Building Robust Transcriptomes with Master Splicing Factors

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 · see citing works

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · see citing works

Super-enhancers in the control of cell identity and disease

Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662 · see citing works

Network motifs: theory and experimental approaches

Alon, U. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2102 · Cited by 3,279 · see citing works

An Introduction to Systems Biology: Design Principles of Biological Circuits

Alon, U. (2006) · doi:10.1201/9781420011432 · Cited by 2,825 · see citing works

Biological robustness

Kitano, H. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1471 · Cited by 2,278 · see citing works

The Strategy of the Genes

Waddington, C. H. (2014) · doi:10.4324/9781315765471 · Cited by 2,153 · see citing works

Frequent pathway mutations of splicing machinery in myelodysplasia

Yoshida, K., Sanada, M., Shiraishi, Y., Nowak, D., Nagata, Y., Yamamoto, R., Sato, Y., Sato-Otsubo, A., Kon, A., Nagasaki, M., et al. (2011) · Nature · doi:10.1038/nature10496 · Cited by 2,029 · see citing works

Noise in eukaryotic gene expression

Blake, W. J., Kærn, M., Cantor, C. R., & Collins, J. J. (2003) · Nature · doi:10.1038/nature01546 · Cited by 1,636 · see citing works

Engineering stability in gene networks by autoregulation

Becskei, A., & Serrano, L. G. (2000) · Nature · doi:10.1038/35014651 · Cited by 1,493 · see citing works

The MicroRNA miR-124 Promotes Neuronal Differentiation by Triggering Brain-Specific Alternative Pre-mRNA Splicing

Makeyev, E. V., Zhang, J., Carrasco, M. A., & Maniatis, T. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.07.015 · Cited by 1,395 · see citing works

Control of the Embryonic Stem Cell State

Young, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.01.032 · Cited by 1,189 · see citing works

RNA and Disease

Cooper, T. A., Wan, L., & Dreyfuss, G. (2009) · Cell · doi:10.1016/j.cell.2009.02.011 · Cited by 1,160 · see citing works

The SR protein family of splicing factors: master regulators of gene expression

Long, J. C., & Cáceres, J. F. (2008) · Biochemical Journal · doi:10.1042/bj20081501 · Cited by 1,125 · see citing works

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

Lewis, B. P., Green, R. E., & Brenner, S. E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0136770100 · Cited by 1,069 · see citing works

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Barbosa-Morais, N. L., Irimia, M., Pan, Q., Xiong, H. Y., Gueroussov, S., Lee, L. J., Slobodeniuc, V., Kutter, C., Watt, S., Çolak, R., et al. (2012) · Science · doi:10.1126/science.1230612 · Cited by 1,063 · see citing works

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

Merkin, J., Russell, C., Chen, P., & Burge, C. B. (2012) · Science · doi:10.1126/science.1228186 · Cited by 972 · 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

Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise

Mendell, J. T., Sharifi, N., Meyers, J. L., Martínez-Murillo, F., & Dietz, H. C. (2004) · Nature Genetics · doi:10.1038/ng1429 · Cited by 880 · see citing works

A Protein–Protein Interaction Network for Human Inherited Ataxias and Disorders of Purkinje Cell Degeneration

Lim, J., Hao, T., Shaw, C., Patel, A. J., Szabó, G., Rual, J.-F., Fisk, C. J., Li, N., Smolyar, A., Hill, D. E., et al. (2006) · Cell · doi:10.1016/j.cell.2006.03.032 · Cited by 789 · see citing works

Negative Autoregulation Speeds the Response Times of Transcription Networks

Rosenfeld, N., Elowitz, M. B., & Alon, U. S. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00994-4 · Cited by 714 · see citing works

Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion

Becskei, A., Séraphin, B., & Serrano, L. G. (2001) · The EMBO Journal · doi:10.1093/emboj/20.10.2528 · Cited by 687 · see citing works

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

Lareau, L. F., Inada, M., Green, R. E., Wengrod, J., & Brenner, S. E. (2007) · Nature · doi:10.1038/nature05676 · Cited by 685 · see citing works

Escaping the Nuclear Confines: Signal-Dependent Pre-mRNA Splicing in Anucleate Platelets

Denis, M. M., Tolley, N. D., Bunting, M., Schwertz, H., Jiang, H., Lindemann, S., Yost, C. C., Rubner, F. J., Albertine, K. H., Swoboda, K. J., et al. (2005) · Cell · doi:10.1016/j.cell.2005.06.015 · Cited by 652 · see citing works

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 · see citing works

Direct Conversion of Fibroblasts to Neurons by Reprogramming PTB-Regulated MicroRNA Circuits

Xue, Y., Ouyang, K., Huang, J., Zhou, Y., Ouyang, H., Li, H., Wang, G., Wu, Q., Wei, C., Bi, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2012.11.045 · Cited by 562 · see citing works

Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decayPreprint

Ni, J. Z., Grate, L. R., Donohue, J. P., Preston, C. G., Nobida, N., O’Brien, G. S., Shiue, L., Clark, T. A., Blume, J. E., & Ares, M. (2007) · Genes & Development · doi:10.1101/gad.1525507 · Cited by 551 · 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

The Neurobiology of Childhood Spinal Muscular Atrophy

Crawford, T. O., & Pardo, C. A. (1996) · Neurobiology of Disease · doi:10.1006/nbdi.1996.0010 · Cited by 523 · 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

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

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 · see citing works

Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins

Huelga, S. C., Vu, A. Q., Arnold, J. D., Liang, T. Y., Liu, P. P., Yan, B. Y., Donohue, J. P., Shiue, L., Hoon, S., Brenner, S., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.02.001 · Cited by 470 · see citing works

An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype

Shapiro, I. M., Cheng, A. W., Flytzanis, N. C., Balsamo, M., Condeelis, J. S., Oktay, M. H., Burge, C. B., & Gertler, F. B. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002218 · Cited by 452 · see citing works

Increased Steady-State Levels of CUGBP1 in Myotonic Dystrophy 1 Are Due to PKC-Mediated Hyperphosphorylation

Kuyumcu-Martinez, N. M., Wang, G., & Cooper, T. A. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.07.027 · Cited by 445 · see citing works

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

Bhatt, D. M., Pandya‐Jones, A., Tong, A.-J., Barozzi, I., Lissner, M. M., Natoli, G., Black, D. L., & Smale, S. T. (2012) · Cell · doi:10.1016/j.cell.2012.05.043 · Cited by 442 · see citing works

Nova-1 Regulates Neuron-Specific Alternative Splicing and Is Essential for Neuronal Viability

Jensen, K. B., Dredge, B. K., Stefani, G., Zhong, R., Buckanovich, R. J., Okano, H. J., Yang, Y. Y. L., & Darnell, R. B. (2000) · Neuron · doi:10.1016/s0896-6273(00)80900-9 · Cited by 426 · see citing works

Autoregulation of Polypyrimidine Tract Binding Protein by Alternative Splicing Leading to Nonsense-Mediated Decay

Wollerton, M., Gooding, C., Wagner, E. J., García-Blanco, M. A., & Smith, C. W. J. (2004) · Molecular Cell · doi:10.1016/s1097-2765(03)00502-1 · Cited by 409 · see citing works

hnRNP Proteins and Splicing Control

Martínez-Contreras, R. D., Cloutier, P., Shkreta, L., Fisette, J., Revil, T., & Chabot, B. (2007) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-77374-2_8 · Cited by 394 · see citing works

An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming

Gabut, M., Samavarchi‐Tehrani, P., Wang, X., Slobodeniuc, V., O’Hanlon, D., Sung, H., Alvarez, M., Talukder, S., Pan, Q., Mazzoni, E. O., et al. (2011) · Cell · doi:10.1016/j.cell.2011.08.023 · Cited by 368 · see citing works

Structure, function and evolution of sex-determining systems in Dipteran insects

Schütt, C., & Nöthiger, R. (2000) · Development · doi:10.1242/dev.127.4.667 · Cited by 352 · see citing works

A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA

Tian, M., & Maniatis, T. (1993) · Cell · doi:10.1016/0092-8674(93)90298-5 · Cited by 345 · see citing works

Positive autoregulation of Sex-lethal by alternative splicing maintains the female determined state in Drosophila

Bell, L. R., Horabin, J. I., Schedl, P. D., & Cline, T. W. (1991) · Cell · doi:10.1016/0092-8674(91)90157-t · Cited by 344 · see citing works

Cancer-associated regulation of alternative splicing

Venables, J. P., Klinck, R., Koh, C., Gervais-Bird, J., Bramard, A., Inkel, L., Durand, M., Couture, S., Froehlich, U., Lapointe, E., et al. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1608 · Cited by 340 · see citing works

Regulation of mammalian spliceosome assembly by a protein phosphorylation mechanism.

Mermoud, J. E., Cohen, P. T., & Lamond, A. I. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06906.x · Cited by 330 · see citing works

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

Han, H. R., Irimia, M., Ross, P. J., Sung, H., Alipanahi, B., David, L., Golipour, A., Gabut, M., Michael, I. P., Nachman, E. N., et al. (2013) · Nature · doi:10.1038/nature12270 · Cited by 326 · see citing works

Negative autoregulation linearizes the dose–response and suppresses the heterogeneity of gene expression

Nevozhay, D., Adams, R., Murphy, K. F., Josić́, K., & Balázsi, G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809901106 · Cited by 319 · see citing works

Crossregulation and Functional Redundancy between the Splicing Regulator PTB and Its Paralogs nPTB and ROD1

Spellman, R., Llorian, M., & Smith, C. W. J. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.016 · Cited by 313 · 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

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 & Development · doi:10.1101/gad.1703108 · Cited by 300 · see citing works

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

Zhang, C., Frias, M. A., Mele, A., Ruggiu, M., Eom, T., Marney, C. B., Wang, H., Licatalosi, D. D., Fak, J. J., & Darnell, R. B. (2010) · Science · doi:10.1126/science.1191150 · Cited by 294 · see citing works

Sex-specific alternative splicing of RNA from the transformer gene results from sequence-dependent splice site blockage

Sosnowski, B. A., Belote, J. M., & McKeown, M. (1989) · Cell · doi:10.1016/0092-8674(89)90426-1 · Cited by 292 · see citing works

Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes

Lim, K., Ferraris, L., Filloux, M. E., Raphael, B. J., & Fairbrother, W. G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1101135108 · Cited by 285 · see citing works

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

Änkö, M., Müller-McNicoll, M., Brandl, H., Curk, T., Gorup, Č., Henry, I., Ule, J., & Neugebauer, K. M. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r17 · Cited by 278 · see citing works

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 276 · see citing works

Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer.Preprint

Lynch, K. W., & Maniatis, T. (1996) · Genes & Development · doi:10.1101/gad.10.16.2089 · Cited by 238 · see citing works

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulationPreprint

Ip, J. Y. Y., Schmidt, D., Pan, Q., Ramani, A. K., Fraser, A. G., Odom, D. T., & Blencowe, B. J. (2010) · Genome Research · doi:10.1101/gr.111070.110 · Cited by 237 · see citing works

The primary sex determination signal of Drosophila acts at the level of transcription

Keyes, L. N., Cline, T. W., & Schedl, P. D. (1992) · Cell · doi:10.1016/0092-8674(92)90036-c · Cited by 227 · 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

The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia

Yang, Y. Y. L., Yin, G. L., & Darnell, R. B. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.22.13254 · Cited by 219 · see citing works

The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function

Gehman, L. T., Meera, P., Stoilov, P., Shiue, L., O'Brien, J. E., Meisler, M. H., Ares, M., Otis, T. S., & Black, D. L. (2012) · Genes & Development · doi:10.1101/gad.182477.111 · Cited by 213 · see citing works

Regulation of CD45 Alternative Splicing by Heterogeneous Ribonucleoprotein, hnRNPLL

Oberdoerffer, S., Moita, L. F., Neems, D. S., Freitas, R. P., Hacohen, N., & Rao, A. (2008) · Science · doi:10.1126/science.1157610 · Cited by 205 · see citing works

Regulation of alternative splicing by the core spliceosomal machineryPreprint

Saltzman, A. L., Pan, Q., & Blencowe, B. J. (2011) · Genes & Development · doi:10.1101/gad.2004811 · Cited by 204 · see citing works

Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay

Saltzman, A. L., Kim, Y. K., Pan, Q., Fagnani, M. M., Maquat, L. E., & Blencowe, B. J. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00361-08 · Cited by 204 · see citing works

Tissue-specific splicing factor gene expression signatures

Grosso, A. R., Gomes, A. Q., Barbosa‐Morais, N. L., Caldeira, S., Thorne, N., Grech, G., Lindern, M. V., & Carmo‐Fonseca, M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn463 · Cited by 195 · see citing works

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 · see citing works

Sex-specific transcriptional regulation by the male and female doublesex proteins of Drosophila.Preprint

Coschigano, K. T., & Wensink, P. C. (1993) · Genes & Development · doi:10.1101/gad.7.1.42 · Cited by 191 · see citing works

Male‐specific lethal 2, a dosage compensation gene of Drosophila, undergoes sex‐specific regulation and encodes a protein with a RING finger and a metallothionein‐like cysteine cluster.

Zhou, S., Yang, Y., Scott, M. J., Pannuti, A., Fehr, K. C., Eisen, A., Koonin, E. V., Fouts, D. L., Wrightsman, R. A., & Manning, J. E. (1995) · The EMBO Journal · doi:10.1002/j.1460-2075.1995.tb07288.x · Cited by 175 · see citing works

Sex determination in insects: a binary decision based on alternative splicing

Salz, H. K. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.03.001 · Cited by 167 · see citing works

Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor

Ninomiya, K., Kataoka, N., & Hagiwara, M. (2011) · The Journal of Cell Biology · doi:10.1083/jcb.201107093 · Cited by 167 · see citing works

SR proteins escort the U4/U6.U5 tri-snRNP to the spliceosome.

Roscigno, R. F., & García-Blanco, M. A. (1995) · PubMed · Cited by 167 · see citing works

The msl-2 dosage compensation gene of Drosophila encodes a putative DNA-binding protein whose expression is sex specifically regulated by Sex-lethal

Bashaw, G. J., & Baker, B. S. (1995) · Development · doi:10.1242/dev.121.10.3245 · Cited by 165 · 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

An inducible change in Fox-1/A2BP1 splicing modulates the alternative splicing of downstream neuronal target exonsPreprint

Lee, J.-A., Tang, Z., & Black, D. L. (2009) · Genes & Development · doi:10.1101/gad.1837009 · Cited by 158 · see citing works

Common Molecular Pathways Mediate Long-Term Potentiation of Synaptic Excitation and Slow Synaptic Inhibition

Huang, C. S., Shi, S.-H., Ule, J., Ruggiu, M., Barker, L. A., Darnell, R. B., Jan, Y. N., & Jan, L. Y. (2005) · Cell · doi:10.1016/j.cell.2005.07.033 · Cited by 157 · see citing works

Cross-Regulation between an Alternative Splicing Activator and a Transcription Repressor Controls Neurogenesis

Raj, B., O'Hanlon, D., Vessey, J. P., Pan, Q., Ray, D., Buckley, N. J., Miller, F. D., & Blencowe, B. J. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.014 · Cited by 143 · see citing works

Auto- and Cross-Regulation of the hnRNP L Proteins by Alternative Splicing

Rossbach, O., Hung, L.-H., Schreiner, S., Grishina, I., Heiner, M., Hui, J., & Bindereif, A. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01689-08 · Cited by 141 · see citing works

MBNL1 and RBFOX2 cooperate to establish a splicing programme involved in pluripotent stem cell differentiation

Venables, J. P., Lapasset, L., Gadea, G., Fort, P., Klinck, R., Irimia, M., Vignal, E., Thibault, P., Prinos, P., Chabot, B., et al. (2013) · Nature Communications · doi:10.1038/ncomms3480 · Cited by 140 · see citing works

Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

Weischenfeldt, J., Waage, J., Tian, G., Zhao, J., Damgaard, I., Jakobsen, J. S., Kristiansen, K., Krogh, A., Wang, J., & Porse, B. T. (2012) · Genome biology · doi:10.1186/gb-2012-13-5-r35 · Cited by 140 · 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

Large-Scale Discovery of ERK2 Substrates Identifies ERK-Mediated Transcriptional Regulation by ETV3

Carlson, S. M., Chouinard, C. R., Labadorf, A. T., Lam, C. J., Schmelzle, K., Fraenkel, E., & White, F. M. (2011) · Science Signaling · doi:10.1126/scisignal.2002010 · Cited by 137 · see citing works

Rbfox2 controls autoregulation in RNA-binding protein networksPreprint

Jangi, M., Boutz, P. L., Paul, P., & Sharp, P. A. (2014) · Genes & Development · doi:10.1101/gad.235770.113 · Cited by 130 · 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

Autoregulation of Fox protein expression to produce dominant negative splicing factors

Damianov, A., & Black, D. L. (2010) · RNA · doi:10.1261/rna.1838210 · Cited by 120 · see citing works

Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells

Lu, Y., Loh, Y., Li, H., Cesana, M., Ficarro, S. B., Parikh, J. R., Salomonis, N., Toh, C.-X. D., Andreadis, S. T., Luckey, C. J., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.04.002 · Cited by 113 · see citing works

Regulatory Dynamics of Synthetic Gene Networks with Positive Feedback

Maeda, Y. T., & Sano, M. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.03.064 · Cited by 110 · see citing works

FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns

Nakaya, T., Alexiou, P., Maragkakis, M., Chang, A., & Mourelatos, Z. (2013) · RNA · doi:10.1261/rna.037804.112 · Cited by 110 · see citing works

RNA splicing regulates the temporal order of TNF-induced gene expression

Hao, S., & Baltimore, D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309990110 · Cited by 91 · see citing works

A cell-based screen for splicing regulators identifies hnRNP LL as a distinct signal-induced repressor ofCD45variable exon 4

Topp, J. D., Jackson, J., Melton, A. A., & Lynch, K. W. (2008) · RNA · doi:10.1261/rna.1212008 · Cited by 90 · see citing works

DEGRADE, MOVE, REGROUP: signaling control of splicing proteins

Heyd, F., & Lynch, K. W. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.04.003 · Cited by 77 · see citing works

RNA‐binding proteins Rbm38 and Rbm24 regulate myogenic differentiation via p21‐dependent and ‐independent regulatory pathways

Miyamoto, S., Hidaka, K., Jin, D., & Morisaki, T. (2009) · Genes to Cells · doi:10.1111/j.1365-2443.2009.01347.x · Cited by 64 · cited 5× · see citing works

The RNA Binding Protein RBM38 (RNPC1) Regulates Splicing during Late Erythroid Differentiation

Heinicke, L. A., Nabet, B., Shen, S., Jiang, P., van Zalen, S., Cieply, B. W., Russell, J., Xing, Y., & Carstens, R. P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078031 · Cited by 51 · see citing works

RNA‐binding motif protein 24 regulates myogenin expression and promotes myogenic differentiation

Jin, D., Hidaka, K., Shirai, M., & Morisaki, T. (2010) · Genes to Cells · doi:10.1111/j.1365-2443.2010.01446.x · Cited by 50 · see citing works

Rbms3 functions in craniofacial development by posttranscriptionally modulating TGF-β signaling

Jayasena, C. S., & Bronner-Fraser, M. E. (2012) · The Journal of Cell Biology · doi:10.1083/jcb.201204138 · Cited by 46 · see citing works

The RNA-binding protein Seb4/RBM24 is a direct target of MyoD and is required for myogenesis during Xenopus early development

Li, H., Bourdelas, A., Carron, C., & Shi, D. (2010) · Mechanisms of Development · doi:10.1016/j.mod.2010.03.002 · Cited by 42 · see citing works

Sexual Back Talk With Evolutionary Implications: Stimulation of the Drosophila Sex-Determination Gene Sex-lethal by Its Target transformer

Siera, S. G., & Cline, T. W. (2008) · Genetics · doi:10.1534/genetics.108.093898 · Cited by 35 · see citing works

Structural and functional conservation of the Drosophila doublesex splicing enhancer repeat elements.

Hertel, K. J., Lynch, K. W., Hsiao, E. C., Liu, E. H., & Maniatis, T. (1996) · PubMed Central · Cited by 35 · see citing works

Knockdown of Hnrnpa0, a del(5q) gene, alters myeloid cell fate in murine cells through regulation of AU-rich transcripts

Young, D. J., Stoddart, A., Nakitandwe, J., Chen, S.-C., Qian, Z. Y., Downing, J. R., & Beau, M. M. L. (2014) · Haematologica · doi:10.3324/haematol.2013.098657 · Cited by 30 · see citing works

King of hearts: a splicing factor rules cardiac proteins

Linke, W. A., & Bücker, S. (2012) · Nature Medicine · doi:10.1038/nm.2762 · Cited by 20 · see citing works

A Splicing Switch for T Cells

Holmes, N. (2008) · Science · doi:10.1126/science.1162294 · Cited by 4 · 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-Mediated Feedback Control of Transcriptional Condensates

Henninger, J. E., Oksuz, O., Shrinivas, K., Sagi, I., LeRoy, G., Zheng, M., Andrews, J. O., Zamudio, A. V., Lazaris, C., Hannett, N. M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.11.030 · Cited by 563 · see citing works

Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing

Amabile, A., Migliara, A., Capasso, P., Biffi, M., Cittaro, D., Naldini, L., & Lombardo, A. (2016) · Cell · doi:10.1016/j.cell.2016.09.006 · Cited by 516 · see citing works

Alternative‐splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics

Urbanski, L. M., Leclair, N. K., & Anczuków, O. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1476 · Cited by 381 · see citing works

The neurogenetics of alternative splicing

Vuong, C. K., Black, D. L., & Zheng, S. (2016) · Nature Reviews Neuroscience · doi:10.1038/nrn.2016.27 · Cited by 340 · see citing works

Intron retention as a component of regulated gene expression programs

Jacob, A. G., & Smith, C. W. J. (2017) · Human Genetics · doi:10.1007/s00439-017-1791-x · Cited by 323 · see citing works

EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression

Pradella, D., Naro, C., Sette, C., & Ghigna, C. (2017) · Molecular Cancer · doi:10.1186/s12943-016-0579-2 · Cited by 325 · see citing works

Lessons from non-canonical splicing

Sibley, C. R., Blázquez, L., & Ule, J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.46 · Cited by 312 · see citing works

Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome

Calixto, C. P. G., Guo, W., James, A. B., Τzioutziou, N. A., Entizne, J. C., Panter, P. E., Knight, H., Nimmo, H. G., Zhang, R., & Brown, J. W. S. (2018) · The Plant Cell · doi:10.1105/tpc.18.00177 · Cited by 296 · see citing works

Proteomic and interactomic insights into the molecular basis of cell functional diversity

Bludau, I., & Aebersold, R. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0231-2 · Cited by 297 · see citing works

Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo

Shirai, C. L., Ley, J. N., White, B. S., Kim, S., Tibbitts, J., Shao, J., Ndonwi, M., Wadugu, B., Duncavage, E. J., Okeyo-Owuor, T., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.04.008 · Cited by 287 · see citing works

Specificity and nonspecificity in RNA–protein interactions

Jankowsky, E., & Harris, M. E. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4032 · Cited by 277 · see citing works

SR Proteins: Binders, Regulators, and Connectors of RNA

Jeong-Yu, S. (2017) · Molecules and Cells · doi:10.14348/molcells.2017.2319 · Cited by 270 · see citing works

Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

Sebestyén, E., Singh, B., Miñana, B., Pagès, A., Mateo, F., Pujana, M. A., Valcárcel, J., & Eyras, E. (2016) · Genome Research · doi:10.1101/gr.199935.115 · Cited by 276 · see citing works

Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects

Rogalska, M. E., Vivori, C., & Valcárcel, J. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00556-8 · Cited by 269 · see citing works

Alternative splicing and the evolution of phenotypic novelty

Bush, S. J., Chen, L., Tovar-Corona, J. M., & Urrutia, A. O. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0474 · Cited by 193 · see citing works

RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPFPreprint

Huang, H., Zhang, J., Harvey, S. E., Hu, X., & Cheng, C. (2017) · Genes & Development · doi:10.1101/gad.305862.117 · Cited by 185 · see citing works

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

Han, H. R., Braunschweig, U., Gonatopoulos-Pournatzis, T., Weatheritt, R. J., Hirsch, C. L., Ha, K., Radovani, E., Nabeel‐Shah, S., Sterne‐Weiler, T., Wang, J., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.01.011 · Cited by 177 · see citing works

The ribosome-engaged landscape of alternative splicing

Weatheritt, R. J., Sterne-Weiler, T., & Blencowe, B. J. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3317 · Cited by 162 · see citing works

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome

Garrido-Martín, D., Borsari, B., Calvo, M., Reverter, F., & Guigó, R. (2021) · Nature Communications · doi:10.1038/s41467-020-20578-2 · Cited by 140 · see citing works

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

Kanitz, A., Gypas, F., Gruber, A. J., Gruber, A. J., Martin, G., & Zavolan, M. (2015) · Genome biology · doi:10.1186/s13059-015-0702-5 · Cited by 141 · see citing works

Therapeutic potential of targeting microRNA‐10b in established intracranial glioblastoma: first steps toward the clinic

Teplyuk, N., Uhlmann, E. J., Gabriely, G., Volfovsky, N., Wang, Y., Teng, J., Karmali, P., Marcusson, E., Peter, M., Mohan, A., et al. (2016) · EMBO Molecular Medicine · doi:10.15252/emmm.201505495 · Cited by 136 · see citing works

Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness

Nguyen, A., Yoshida, M., Goodarzi, H., & Tavazoie, S. F. (2016) · Nature Communications · doi:10.1038/ncomms11246 · Cited by 136 · see citing works

Untitled work

van den Hoogenhof (2016) · doi:10.1161/circresaha.115.307872 · Cited by 134 · see citing works

Mammalian gene expression variability is explained by underlying cell state

Foreman, R., & Wollman, R. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199146 · Cited by 126 · see citing works

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

Gonatopoulos-Pournatzis, T., Wu, M., Braunschweig, U., Roth, J. F., Han, H. R., Best, A. J., Raj, B., Aregger, M., O’Hanlon, D., Ellis, J. D., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.008 · Cited by 119 · see citing works

The Features and Regulation of Co-transcriptional Splicing in Arabidopsis

Zhu, D., Mao, F., Tian, Y., Lin, X., Gu, L., Gu, H., Qu, L., Wu, Y., & Wu, Z. (2019) · Molecular Plant · doi:10.1016/j.molp.2019.11.004 · Cited by 91 · see citing works

Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state

Yarden Katz, A., Li, F., Lambert, N. J., Sokol, E. S., Tam, W. L., Cheng, A. W., Airoldi, E. M., Lengner, C. J., Gupta, P. B., Yu, Z., et al. (2014) · eLife · doi:10.7554/elife.03915 · Cited by 90 · see citing works

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

Blázquez, L., Emmett, W., Faraway, R., Pineda, J. M. B., Bajew, S., Gohr, A., Haberman, N., Sibley, C. R., Bradley, R. K., Irimia, M., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.09.033 · Cited by 84 · see citing works

Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Wu, L.-S., Cheng, W.-C., Chen, C.-Y., Wu, M.-C., Wang, Y., Tseng, Y.-H., Chuang, T., & Shen, C. ‐. J. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0674-x · Cited by 69 · see citing works

Antisense Oligonucleotides Promote Exon Inclusion and Correct the Common c.-32-13T>G GAA Splicing Variant in Pompe Disease

van der Wal, E., Bergsma, A. J., Pijnenburg, J. M., van der Ploeg, A. T., & Pijnappel, W. W. M. P. (2017) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2017.03.001 · Cited by 69 · see citing works

Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling

Mallory, M. J., Allon, S. J., Qiu, J., Gazzara, M. R., Tapescu, I., Martínez, N. M., Fu, X., & Lynch, K. W. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1423695112 · Cited by 66 · see citing works

RNA Binding Protein Ptbp2 Is Essential for Male Germ Cell Development

Zagore, L. L., Grabinski, S. E., Sweet, T. J., Hannigan, M. M., Sramkoski, R. M., Li, Q., & Licatalosi, D. D. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.00676-15 · Cited by 62 · see citing works

The determinants of alternative RNA splicing in human cells

Ramanouskaya, T. V., & Grinev, V. V. (2017) · Molecular Genetics and Genomics · doi:10.1007/s00438-017-1350-0 · Cited by 66 · see citing works

Not only cancer: the long non-coding RNA MALAT1 affects the repertoire of alternatively spliced transcripts and circular RNAs in multiple sclerosis

Cardamone, G., Paraboschi, E. M., Soldà, G., Cantoni, C., Supino, D., Piccio, L. M., Duga, S., & Asselta, R. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy438 · Cited by 66 · see citing works

GAA Deficiency in Pompe Disease Is Alleviated by Exon Inclusion in iPSC-Derived Skeletal Muscle Cells

van der Wal, E., Bergsma, A. J., van Gestel, T. J. M., Groen, S. L. M. I. ‘., Zaehres, H., Araúzo-Bravo, M. J., Schöler, H. R., van der Ploeg, A. T., & Pijnappel, W. W. M. P. (2017) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2017.03.002 · Cited by 65 · see citing works

Towards understanding pre-mRNA splicing mechanisms and the role of SR proteins

Sahebi, M., Hanafi, M. M., van Wijnen, A. J., Azizi, P., Abiri, R., Ashkani, S., & Taheri, S. (2016) · Gene · doi:10.1016/j.gene.2016.04.057 · Cited by 62 · see citing works

The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

Llorian, M., Gooding, C., Bellora, N., Hallegger, M., Buckroyd, A., Wang, X., Rajgor, D., Kayikci, M., Feltham, J., Ule, J., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw560 · Cited by 58 · 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

A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate

Foley, S. W., Gosai, S. J., Wang, D., Selamoglu, N., Sollitti, A. C., Köster, T., Steffen, A., Lyons, E. H., Daldal, F., Garcia, B. A., et al. (2017) · Developmental Cell · doi:10.1016/j.devcel.2017.03.018 · Cited by 59 · see citing works

Autoregulation of RBM10 and cross-regulation of RBM10/RBM5 via alternative splicing-coupled nonsense-mediated decay

Sun, Y., Bao, Y., Han, W., Song, F., Shen, X., Zhao, J., Zuo, J., Saffen, D. W., Chen, W., Wang, Z., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx508 · Cited by 56 · see citing works

RBM10: Structure, functions, and associated diseases

Inoue, A. (2021) · Gene · doi:10.1016/j.gene.2021.145463 · Cited by 57 · see citing works

Molecular functions and specific roles of circRNAs in the cardiovascular system

Holdt, L. M., Kohlmaier, A., & Teupser, D. (2018) · Non-coding RNA Research · doi:10.1016/j.ncrna.2018.05.002 · Cited by 55 · see citing works

The evolution of posttranscriptional regulation

Schaefke, B., Sun, W., Li, Y., Fang, L., & Chen, W. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1485 · Cited by 53 · see citing works

ALU non-B-DNA conformations, flipons, binary codes and evolution

Herbert, A. G. (2020) · Royal Society Open Science · doi:10.1098/rsos.200222 · Cited by 52 · see citing works

Splicing factor BUD31 promotes ovarian cancer progression through sustaining the expression of anti-apoptotic BCL2L12

Wang, Z., Wang, S., Qin, J., Zhang, X., Lü, G., Liu, H., Guo, H., Wu, L., Shender, V. О., Shao, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34042-w · Cited by 48 · see citing works

αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome

Ji, X., Park, J. W., Bahrami‐Samani, E., Lin, L., Duncan-Lewis, C., Pherribo, G. J., Xing, Y., & Liebhaber, S. A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw088 · Cited by 44 · see citing works

Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers

Nakagaki-Silva, E. E., Gooding, C., Llorian, M., Jacob, A. G., Richards, F., Buckroyd, A., Sinha, S., & Smith, C. W. J. (2019) · eLife · doi:10.7554/elife.46327 · Cited by 42 · see citing works

Aberrant Expression of a Non-muscle RBFOX2 Isoform Triggers Cardiac Conduction Defects in Myotonic Dystrophy

Misra, C., Bangru, S., Lin, F., Lam, K. L. H., Koenig, S. N., Lubbers, E. R., Hedhli, J., Murphy, N. P., Parker, D. J., Dobrucki, L. W., et al. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.01.037 · Cited by 46 · see citing works

Calcium Channel CaVα1 Splice Isoforms - Tissue Specificity and Drug Action

Lipscombe, D., & Andrade, A. (2015) · Current Molecular Pharmacology · doi:10.2174/1874467208666150507103215 · Cited by 45 · see citing works

Splicing dysregulation in cancer: from mechanistic understanding to a new class of therapeutic targets

Wang, Y., Bao, Y., Zhang, S., & Wang, Z. (2020) · Science China Life Sciences · doi:10.1007/s11427-019-1605-0 · Cited by 44 · see citing works

m6A‐mediated alternative splicing coupled with nonsense‐mediated mRNA decay regulates SAM synthetase homeostasis

Watabe, E., Togo‐Ohno, M., Ishigami, Y., Wani, S., Hirota, K., Kimura‐Asami, M., Hasan, S., Takei, S., Fukamizu, A., Suzuki, Y., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2020106434 · Cited by 44 · see citing works

Therapeutic Targeting of Alternative Splicing: A New Frontier in Cancer Treatment

Murphy, A., Li, A. H., Li, P., & Sun, H. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.868664 · Cited by 43 · see citing works

Emerging roles of RNA-binding proteins in plant development

Cho, H., Cho, H. S., & Hwang, I. (2019) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2019.03.016 · Cited by 40 · see citing works

AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors

Hu, J., Khodadadi‐Jamayran, A., Mao, M., Shah, K. K., Yang, Z., Nasim, T., Wang, Z., & Jiang, H. (2016) · Nature Communications · doi:10.1038/ncomms13347 · Cited by 37 · see citing works

ZFR coordinates crosstalk between RNA decay and transcription in innate immunity

Haque, N., Ouda, R., Chen, C., Ozato, K., & Hogg, J. R. (2018) · Nature Communications · doi:10.1038/s41467-018-03326-5 · Cited by 36 · see citing works

Challenges and approaches to predicting RNA with multiple functional structures

Schroeder, S. J. (2018) · RNA · doi:10.1261/rna.067827.118 · Cited by 38 · see citing works

Generation of functionally distinct isoforms of PTBP3 by alternative splicing and translation initiation

Tan, L.-Y., Whitfield, P. D., Llorian, M., Monzón‐Casanova, E., Díaz‐Muñoz, M. D., Turner, M., & Smith, C. W. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv429 · Cited by 38 · see citing works

Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources

Sulakhe, D., D’Souza, M., Wang, S., Balasubramanian, S., Athri, P., Xie, B., Canzar, S., Gady Agam, B., Gilliam, T. C., & Maltsev, N. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby047 · Cited by 33 · see citing works

Cis‐regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis

Wang, X., Yang, M., Ren, D., Terzaghi, W., Deng, X., & He, G. (2018) · The Plant Journal · doi:10.1111/tpj.14142 · Cited by 37 · see citing works

Alternative Splicing in Genetic Diseases: Improved Diagnosis and Novel Treatment Options

Bergsma, A. J., van der Wal, E., Broeders, M., van der Ploeg, A. T., & Pijnappel, W. W. M. P. (2017) · International review of cytology · doi:10.1016/bs.ircmb.2017.07.008 · Cited by 36 · see citing works

Predominant contribution of cis‐regulatory divergence in the evolution of mouse alternative splicing

Gao, Q., Sun, W., Ballegeer, M., Libert, C., & Chen, W. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145970 · Cited by 34 · see citing works

Dynamics and Functional Roles of Splicing Factor Autoregulation

Ding, F., Su, C. J., Edmonds, K. K., Liang, G., & Elowitz, M. B. (2021) · Cell Reports · doi:10.1016/j.celrep.2022.110985 · Cited by 35 · see citing works

LEFKOTHEA Regulates Nuclear and Chloroplast mRNA Splicing in Plants

Δάρας, Γ., Rigas, S., Alatzas, A., Samiotaki, M. K., Chatzopoulos, D., Tsitsekian, D., Papadaki, V., Templalexis, D., Μπανίλας, Γ. Π., Athanasiadou, A.-M., et al. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.07.024 · Cited by 33 · see citing works

Oligonucleotide-based systems: DNA, microRNAs, DNA/RNA aptamers

Jolly, P., Estrela, P., & Ladomery, M. (2016) · Essays in Biochemistry · doi:10.1042/ebc20150004 · Cited by 33 · see citing works

Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries

Mikl, M., Hamburg, A., Pilpel, Y., & Segal, E. (2019) · Nature Communications · doi:10.1038/s41467-019-12642-3 · Cited by 31 · see citing works

A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior

Ehrmann, I. E., Gazzara, M. R., Pagliarini, V., Dalgliesh, C., Chadegani, M. K., Xu, Y., Cesari, E., Danilenko, M., MacLennan, M., Lowdon, K., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.12.002 · Cited by 30 · see citing works

Comprehensive Analysis of the Global Protein Changes That Occur During Salivary Gland Degeneration in Female Ixodid Ticks Haemaphysalis longicornis

Wang, H., Zhang, X., Wang, X., Zhang, B., Wang, M., Yang, X., Han, X., Wang, R., Ren, S., Hu, Y., et al. (2019) · Frontiers in Physiology · doi:10.3389/fphys.2018.01943 · Cited by 30 · see citing works

THO Complex-Dependent Posttranscriptional Control Contributes to Vascular Smooth Muscle Cell Fate Decision

Yuan, X., Zhang, T., Yao, F., Liao, Y., Liu, F., Ren, Z., Han, L., Diao, L., Li, Y., Zhou, B., et al. (2018) · Circulation Research · doi:10.1161/circresaha.118.313527 · Cited by 28 · see citing works

The RNA‐binding protein caper is required for sensory neuron development in Drosophila melanogaster

Olesnicky, E. C., Bono, J. M., Bell, L. A., Schachtner, L. T., & Lybecker, M. C. (2017) · Developmental Dynamics · doi:10.1002/dvdy.24523 · Cited by 27 · see citing works

Modulation of alternative splicing during early infection of human primary B lymphocytes with Epstein-Barr virus (EBV): a novel function for the viral EBNA-LP protein

Manet, É., Polvèche, H., Mure, F., Mrozek-Górska, P., Roisné-Hamelin, F., Hammerschmidt, W., Auboeuf, D., & Gruffat, H. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab787 · Cited by 25 · see citing works

Regulation of splicing and circularisation of RNA in epithelial mesenchymal plasticity

Neumann, D., Goodall, G. J., & Gregory, P. A. (2017) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2017.08.008 · Cited by 25 · see citing works

Variant snRNPs: New players within the spliceosome system

Vazquez‐Arango, P., & O’Reilly, D. (2017) · RNA Biology · doi:10.1080/15476286.2017.1373238 · Cited by 23 · see citing works

Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate

Fagg, W. S., Liu, N., Braunschweig, U., de Castro, K. L. P., Chen, X., Ditmars, F. S., Widen, S. G., Donohue, J. P., Módis, K., Russell, W. K., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac327 · Cited by 21 · see citing works

How alternative splicing changes the properties of plant proteins

Kashkan, I., Timofeyenko, K., & Růžička, K. (2022) · Quantitative Plant Biology · doi:10.1017/qpb.2022.9 · Cited by 20 · see citing works

Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control

Danilenko, M., Dalgliesh, C., Pagliarini, V., Naro, C., Ehrmann, I. E., Feracci, M., Chadegani, M. K., Tyson-Capper, A. J., Clowry, G. J., Fort, P., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1277 · Cited by 20 · see citing works

Opposing roles of miR‐294 and MBNL1/2 in shaping the gene regulatory network of embryonic stem cells

Wu, D., Gu, K., Yu, J., Fu, X., Wang, X., Guo, W., Liao, L., Zhu, H. M., Zhang, X., Hui, J., et al. (2018) · EMBO Reports · doi:10.15252/embr.201745657 · Cited by 20 · see citing works

Post‐Transcriptional Noise Control

Hansen, M. M. K., & Weinberger, L. S. (2019) · BioEssays · doi:10.1002/bies.201900044 · Cited by 17 · see citing works

Alternative splicing coupled with transcript degradation modulates OAS1g antiviral activity

Frankiw, L. S., Mann, M., Li, G., Joglekar, A. V., & Baltimore, D. (2019) · RNA · doi:10.1261/rna.073825.119 · Cited by 20 · see citing works

An engineered RNA binding protein with improved splicing regulation

Hale, M. A., Richardson, J. I., Day, R. C., McConnell, O. L., Arboleda, J. D., Wang, E. T., & Berglund, J. A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1304 · Cited by 19 · see citing works

Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing

Tejedor, J. R., Tilgner, H., Iannone, C., Guigó, R., & Valcárcel, J. (2015) · RNA · doi:10.1261/rna.049890.115 · Cited by 19 · see citing works

An Alternative Splicing Program for Mouse Craniofacial Development

Hooper, J. E., Jones, K. L., Smith, F. J., Williams, T., & Li, H. (2020) · Frontiers in Physiology · doi:10.3389/fphys.2020.01099 · Cited by 18 · see citing works

HNF1A and A1CF coordinate a beta cell transcription-splicing axis that is disrupted in type 2 diabetes

Bernardo, E., Vas, M. G. D., Balboa, D., Cuenca-Ardura, M., Bonàs‐Guarch, S., Planas-Fèlix, M., Mollandin, F., Torrens-Dinarès, M., Maestro, M. A., García-Hurtado, J., et al. (2025) · Cell Metabolism · doi:10.1016/j.cmet.2025.07.007 · Cited by 17 · see citing works

Alternative splicing decouples local from global PRC2 activity

Arecco, N., Mocavini, I., Blanco, E., Ballaré, C., Libman, E., Bonnal, S., Irimia, M., & Croce, L. D. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.011 · Cited by 17 · see citing works

Emerging properties of nuclear RNP biogenesis and export

Oeffinger, M., & Montpetit, B. (2015) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2015.04.007 · Cited by 15 · 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

Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states

Yang, Y., Yang, Y., Yuan, J., Shen, X., Li, J. J., & Li, J. J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1256 · Cited by 13 · see citing works

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing

Pacini, C., & Koziol, M. J. (2018) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2017.0073 · Cited by 13 · see citing works

Phosphorylation of the smooth muscle master splicing regulator RBPMS regulates its splicing activity

Barnhart, M. D., Yang, Y. A., Nakagaki-Silva, E. E., Hammond, T. H., Pizzinga, M., Gooding, C., Stott, K. M., & Smith, C. W. J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1048 · Cited by 14 · see citing works

Splicing regulation of GFPT1 muscle-specific isoform and its roles in glucose metabolisms and neuromuscular junction

Farshadyeganeh, P., Nazim, M., Zhang, R., Ohkawara, B., Nakajima, K., Rahman, M. A., Nasrin, F., Ito, M., Takeda, J., Ohe, K., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107746 · Cited by 13 · see citing works

Cell-type-resolved alternative splicing patterns in mouse liver

Wu, P., Zhou, D., Lin, W., Li, Y., Wei, H., Qian, X., Jiang, Y., & He, F. (2017) · DNA Research · doi:10.1093/dnares/dsx055 · Cited by 13 · see citing works

Modulation of Yorkie activity by alternative splicing is required for developmental stability

Srivastava, D., de Toledo, M., Manchon, L., Tazi, J., & Juge, F. (2020) · The EMBO Journal · doi:10.15252/embj.2020104895 · Cited by 13 · see citing works

Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein–RNA Interactions

Sibley, C. R. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7213-5_29 · Cited by 12 · see citing works

Tra2beta-Dependent Regulation of RIO Kinase 3 Splicing During Rift Valley Fever Virus Infection Underscores the Links Between Alternative Splicing and Innate Antiviral Immunity

White, L. A., Bisom, T. C., Grimes, H. L., Hayashi, M., Lanchy, J.-M., & Lodmell, J. S. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.799024 · Cited by 12 · see citing works

The ACE I/D polymorphism does not explain heterogeneity of natural course and response to enzyme replacement therapy in Pompe disease

Kuperus, E., van der Meijden, J. C., Groen, S. L. M. I. ‘., Kroos, M. A., Hoogeveen‐Westerveld, M., Rizopoulos, D., Martinez, M., Kruijshaar, M. E., van Doorn, P. A., van der Beek, N. A. M. E., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0208854 · Cited by 12 · see citing works

Cell-type specific regulator RBPMS switches alternative splicing via higher-order oligomerization and heterotypic interactions with other splicing regulators

Yang, Y. A., Lee, G. C., Nakagaki-Silva, E. E., Huang, Y., Peacey, M., Partridge, R., Gooding, C., & Smith, C. W. J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad652 · Cited by 11 · see citing works

Glycine-rich RNA-binding cofactor RZ1AL is associated with tomato ripening and development

Li, X., Yang, Y., Zeng, N., Qu, G., Fu, D., Zhu, B., Luo, Y., Ostersetzer‐Biran, O., & Zhu, H. (2022) · Horticulture Research · doi:10.1093/hr/uhac134 · Cited by 11 · see citing works

Bespoke RNA recognition by Pumilios

Edwards, T. A. (2015) · Biochemical Society Transactions · doi:10.1042/bst20150072 · Cited by 11 · see citing works

Identification of a de novo FOXP1 mutation and incidental discovery of inherited genetic variants contributing to a case of autism spectrum disorder and epilepsy

Jay, K., Mitra, A., Harding, T., Matthes, D., & Ness, B. V. (2019) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.751 · Cited by 10 · see citing works

Networks of Splice Factor Regulation by Unproductive Splicing Coupled With Nonsense Mediated mRNA DecayPreprint

Desai, A. M., Hu, Z., French, C. E., Lloyd, J. P. B., & Brenner, S. E. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.20.107375 · Cited by 9 · see citing works

CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Aghamirzaie, D., Collakova, E., Li, S., & Grene, R. (2016) · BMC Genomics · doi:10.1186/s12864-016-3172-6 · Cited by 12 · see citing works

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

Papasaikas, P., Ramon Tejedor, J., Vigevani, L., & Valcárcel, J. (2015) · Figshare · doi:10.6084/m9.figshare.1575696

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

Reconstruction of composite regulator-target splicing networks from high-throughput transcriptome data

Papasaikas, P., Rao, A. U. K., Huggins, P. M., Valcárcel, J., & Lopez, A. J. (2015) · BMC Genomics · doi:10.1186/1471-2164-16-s10-s7 · Cited by 20 · see citing works

SR splicing regulator results in tissue-specific

Qi, J., Su, S., McGuffin, M. E., & Mattox, W. (2006)