Results 1 to 10 of about 8,160,610 (250)

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

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, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Zoonomia Consortium‡, Hiller M.   +13 more
europepmc   +2 more sources

PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. [PDF]

PeerJ, 2023
Background Gene-gene co-expression correlations measured by mRNA-sequencing (RNA-seq) can be used to predict gene annotations based on the co-variance structure within these data.
Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma'ayan A.   +5 more
europepmc   +2 more sources

GENCODE 2025: reference gene annotation for human and mouse. [PDF]

Nucleic Acids Res
GENCODE 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, Carbonell-Sala S, Diekhans M, Martinez JG, Hunt T, Jungreis I, Loveland JE, Arnan C, Barnes I, Bennett R, Berry A, Bignell A, Cerdán-Vélez D, Cochran K, Cortés LT, Davidson C, Donaldson S, Dursun C, Fatima R, Hardy M, Hebbar P, Hollis Z, James BT, Jiang Y, Johnson R, Kaur G, Kay M, Mangan RJ, Maquedano M, Gómez LM, Mathlouthi N, Merritt R, Ni P, Palumbo E, Perteghella T, Pozo F, Raj S, Sisu C, Steed E, Sumathipala D, Suner MM, Uszczynska-Ratajczak B, Wass E, Yang YT, Zhang D, Finn RD, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Birney E, Martin FJ, Frankish A.   +55 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, Tan H, Liu J, Lee H, Jung H, Kumar H, Zhou X.   +6 more
europepmc   +2 more sources

Annotation matters: the effect of structural gene annotation on orthology inference. [PDF]

Bioinformatics
Motivation In silico gene annotation, the process of identifying the genes present in a genome, remains a challenging task. As genome assemblies rapidly increase, the corresponding gene models and repertoires often fall short in quality. Despite advances
Prieto-Baños S, Nevers Y, Altenhoff A, Warwick Vesztrocy A, Dessimoz C, Glover NM.   +5 more
europepmc   +2 more sources

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update).

Nucleic Acids Research, 2022
DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report
H Clifford Lane, Weizhong Chang
exaly   +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, Steinborn M, Scholz S, Dey D, Weber APM, Denton AK.   +5 more
europepmc   +2 more sources

The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes. [PDF]

BMC Genomics, 2021
The nematode Pristionchus pacificus is an established model organism for comparative studies with Caenorhabditis elegans. Over the past years, it developed into an independent animal model organism for elucidating the genetic basis of phenotypic ...
Rödelsperger C.
europepmc   +2 more sources

DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns

Nucleic Acids Research, 2019
Annotation of gene expression in prokaryotes often finds itself corrected due to small variations of the annotated gene regions observed between different (sub)-species.
Jim Clauwaert, Willem Waegeman, Gerben Menschaert   +2 more
exaly   +2 more sources