GENCODE 2021

“…<jats:title>Abstract</jats:title> <jats:p>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. …”
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GENCODE 2021 by Boix, Carles

“…<jats:title>Abstract</jats:title> <jats:p>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. …”
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The GENCODE human gene set by Searle, S., Frankish, A., Bignell, A., Aken, B., Derrien, Thomas, Diekhans, M., Harte, R., Howald, C., Kokocinski, F., Lin, M., Tress, M., Van Baren, M., Barnes, I., Hunt, T., Carvalho-Silva, D., Davidson, C., Donaldson, S., Gilbert, J., Kay, M., Lloyd, D., Loveland, J., Mudge, J., Snow, C., Vamathevan, J., Wilming, L., Brent, M., Gerstein, Mark B., Guigo, Roderic, Kellis, Manolis, Reymond, A., Zadissa, A., Valencia, A., Harrow, J., Hubbard, T.

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GENCODE reference annotation for the human and mouse genomes

“…The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend theGENCODE gene annotation. …”
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GENCODE reference annotation for the human and mouse genomes by 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

“…The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend theGENCODE gene annotation. …”
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GENCODE: The reference human genome annotation for The ENCODE Project by Lin, Michael F., Kellis, Manolis

“…The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. …”
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Human Transcriptome and Chromatin Modifications: An ENCODE Perspective by Li Shen, Inchan Choi, Eric J. Nestler, Kyoung-Jae Won

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Improved definition of the mouse transcriptome via targeted RNA sequencing by Bussotti, G, Leonardi, T, Clark, M, Mercer, T, Crawford, J, Malquori, L, Notredame, C, Dinger, M, Mattick, J, Enright, A

“…Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. …”

Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome by Michael John Milligan, Erin eHarvey, Albert eYu, Ashleigh eMorgan, Caio eDamski, Daniela-Lee eSmith, Eden eZhang, Jothini eSivananthan, Jonathan eBerengut, Radhini eSubramaniam, Aleksandra eSkoric, Scott eCollins, Kevin V Morris, Kevin V Morris, Leonard eLipovich

“…As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72); Retroposed Pseudogenes V5 (processed only) and Yale Pseudo60 (processed and unprocessed, Ensembl 60); two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. …”
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Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci by Jungreis, Irwin, He, Liang, Li, Yue, Kellis, Manolis

“…We analyze more than 1000 highscoring human PhyloCSF regions and confidently add 144 conserved protein-coding genes to the GENCODE gene set, as well as additional coding regions within 236 previously annotated protein-coding genes, and 169 pseudogenes, most of them disabled after primates diverged. …”
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AnnoTrack - a tracking system for genome annotation by Hubbard Tim, Harrow Jennifer, Kokocinski Felix

“…</p> <p>Results</p> <p>As part of the scale-up phase of the ENCODE project (Encyclopedia of DNA Elements), the aim of the GENCODE project is to produce a highly accurate evidence-based reference gene annotation for the human genome. …”
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Mechanisms of Long Non-Coding RNA in Breast Cancer by Bianca Giuliani, Chiara Tordonato, Francesco Nicassio

“…So far, about 19,000 lncRNAs genes have been annotated in the human genome (Gencode 41), nearly matching the number of protein-coding genes. …”
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Transcript assembly and annotations: Bias and adjustment. by Qimin Zhang, Mingfu Shao

“…The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between their methodologies and information resources can lead to significant differences. …”
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SNP_TATA_COMPARATOR: Web SERVICE FOR COMPARISON OF SNPs WITHIN GENE PROMOTЕRS ASSOCIATED WITH HUMAN DISEASES USING THE EQUILIBRIUM EQUATION OF THE TBP/TATA COMPLEX by D. A. Rasskazov, K. V. Gunbin, P. M. Ponomarenko, O. V. Vishnevsky, M. P. Ponomarenko, D. A. Afonnikov

“…Data of individual deviations from the reference human genome (Ensembl, rel. 68, i.e. the variant of human genome commonly accepted as datum in comparison analysis) are accessible for free in the real-time mode. Also, data from the GENCODE database (rel. 17) are automatically invoked. …”
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Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. by Rozita Akrami, Anders Jacobsen, Jessica Hoell, Nikolaus Schultz, Chris Sander, Erik Larsson

“…Here, we report on a genomic analysis of GENCODE lncRNAs in high-grade serous ovarian adenocarcinoma, based on The Cancer Genome Atlas (TCGA) molecular profiles. …”
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CI-SpliceAI-Improving machine learning predictions of disease causing splicing variants using curated alternative splice sites. by Yaron Strauch, Jenny Lord, Mahesan Niranjan, Diana Baralle

“…Limiting the data to only validated and manual annotated primary and alternatively spliced GENCODE sites in training may improve predictive abilities. …”
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CaTCH: Calculating transcript complexity of human genes by Koushiki Basu, Anubha Dey, Manjari Kiran

“…According to the latest GENCODE annotations, most genes have less than four transcripts, positively correlating with the number of exons. …”
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CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure by Ales Varabyou, Markus J. Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao, Sukhwan Park, Jakob Heinz, Christopher Pockrandt, Alaina Shumate, Natalia Rincon, Daniela Puiu, Martin Steinegger, Steven L. Salzberg, Mihaela Pertea

“…It includes all MANE transcripts and at least one transcript for most RefSeq and GENCODE genes. On the CHM13 human genome, the CHESS 3 catalog contains an additional 129 protein-coding genes. …”
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Genome-Wide Differential Transcription of Long Noncoding RNAs in Psoriatic Skin by Valerie M. Stacey, Sulev Kõks

“…We computationally screened lncRNA transcripts as annotated by GENCODE across the human genome and compared transcription in psoriatic and healthy samples from two separate studies. …”
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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis by Carlevaro-Fita, Joana, Lanzós, Andrés, Feuerbach, Lars, Hong, Chen, Mas-Ponte, David, Pedersen, Jakob Skou, Johnson, Rory, Kellis, Manolis, PCAWG Drivers and Functional Interpretation Group

“…Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. …”
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