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1. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Author

Pardo-Palacios, Francisco J., Wang, Dingjie, Reese, Fairlie, Diekhans, Mark, Carbonell-Sala, Sílvia, Williams, Brian, Loveland, Jane E., De María, Maite, Adams, Matthew S., Balderrama-Gutierrez, Gabriela, Behera, Amit K., Gonzalez Martinez, Jose M., Hunt, Toby, Lagarde, Julien, Liang, Cindy E., Li, Haoran, Meade, Marcus Jerryd, Moraga Amador, David A., Prjibelski, Andrey D., Birol, Inanc, Bostan, Hamed, Brooks, Ashley M., Çelik, Muhammed Hasan, Chen, Ying, Du, Mei R. M., Felton, Colette, Göke, Jonathan, Hafezqorani, Saber, Herwig, Ralf, Kawaji, Hideya, Lee, Joseph, Li, Jian-Liang, Lienhard, Matthias, Mikheenko, Alla, Mulligan, Dennis, Nip, Ka Ming, Pertea, Mihaela, Ritchie, Matthew E., Sim, Andre D., Tang, Alison D., Wan, Yuk Kei, Wang, Changqing, Wong, Brandon Y., Yang, Chen, Barnes, If, Berry, Andrew E., Capella-Gutierrez, Salvador, Cousineau, Alyssa, Dhillon, Namrita, Fernandez-Gonzalez, Jose M., Ferrández-Peral, Luis, Garcia-Reyero, Natàlia, Götz, Stefan, Hernández-Ferrer, Carles, Kondratova, Liudmyla, Liu, Tianyuan, Martinez-Martin, Alessandra, Menor, Carlos, Mestre-Tomás, Jorge, Mudge, Jonathan M., Panayotova, Nedka G., Paniagua, Alejandro, Repchevsky, Dmitry, Ren, Xingjie, Rouchka, Eric, Saint-John, Brandon, Sapena, Enrique, Sheynkman, Leon, Smith, Melissa Laird, Suner, Marie-Marthe, Takahashi, Hazuki, Youngworth, Ingrid A., Carninci, Piero, Denslow, Nancy D., Guigó, Roderic, Hunter, Margaret E., Maehr, Rene, Shen, Yin, Tilgner, Hagen U., Wold, Barbara J., Vollmers, Christopher, Frankish, Adam, Au, Kin Fai, Sheynkman, Gloria M., Mortazavi, Ali, Conesa, Ana, and Brooks, Angela N.

Published
2024
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2. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Author

Jain, Shantanu, Bakolitsa, Constantina, Brenner, Steven E, Radivojac, Predrag, Moult, John, Repo, Susanna, Hoskins, Roger A, Andreoletti, Gaia, Barsky, Daniel, Chellapan, Ajithavalli, Chu, Hoyin, Dabbiru, Navya, Kollipara, Naveen K, Ly, Melissa, Neumann, Andrew J, Pal, Lipika R, Odell, Eric, Pandey, Gaurav, Peters-Petrulewicz, Robin C, Srinivasan, Rajgopal, Yee, Stephen F, Yeleswarapu, Sri Jyothsna, Zuhl, Maya, Adebali, Ogun, Patra, Ayoti, Beer, Michael A, Hosur, Raghavendra, Peng, Jian, Bernard, Brady M, Berry, Michael, Dong, Shengcheng, Boyle, Alan P, Adhikari, Aashish, Chen, Jingqi, Hu, Zhiqiang, Wang, Robert, Wang, Yaqiong, Miller, Maximilian, Wang, Yanran, Bromberg, Yana, Turina, Paola, Capriotti, Emidio, Han, James J, Ozturk, Kivilcim, Carter, Hannah, Babbi, Giulia, Bovo, Samuele, Di Lena, Pietro, Martelli, Pier Luigi, Savojardo, Castrense, Casadio, Rita, Cline, Melissa S, De Baets, Greet, Bonache, Sandra, Diez, Orland, Gutierrez-Enriquez, Sara, Fernandez, Alejandro, Montalban, Gemma, Ootes, Lars, Ozkan, Selen, Padilla, Natalia, Riera, Casandra, De la Cruz, Xavier, Diekhans, Mark, Huwe, Peter J, Wei, Qiong, Xu, Qifang, Dunbrack, Roland L, Gotea, Valer, Elnitski, Laura, Margolin, Gennady, Fariselli, Piero, Kulakovskiy, Ivan V, Makeev, Vsevolod J, Penzar, Dmitry D, Vorontsov, Ilya E, Favorov, Alexander V, Forman, Julia R, Hasenahuer, Marcia, Fornasari, Maria S, Parisi, Gustavo, Avsec, Ziga, Celik, Muhammed H, Thi, Yen Duong Nguyen, Gagneur, Julien, Shi, Fang-Yuan, Edwards, Matthew D, Guo, Yuchun, Tian, Kevin, Zeng, Haoyang, Gifford, David K, Goke, Jonathan, Zaucha, Jan, Gough, Julian, Ritchie, Graham RS, Frankish, Adam, Mudge, Jonathan M, Harrow, Jennifer, Young, Erin L, and Yu, Yao

Subjects
Biological Sciences, Genetics, Human Genome, 2.1 Biological and endogenous factors, Good Health and Well Being, Humans, Computational Biology, Mutation, Missense, Phenotype, Critical Assessment of Genome Interpretation Consortium, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.ResultsPerformance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.ConclusionsResults show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Published
2024

5. Standardized annotation of translated open reading frames

Author

Mudge, Jonathan M, Ruiz-Orera, Jorge, Prensner, John R, Brunet, Marie A, Calvet, Ferriol, Jungreis, Irwin, Gonzalez, Jose Manuel, Magrane, Michele, Martinez, Thomas F, Schulz, Jana Felicitas, Yang, Yucheng T, Albà, M Mar, Aspden, Julie L, Baranov, Pavel V, Bazzini, Ariel A, Bruford, Elspeth, Martin, Maria Jesus, Calviello, Lorenzo, Carvunis, Anne-Ruxandra, Chen, Jin, Couso, Juan Pablo, Deutsch, Eric W, Flicek, Paul, Frankish, Adam, Gerstein, Mark, Hubner, Norbert, Ingolia, Nicholas T, Kellis, Manolis, Menschaert, Gerben, Moritz, Robert L, Ohler, Uwe, Roucou, Xavier, Saghatelian, Alan, Weissman, Jonathan S, and van Heesch, Sebastiaan

Subjects
Molecular Sequence Annotation, Open Reading Frames, Protein Biosynthesis, Ribosomes
Published
2022

6. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

Author

Sweeney, Blake A, Petrov, Anton I, Ribas, Carlos E, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Seemann, Stefan E, Gorodkin, Jan, Cannone, Jamie J, Gutell, Robin R, Kay, Simon, Marygold, Steven, dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M, Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P, Lowe, Todd M, Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G, Ma, Lina, Zhang, Zhang, Volders, Pieter-Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J, Kalvari, Ioanna, Nawrocki, Eric P, Petrov, Anton S, Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M, Hoksza, David, Lovering, Ruth C, Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, and Weinberg, Zasha

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Animals, Apicomplexa, Base Sequence, Betacoronavirus, Databases, Nucleic Acid, Fungi, Gene Ontology, Humans, Internet, Molecular Sequence Annotation, Nucleic Acid Conformation, RNA, Untranslated, Sequence Analysis, RNA, Software, RNAcentral Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.

Published
2021

7. Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames

Author

Sandmann, Clara-L., Schulz, Jana F., Ruiz-Orera, Jorge, Kirchner, Marieluise, Ziehm, Matthias, Adami, Eleonora, Marczenke, Maike, Christ, Annabel, Liebe, Nina, Greiner, Johannes, Schoenenberger, Aaron, Muecke, Michael B., Liang, Ning, Moritz, Robert L., Sun, Zhi, Deutsch, Eric W., Gotthardt, Michael, Mudge, Jonathan M., Prensner, John R., Willnow, Thomas E., Mertins, Philipp, van Heesch, Sebastiaan, and Hubner, Norbert

Published
2023
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9. SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility

Author

Silvennoinen, Katri, Gawel, Kinga, Tsortouktzidis, Despina, Pitsch, Julika, Alhusaini, Saud, van Loo, Karen M. J., Picardo, Richard, Michalak, Zuzanna, Pagni, Susanna, Martins Custodio, Helena, Mills, James, Whelan, Christopher D., de Zubicaray, Greig I., McMahon, Katie L., van der Ent, Wietske, Kirstein-Smardzewska, Karolina J., Tiraboschi, Ettore, Mudge, Jonathan M., Frankish, Adam, Thom, Maria, Wright, Margaret J., Thompson, Paul M., Schoch, Susanne, Becker, Albert J., Esguerra, Camila V., and Sisodiya, Sanjay M.

Published
2022
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10. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

Author

Morales, Joannella, Pujar, Shashikant, Loveland, Jane E., Astashyn, Alex, Bennett, Ruth, Berry, Andrew, Cox, Eric, Davidson, Claire, Ermolaeva, Olga, Farrell, Catherine M., Fatima, Reham, Gil, Laurent, Goldfarb, Tamara, Gonzalez, Jose M., Haddad, Diana, Hardy, Matthew, Hunt, Toby, Jackson, John, Joardar, Vinita S., Kay, Michael, Kodali, Vamsi K., McGarvey, Kelly M., McMahon, Aoife, Mudge, Jonathan M., Murphy, Daniel N., Murphy, Michael R., Rajput, Bhanu, Rangwala, Sanjida H., Riddick, Lillian D., Thibaud-Nissen, Françoise, Threadgold, Glen, Vatsan, Anjana R., Wallin, Craig, Webb, David, Flicek, Paul, Birney, Ewan, Pruitt, Kim D., Frankish, Adam, Cunningham, Fiona, and Murphy, Terence D.

Published
2022
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14. Transcript expression-aware annotation improves rare variant interpretation

Author

Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, and Mudge, Jonathan M.

Subjects
Genetic variation -- Analysis -- Usage, Human genome -- Identification and classification -- Analysis -- Usage, Genetic transcription -- Usage -- Analysis, Citation indexes -- Management -- Analysis -- Usage, Company business management, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD).sup.1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the 'proportion expressed across transcripts', which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project.sup.2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies. A novel variant annotation metric that quantifies the level of expression of genetic variants across tissues is validated in the Genome Aggregation Database (gnomAD) and is shown to improve rare variant interpretation., Author(s): Beryl B. Cummings [sup.1] [sup.2] [sup.3] , Konrad J. Karczewski [sup.1] [sup.2] , Jack A. Kosmicki [sup.1] [sup.2] [sup.4] , Eleanor G. Seaby [sup.1] [sup.2] [sup.5] , Nicholas A. [...]

Published
2020
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15. Current status and new features of the Consensus Coding Sequence database

Author

Farrell, Catherine M, O’Leary, Nuala A, Harte, Rachel A, Loveland, Jane E, Wilming, Laurens G, Wallin, Craig, Diekhans, Mark, Barrell, Daniel, Searle, Stephen MJ, Aken, Bronwen, Hiatt, Susan M, Frankish, Adam, Suner, Marie-Marthe, Rajput, Bhanu, Steward, Charles A, Brown, Garth R, Bennett, Ruth, Murphy, Michael, Wu, Wendy, Kay, Mike P, Hart, Jennifer, Rajan, Jeena, Weber, Janet, Snow, Catherine, Riddick, Lillian D, Hunt, Toby, Webb, David, Thomas, Mark, Tamez, Pamela, Rangwala, Sanjida H, McGarvey, Kelly M, Pujar, Shashikant, Shkeda, Andrei, Mudge, Jonathan M, Gonzalez, Jose M, Gilbert, James GR, Trevanion, Stephen J, Baertsch, Robert, Harrow, Jennifer L, Hubbard, Tim, Ostell, James M, Haussler, David, and Pruitt, Kim D

Subjects
Human Genome, Genetics, Animals, Databases, Genetic, Exons, Genomics, Humans, Internet, Mice, Molecular Sequence Annotation, Proteins, Sequence Analysis, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.

Published
2014

17. Ensembl 2024

Author

Harrison, Peter W, primary, Amode, M Ridwan, additional, Austine-Orimoloye, Olanrewaju, additional, Azov, Andrey G, additional, Barba, Matthieu, additional, Barnes, If, additional, Becker, Arne, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bhai, Jyothish, additional, Bhurji, Simarpreet Kaur, additional, Boddu, Sanjay, additional, Branco Lins, Paulo R, additional, Brooks, Lucy, additional, Ramaraju, Shashank Budhanuru, additional, Campbell, Lahcen I, additional, Martinez, Manuel Carbajo, additional, Charkhchi, Mehrnaz, additional, Chougule, Kapeel, additional, Cockburn, Alexander, additional, Davidson, Claire, additional, De Silva, Nishadi H, additional, Dodiya, Kamalkumar, additional, Donaldson, Sarah, additional, El Houdaigui, Bilal, additional, Naboulsi, Tamara El, additional, Fatima, Reham, additional, Giron, Carlos Garcia, additional, Genez, Thiago, additional, Grigoriadis, Dionysios, additional, Ghattaoraya, Gurpreet S, additional, Martinez, Jose Gonzalez, additional, Gurbich, Tatiana A, additional, Hardy, Matthew, additional, Hollis, Zoe, additional, Hourlier, Thibaut, additional, Hunt, Toby, additional, Kay, Mike, additional, Kaykala, Vinay, additional, Le, Tuan, additional, Lemos, Diana, additional, Lodha, Disha, additional, Marques-Coelho, Diego, additional, Maslen, Gareth, additional, Merino, Gabriela Alejandra, additional, Mirabueno, Louisse Paola, additional, Mushtaq, Aleena, additional, Hossain, Syed Nakib, additional, Ogeh, Denye N, additional, Sakthivel, Manoj Pandian, additional, Parker, Anne, additional, Perry, Malcolm, additional, Piližota, Ivana, additional, Poppleton, Daniel, additional, Prosovetskaia, Irina, additional, Raj, Shriya, additional, Pérez-Silva, José G, additional, Salam, Ahamed Imran Abdul, additional, Saraf, Shradha, additional, Saraiva-Agostinho, Nuno, additional, Sheppard, Dan, additional, Sinha, Swati, additional, Sipos, Botond, additional, Sitnik, Vasily, additional, Stark, William, additional, Steed, Emily, additional, Suner, Marie-Marthe, additional, Surapaneni, Likhitha, additional, Sutinen, Kyösti, additional, Tricomi, Francesca Floriana, additional, Urbina-Gómez, David, additional, Veidenberg, Andres, additional, Walsh, Thomas A, additional, Ware, Doreen, additional, Wass, Elizabeth, additional, Willhoft, Natalie L, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Giorgetti, Stefano, additional, Haggerty, Leanne, additional, Ilsley, Garth R, additional, Keatley, Jon, additional, Loveland, Jane E, additional, Moore, Benjamin, additional, Mudge, Jonathan M, additional, Naamati, Guy, additional, Tate, John, additional, Trevanion, Stephen J, additional, Winterbottom, Andrea, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Cunningham, Fiona, additional, Dyer, Sarah, additional, Finn, Robert D, additional, Martin, Fergal J, additional, and Yates, Andrew D, additional

Published
2023
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18. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Author

Pardo-Palacios, Francisco J., primary, Wang, Dingjie, additional, Reese, Fairlie, additional, Diekhans, Mark, additional, Carbonell-Sala, Sílvia, additional, Williams, Brian, additional, Loveland, Jane E., additional, De María, Maite, additional, Adams, Matthew S., additional, Balderrama-Gutierrez, Gabriela, additional, Behera, Amit K., additional, Gonzalez, Jose M., additional, Hunt, Toby, additional, Lagarde, Julien, additional, Liang, Cindy E., additional, Li, Haoran, additional, Meade, Marcus Jerryd, additional, Amador, David A. Moraga, additional, Prjibelski, Andrey D., additional, Birol, Inanc, additional, Bostan, Hamed, additional, Brooks, Ashley M., additional, Çelik, Muhammed Hasan, additional, Chen, Ying, additional, Du, Mei R.M., additional, Felton, Colette, additional, Göke, Jonathan, additional, Hafezqorani, Saber, additional, Herwig, Ralf, additional, Kawaji, Hideya, additional, Lee, Joseph, additional, Li, Jian-Liang, additional, Lienhard, Matthias, additional, Mikheenko, Alla, additional, Mulligan, Dennis, additional, Nip, Ka Ming, additional, Pertea, Mihaela, additional, Ritchie, Matthew E., additional, Sim, Andre D., additional, Tang, Alison D., additional, Wan, Yuk Kei, additional, Wang, Changqing, additional, Wong, Brandon Y., additional, Yang, Chen, additional, Barnes, If, additional, Berry, Andrew, additional, Capella, Salvador, additional, Dhillon, Namrita, additional, Fernandez-Gonzalez, Jose M., additional, Ferrández-Peral, Luis, additional, Garcia-Reyero, Natàlia, additional, Goetz, Stefan, additional, Hernández-Ferrer, Carles, additional, Kondratova, Liudmyla, additional, Liu, Tianyuan, additional, Martinez-Martin, Alessandra, additional, Menor, Carlos, additional, Mestre-Tomás, Jorge, additional, Mudge, Jonathan M., additional, Panayotova, Nedka G., additional, Paniagua, Alejandro, additional, Repchevsky, Dmitry, additional, Rouchka, Eric, additional, Saint-John, Brandon, additional, Sapena, Enrique, additional, Sheynkman, Leon, additional, Smith, Melissa Laird, additional, Suner, Marie-Marthe, additional, Takahashi, Hazuki, additional, Youngworth, Ingrid Ashley, additional, Carninci, Piero, additional, Denslow, Nancy D., additional, Guigó, Roderic, additional, Hunter, Margaret E., additional, Tilgner, Hagen U., additional, Wold, Barbara J., additional, Vollmers, Christopher, additional, Frankish, Adam, additional, Au, Kin Fai, additional, Sheynkman, Gloria M., additional, Mortazavi, Ali, additional, Conesa, Ana, additional, and Brooks, Angela N., additional

Published
2023
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21. Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

Author

Steward, Charles A., Roovers, Jolien, Suner, Marie-Marthe, Gonzalez, Jose M., Uszczynska-Ratajczak, Barbara, Pervouchine, Dmitri, Fitzgerald, Stephen, Viola, Margarida, Stamberger, Hannah, Hamdan, Fadi F., Ceulemans, Berten, Leroy, Patricia, Nava, Caroline, Lepine, Anne, Tapanari, Electra, Keiller, Don, Abbs, Stephen, Sanchis-Juan, Alba, Grozeva, Detelina, Rogers, Anthony S., Diekhans, Mark, Guigó, Roderic, Petryszak, Robert, Minassian, Berge A., Cavalleri, Gianpiero, Vitsios, Dimitrios, Petrovski, Slavé, Harrow, Jennifer, Flicek, Paul, Lucy Raymond, F., Lench, Nicholas J., Jonghe, Peter De, Mudge, Jonathan M., Weckhuysen, Sarah, Sisodiya, Sanjay M., and Frankish, Adam

Published
2019
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25. GENCODE: reference annotation for the human and mouse genomes in 2023

Author

Frankish, Adam, primary, Carbonell-Sala, Sílvia, additional, Diekhans, Mark, additional, Jungreis, Irwin, additional, Loveland, Jane E, additional, Mudge, Jonathan M, additional, Sisu, Cristina, additional, Wright, James C, additional, Arnan, Carme, additional, Barnes, If, additional, Banerjee, Abhimanyu, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bignell, Alexandra, additional, Boix, Carles, additional, Calvet, Ferriol, additional, Cerdán-Vélez, Daniel, additional, Cunningham, Fiona, additional, Davidson, Claire, additional, Donaldson, Sarah, additional, Dursun, Cagatay, additional, Fatima, Reham, additional, Giorgetti, Stefano, additional, Giron, Carlos Garcıa, additional, Gonzalez, Jose Manuel, additional, Hardy, Matthew, additional, Harrison, Peter W, additional, Hourlier, Thibaut, additional, Hollis, Zoe, additional, Hunt, Toby, additional, James, Benjamin, additional, Jiang, Yunzhe, additional, Johnson, Rory, additional, Kay, Mike, additional, Lagarde, Julien, additional, Martin, Fergal J, additional, Gómez, Laura Martínez, additional, Nair, Surag, additional, Ni, Pengyu, additional, Pozo, Fernando, additional, Ramalingam, Vivek, additional, Ruffier, Magali, additional, Schmitt, Bianca M, additional, Schreiber, Jacob M, additional, Steed, Emily, additional, Suner, Marie-Marthe, additional, Sumathipala, Dulika, additional, Sycheva, Irina, additional, Uszczynska-Ratajczak, Barbara, additional, Wass, Elizabeth, additional, Yang, Yucheng T, additional, Yates, Andrew, additional, Zafrulla, Zahoor, additional, Choudhary, Jyoti S, additional, Gerstein, Mark, additional, Guigo, Roderic, additional, Hubbard, Tim J P, additional, Kellis, Manolis, additional, Kundaje, Anshul, additional, Paten, Benedict, additional, Tress, Michael L, additional, and Flicek, Paul, additional

Published
2022
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26. Ensembl 2023

Author

Martin, Fergal J, primary, Amode, M Ridwan, additional, Aneja, Alisha, additional, Austine-Orimoloye, Olanrewaju, additional, Azov, Andrey G, additional, Barnes, If, additional, Becker, Arne, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bhai, Jyothish, additional, Bhurji, Simarpreet Kaur, additional, Bignell, Alexandra, additional, Boddu, Sanjay, additional, Branco Lins, Paulo R, additional, Brooks, Lucy, additional, Ramaraju, Shashank Budhanuru, additional, Charkhchi, Mehrnaz, additional, Cockburn, Alexander, additional, Da Rin Fiorretto, Luca, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, Donaldson, Sarah, additional, El Houdaigui, Bilal, additional, El Naboulsi, Tamara, additional, Fatima, Reham, additional, Giron, Carlos Garcia, additional, Genez, Thiago, additional, Ghattaoraya, Gurpreet S, additional, Martinez, Jose Gonzalez, additional, Guijarro, Cristi, additional, Hardy, Matthew, additional, Hollis, Zoe, additional, Hourlier, Thibaut, additional, Hunt, Toby, additional, Kay, Mike, additional, Kaykala, Vinay, additional, Le, Tuan, additional, Lemos, Diana, additional, Marques-Coelho, Diego, additional, Marugán, José Carlos, additional, Merino, Gabriela Alejandra, additional, Mirabueno, Louisse Paola, additional, Mushtaq, Aleena, additional, Hossain, Syed Nakib, additional, Ogeh, Denye N, additional, Sakthivel, Manoj Pandian, additional, Parker, Anne, additional, Perry, Malcolm, additional, Piližota, Ivana, additional, Prosovetskaia, Irina, additional, Pérez-Silva, José G, additional, Salam, Ahamed Imran Abdul, additional, Saraiva-Agostinho, Nuno, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sinha, Swati, additional, Sipos, Botond, additional, Stark, William, additional, Steed, Emily, additional, Sukumaran, Ranjit, additional, Sumathipala, Dulika, additional, Suner, Marie-Marthe, additional, Surapaneni, Likhitha, additional, Sutinen, Kyösti, additional, Szpak, Michal, additional, Tricomi, Francesca Floriana, additional, Urbina-Gómez, David, additional, Veidenberg, Andres, additional, Walsh, Thomas A, additional, Walts, Brandon, additional, Wass, Elizabeth, additional, Willhoft, Natalie, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Giorgetti, Stefano, additional, Haggerty, Leanne, additional, Ilsley, Garth R, additional, Loveland, Jane E, additional, Moore, Benjamin, additional, Mudge, Jonathan M, additional, Tate, John, additional, Thybert, David, additional, Trevanion, Stephen J, additional, Winterbottom, Andrea, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Ruffier, Magali, additional, Cunningham, Fiona, additional, Dyer, Sarah, additional, Finn, Robert D, additional, Howe, Kevin L, additional, Harrison, Peter W, additional, Yates, Andrew D, additional, and Flicek, Paul, additional

Published
2022
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27. Standardized annotation of translated open reading frames

Author

Wellcome Trust, National Human Genome Research Institute (US), European Molecular Biology Laboratory, National Institutes of Health (US), State Secretariat for Education, Research and Innovation (Switzerland), Stowers Institute for Medical Research, Cancer Prevention and Research Institute of Texas, Howard Hughes Medical Institute, Russian Science Foundation, European Research Council, European Commission, Fondation Leducq, Canadian Institutes of Health Research, Canada Research Chairs, National Science Foundation (US), Medical Research Council (UK), Fonds de Recherche du Québec, Mudge, Jonathan M., Ruiz-Orera, Jorge, Prensner, John R., Brunet, Marie A., Calvet, Ferriol, Jungreis, Irwin, González, José Manuel, Magrane, Michele, Martinez, Thomas F., Felicitas Schulz, Jana, Yang, Yucheng T., Albà, M. Mar, Aspden, Julie Louise, Baranov, Pavel V., Bazzini, Ariel A., Bruford, Elspeth, Martín, María Jesús, Calviello, Lorenzo, Chen, Jin, Couso, Juan Pablo, Deutsch, Eric W., Flicek, Paul, Frankish, Adam, Gerstein, Mark, Hubner, Norbert, Ingolia, Nicholas T., Kellis, Manolis, Menschaert, Gerben, Moritz, Robert L., Ohler, Uwe, Roucou, Xavier, Saghatelian, Alan, Weissman, Jonathan S., Heesch, Sebastiaan van, Wellcome Trust, National Human Genome Research Institute (US), European Molecular Biology Laboratory, National Institutes of Health (US), State Secretariat for Education, Research and Innovation (Switzerland), Stowers Institute for Medical Research, Cancer Prevention and Research Institute of Texas, Howard Hughes Medical Institute, Russian Science Foundation, European Research Council, European Commission, Fondation Leducq, Canadian Institutes of Health Research, Canada Research Chairs, National Science Foundation (US), Medical Research Council (UK), Fonds de Recherche du Québec, Mudge, Jonathan M., Ruiz-Orera, Jorge, Prensner, John R., Brunet, Marie A., Calvet, Ferriol, Jungreis, Irwin, González, José Manuel, Magrane, Michele, Martinez, Thomas F., Felicitas Schulz, Jana, Yang, Yucheng T., Albà, M. Mar, Aspden, Julie Louise, Baranov, Pavel V., Bazzini, Ariel A., Bruford, Elspeth, Martín, María Jesús, Calviello, Lorenzo, Chen, Jin, Couso, Juan Pablo, Deutsch, Eric W., Flicek, Paul, Frankish, Adam, Gerstein, Mark, Hubner, Norbert, Ingolia, Nicholas T., Kellis, Manolis, Menschaert, Gerben, Moritz, Robert L., Ohler, Uwe, Roucou, Xavier, Saghatelian, Alan, Weissman, Jonathan S., and Heesch, Sebastiaan van

Abstract

Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’ of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (UTRs) of protein-coding genes. However, reference gene annotation projects have been circumspect in their incorporation of these ORFs because of uncertainties about their experimental reproducibility and physiological roles. Yet, it is clear that certain ‘Ribo-seq ORFs’ make stable proteins, others mediate gene regulation, and many have medical implications. Ultimately, the absence of standardized ORF annotation has created a circular problem: while Ribo-seq ORFs remain unrecognized by reference annotation databases, this lack of recognition will thwart studies examining their roles. Here, we outline a community-led effort involving Ensembl/GENCODE, the HUGO Gene Nomenclature Committee (HGNC), UniProtKB, HUPO/HPP and PeptideAtlas to produce a standardized catalog of 7,264 human Ribo-seq ORFs; a path to bring protein-level evidence for Ribo-seq ORFs into reference annotation databases; and a roadmap to facilitate research in the global community.

Published
2022

28. GENCODE reference annotation for the human and mouse genomes

Author

Frankish, Adam, Diekhans, Mark, Ferreira, Anne-Maud, Johnson, Rory, Jungreis, Irwin, Loveland, Jane, Mudge, Jonathan M, Sisu, Cristina, Wright, James, Armstrong, Joel, Barnes, If, Berry, Andrew, Bignell, Alexandra, Carbonell Sala, Silvia, Chrast, Jacqueline, Cunningham, Fiona, Di Domenico, Tomás, Donaldson, Sarah, Fiddes, Ian T, García Girón, Carlos, Gonzalez, Jose Manuel, Grego, Tiago, Hardy, Matthew, Hourlier, Thibaut, Hunt, Toby, Izuogu, Osagie G, Lagarde, Julien, Martin, Fergal J, Martínez, Laura, Mohanan, Shamika, Muir, Paul, Navarro, Fabio C P, Parker, Anne, Pei, Baikang, Pozo, Fernando, Ruffier, Magali, Schmitt, Bianca M, Stapleton, Eloise, Suner, Marie-Marthe, Sycheva, Irina, Uszczynska-Ratajczak, Barbara, Xu, Jinuri, Yates, Andrew, Zerbino, Daniel, Zhang, Yan, Aken, Bronwen, Choudhary, Jyoti S, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J P, Kellis, Manolis, Paten, Benedict, Reymond, Alexandre, Tress, Michael L, Flicek, Paul, Frankish, Adam, Diekhans, Mark, Ferreira, Anne-Maud, Johnson, Rory, Jungreis, Irwin, Loveland, Jane, Mudge, Jonathan M, Sisu, Cristina, Wright, James, Armstrong, Joel, Barnes, If, Berry, Andrew, Bignell, Alexandra, Carbonell Sala, Silvia, Chrast, Jacqueline, Cunningham, Fiona, Di Domenico, Tomás, Donaldson, Sarah, Fiddes, Ian T, García Girón, Carlos, Gonzalez, Jose Manuel, Grego, Tiago, Hardy, Matthew, Hourlier, Thibaut, Hunt, Toby, Izuogu, Osagie G, Lagarde, Julien, Martin, Fergal J, Martínez, Laura, Mohanan, Shamika, Muir, Paul, Navarro, Fabio C P, Parker, Anne, Pei, Baikang, Pozo, Fernando, Ruffier, Magali, Schmitt, Bianca M, Stapleton, Eloise, Suner, Marie-Marthe, Sycheva, Irina, Uszczynska-Ratajczak, Barbara, Xu, Jinuri, Yates, Andrew, Zerbino, Daniel, Zhang, Yan, Aken, Bronwen, Choudhary, Jyoti S, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J P, Kellis, Manolis, Paten, Benedict, Reymond, Alexandre, Tress, Michael L, and Flicek, Paul

Abstract

© 2018 The Author(s). The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend theGENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.

Published
2022

31. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Author

Pardo-Palacios, Francisco J., Wang, Dingjie, Reese, Fairlie, Diekhans, Mark, Carbonell-Sala, Sílvia, Williams, Brian, Loveland, Jane E., Adams, Matthew S., Balderrama-Gutierrez, Gabriela, Behera, Amit K., María, Maite De, Gonzalez, Jose M., Hunt, Toby, Lagarde, Julien, Li, Haoran, Liang, Cindy E., Prjibelski, Andrey D., Sheynkman, Leon, Amador, David Moraga, Barnes, If, Berry, Andrew, Çelik, Muhammed Hasan, Garcia-Reyero, Natàlia, Goetz, Stefan, Kondratova, Liudmyla, Martinez-Tomas, Jorge, Menor, Carlos, Mudge, Jonathan M., Paniagua, Alejandro, Suner, Marie-Marthe, Takahashi, Hazuki, Tang, Alison D., Youngworth, Ingrid Ashley, Carninci, Piero, Denslow, Nancy, Guigó, Roderic, Hunter, Margaret E., Tilgner, Hagen U., Wold, Barbara J., Vollmers, Christopher, Frankish, Adam, Au, Kin Fai, Sheynkman, Gloria M., Conesa, Ana, Mortazavi, Ali, and Brooks, Angela N.

Abstract

With increased usage of long-read sequencing technologies to perform transcriptome analyses, there becomes a greater need to evaluate different methodologies including library preparation, sequencing platform, and computational analysis tools. Here, we report the study design of a community effort called the Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium, whose goals are characterizing the strengths and remaining challenges in using long-read approaches to identify and quantify the transcriptomes of both model and non-model organisms. The LRGASP organizers have generated cDNA and direct RNA datasets in human, mouse, and manatee samples using different protocols followed by sequencing on Illumina, Pacific Biosciences, and Oxford Nanopore Technologies platforms. Participants will use the provided data to submit predictions for three challenges: transcript isoform detection with a high-quality genome, transcript isoform quantification, and de novo transcript isoform identification. Evaluators from different institutions will determine which pipelines have the highest accuracy for a variety of metrics using benchmarks that include spike-in synthetic transcripts, simulated data, and a set of undisclosed, manually curated transcripts by GENCODE. We also describe plans for experimental validation of predictions that are platform-specific and computational tool-specific. We believe that a community effort to evaluate long-read RNA-seq methods will help move the field toward a better consensus on the best approaches to use for transcriptome analyses. Items: The LRGASP Registered Report Supplementary File Supplementary Figures Supplementary Table 1

Published
2022
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33. GENCODE: reference annotation for the human and mouse genomes in 2023.

Author

Frankish, Adam, Carbonell-Sala, Sílvia, Diekhans, Mark, Jungreis, Irwin, Loveland, Jane E, Mudge, Jonathan M, Sisu, Cristina, Wright, James C, Arnan, Carme, Barnes, If, Banerjee, Abhimanyu, Bennett, Ruth, Berry, Andrew, Bignell, Alexandra, Boix, Carles, Calvet, Ferriol, Cerdán-Vélez, Daniel, Cunningham, Fiona, Davidson, Claire, and Donaldson, Sarah

Published
2023
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34. Ensembl 2022

Author

Cunningham, Fiona, primary, Allen, James E, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Austine-Orimoloye, Olanrewaju, additional, Azov, Andrey G, additional, Barnes, If, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bhai, Jyothish, additional, Bignell, Alexandra, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Brooks, Lucy, additional, Charkhchi, Mehrnaz, additional, Cummins, Carla, additional, Da Rin Fioretto, Luca, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, Donaldson, Sarah, additional, El Houdaigui, Bilal, additional, El Naboulsi, Tamara, additional, Fatima, Reham, additional, Giron, Carlos Garcia, additional, Genez, Thiago, additional, Martinez, Jose Gonzalez, additional, Guijarro-Clarke, Cristina, additional, Gymer, Arthur, additional, Hardy, Matthew, additional, Hollis, Zoe, additional, Hourlier, Thibaut, additional, Hunt, Toby, additional, Juettemann, Thomas, additional, Kaikala, Vinay, additional, Kay, Mike, additional, Lavidas, Ilias, additional, Le, Tuan, additional, Lemos, Diana, additional, Marugán, José Carlos, additional, Mohanan, Shamika, additional, Mushtaq, Aleena, additional, Naven, Marc, additional, Ogeh, Denye N, additional, Parker, Anne, additional, Parton, Andrew, additional, Perry, Malcolm, additional, Piližota, Ivana, additional, Prosovetskaia, Irina, additional, Sakthivel, Manoj Pandian, additional, Salam, Ahamed Imran Abdul, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Pérez-Silva, José G, additional, Stark, William, additional, Steed, Emily, additional, Sutinen, Kyösti, additional, Sukumaran, Ranjit, additional, Sumathipala, Dulika, additional, Suner, Marie-Marthe, additional, Szpak, Michal, additional, Thormann, Anja, additional, Tricomi, Francesca Floriana, additional, Urbina-Gómez, David, additional, Veidenberg, Andres, additional, Walsh, Thomas A, additional, Walts, Brandon, additional, Willhoft, Natalie, additional, Winterbottom, Andrea, additional, Wass, Elizabeth, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Frankish, Adam, additional, Giorgetti, Stefano, additional, Haggerty, Leanne, additional, Hunt, Sarah E, additional, IIsley, Garth R, additional, Loveland, Jane E, additional, Martin, Fergal J, additional, Moore, Benjamin, additional, Mudge, Jonathan M, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Tate, John, additional, Thybert, David, additional, Trevanion, Stephen J, additional, Dyer, Sarah, additional, Harrison, Peter W, additional, Howe, Kevin L, additional, Yates, Andrew D, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2021
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35. A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

Author

Mudge, Jonathan M., primary, Ruiz-Orera, Jorge, additional, Prensner, John R., additional, Brunet, Marie A., additional, Gonzalez, Jose Manuel, additional, Magrane, Michele, additional, Martinez, Thomas, additional, Schulz, Jana Felicitas, additional, Yang, Yucheng T., additional, Albà, M. Mar, additional, Baranov, Pavel V., additional, Bazzini, Ariel, additional, Bruford, Elspeth, additional, Martin, Maria Jesus, additional, Carvunis, Anne-Ruxandra, additional, Chen, Jin, additional, Couso, Juan Pablo, additional, Flicek, Paul, additional, Frankish, Adam, additional, Gerstein, Mark, additional, Hubner, Norbert, additional, Ingolia, Nicholas T., additional, Menschaert, Gerben, additional, Ohler, Uwe, additional, Roucou, Xavier, additional, Saghatelian, Alan, additional, Weissman, Jonathan, additional, and van Heesch, Sebastiaan, additional

Published
2021
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36. GENCODE 2021

Author

Frankish, Adam, Diekhans, Mark, Jungreis, Irwin, Lagarde, Julien, Loveland, Jane E, Mudge, Jonathan M, Sisu, Cristina, Wright, James C, Armstrong, Joel, Barnes, If, Berry, Andrew, Bignell, Alexandra, Boix, Carles, Carbonell Sala, Silvia, Cunningham, Fiona, Di Domenico, Tomás, Donaldson, Sarah, Fiddes, Ian T, García Girón, Carlos, Gonzalez, Jose Manuel, Grego, Tiago, Hardy, Matthew, Hourlier, Thibaut, Howe, Kevin L, Hunt, Toby, Izuogu, Osagie G, Johnson, Rory, Martin, Fergal J, Martínez, Laura, Mohanan, Shamika, Muir, Paul, Navarro, Fabio C P, Parker, Anne, Pei, Baikang, Pozo, Fernando, Riera, Ferriol Calvet, Ruffier, Magali, Schmitt, Bianca M, Stapleton, Eloise, Suner, Marie-Marthe, Sycheva, Irina, Uszczynska-Ratajczak, Barbara, Wolf, Maxim Y, Xu, Jinuri, Yang, Yucheng T, Yates, Andrew, Zerbino, Daniel, Zhang, Yan, Choudhary, Jyoti S, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J P, Kellis, Manolis, Paten, Benedict, Tress, Michael L, and Flicek, Paul

Subjects
ComputingMethodologies_PATTERNRECOGNITION, 610 Medicine & health
Abstract

The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Published
2021
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37. RNAcentral 2021:Secondary structure integration, improved sequence search and new member databases

Author

Sweeney, Blake A., Petrov, Anton I., Ribas, Carlos E., Finn, Robert D., Bateman, Alex, Szymanski, MacIej, Karlowski, Wojciech M., Seemann, Stefan E., Gorodkin, Jan, Cannone, Jamie J., Gutell, Robin R., Kay, Simon, Marygold, Steven, Dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M., Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P., Lowe, Todd M., Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G., Ma, Lina, Zhang, Zhang, Volders, Pieter Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J., Kalvari, Ioanna, Nawrocki, Eric P., Petrov, Anton S., Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M., Hoksza, David, Lovering, Ruth C., Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, Weinberg, Zasha, Sweeney, Blake A., Petrov, Anton I., Ribas, Carlos E., Finn, Robert D., Bateman, Alex, Szymanski, MacIej, Karlowski, Wojciech M., Seemann, Stefan E., Gorodkin, Jan, Cannone, Jamie J., Gutell, Robin R., Kay, Simon, Marygold, Steven, Dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M., Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P., Lowe, Todd M., Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G., Ma, Lina, Zhang, Zhang, Volders, Pieter Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J., Kalvari, Ioanna, Nawrocki, Eric P., Petrov, Anton S., Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M., Hoksza, David, Lovering, Ruth C., Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, and Weinberg, Zasha

Abstract

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.

Published
2021

38. Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Martinez-Gomez, Laura, Abascal, Federico, Jungreis, Irwin, Pozo, Fernando, Kellis, Manolis, Mudge, Jonathan M, Tress, Michael L, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Martinez-Gomez, Laura, Abascal, Federico, Jungreis, Irwin, Pozo, Fernando, Kellis, Manolis, Mudge, Jonathan M, and Tress, Michael L

Abstract

Transposable elements colonize genomes and with time may end up being incorporated into functional regions. SINE Alu elements, which appeared in the primate lineage, are ubiquitous in the human genome and more than a thousand overlap annotated coding exons. Although almost all Alu-derived coding exons appear to be in alternative transcripts, they have been incorporated into the main coding transcript in at least 11 genes. The extent to which Alu regions are incorporated into functional proteins is unclear, but we detected reliable peptide evidence to support the translation to protein of 33 Alu-derived exons. All but one of the Alu elements for which we detected peptides were frame-preserving and there was proportionally seven times more peptide evidence for Alu elements as for other primate exons. Despite this strong evidence for translation to protein we found no evidence of selection, either from cross species alignments or human population variation data, among these Alu-derived exons. Overall, our results confirm that SINE Alu elements have contributed to the expansion of the human proteome, and this contribution appears to be stronger than might be expected over such a relatively short evolutionary timeframe. Despite this, the biological relevance of these modifications remains open to question., National Human Genome Research Institute (Grants 2-U41-HG007234 and R01-HG004037)

Published
2021

39. Author Correction: Transcript expression-aware annotation improves rare variant interpretation

Author

Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, and Mudge, Jonathan M.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41586-020-03175-7, Author(s): Beryl B. Cummings [sup.1] [sup.2] [sup.3], Konrad J. Karczewski [sup.1] [sup.2], Jack A. Kosmicki [sup.1] [sup.2] [sup.4], Eleanor G. Seaby [sup.1] [sup.2] [sup.5], Nicholas A. Watts [sup.1] [sup.2], Moriel [...]

Published
2021
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40. Transcript expression-aware annotation improves rare variant interpretation

Author

Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, Mudge, Jonathan M., Karjalainen, Juha, Satterstrom, F. Kyle, O’Donnell-Luria, Anne H., Poterba, Timothy, Seed, Cotton, Solomonson, Matthew, Alföldi, Jessica, Armean, Irina M., Banks, Eric, Bergelson, Louis, Cibulskis, Kristian, Collins, Ryan L., Connolly, Kristen M., Covarrubias, Miguel, Daly, Mark J., Donnelly, Stacey, Farjoun, Yossi, Ferriera, Steven, Francioli, Laurent, Gabriel, Stacey, Gauthier, Laura D., Gentry, Jeff, Gupta, Namrata, Jeandet, Thibault, Kaplan, Diane, Laricchia, Kristen M., Llanwarne, Christopher, Minikel, Eric V., Munshi, Ruchi, Neale, Benjamin M., Novod, Sam, Petrillo, Nikelle, Roazen, David, Ruano-Rubio, Valentin, Saltzman, Andrea, Lehtimäki, Terho, Mattila, Kari M., Suvisaari, Jaana, Tampere University, Clinical Medicine, Department of Clinical Chemistry, Centre of Excellence in Complex Disease Genetics, HUS Abdominal Center, Department of Medicine, Clinicum, Gastroenterologian yksikkö, HUS Psychiatry, Department of Psychiatry, HUS Neurocenter, Department of Neurosciences, Neurologian yksikkö, Institute for Molecular Medicine Finland, Department of Public Health, Aarno Palotie / Principal Investigator, Genomics of Neurological and Neuropsychiatric Disorders, Biosciences, Samuli Olli Ripatti / Principal Investigator, Complex Disease Genetics, and Biostatistics Helsinki

Subjects
Male, Transcription, Genetic, Autism Spectrum Disorder, Developmental Disabilities, Datasets as Topic, Haploinsufficiency, Human genetic variation, Genome, Exon, 0302 clinical medicine, Loss of Function Mutation, Disease, Poisson Distribution, Exome sequencing, 0303 health sciences, education.field_of_study, Multidisciplinary, Disease genetics, ARRHYTHMIA, 1184 Genetics, developmental biology, physiology, Genome Aggregation Database Production Team, Exons, Female, Medical genomics, GENES, Genotype, General Science & Technology, Population, Computational biology, Biology, 3121 Internal medicine, Article, DNA sequencing, 03 medical and health sciences, Rare Diseases, Intellectual Disability, Exome Sequencing, Humans, RNA, Messenger, Author Correction, Transcriptomics, education, Gene, 030304 developmental biology, MUTATIONS, Alternative splicing, Reproducibility of Results, Molecular Sequence Annotation, Genome Aggregation Database Consortium, 3111 Biomedicine, Transcriptome, 030217 neurology & neurosurgery
Abstract

The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD)1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the ‘proportion expressed across transcripts’, which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies., A novel variant annotation metric that quantifies the level of expression of genetic variants across tissues is validated in the Genome Aggregation Database (gnomAD) and is shown to improve rare variant interpretation.

Published
2020

41. GENCODE 2021

Author

Frankish, Adam, primary, Diekhans, Mark, additional, Jungreis, Irwin, additional, Lagarde, Julien, additional, Loveland, Jane E, additional, Mudge, Jonathan M, additional, Sisu, Cristina, additional, Wright, James C, additional, Armstrong, Joel, additional, Barnes, If, additional, Berry, Andrew, additional, Bignell, Alexandra, additional, Boix, Carles, additional, Carbonell Sala, Silvia, additional, Cunningham, Fiona, additional, Di Domenico, Tomás, additional, Donaldson, Sarah, additional, Fiddes, Ian T, additional, García Girón, Carlos, additional, Gonzalez, Jose Manuel, additional, Grego, Tiago, additional, Hardy, Matthew, additional, Hourlier, Thibaut, additional, Howe, Kevin L, additional, Hunt, Toby, additional, Izuogu, Osagie G, additional, Johnson, Rory, additional, Martin, Fergal J, additional, Martínez, Laura, additional, Mohanan, Shamika, additional, Muir, Paul, additional, Navarro, Fabio C P, additional, Parker, Anne, additional, Pei, Baikang, additional, Pozo, Fernando, additional, Riera, Ferriol Calvet, additional, Ruffier, Magali, additional, Schmitt, Bianca M, additional, Stapleton, Eloise, additional, Suner, Marie-Marthe, additional, Sycheva, Irina, additional, Uszczynska-Ratajczak, Barbara, additional, Wolf, Maxim Y, additional, Xu, Jinuri, additional, Yang, Yucheng T, additional, Yates, Andrew, additional, Zerbino, Daniel, additional, Zhang, Yan, additional, Choudhary, Jyoti S, additional, Gerstein, Mark, additional, Guigó, Roderic, additional, Hubbard, Tim J P, additional, Kellis, Manolis, additional, Paten, Benedict, additional, Tress, Michael L, additional, and Flicek, Paul, additional

Published
2020
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42. Non‐coding regulatory elements: Potential roles in disease and the case of epilepsy.

Author

Pagni, Susanna, Mills, James D., Frankish, Adam, Mudge, Jonathan M., and Sisodiya, Sanjay M.

Subjects
GENE enhancers, RIBOSOMAL DNA, NON-coding DNA, LINCRNA, EPILEPSY, RIBOSOMAL RNA, PARKINSON'S disease
Abstract

Non‐coding DNA (ncDNA) refers to the portion of the genome that does not code for proteins and accounts for the greatest physical proportion of the human genome. ncDNA includes sequences that are transcribed into RNA molecules, such as ribosomal RNAs (rRNAs), microRNAs (miRNAs), long non‐coding RNAs (lncRNAs) and un‐transcribed sequences that have regulatory functions, including gene promoters and enhancers. Variation in non‐coding regions of the genome have an established role in human disease, with growing evidence from many areas, including several cancers, Parkinson's disease and autism. Here, we review the features and functions of the regulatory elements that are present in the non‐coding genome and the role that these regions have in human disease. We then review the existing research in epilepsy and emphasise the potential value of further exploring non‐coding regulatory elements in epilepsy. In addition, we outline the most widely used techniques for recognising regulatory elements throughout the genome, current methodologies for investigating variation and the main challenges associated with research in the field of non‐coding DNA. [ABSTRACT FROM AUTHOR]

Published
2022
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44. Ensembl 2021

Author

Howe, Kevin L, primary, Achuthan, Premanand, additional, Allen, James, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Azov, Andrey G, additional, Bennett, Ruth, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Charkhchi, Mehrnaz, additional, Cummins, Carla, additional, Da Rin Fioretto, Luca, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, El Houdaigui, Bilal, additional, Fatima, Reham, additional, Gall, Astrid, additional, Garcia Giron, Carlos, additional, Grego, Tiago, additional, Guijarro-Clarke, Cristina, additional, Haggerty, Leanne, additional, Hemrom, Anmol, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Juettemann, Thomas, additional, Kaikala, Vinay, additional, Kay, Mike, additional, Lavidas, Ilias, additional, Le, Tuan, additional, Lemos, Diana, additional, Gonzalez Martinez, Jose, additional, Marugán, José Carlos, additional, Maurel, Thomas, additional, McMahon, Aoife C, additional, Mohanan, Shamika, additional, Moore, Benjamin, additional, Muffato, Matthieu, additional, Oheh, Denye N, additional, Paraschas, Dimitrios, additional, Parker, Anne, additional, Parton, Andrew, additional, Prosovetskaia, Irina, additional, Sakthivel, Manoj P, additional, Salam, Ahamed I Abdul, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Steed, Emily, additional, Szpak, Michal, additional, Szuba, Marek, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Threadgold, Glen, additional, Walts, Brandon, additional, Winterbottom, Andrea, additional, Chakiachvili, Marc, additional, Chaubal, Ameya, additional, De Silva, Nishadi, additional, Flint, Bethany, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, IIsley, Garth R, additional, Langridge, Nick, additional, Loveland, Jane E, additional, Martin, Fergal J, additional, Mudge, Jonathan M, additional, Morales, Joanella, additional, Perry, Emily, additional, Ruffier, Magali, additional, Tate, John, additional, Thybert, David, additional, Trevanion, Stephen J, additional, Cunningham, Fiona, additional, Yates, Andrew D, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2020
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47. Transcript expression-aware annotation improves rare variant discovery and interpretation

Author

Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, Mudge, Jonathan M., Karjalainen, Juha, Satterstrom, F. Kyle, O’Donnell-Luria, Anne, Poterba, Timothy, Seed, Cotton, Solomonson, Matthew, Alföldi, Jessica, Daly, Mark J., and MacArthur, Daniel G.

Subjects
0303 health sciences, 03 medical and health sciences, Annotation, 0302 clinical medicine, Computational biology, Biology, 030217 neurology & neurosurgery, 030304 developmental biology, Gene transcript, Interpretation (model theory)
Abstract

The acceleration of DNA sequencing in patients and population samples has resulted in unprecedented catalogues of human genetic variation, but the interpretation of rare genetic variants discovered using such technologies remains extremely challenging. A striking example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Through manual curation of putative loss of function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD)(1), we show that one explanation for this paradox involves alternative mRNA splicing, which allows exons of a gene to be expressed at varying levels across cell types. Currently, no existing annotation tool systematically incorporates this exon expression information into variant interpretation. Here, we develop a transcript-level annotation metric, the proportion expressed across transcripts (pext), which summarizes isoform quantifications for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression project(2) (GTEx) and show that it clearly differentiates between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder (ASD) and developmental disorders and intellectual disability (DD/ID) to show that pLoF variants in weakly expressed regions have effect sizes similar to those of synonymous variants, while pLoF variants in highly expressed exons are most strongly enriched among cases versus controls. Our annotation is fast, flexible, and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for rare disease diagnosis, rare variant burden analyses in complex disorders, and curation and prioritization of variants in recall-by-genotype studies.

Published
2019

48. Ensembl 2020

Author

Yates, Andrew D, primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Allen, James, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Azov, Andrey G, additional, Bennett, Ruth, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Marugán, José Carlos, additional, Cummins, Carla, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, Fatima, Reham, additional, Gall, Astrid, additional, Giron, Carlos Garcia, additional, Gil, Laurent, additional, Grego, Tiago, additional, Haggerty, Leanne, additional, Haskell, Erin, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Janacek, Sophie H, additional, Juettemann, Thomas, additional, Kay, Mike, additional, Lavidas, Ilias, additional, Le, Tuan, additional, Lemos, Diana, additional, Martinez, Jose Gonzalez, additional, Maurel, Thomas, additional, McDowall, Mark, additional, McMahon, Aoife, additional, Mohanan, Shamika, additional, Moore, Benjamin, additional, Nuhn, Michael, additional, Oheh, Denye N, additional, Parker, Anne, additional, Parton, Andrew, additional, Patricio, Mateus, additional, Sakthivel, Manoj Pandian, additional, Abdul Salam, Ahamed Imran, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sycheva, Mira, additional, Szuba, Marek, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Threadgold, Glen, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Winterbottom, Andrea, additional, Zadissa, Amonida, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, IIsley, Garth, additional, Kostadima, Myrto, additional, Langridge, Nick, additional, Loveland, Jane E, additional, Martin, Fergal J, additional, Morales, Joannella, additional, Mudge, Jonathan M, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Trevanion, Stephen J, additional, Cunningham, Fiona, additional, Howe, Kevin L, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2019
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49. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

Author

Mudge, Jonathan M., primary, Jungreis, Irwin, additional, Hunt, Toby, additional, Gonzalez, Jose Manuel, additional, Wright, James C., additional, Kay, Mike, additional, Davidson, Claire, additional, Fitzgerald, Stephen, additional, Seal, Ruth, additional, Tweedie, Susan, additional, He, Liang, additional, Waterhouse, Robert M., additional, Li, Yue, additional, Bruford, Elspeth, additional, Choudhary, Jyoti S., additional, Frankish, Adam, additional, and Kellis, Manolis, additional

Published
2019
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50. Cell type specific novel lincRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas

Author

Grassi, Luigi, primary, Izuogu, Osagie G., additional, Jorge, Natasha A.N., additional, Seyres, Denis, additional, Bustamante, Mariona, additional, Burden, Frances, additional, Farrow, Samantha, additional, Farahi, Neda, additional, Martin, Fergal J., additional, Frankish, Adam, additional, Mudge, Jonathan M., additional, Kostadima, Myrto, additional, Petersen, Romina, additional, Lambourne, John J., additional, Rowlston, Sophia, additional, Martin-Rendon, Enca, additional, Clarke, Laura, additional, Downes, Kate, additional, Estivill, Xavier, additional, Flicek, Paul, additional, Martens, Joost H.A., additional, Yaspo, Marie-Laure, additional, Stunnenberg, Hendrik G., additional, Ouwehand, Willem H., additional, Passetti, Fabio, additional, Turro, Ernest, additional, and Frontini, Mattia, additional

Published
2019
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