Evidence map›Paper›PMID 37904256›Full record

ArticleGenome biology2023

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure.

Ales Varabyou, Markus J Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao, Sukhwan Park, Jakob Heinz, Christopher Pockrandt, Alaina Shumate and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.

0numbers the graph read from it
0cells of the map it votes in
44citing papers in PubMed
8.5field-weighted citation impact, top 2% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

44 citing papers in PubMed, 55 citations in OpenAlex.

  1. Article
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  4. Testing the reliability of AI-generated protein structures.bioRxiv : the preprint server for biology · 2026
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  6. Review
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  11. Review
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  14. Review
  15. Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes.bioRxiv : the preprint server for biology · 2025
    Article
  16. Article
  17. Isoswitching drives the aging process in human brains.bioRxiv : the preprint server for biology · 2025
    Article
  18. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors at 2 institutions in 2 countries.

Ales VarabyouCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. ales.varabyou@jhu.edu.ORCID 0000-0003-1060-7212
Markus J SommerCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Beril ErdogduCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Ida ShinderCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Ilia MinkinCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Kuan-Hao ChaoCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Sukhwan ParkSchool of Biological Sciences, Seoul National University, Seoul, South Korea.
Jakob HeinzCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Christopher PockrandtCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Alaina ShumateCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Natalia RinconCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Daniela PuiuCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Martin SteineggerSchool of Biological Sciences, Seoul National University, Seoul, South Korea.
Steven L SalzbergCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
Mihaela PerteaCenter for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. mpertea@jhu.edu.
Johns Hopkins University · USSeoul National University · KR

Funding

Computational Methods for Genome Assembly, Transcript Assembly, and Variant DiscoveryR01HG006677 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2011 to 2025
$10.7M
Computational Methods for Microbial and Microbiome Sequence AnalysisR35GM130151 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Steven L. Salzberg · 2019 to 2026
$2.9M
Comprehensive Human Expressed Sequences in Brain (CHESS-BRAIN) and their roles in neuropsychiatric illnessR01MH123567 · NIMH · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2021 to 2025
$2.8M
NHGRI NIH HHS R01 HG006677NIGMS NIH HHS R35 GM130151NIMH NIH HHS R01 MH123567
6 · The paper itself

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 .

Indexed as

Genome, HumanProteinsAlgorithmsHumansMolecular Sequence AnnotationPhylogenySoftwareProteins

Identifiers

PMID37904256
PMCPMC10614308
OpenAlexW4388022000

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.