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...

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Manylion Llyfryddiaeth
Prif Awduron:	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
Fformat:	Journal article
Iaith:	English
Cyhoeddwyd:	Oxford University Press 2024

Eitemau Tebyg

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Questing benchmarks for the current ratio: An analysis of the Warsaw Stock Exchange firms
gan: Piotr Wójtowicz
Cyhoeddwyd: (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
gan: Gustavo Bravo-Ruiz, et al.
Cyhoeddwyd: (2017-09-01)

Focusing in Orthologic
gan: Olivier Laurent
Cyhoeddwyd: (2017-07-01)

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

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

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

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

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

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

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