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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
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Abstract
CHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current genome annotation by integrating the latest reference data and algorithms, machine learning techniques for noise filtering, and new protein structure prediction methods. CHESS 3 contains 41,356 genes, including 19,839 protein-coding genes and 158,377 transcripts, with 14,863 protein-coding transcripts not in other catalogs. 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. CHESS 3 is available at http://ccb.jhu.edu/chess .
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Cites
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Cited by
Sorted by citations
Upstream open reading frames may contain hundreds of novel human exons
Ji, H. J., & Salzberg, S. L. (2024) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1012543 · Cited by 6
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Metadata
- Authors
- Varabyou, A., Sommer, M. J., Erdogdu, B., Shinder, I., Minkin, I., Chao, K.-H., Park, S., Heinz, J., Pockrandt, C., Shumate, A., Rincon, N., Puiu, D., Steinegger, M., Salzberg, S. L., & Pertea, M.
- Affiliations
- Johns Hopkins University (US)
- Seoul National University (KR)
- Corresponding author
- Varabyou, Ales
- Salzberg, Steven L.
- Pertea, Mihaela
- ORCID
- Venue
- Genome Biology
- Published
- 2023-10-30
- Volume
- 24
- Issue
- 1
- Pages
- 249-249
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC10614308
- OpenAlex
- W4388022000
- Cited by
- 54
- References
- 13
- Citations by year
- 2026: 14 · 2025: 23 · 2024: 13 · 2023: 4
- FWCI
- 4.81
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Seoul National University Open Repository (Seoul National University) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- National Institute of Mental Health (R01 MH123567)
- National Human Genome Research Institute (R01 HG006677)
- National Institute of General Medical Sciences (R35 GM130151)
- Directorate for Biological Sciences (DBI-1759518)
- National Research Foundation of Korea (2019R1-A6A1-A10073437, 2020M3-A9G7-103933, 2021-R1C1-C102065, 2021-M3A9-I4021220)
- Samsung DS research fund
- Creative-Pioneering Researchers Program at Seoul National University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- transcriptome, RNA-seq, genome annotation, protein-coding genes, transcriptome assembly, Manes, protein structure prediction, noise reduction, human body sites
- MeSH terms
- Algorithms, Humans, Phylogeny, Proteins, Software, Genome, Human, Molecular Sequence Annotation
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