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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Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow by James C. Wright, Jonathan Mudge, Hendrik Weisser, Mitra P. Barzine, Jose M. Gonzalez, Alvis Brazma, Jyoti S. Choudhary, Jennifer Harrow

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GenCoder: A Generative AI-Based Adaptive Intra-Vehicle Intrusion Detection System by Mikhail Smolin

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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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Rare Splice Variants in Long Non-Coding RNAs by Rituparno Sen, Gero Doose, Peter F. Stadler

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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. …”

lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA. by Shaoli Das, Suman Ghosal, Rituparno Sen, Jayprokas Chakrabarti

“…The lncRNA targets of human miRNAs (up to GENCODE 11) are downloaded from miRCode database. miRNA targets on the rest of the GENCODE 19 lncRNAs are predicted by our algorithm for finding seed-matched target sites. …”
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Imaging Mass Cytometric Analysis of Postmortem Tissues Reveals Dysregulated Immune Cell and Cytokine Responses in Multiple Organs of COVID-19 Patients by Chong Wang, Chong Wang, Jiqian Xu, Shaoyuan Wang, Shangwen Pan, Jiancheng Zhang, Yang Han, Yang Han, Yang Han, Muhan Huang, Muhan Huang, Di Wu, Di Wu, Qingyu Yang, Xiaobo Yang, Yang Yang, Ting Shu, Ting Shu, Xiaojing Zou, Ruiting Li, Yufeng Luo, Runqing Yao, Yaxin Wang, Yang Qiu, Yang Qiu, Yu Wang, Ding-Yu Zhang, Qun Yao, Yongpan Yan, Xi Zhou, Xi Zhou, Xi Zhou, You Shang, You Shang, You Shang

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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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Amynthas corticis genome reveals molecular mechanisms behind global distribution by Xing Wang, Yi Zhang, Yufeng Zhang, Mingming Kang, Yuanbo Li, Samuel W. James, Yang Yang, Yanmeng Bi, Hao Jiang, Yi Zhao, Zhenjun Sun

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The 4p16.3 Parkinson Disease Risk Locus Is Associated with GAK Expression and Genes Involved with the Synaptic Vesicle Membrane. by Michael W Nagle, Jeanne C Latourelle, Adam Labadorf, Alexandra Dumitriu, Tiffany C Hadzi, Thomas G Beach, Richard H Myers

“…Furthermore, carriers of 4p16.3 PD GWAS risk SNPs show decreased expression of one of these transcripts, GAK25 (Gencode Transcript 009), which correlates with the expression of genes functioning in the synaptic vesicle membrane. …”
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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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Impact of human gene annotations on RNA-seq differential expression analysis by Yu Hamaguchi, Chao Zeng, Michiaki Hamada

“…Results Using “mappability”, a metric of the complexity of gene annotation, we compared three distinct human gene annotations, GENCODE, RefSeq, and NONCODE, and evaluated how mappability affected DE analysis. …”
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Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements by Jeong-An Gim, Hong-Seok Ha, Kung Ahn, Dae-Soo Kim, Heui-Soo Kim

“…In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. …”
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