Impact of gene annotation choice on the quantification of RNA-seq data [PDF]
BMC Bioinformatics, 2022 Background RNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression levels of genes from RNA-seq data is to map reads to a reference genome and then count mapped reads to ...
David Chisanga, Yang Liao, Wei Shi
doaj +3 more sources
FusionGDB: fusion gene annotation DataBase. [PDF]
Nucleic Acids Res, 2019 Gene fusion is one of the hallmarks of cancer genome via chromosomal rearrangement initiated by DNA double-strand breakage. To date, many fusion genes (FGs) have been established as important biomarkers and therapeutic targets in multiple cancer types ...
Kim P, Zhou X.
europepmc +5 more sources
Integrating gene annotation with orthology inference at scale. [PDF]
Science, 2023 Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability.
Kirilenko BM +13 more
europepmc +2 more sources
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. [PDF]
Nucleic Acids Res, 2022 A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies.
Kim P +6 more
europepmc +2 more sources
GENCODE 2025: reference gene annotation for human and mouse. [PDF]
Nucleic Acids ResGENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity.
Mudge JM +55 more
europepmc +2 more sources
Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning. [PDF]
Bioinformatics, 2021 Motivation Current state-of-the-art tools for the de novo annotation of genes in eukaryotic genomes have to be specifically fitted for each species and still often produce annotations that can be improved much further.
Stiehler F +5 more
europepmc +2 more sources
Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models [PDF]
BMC Genomics, 2019 Background The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms.
Jeanne Wilbrandt +3 more
doaj +3 more sources
Frontiers in Microbiology, 2022 Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes.
Varada Khot +11 more
doaj +2 more sources
Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus. [PDF]
Sci Rep, 2019 Nematodes such as Caenorhabditis elegans are powerful systems to study basically all aspects of biology. Their species richness together with tremendous genetic knowledge from C.
Rödelsperger C +9 more
europepmc +2 more sources
Gene Annotation in High Schools: Successful Student Pipeline and Teacher Professional Development in Bioscience Using GENI-ACT [PDF]
Frontiers in Microbiology, 2021 Knowledge of genomics is an essential component of science for high school student health literacy. However, few high school teachers have received genomics training or any guidance on how to teach the subject to their students. This project explored the
Stephen T. Koury +3 more
doaj +2 more sources