KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences
Z Zhang - Genomics, Proteomics and Bioinformatics, 2022 - academic.oup.com
Abstract KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective
pressure on both coding and non-coding sequences. Similar to the nonsynonymous …
pressure on both coding and non-coding sequences. Similar to the nonsynonymous …
LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations
Z Li, L Liu, C Feng, Y Qin, J Xiao… - Nucleic Acids …, 2023 - academic.oup.com
LncBook, a comprehensive resource of human long non-coding RNAs (lncRNAs), has been
used in a wide range of lncRNA studies across various biological contexts. Here, we present …
used in a wide range of lncRNA studies across various biological contexts. Here, we present …
Discovering microproteins: making the most of ribosome profiling data
Building a reference set of protein-coding open reading frames (ORFs) has revolutionized
biological process discovery and understanding. Traditionally, gene models have been …
biological process discovery and understanding. Traditionally, gene models have been …
[HTML][HTML] What can ribo-seq, immunopeptidomics, and proteomics tell us about the noncanonical proteome?
Abstract Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of
the human genome and proteome by illuminating thousands of noncanonical sites of …
the human genome and proteome by illuminating thousands of noncanonical sites of …
[HTML][HTML] Small open Reading frame-encoded Micro-peptides: an emerging protein world
X Dong, K Zhang, C Xun, T Chu, S Liang… - International Journal of …, 2023 - mdpi.com
Small open reading frames (sORFs) are often overlooked features in genomes. In the past,
they were labeled as noncoding or “transcriptional noise”. However, accumulating evidence …
they were labeled as noncoding or “transcriptional noise”. However, accumulating evidence …
NPInter v5. 0: ncRNA interaction database in a new era
Y Zheng, H Luo, X Teng, X Hao, X Yan… - Nucleic acids …, 2023 - academic.oup.com
Noncoding RNAs (ncRNAs) play key regulatory roles in biological processes by interacting
with other biomolecules. With the development of high-throughput sequencing and …
with other biomolecules. With the development of high-throughput sequencing and …
OpenProt 2.0 builds a path to the functional characterization of alternative proteins
The OpenProt proteogenomic resource (https://www. openprot. org/) provides users with a
complete and freely accessible set of non-canonical or alternative open reading frames …
complete and freely accessible set of non-canonical or alternative open reading frames …
EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments
B Zhou, B Ji, C Shen, X Zhang, X Yu… - Nucleic Acids …, 2024 - academic.oup.com
Long noncoding RNAs (lncRNAs) have emerged as crucial regulators across diverse
biological processes and diseases. While high-throughput sequencing has enabled lncRNA …
biological processes and diseases. While high-throughput sequencing has enabled lncRNA …
Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling
Upstream open reading frames (uORFs) are typically defined as translation sites located
within the 5′ untranslated region upstream of the main protein coding sequence (CDS) of …
within the 5′ untranslated region upstream of the main protein coding sequence (CDS) of …
The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research
F Manske, L Ogoniak, L Jürgens… - Nucleic Acids …, 2023 - academic.oup.com
Upstream open reading frames (uORFs) are initiated by AUG or near-cognate start codons
and have been identified in the transcript leader sequences of the majority of eukaryotic …
and have been identified in the transcript leader sequences of the majority of eukaryotic …