New developments for the Quest for Orthologs benchmark service

New developments for the Quest for Orthologs benchmark service

The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengt...

Deskribapen osoa

Xehetasun bibliografikoak
Egile Nagusiak:	Altenhoff, A, Nevers, Y, Tran, V, Jyothi, D, Martin, M, Cosentino, S, Majidian, S, Marcet-Houben, M, Fuentes-Palacios, D, Persson, E, Walsh, T, Lecompte, O, Gabaldón, T, Kelly, S, Hu, Y, Iwasaki, W, Capella-Gutierrez, S, Dessimoz, C, Thomas, P, Ebersberger, I, Sonnhammer, E
Formatua:	Journal article
Hizkuntza:	English
Argitaratua:	Oxford University Press 2024

Antzeko izenburuak

The Quest for Orthologs orthology benchmark service in 2022
nork: Nevers, Y, et al.
Argitaratua: (2022)

The Quest for Orthologs benchmark service and consensus calls in 2020
nork: Altenhoff, AM, et al.
Argitaratua: (2020)

Quest for Orthologs in the Era of Biodiversity Genomics
nork: Langschied, F, et al.
Argitaratua: (2024)

Phylogenetic and functional assessment of orthologs inference projects and methods.
nork: Adrian M Altenhoff, et al.
Argitaratua: (2009-01-01)

Inferring hierarchical orthologous groups from orthologous gene pairs.
nork: Adrian M Altenhoff, et al.
Argitaratua: (2013-01-01)

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.
nork: Adrian M Altenhoff, et al.
Argitaratua: (2012-01-01)

The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.
nork: Daniel A Dalquen, et al.
Argitaratua: (2013-01-01)

Domainoid: domain-oriented orthology inference
nork: Emma Persson, et al.
Argitaratua: (2019-10-01)

DrosOMA: the Drosophila Orthologous Matrix browser [version 2; peer review: 2 approved]
nork: Robert M. Waterhouse, et al.
Argitaratua: (2024-01-01)

Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi
nork: Capella-Gutiérrez Salvador, et al.
Argitaratua: (2012-05-01)

Domain architecture conservation in orthologs
nork: Pekkari Isabella, et al.
Argitaratua: (2011-08-01)

Orthology confers intron position conservation
nork: Forslund Kristoffer, et al.
Argitaratua: (2010-07-01)

Algorithm of OMA for large-scale orthology inference
nork: Gonnet Gaston H, et al.
Argitaratua: (2008-12-01)

Algorithm of OMA for large-scale orthology inference
nork: Gonnet Gaston H, et al.
Argitaratua: (2009-07-01)

How to build phylogenetic species trees with OMA [version 2; peer review: 2 approved]
nork: Yannis Nevers, et al.
Argitaratua: (2022-02-01)

Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus
nork: Maria Augusta C. Horta, et al.
Argitaratua: (2022-08-01)

The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome.
nork: Marina Marcet-Houben, et al.
Argitaratua: (2009-01-01)

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage.
nork: Marina Marcet-Houben, et al.
Argitaratua: (2015-08-01)

Protein length distribution is remarkably uniform across the tree of life
nork: Yannis Nevers, et al.
Argitaratua: (2023-06-01)

Functional characterization in <it>Caenorhabditis elegans </it>of transmembrane worm-human orthologs
nork: Baillie David L, et al.
Argitaratua: (2004-11-01)

SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models
nork: Salvatore Cosentino, et al.
Argitaratua: (2024-07-01)

Quality of computationally inferred gene ontology annotations.
nork: Nives Skunca, et al.
Argitaratua: (2012-05-01)

HaMStR: Profile hidden markov model based search for orthologs in ESTs
nork: Strauss Sascha, et al.
Argitaratua: (2009-07-01)

Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved]
nork: Monique Zahn-Zabal, et al.
Argitaratua: (2020-01-01)

Assigning confidence scores to homoeologs using fuzzy logic
nork: Natasha M. Glover, et al.
Argitaratua: (2019-01-01)

Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire
nork: Marina Marcet-Houben, et al.
Argitaratua: (2024-11-01)

OrthoInspector: comprehensive orthology analysis and visual exploration
nork: Lecompte Odile, et al.
Argitaratua: (2011-01-01)

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.
nork: Kalliopi Trachana, et al.
Argitaratua: (2014-01-01)

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events
nork: Irene Julca, et al.
Argitaratua: (2018-01-01)

Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology
nork: Lucas D. Wittwer, et al.
Argitaratua: (2014-10-01)

Questing benchmarks for the current ratio: An analysis of the Warsaw Stock Exchange firms
nork: Piotr Wójtowicz
Argitaratua: (2022-12-01)

Regulatory Mechanisms of a Highly Pectinolytic Mutant of Penicillium occitanis and Functional Analysis of a Candidate Gene in the Plant Pathogen Fusarium oxysporum
nork: Gustavo Bravo-Ruiz, et al.
Argitaratua: (2017-09-01)

Focusing in Orthologic
nork: Olivier Laurent
Argitaratua: (2017-07-01)

Assessment of orthologous splicing isoforms in human and mouse orthologous genes
nork: Horner David S, et al.
Argitaratua: (2010-10-01)

Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi
nork: Miquel Àngel Schikora-Tamarit, et al.
Argitaratua: (2021-04-01)

The Plant Orthology Browser: An Orthology and Gene-Order Visualizer for Plant Comparative Genomics
nork: Dan Tulpan, et al.
Argitaratua: (2017-03-01)

How Uninformed is the Average Data Subject? A Quest for Benchmarks in EU Personal Data Protection
nork: Gloria González Fuster
Argitaratua: (2014-11-01)

Scaffolding low quality genomes using orthologous protein sequences.
nork: Li, Y, et al.
Argitaratua: (2013)

Improving the specificity of high-throughput ortholog prediction
nork: Horsman Benjamin GS, et al.
Argitaratua: (2006-05-01)

Internet News Headlines: Ontological and Orthological Aspects
nork: E. N. Shirokova
Argitaratua: (2021-12-01)