The status of the human gene catalogue

P Amaral, S Carbonell-Sala, FM De La Vega, T Faial… - Nature, 2023 - nature.com
Scientists have been trying to identify every gene in the human genome since the initial draft
was published in 2001. In the years since, much progress has been made in identifying …

Evolution and implications of de novo genes in humans

LA Broeils, J Ruiz-Orera, B Snel, N Hubner… - Nature ecology & …, 2023 - nature.com
Genes and translated open reading frames (ORFs) that emerged de novo from previously
non-coding sequences provide species with opportunities for adaptation. When aberrantly …

The ProteomeXchange consortium at 10 years: 2023 update

EW Deutsch, N Bandeira, Y Perez-Riverol… - Nucleic acids …, 2023 - academic.oup.com
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput
proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www …

Genenames. org: the HGNC resources in 2023

RL Seal, B Braschi, K Gray, TEM Jones… - Nucleic Acids …, 2023 - academic.oup.com
Abstract The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and
names to human genes. The HGNC database (www. genenames. org) currently contains …

GENCODE: reference annotation for the human and mouse genomes in 2023

A Frankish, S Carbonell-Sala, M Diekhans… - Nucleic acids …, 2023 - academic.oup.com
GENCODE produces high quality gene and transcript annotation for the human and mouse
genomes. All GENCODE annotation is supported by experimental data and serves as a …

Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames

CL Sandmann, JF Schulz, J Ruiz-Orera, M Kirchner… - Molecular cell, 2023 - cell.com
All species continuously evolve short open reading frames (sORFs) that can be templated
for protein synthesis and may provide raw materials for evolutionary adaptation. We …

What can Ribo-Seq, immunopeptidomics, and proteomics tell us about the noncanonical proteome?

JR Prensner, JG Abelin, LW Kok, KR Clauser… - Molecular & Cellular …, 2023 - Elsevier
Abstract Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of
the human genome and proteome by illuminating thousands of noncanonical sites of …

[HTML][HTML] Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma

DA Hofman, J Ruiz-Orera, I Yannuzzi, R Murugesan… - Molecular Cell, 2024 - cell.com
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation.
Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively …

The 2022 report on the human proteome from the HUPO human proteome project

GS Omenn, L Lane, CM Overall, C Pineau… - Journal of proteome …, 2022 - ACS Publications
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP)
show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 …

Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features

H Yang, Q Li, EK Stroup, S Wang, Z Ji - Nature communications, 2024 - nature.com
Studies have revealed dozens of functional peptides in putative 'noncoding'regions and
raised the question of how many proteins are encoded by noncanonical open reading …