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...

Bibliográfalaš dieđut
Váldodahkkit:	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
Materiálatiipa:	Journal article
Giella:	English
Almmustuhtton:	Oxford University Press 2024

Geahča maid

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Focusing in Orthologic
Dahkki: Olivier Laurent
Almmustuhtton: (2017-07-01)

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

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

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

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

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

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

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