., & Chao, M. V. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600253 · Cited by 139 · see citing works

The GIT Family of Proteins Forms Multimers and Associates with the Presynaptic Cytomatrix Protein Piccolo

Kim, S.-H., Ko, J., Shin, H., Lee, J.-R., Lim, C., Han, J., Altrock, W. D., Garner, C. C., Gundelfinger, E. D., Premont, R. T., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m212287200 · Cited by 139 · see citing works

Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing

Baek, D., & Green, P. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506139102 · Cited by 138 · see citing works

Expression ofreelin, the gene responsible for the reeler mutation, in embryonic development and adulthood in the mouse

Ikeda, Y., & Terashima, T. (1997) · Developmental Dynamics · doi:10.1002/(sici)1097-0177(199710)210:2 · Cited by 138 · see citing works

The GIT Family of ADP-ribosylation Factor GTPase-activating Proteins

Premont, R. T., Claing, A., Vitale, N., Perry, S. J., & Lefkowitz, R. J. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.29.22373 · Cited by 136 · see citing works

Spongiform Degeneration in mahoganoid Mutant Mice

He, L., Lu, X., Jolly, A. F., Eldridge, A. G., Watson, S. J., Jackson, P. K., Barsh, G. S., & Gunn, T. M. (2003) · Science · doi:10.1126/science.1079694 · Cited by 135 · see citing works

Molecular Characterization of abLIM, a Novel Actin-binding and Double Zinc Finger Protein

Roof, D. J., Hayes, A., Adamian, M., Chishti, A. H., & Li, T. (1997) · The Journal of Cell Biology · doi:10.1083/jcb.138.3.575 · Cited by 131 · see citing works

Cannabinoid Receptor-induced Neurite Outgrowth Is Mediated by Rap1 Activation through Gαo/i-triggered Proteasomal Degradation of Rap1GAPII

Jordan, J. D., He, J. C., Eungdamrong, N. J., Gomes, I., Ali, W., Nguyen, T., Bivona, T. G., Philips, M. R., Devi, L. A., & Iyengar, R. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m411521200 · Cited by 130 · see citing works

The molecular machinery of synaptic vesicle exocytosis

Li, L., & Chin, L. (2003) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-003-2240-7 · Cited by 126 · see citing works

Proteomic Analysis of β1-Adrenergic Receptor Interactions with PDZ Scaffold Proteins

He, J., Bellini, M., Inuzuka, H., Xu, J., Xiong, Y., Yang, X., Castleberry, A. M., & Hall, R. A. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m509503200 · Cited by 126 · see citing works

Molecular Cloning of a Novel Potassium-dependent Sodium-Calcium Exchanger from Rat Brain

Tsoi, M., Rhee, K.-H., Bungard, D., Li, X., Lee, S.-L., Auer, R. N., & Lytton, J. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.7.4155 · Cited by 124 · see citing works

Expression of Meis and Pbx genes and their protein products in the developing telencephalon: implications for regional differentiation

Toresson, H., Parmar, M., & Campbell, K. (2000) · Mechanisms of Development · doi:10.1016/s0925-4773(00)00324-5 · Cited by 124 · see citing works

A Structure-based Model of the c-Myc/Bin1 Protein Interaction Shows Alternative Splicing of Bin1 and c-Myc Phosphorylation are Key Binding Determinants

Pineda‐Lucena, A., Ho, C. S. W., Mao, D. Y. L., Sheng, Y., Laister, R. C., Muhandiram, R., Lü, Y., Seet, B. T., Katz, S., Szyperski, T., et al. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.05.046 · Cited by 124 · see citing works

NIBP, a Novel NIK and IKKβ-binding Protein That Enhances NF-κB Activation

Hu, W.-H., Pendergast, J. S., Mo, X.-M., Brambilla, R., Bracchi-Ricard, V. C., Li, F., Walters, W. M., Blits, B., He, L., Schaal, S. M., et al. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m501670200 · Cited by 122 · see citing works

The Mechanism for Regulation of the F-actin Binding Activity of IQGAP1 by Calcium/Calmodulin

Mateer, S. C., McDaniel, A. E., Nicolas, V., Habermacher, G. M., Lin, M.-J., Cromer, D. A., King, M. E., & Bloom, G. S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m109535200 · Cited by 119 · see citing works

Alternative splicing modulates the frequency‐dependent response of CaMKII to Ca2+ oscillations

Bayer, K. U., Koninck, P. D., & Schulman, H. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf360 · Cited by 112 · see citing works

Deficient long‐term synaptic depression in the rostral cerebellum correlated with impaired motor learning in phospholipase C β4 mutant mice

Miyata, M., Kim, H., Hashimoto, K., Lee, T., Cho, S. Y., Jiang, H., Wu, Y., Jun, K., Wu, D., Kano, M., et al. (2001) · European Journal of Neuroscience · doi:10.1046/j.0953-816x.2001.01570.x · Cited by 111 · see citing works

Molecular cloning of the cDNA for stimulatory GDP/GTP exchange protein for smg p21s (ras p21-like small GTP-binding proteins) and characterization of stimulatory GDP/GTP exchange protein.

Kaibuchi, K., Mizuno, T., Fujioka, H., Yamamoto, T. S., Kishi, K., Fukumoto, Y., Hori, Y., & Takai, Y. (1991) · Molecular and Cellular Biology · doi:10.1128/mcb.11.5.2873 · Cited by 110 · see citing works

CPG2

Cottrell, J. R., Borók, E., Horváth, T. L., & Nedivi, E. (2004) · Neuron · doi:10.1016/j.neuron.2004.10.025 · Cited by 108 · see citing works

Identification and Characterization of RA-GEF-2, a Rap Guanine Nucleotide Exchange Factor That Serves as a Downstream Target of M-Ras

Gao, X., Satoh, T., Liao, Y., Song, C., Hu, C.-D., Kariya, K.-I., & Kataoka, T. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m105760200 · Cited by 106 · see citing works

Interactions between Chip and the Achaete/Scute–Daughterless Heterodimers Are Required for Pannier-Driven Proneural Patterning

Ramain, P., Khechumian, R., Khetchoumian, K., Arbogast, N., Ackermann, C., & Heitzler, P. (2000) · Molecular Cell · doi:10.1016/s1097-2765(05)00079-1 · Cited by 104 · see citing works

p38 Mitogen-Activated Protein Kinase

Kerkelä, R., & Force, T. L. (2006) · Journal of the American College of Cardiology · doi:10.1016/j.jacc.2006.05.005 · Cited by 104 · see citing works

The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons

Minovitsky, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki210 · Cited by 103 · see citing works

Loss of Ca2+/Calmodulin Kinase Kinase β Affects the Formation of Some, But Not All, Types of Hippocampus-Dependent Long-Term Memory

Peters, M., Mizuno, K., Ris, L., Angelo, M., Godaux, E., & Giese, K.-P. (2003) · Journal of Neuroscience · doi:10.1523/jneurosci.23-30-09752.2003 · Cited by 102 · see citing works

Loss of mitogen-activated protein kinase kinase kinase 4 (MEKK4) results in enhanced apoptosis and defective neural tube development

Chi, H., Sarkisian, M. R., RAKIC, P. T., & Flavell, R. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500026102 · Cited by 102 · see citing works

The Expression Patterns of Guidance Receptors, DCC and Neogenin, Are Spatially and Temporally Distinct throughout Mouse Embryogenesis

Gad, J. M., Keeling, S. L., Wilks, A. F., Tan, S., & Cooper, H. M. (1997) · Developmental Biology · doi:10.1006/dbio.1997.8756 · Cited by 101 · see citing works

Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data

Le, K., Mitsouras, K., Roy, M., Wang, Q., Xu, Q., Nelson, S. F., & Lee, C. J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh173 · Cited by 100 · see citing works

Intersectin Regulates Fission and Internalization of Caveolae in Endothelial Cells

Predescu, S. A., Predescu, D. N., Timblin, B. K., Stan, R. V., & Malik, A. B. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-01-0041 · Cited by 100 · see citing works

Synaptogyrins Regulate Ca2+-dependent Exocytosis in PC12 Cells*

Sugita, S., Janz, R., & Südhof, T. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.27.18893 · Cited by 99 · see citing works

MAGI-1: A Widely Expressed, Alternatively Spliced Tight Junction Protein

Laura, R. P., Ross, S., Koeppen, H., & Lasky, L. A. (2002) · Experimental Cell Research · doi:10.1006/excr.2002.5475 · Cited by 98 · see citing works

Deciphering the splicing code

Barash, Y., Calarco, J. A., Gao, W., Pan, Q., Wang, X., Ofer Shai, A., Blencowe, B. J., & Frey, B. J. (2010) · Nature · doi:10.1038/nature09000 · Cited by 891 · see citing works

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

Ule, J., & Blencowe, B. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.017 · Cited by 780 · see citing works

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 760 · see citing works

Functional consequences of developmentally regulated alternative splicing

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

A single-molecule long-read survey of the human transcriptome

Sharon, D., Tilgner, H., Grubert, F., & Snyder, M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2705 · Cited by 701 · see citing works

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

Irimia, M., Weatheritt, R. J., Ellis, J. D., Parikshak, N. N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O’Hanlon, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.035 · Cited by 693 · see citing works

A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart

Kalsotra, A., Xiao, X., Ward, A. J., Castle, J. C., Johnson, J. M., Burge, C. B., & Cooper, T. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809045105 · Cited by 508 · see citing works

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 · see citing works

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoformsPreprint

Tapial, J., Ha, K., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Márquez, Y., et al. (2017) · Genome Research · doi:10.1101/gr.220962.117 · Cited by 427 · see citing works

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

Gupta, I., Collier, P. G., Haase, B., Mahfouz, A., Joglekar, A., Floyd, T., Koopmans, F., Barres, B., Smit, A. B., Sloan, S. A., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4259 · Cited by 343 · see citing works

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

Castle, J. C., Zhang, C., Shah, J. K., Kulkarni, A., Kalsotra, A., Cooper, T. A., & Johnson, J. M. (2008) · Nature Genetics · doi:10.1038/ng.264 · Cited by 319 · see citing works

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2

Zhang, C., Zhang, Z., Castle, J., Sun, S., Johnson, J., Krainer, A. R., & Zhang, M. Q. (2008) · Genes &amp; Development · doi:10.1101/gad.1703108 · Cited by 300 · see citing works

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

Joglekar, A., Prjibelski, A., Mahfouz, A., Collier, P., Lin, S., Schlusche, A. K., Marrocco, J., Williams, S. R., Haase, B., Hayes, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20343-5 · Cited by 229 · see citing works

Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein

Calarco, J. A., Superina, S., O'Hanlon, D., Gabut, M., Raj, B., Pan, Q., Skalska, U., Clarke, L., Gelinas, D., van der Kooy, D., et al. (2009) · Cell · doi:10.1016/j.cell.2009.06.012 · Cited by 225 · see citing works

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

Bottomly, D., Walter, N. A. R., Hunter, J. E., Darakjian, P., Kawane, S., Buck, K. J., Searles, R. P., Mooney, M. A., McWeeney, S. K., & HITZEMANN, R. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017820 · Cited by 225 · see citing works

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

Tilgner, H., Jahanbani, F., Blauwkamp, T., Moshrefi, A., Jaeger, E., Chen, F., Harel, I., Bustamante, C. D., Rasmussen, M., & Snyder, M. P. (2015) · Nature Biotechnology · doi:10.1038/nbt.3242 · Cited by 223 · see citing works

Alternative splicing: current perspectives

Kim, E., Goren, A., & Ast, G. (2007) · BioEssays · doi:10.1002/bies.20692 · Cited by 218 · see citing works

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

Blencowe, B. J., Ahmad, S., & Lee, L. J. (2009) · Genes &amp; Development · doi:10.1101/gad.1788009 · Cited by 168 · see citing works

Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development

Giudice, J., Xia, Z., Wang, E. T., Scavuzzo, M. A., Ward, A. J., Kalsotra, A., Wang, W., Wehrens, X. H. T., Burge, C. B., Li, W., et al. (2014) · Nature Communications · doi:10.1038/ncomms4603 · Cited by 161 · see citing works

Global analysis of alternative splicing differences between humans and chimpanzeesPreprint

Calarco, J. A., Xing, Y., Cáceres, M., Calarco, J. P., Xiao, X. G., Pan, Q., Lee, C. J., Preuss, T. M., & Blencowe, B. J. (2007) · Genes & Development · doi:10.1101/gad.1606907 · Cited by 158 · see citing works

Multiple and Specific mRNA Processing Targets for the Major Human hnRNP Proteins

Venables, J. P., Koh, C., Froehlich, U., Lapointe, E., Couture, S., Inkel, L., Bramard, A., Paquet, É. R., Watier, V., Durand, M., et al. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00726-08 · Cited by 155 · see citing works

Genome-wide Analysis of Alternative Pre-mRNA Splicing

Ben-Dov, C., Hartmann, B., Lundgren, J., & Valcárcel, J. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.r700033200 · Cited by 151 · see citing works

Alternative splicing: global insights

Hallegger, M., Llorian, M., & Smith, C. W. J. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07521.x · Cited by 143 · see citing works

Splicing factor and exon profiling across human tissues

de la Grange, P., Gratadou, L., Delord, M., Dutertre, M., & Auboeuf, D. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq008 · Cited by 127 · see citing works

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 · see citing works

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 97 · see citing works

A systematic analysis of intronic sequences downstream of 5′ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulationPreprint

Aznarez, I., Barash, Y., Ofer Shai, A., He, D., Zielenski, J., Tsui, L., Parkinson, J., Frey, B. J., Rommens, J. M., & Blencowe, B. J. (2008) · Genome Research · doi:10.1101/gr.073155.107 · Cited by 94 · see citing works

Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression

Ferrarese, R., Harsh, G. R., Yadav, A. K., Bug, E., Maticzka, D., Reichardt, W., Dombrowski, S. M., Miller, T. E., Masilamani, A. P., Dai, F., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci68836 · Cited by 92 · see citing works

Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation

Schor, I. E., Fiszbein, A., Petrillo, E., & Kornblihtt, A. R. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.167 · Cited by 90 · see citing works

The splicing landscape is globally reprogrammed during male meiosis

Schmid, R., Grellscheid, S. N., Ehrmann, I. E., Dalgliesh, C., Danilenko, M., Paronetto, M. P., Pedrotti, S., Grellscheid, D., Dixon, R. J., Sette, C., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt811 · Cited by 89 · see citing works

Global analysis of mRNA splicing

Moore, M. J., & Silver, P. A. (2007) · RNA · doi:10.1261/rna.868008 · Cited by 79 · see citing works

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 · see citing works

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

Tilgner, H., Jahanbani, F., Gupta, I., Collier, P., Wei, E., Rasmussen, M., & Snyder, M. (2018) · Genome Research · doi:10.1101/gr.230516.117 · Cited by 71 · see citing works

Applications of deep learning in understanding gene regulation

Li, Z., Gao, E., Zhou, J., Han, W., Xu, X., & Gao, X. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2022.100384 · Cited by 68 · see citing works

Multiple splice defects in ABCA1cause low HDL-C in a family with Hypoalphalipoproteinemia and premature coronary disease

Rhyne, J., Mantaring, M. M., GARDNER, D. F., & Miller, M. J. (2009) · BMC Medical Genetics · doi:10.1186/1471-2350-10-1 · Cited by 67 · see citing works

Regulation of mRNA splicing by MeCP2 via epigenetic modifications in the brain

Cheng, T., Chen, J., Wan, H., Tang, B., Tian, W., Liao, L., & Qiu, Z. (2017) · Scientific Reports · doi:10.1038/srep42790 · Cited by 62 · see citing works

Quantitative regulation of alternative splicing in evolution and development

Irimia, M., Rukov, J. L., Roy, S. W., Vinther, J., & García‐Fernàndez, J. (2009) · BioEssays · doi:10.1002/bies.080092 · Cited by 61 · see citing works

Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis

Yamamoto, M. L., Clark, T. A., Gee, S. L., Kang, J.-A., Schweitzer, A. C., Wickrema, A., & Conboy, J. G. (2009) · Blood · doi:10.1182/blood-2008-05-160325 · Cited by 59 · see citing works

MECHANISMS IN ENDOCRINOLOGY: Alternative splicing: the new frontier in diabetes research

Juan‐Mateu, J., Villate, O., & Eizirik, D. L. (2016) · European Journal of Endocrinology · doi:10.1530/eje-15-0916 · Cited by 58 · see citing works

Getting the Entire Message: Progress in Isoform Sequencing

Hardwick, S. A., Joglekar, A., Flicek, P., Frankish, A., & Tilgner, H. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00709 · Cited by 56 · see citing works

Variants Affecting Exon Skipping Contribute to Complex Traits

Lee, Y., Gamazon, E. R., Rebman, E., Lee, Y., Lee, S., Dolan, M. E., Cox, N. J., & Lussier, Y. A. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002998 · Cited by 55 · see citing works

Triple-Stage Mass Spectrometry Unravels the Heterogeneity of an Endogenous Protein Complex

Ben-Nissan, G., Belov, M. E., Morgenstern, D., Levin, Y., Dym, O., Arkind, G., Lipson, C., Makarov, A. A., & Sharon, M. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b00518 · Cited by 54 · see citing works

RBFOX2 alters splicing outcome in distinct binding modes with multiple protein partners

Zhou, D., Couture, S., Scott, M. S., & Elela, S. A. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab595 · Cited by 51 · see citing works

Neuronal activity-regulated alternative mRNA splicing

Hermey, G., Blüthgen, N., & Kuhl, D. (2017) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2017.06.002 · Cited by 50 · see citing works

Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals

Torres-Méndez, A., Pop, S., Bonnal, S., Almudí, I., Avola, A., Roberts, R. J. V., Paolantoni, C., Alcaina‐Caro, A., Anduaga, A. M., Haussmann, I. U., et al. (2022) · Science Advances · doi:10.1126/sciadv.abk0445 · Cited by 49 · see citing works

Isoform switching of steroid receptor co-activator-1 attenuates glucocorticoid-induced anxiogenic amygdala CRH expression

Zalachoras, I., Verhoeve, S. L., Toonen, L. J. A., van Weert, L. T. C. M., van Vlodrop, A. M., Mol, I., Meelis, W., de Kloet, E. R., & Meijer, O. C. (2016) · Molecular Psychiatry · doi:10.1038/mp.2016.16 · Cited by 40 · see citing works

TMEM16A alternative splicing coordination in breast cancer

Ubby, I., Bussani, E., Colonna, A., Stacul, G., Locatelli, M., Scudieri, P., Galietta, L. J. V., & Pagani, F. (2013) · Molecular Cancer · doi:10.1186/1476-4598-12-75 · Cited by 39 · see citing works

Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor<i>Nova1</i>

Irimia, M., Denuc, A., Ferran, J. L., Pernaute, B., Puelles, L., Roy, S. W., Garcia-Fernàndez, J., & Marfany, G. (2012) · RNA Biology · doi:10.4161/rna.9.1.18387 · Cited by 38 · see citing works

Genome-wide analysis of alternative splicing during human heart development

Wang, H., Chen, Y., Li, X., Chen, G., Zhong, L., Chen, G., Liao, Y., Liao, W., & Bin, J. (2016) · Scientific Reports · doi:10.1038/srep35520 · Cited by 35 · see citing works

mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance

Hoen, P. A. C. ’., Hirsch, M., de Meijer, E. J., de Menezes, R. X., van Ommen, G. J., & den Dunnen, J. T. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq790 · Cited by 34 · see citing works

Downstream intronic splicing enhancers

Venables, J. P. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.08.012 · Cited by 33 · see citing works

Quantitative analysis of 5HT2C receptor RNA editing patterns in psychiatric disorders

O’Neil, R. T., & Emeson, R. B. (2011) · Neurobiology of Disease · doi:10.1016/j.nbd.2011.08.026 · Cited by 33 · see citing works

Repeat-associated RNA structure and aberrant splicing

Hale, M. A., Johnson, N. E., & Berglund, J. A. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.07.006 · Cited by 33 · see citing works

Technologies for the Global Discovery and Analysis of Alternative Splicing

Calarco, J. A., Saltzman, A. L., Ip, J. Y. Y., & Blencowe, B. J. (2007) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-77374-2_5 · Cited by 33 · see citing works

Assessing long-distance RNA sequence connectivity via RNA-templated DNA–DNA ligation

Roy, C. K., Olson, S., Graveley, B. R., Zamore, P. D., & Moore, M. J. (2015) · eLife · doi:10.7554/elife.03700 · Cited by 32 · see citing works

Exposing the subunit diversity within protein complexes: A mass spectrometry approach

Rozen, S., Tieri, A., Ridner, G., Stark, A.-K., Schmaler, T., Ben‐Nissan, G., Dubiel, W., & Sharon, M. (2013) · Methods · doi:10.1016/j.ymeth.2012.12.013 · Cited by 31 · see citing works

Characterization of splice variants of the genes encoding human mitochondrial HMG-CoA lyase and HMG-CoA synthase, the main enzymes of the ketogenesis pathway

Puisac, B., Ramos, M., Arnedo, M., Menao, S., Gil‐Rodríguez, M. C., Teresa‐Rodrigo, M. E., Pié, Á., Karam, J. C. D., Wesselink, J., Gimenez-Lopez, I., et al. (2011) · Molecular Biology Reports · doi:10.1007/s11033-011-1270-8 · Cited by 31 · see citing works

Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegansPreprint

Koterniak, B., Pilaka, P. P., Gracida, X., Schneider, L.-M., Pritišanac, I., Zhang, Y., & Calarco, J. A. (2020) · Genome Research · doi:10.1101/gr.267328.120 · Cited by 31 · see citing works

LSCplus: a fast solution for improving long read accuracy by short read alignment

Hu, R., Sun, G., & Sun, X. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1316-y · Cited by 28 · see citing works

The aberrant splicing of BAF45d links splicing regulation and transcription in glioblastoma

Aldave, G., González-Huarriz, M., Rubio, Á., Romero, J. P., Ravi, D. G., Miñana, B., Cuadrado‐Tejedor, M., García‐Osta, A., Verhaak, R. G. W., Xipell, E., et al. (2018) · Neuro-Oncology · doi:10.1093/neuonc/noy007 · Cited by 27 · see citing works

Efficient in Vivo Manipulation of Alternative Pre-mRNA Splicing Events Using Antisense Morpholinos in Mice

Parra, M., Gee, S. L., Mohandas, N., & Conboy, J. G. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.158154 · Cited by 25 · see citing works

Antisense-Mediated RNA Targeting: Versatile and Expedient Genetic Manipulation in the Brain

Zalachoras, I., Evers, M. M., van Roon-Mom, W. M. C., Aartsma-Rus, A. M., & Meijer, O. C. (2011) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2011.00010 · Cited by 24 · see citing works

Model-based detection of alternative splicing signals

Barash, Y., Blencowe, B. J., & Frey, B. J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq200 · Cited by 22 · see citing works

From words to complete phrases: insight into single-cell isoforms using short and long reads

Joglekar, A., Foord, C., Jarroux, J., Pollard, S., & Tilgner, H. (2023) · Transcription · doi:10.1080/21541264.2023.2213514 · Cited by 20 · see citing works

Systems analysis of alternative splicing and its regulation

Xiao, X. G., & Lee, J. (2010) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.84 · Cited by 20 · see citing works

Role of thePreprint

Artokca, I. (2015) · SSRN Electronic Journal · Cited by 20 · see citing works

The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation

Mantica, F., & Irimia, M. (2022) · Annual Review of Genetics · doi:10.1146/annurev-genet-071719-020653 · Cited by 19 · see citing works

Long noncoding RNA PM maintains cerebellar synaptic integrity and Cbln1 activation via Pax6/Mll1-mediated H3K4me3

Jin, Y., Zhang, B., Lu, J., Song, Y., Wang, W., Zhang, W., Shao, F., Gong, M., Wang, M., Liang, X., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001297 · Cited by 17 · see citing works

Cell-Specific RNA Binding Protein Rbfox2 Regulates Ca_V2.2 mRNA Exon Composition and Ca_V2.2 Current Size

Allen, S. E., Toro, C. P., Andrade, A., López-Soto, E. J., Denome, S., & Lipscombe, D. (2017) · eneuro · doi:10.1523/eneuro.0332-16.2017 · Cited by 17 · see citing works

Comparative transcriptome profiles of Schistosoma japonicum larval stages: Implications for parasite biology and host invasion

Cheng, S., Zhu, B., Luo, F., Lin, X., Sun, C., You, Y., Yi, C., Xu, B., Wang, J., Lü, Y., et al. (2022) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0009889 · Cited by 16 · see citing works

An exon-centric perspective1Canadian Society of Molecular Biosciences (CSMB) Senior Investigator Award

Blencowe, B. J. (2012) · Biochemistry and Cell Biology · doi:10.1139/o2012-019 · Cited by 15 · see citing works

Novel Kidins220/ARMS Splice Isoforms: Potential Specific Regulators of Neuronal and Cardiovascular Development

Schmieg, N., Thomas, C., Yabe, A., Lynch, D. S., Iglesias, T., Chakravarty, P., & Schiavo, G. (2015) · PLoS ONE · doi:10.1371/journal.pone.0129944 · Cited by 15 · see citing works

Antisense-mediated isoform switching of steroid receptor coactivator-1 in the central nucleus of the amygdala of the mouse brain

Zalachoras, I., Grootaers, G., van Weert, L. T. C. M., Aubert, Y., de Kreij, S. R., Datson, N. A., van Roon‐Mom, W., Aartsma-Rus, A. M., & Meijer, O. C. (2013) · BMC Neuroscience · doi:10.1186/1471-2202-14-5 · Cited by 14 · see citing works

Regulation of Tissue-Specific Alternative Splicing: C. elegans as a Model System

Gracida, X., Norris, A. D., & Calarco, J. A. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-29073-7_10 · Cited by 14 · see citing works

Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods

Alfonso-Gonzalez, C., & Hilgers, V. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00895-4 · Cited by 13 · see citing works

Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state

Hu, W., Foord, C., Hsu, J., Fan, L., Corley, M. J., Lanjewar, S. N., Xu, S., Belchikov, N., He, Y., Pang, A. P. S., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02734-5 · Cited by 14 · see citing works

Coexpression and Cosplicing Network Approaches for the Study of Mammalian Brain Transcriptomes

Iancu, O. D., Colville, A. M., Darakjian, P., & HITZEMANN, R. J. (2014) · International review of neurobiology · doi:10.1016/b978-0-12-801105-8.00004-7 · Cited by 12 · see citing works

Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States

Ciampi, L., Serrano, L. G., & Irimia, M. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00020-1 · Cited by 10 · see citing works

The Challenge to Search for New Nervous System Disease Biomarker Candidates: the Opportunity to Use the Proteogenomics Approach

Nery, T. G. M., Silva, E., Tavares, R., & Passetti, F. (2018) · Journal of Molecular Neuroscience · doi:10.1007/s12031-018-1220-1 · Cited by 7 · see citing works

Deep learning for regulatory genomics: a survey of models, challenges, and applications

Ismail, F. N., Sengupta, A., & Amarasoma, S. (2025) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf271 · Cited by 7 · see citing works

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse

Peng, T., Xue, C., Bi, J., Li, T., Wang, X., Zhang, X., & Li, Y. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-191 · Cited by 7 · see citing works

How do RNA sequence, DNA sequence, and chromatin properties regulate splicing?

Ringrose, L. (2010) · F1000 Biology Reports · doi:10.3410/b2-74 · Cited by 7 · see citing works

Playing inside the genes

Schor, I. E., & Kornblihtt, A. R. (2009) · Communicative & Integrative Biology · doi:10.4161/cib.2.4.8550 · Cited by 7 · see citing works

Statistical and Computational Studies on Alternative Splicing

Chen, L. (2011) · Springer eBooks · doi:10.1007/978-3-642-16345-6_2 · Cited by 6 · see citing works

Interspliced transcription chimeras: Neglected pathological mechanism infiltrating gene accession queries?

Tolvanen, M. E. E., Ojala, P. J., Törönen, P., Anderson, H., Partanen, J., & Turpeinen, H. (2008) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2008.11.002 · Cited by 4 · see citing works

Splicing Code Modeling

Barash, Y., & Vaquero-Garcia, J. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-1-4939-1221-6_13 · Cited by 3 · see citing works

Alternative Splice Site Selection

Coelho, M. B., & Smith, C. W. J. (2012) · Wiley eBooks · doi:10.1002/9783527636778.ch8 · Cited by 2 · see citing works

Machine learning in computational biology: models of alternative splicing

Ofer Shai, A. (2009) · TSpace (University of Toronto) · Cited by 2 · see citing works

DNA Chip Analysis in Genome Discovery

Nazar, R. N., & Robb, J. (2011) · Wiley eBooks · doi:10.1002/9781119977438.ch2 · Cited by 2 · see citing works

Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates

Zhao, S., Kim, J., & Heber, S. (2009) · Lecture notes in computer science · doi:10.1007/978-3-642-01551-9_27 · Cited by 2 · see citing works

Integrated detection and quantification of aberrant transcripts with novel splicing eventsPreprint

Agrawal, I., Lim, Y. S., Sanford, E., Ho, W. Y., Ling, S., & Tucker‐Kellogg, G. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.02.635191 · Cited by 2 · see citing works

Alternative microexon splicing code for a four-amino acid peptide of PTPRD governs behavioral development

Imai, A., Izumi, H., Ito, N., Ogiso, H., Kitajima, Y., Kawase, S., Sendo, M., Azechi, K., Tabata, T., Koshidaka, Y., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2515310123 · Cited by 1 · see citing works

Multimodal bioinformatic analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles

Shalev, I., Somekh, J., & Eran, A. (2021) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2021-108193 · Cited by 1 · see citing works

Nitric oxide drives proteomic diversity through alternative splicing

Schindler, J. C., Seth, P., Hausladen, A., Chan, E. R., Yang, J., Qin, J., Qian, Z., Seth, D., Lundberg, K. C., Luna, J. M., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.04.024 · Cited by 1 · see citing works

Pulmonary remodeling in asthma

Lieberman, P. (2010) · F1000 Medicine Reports · doi:10.3410/m2-74 · Cited by 1 · see citing works

The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites

Glauser, D. A. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-364 · Cited by 1 · see citing works

The Merit of Alternative Messenger RNA Splicing as a New Mine for the Next Generation Ovarian Cancer Biomarkers

Brosseau, J., & Elela, S. A. (2013) · InTech eBooks · doi:10.5772/53976 · Cited by 1 · see citing works

Linear Programming and Integer Linear Programming in Bioinformatics

Andreotti, S. (2015) · Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver · doi:10.17169/refubium-17199 · Cited by 1 · see citing works

An in silico assessment of alternatively spliced isoforms in the mouse brain using RNA-Seq

Bottomly, D. (2009) · doi:10.6083/m4wd3xjh · Cited by 1 · see citing works

Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanismPreprint

Sidorov, S., Pal, K., Lenhard, B., & Luscombe, N. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.28.625692 · Cited by 1 · see citing works

Computational analyses of alternative splicing microarray data

Fagnani, M. M. (2008) · TSpace (University of Toronto)

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 167 · see citing works

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 · see citing works

Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegansPreprint

Koterniak, B., Pilaka, P. P., Gracida, X., Schneider, L.-M., Pritišanac, I., Zhang, Y., & Calarco, J. A. (2020) · Genome Research · doi:10.1101/gr.267328.120 · Cited by 31 · see citing works

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform

Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A. L., Mohammad, N., Babak, T., Siu, H., Hughes, T. R., Morris, Q. D., et al. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.12.004 · Cited by 323 · see citing works