[HTML][HTML] Systematic identification of smORFs in domestic silkworm (Bombyx mori)

L Wan, W Xiao, Z Huang, A Zhou, Y Jiang, B Zou, B Liu… - PeerJ, 2023 - peerj.com
The silkworm (Bombyx mori) is not only an excellent model species, but also an important
agricultural economic insect. Taking it as the research object, its advantages of low …

CPPred-sORF: coding potential prediction of sORF based on non-AUG

X Tong, X Hong, J Xie, S Liu - BioRxiv, 2020 - biorxiv.org
In recent years, researchers have discovered thousands of sORFs that can encode
micropeptides, and more and more discoveries that non-AUG codons can be used as …

How to overcome constraints imposed by microsporidian genome features to ensure gene prediction?

E Peyretaillade, RF Akossi, J Tournayre… - Journal of Eukaryotic …, 2024 - Wiley Online Library
Since the advent of sequencing techniques and due to their continuous evolution, it has
become easier and less expensive to obtain the complete genome sequence of any …

Rise of bacterial small proteins and peptides in therapeutic applications

R Shelin, S Meenakshi - Protein and Peptide Letters, 2023 - ingentaconnect.com
Background: Polypeptides that comprise less than 100 amino acids (50 amino acids in some
cases) are referred to as small proteins (SPs), however, as of date, there is no strict …

[HTML][HTML] Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses

S Leblanc, MA Brunet - Computational and Structural Biotechnology …, 2020 - Elsevier
The Zika virus is a flavivirus that can cause fulminant outbreaks and lead to Guillain-Barré
syndrome, microcephaly and fetal demise. Like other flaviviruses, the Zika virus is …

Multi-omics annotation of human long non-coding RNAs

Q Li, Z Li, C Feng, S Jiang, Z Zhang… - Biochemical Society …, 2020 - portlandpress.com
LncRNAs (long non-coding RNAs) are pervasively transcribed in the human genome and
also extensively involved in a variety of essential biological processes and human diseases …

A systematic evaluation revealed that detecting translated non-canonical ORFs from ribosome profiling data remains challenging

T Lei, Y Chang, C Yao, H Zhang - bioRxiv, 2022 - biorxiv.org
Non-canonical open reading frames (ORFs), which are ORFs that are not included in
reference genome annotations, are gaining more and more research interest in recent …

[HTML][HTML] Translational buffering by ribosome stalling in upstream open reading frames

TA Bottorff, H Park, AP Geballe… - PLoS genetics, 2022 - journals.plos.org
Upstream open reading frames (uORFs) are present in over half of all human mRNAs.
uORFs can potently regulate the translation of downstream open reading frames through …

Newfound coding potential of transcripts unveils missing members of human protein communities

S Leblanc, MA Brunet, JF Jacques… - Genomics …, 2023 - academic.oup.com
Recent proteogenomic approaches have led to the discovery that regions of the
transcriptome previously annotated as non-coding regions [ie, untranslated regions (UTRs) …

[HTML][HTML] A genomic approach to analyze the cold adaptation of yeasts isolated from Italian Alps

B Turchetti, P Buzzini, M Baeza - Frontiers in Microbiology, 2022 - frontiersin.org
Microorganisms including yeasts are responsible for mineralization of organic matter in cold
regions, and their characterization is critical to elucidate the ecology of such environments …