Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms. by Hongyang Li, Ridvan Eksi, Daiyao Yi, Bradley Godfrey, Lisa R Mathew, Christopher L O'Connor, Markus Bitzer, Matthias Kretzler, Rajasree Menon, Yuanfang Guan

“…These transcripts were then validated using transcripts of the same samples by the traditional Illumina RNA-Seq protocol, distinct Illumina RNA-Seq short reads from European Renal cDNA Bank (ERCB) samples, and annotated GENCODE transcript list, thus identifying novel transcripts. …”
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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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TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association by Seo-Won Choi, Jin-Wu Nam

“…TERIUS was able to successfully re-classify GENCODE and miTranscriptome lncRNA annotations. We believe that TERIUS can benefit construction of extensive and accurate non-coding transcriptome maps in many genomes.…”
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Long non-coding RNA expression profiles in hereditary haemorrhagic telangiectasia. by Pernille M Tørring, Martin Jakob Larsen, Anette D Kjeldsen, Lilian Bomme Ousager, Qihua Tan, Klaus Brusgaard

“…The microarray probes were annotated using the GENCODE v.16 dataset, identifying 4,810 probes mapping to 2,811 lncRNAs. …”
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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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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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UROPA: a tool for Universal RObust Peak Annotation by Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso

“…UROPA can incorporate reference annotation files (GTF) from different sources (Gencode, Ensembl, RefSeq), as well as custom reference annotation files. …”
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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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GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation by Monah Abou Alezz, Ludovica Celli, Giulia Belotti, Antonella Lisa, Silvia Bione

“…In this study, we exploited recent annotations by GENCODE to characterize the genomic and splicing features of long non-coding genes in comparison with protein-coding ones, both in human and mouse. …”
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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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Development and validation of ferroptosis-related lncRNAs prognosis signatures in kidney renal clear cell carcinoma by Xiao-Liang Xing, Zhi-Yong Yao, Jialan Ou, Chaoqun Xing, Feng Li

“…Lists of ferroptosis-related genes and long non-coding RNAs were obtained from the FerrDb and GENCODE databases, respectively. The candidate prognostic signatures were screened by Cox regression analyses and least absolute shrinkage and selection operator analyses. …”
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Gene processing control loops suggested by sequencing, splicing, and RNA folding by Perkins Diana O, Jeffries Clark D, Guan Xiaojun

“…All 16-base source sequences in the UCSC Human Genome Browser are within the 14 instances of RNU1 genes listed in wgEncodeGencodeAutoV3. Furthermore, 10 of the 14 instances of the sequence are also within a common 28-nt hairpin-forming subsequence of RNU1.…”
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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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Identification of PBMC-based molecular signature associational with COVID-19 disease severity by Hibah Shaath, Nehad M. Alajez

“…We employed computational and transcriptome analyses of publicly available datasets from PBMCs from 126 patients with COVID-19 admitted to ICU (n = 50), COVID-19 not admitted to ICU (n = 50), non-COVID-19 admitted to ICU (n = 16) and non-COVID-19 not admitted to ICU (n = 10), and utilized the Gencode V33 assembly to analyze protein coding mRNA and long noncoding RNA (lncRNA) transcriptomes in the context of disease severity. …”
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Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach by Yi Zhang, Xinan Liu, James MacLeod, Jinze Liu

“…We show (I) DeepSplice outperforms state-of-the-art methods for splice site classification when applied to the popular benchmark dataset HS3D, (II) DeepSplice shows high accuracy for splice junction classification with GENCODE annotation, and (III) the application of DeepSplice to classify putative splice junctions generated by Rail-RNA alignment of 21,504 human RNA-seq data significantly reduces 43 million candidates into around 3 million highly confident novel splice junctions. …”
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The value of primary transcripts to the clinical and non‐clinical genomics community: Survey results and roadmap for improvements by Joannella Morales, Aoife C. McMahon, Jane Loveland, Emily Perry, Adam Frankish, Sarah Hunt, Irina M. Armean, Paul Flicek, Fiona Cunningham

“…First, both RefSeq and Ensembl/GENCODE produce transcript sets in common use, but there is currently no easy way to translate between the two. …”
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Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. by Gascoigne, D, Cheetham, S, Cattenoz, P, Clark, M, Amaral, P, Taft, R, Wilhelm, D, Dinger, M, Mattick, J

“…RESULTS: To demonstrate the efficacy of Pinstripe for large-scale analysis, we applied Pinstripe's reverse peptide mapping pipeline to a transcript library including de novo assembled transcriptomes from the human Illumina Body Atlas (IBA2) and GENCODE v10 gene annotations, and the EBI Proteomics Identifications Database (PRIDE) peptide database. …”

Human gene and disease associations for clinical‐genomics and precision medicine research by Zeeshan Ahmed, Saman Zeeshan, Dinesh Mendhe, XinQi Dong

“…Our focus here is to create a comprehensive database with mobile access to all available, authentic and actionable genes, SNPs, and classified diseases and drugs collected from different clinical and genomics databases worldwide, including Ensembl, GenCode, ClinVar, GeneCards, DISEASES, HGMD, OMIM, GTR, CNVD, Novoseek, Swiss‐Prot, LncRNADisease, Orphanet, GWAS Catalog, SwissVar, COSMIC, WHO, and FDA. …”
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