The DOI matches its Crossref record; 17 of the 17 references it cites were found in a registry or an index.
The human splicing code reveals new insights into the genetic determinants of disease
Open accessAbstract
Predicting defects in RNA splicing: Most eukaryotic messenger RNAs (mRNAs) are spliced to remove introns. Splicing generates uninterrupted open reading frames that can be translated into proteins. Splicing is often highly regulated, generating alternative spliced forms that code for variant proteins in different tissues. RNA-binding proteins that bind specific sequences in the mRNA regulate splicing. Xiong et al. develop a computational model that predicts splicing regulation for any mRNA sequence (see the Perspective by Guigó and Valcárcel). They use this to analyze more than half a million mRNA splicing sequence variants in the human genome. They are able to identify thousands of known disease-causing mutations, as well as many new disease candidates, including 17 new autism-linked genes. Science , this issue 10.1126/science.1254806 ; see also p. 124
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Cites
A method and server for predicting damaging missense mutations.
Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010) · Nature Methods · doi:10.1038/nmeth0410-248 · Cited by 13,194
Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013
FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism
Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.013 · Cited by 2,072
Functional impact of global rare copy number variation in autism spectrum disorders
Pinto, D., Pagnamenta, A. T., Klei, L., Anney, R., Merico, D., Regan, R., Conroy, J., Magalhaes, T. R., Correia, C., Abrahams, B. S., et al. (2010) · Nature · doi:10.1038/nature09146 · Cited by 2,013 · cited 1×
“The analysis reveals interesting candidates, and only CTNND2 and PTEN have been previously implicated or suggested to play a role in ASD (35, 43).”
BackgroundSelf-citationTranscriptome and genome sequencing uncovers functional variation in humans
The Geuvadis Consortium, Lappalainen, T., Sammeth, M., Friedländer, M. R., ‘t Hoen, P. A. C., Monlong, J., Rivas, M. A., Gonzàlez-Porta, M., Kurbatova, N., Griebel, T., et al. (2013) · Nature · doi:10.1038/nature12531 · Cited by 1,888
Transcriptomic Analysis of Autistic Brain Reveals Convergent Molecular Pathology
Voineagu, I., Wang, X., Johnston, P., Lowe, J. K., Tian, Y., Horvath, S., Mill, J., Cantor, R. M., Blencowe, B. J., & Geschwind, D. H. (2011) · Nature · doi:10.1038/nature10110 · Cited by 1,874 · cited 1×
“are extensively alternatively spliced (40), as well as by recent transcriptomic analyses showing consistent deviations in alternative splicing patterns in the cortical regions of ASD cases (41).”
BackgroundSelf-citationNeuroligins and neurexins link synaptic function to cognitive disease
Südhof, T. C. (2008) · Nature · doi:10.1038/nature07456 · Cited by 1,849
Improving RNA-Seq expression estimates by correcting for fragment bias
Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. L., & Pachter, L. (2011) · Genome Biology · doi:10.1186/gb-2011-12-3-r22 · Cited by 1,725
Evolution and functional impact of rare coding variation from deep sequencing of human exomes
Tennessen, J. A., Bigham, A. W., O’Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., et al. (2012) · Science · doi:10.1126/science.1219240 · Cited by 1,613
A compendium of RNA-binding motifs for decoding gene regulation
Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature · doi:10.1038/nature12311 · Cited by 1,480 · cited 3×
“Because the model was built using the reference genome only, its performance was first validated using held-out data, including additional RNA-seq (54), RT-PCR, RBP binding (14), and MBNL knockdown (15) data sets.”
BackgroundMethodSelf-citationThe evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature · doi:10.1038/nature10532 · Cited by 1,248
Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., Carnevali, P., Nazarenko, I., Nilsen, G. B., Yeung, G., et al. (2010) · Science · doi:10.1126/science.1181498 · Cited by 1,212
A high-resolution map of human evolutionary constraint using 29 mammals
Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature · doi:10.1038/nature10530 · Cited by 1,108
The Human Gene Mutation Database: 2008 update
Stenson, P. D., Mort, M., Ball, E. V., Howells, K., Phillips, A. D., Thomas, N. S., & Cooper, D. N. (2009) · Genome Medicine · doi:10.1186/gm13 · Cited by 873
A genome-wide scan for common alleles affecting risk for autism
Anney, R., Klei, L., Pinto, D., Regan, R., Conroy, J., Magalhaes, T. R., Correia, C., Abrahams, B. S., Sykes, N., Pagnamenta, A. T., et al. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq307 · Cited by 593
Self-citationIntegrative 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
Uddin, M., Tammimies, K., Pellecchia, G., Alipanahi, B., Hu, P., Wang, Z., Pinto, D., Lau, L., Nalpathamkalam, T., Marshall, C. R., et al. (2014) · Nature Genetics · doi:10.1038/ng.2980 · Cited by 163
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LeCun, Y., Bengio, Y., & Hinton, G. (2015) · Nature · doi:10.1038/nature14539 · Cited by 84,126
A guide to deep learning in healthcare
Esteva, A., Robicquet, A., Ramsundar, B., Kuleshov, V., DePristo, M., Chou, K., Cui, C., Corrado, G., Thrun, S., & Dean, J. (2019) · Nature Medicine · doi:10.1038/s41591-018-0316-z · Cited by 5,312
Efficient Processing of Deep Neural Networks: A Tutorial and Survey
Sze, V., Chen, Y.-H., Yang, T.-J., & Emer, J. S. (2017) · Proceedings of the IEEE · doi:10.1109/jproc.2017.2761740 · Cited by 4,215
“• Medical DNNs: They have played an important role in genomics to gain insight into the genetics of diseases such as autism, cancers, and spinal muscular atrophy [24]–[27].”
CADD: predicting the deleteriousness of variants throughout the human genome
Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J., & Kircher, M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1016 · Cited by 3,534
Applications of machine learning in drug discovery and development
Vamathevan, J., Clark, D., Czodrowski, P., Dunham, I., Ferran, E., Lee, G., Li, B., Madabhushi, A., Shah, P., Spitzer, M., et al. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-019-0024-5 · Cited by 3,228
Metadata
- Authors
- Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K. C., Hua, Y., Gueroussov, S., Najafabadi, H. S., Hughes, T. R., Morris, Q., Barash, Y., Krainer, A. R., Jojic, N., Scherer, S. W., Blencowe, B. J., & Frey, B. J.
- Venue
- Science
- Published
- 2015-01-09
- Volume
- 347
- Issue
- 6218
- Pages
- 1254806-1254806
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2088338354
- Cited by
- 1,220
- References
- 17
- FWCI
- 34.56
- Type
- journal article
- Language
- en
- Open access
- green
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