Search Results - "Altenhoff, Adrian"

Phylogenetic and functional assessment of orthologs inference projects and methods by Altenhoff, Adrian M, Dessimoz, Christophe

“…Accurate genome-wide identification of orthologs is a central problem in comparative genomics, a fact reflected by the numerous orthology identification…”
Get full text

Inferring hierarchical orthologous groups from orthologous gene pairs by Altenhoff, Adrian M, Gil, Manuel, Gonnet, Gaston H, Dessimoz, Christophe

“…Hierarchical orthologous groups are defined as sets of genes that have descended from a single common ancestor within a taxonomic range of interest…”
Get full text

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more by Altenhoff, Adrian M, Train, Clément-Marie, Gilbert, Kimberly J, Mediratta, Ishita, Mendes de Farias, Tarcisio, Moi, David, Nevers, Yannis, Radoykova, Hale-Seda, Rossier, Victor, Warwick Vesztrocy, Alex, Glover, Natasha M, Dessimoz, Christophe

“…Abstract OMA is an established resource to elucidate evolutionary relationships among genes from currently 2326 genomes covering all domains of life. OMA…”
Get full text

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs by Altenhoff, Adrian M, Studer, Romain A, Robinson-Rechavi, Marc, Dessimoz, Christophe

“…The function of most proteins is not determined experimentally, but is extrapolated from homologs. According to the "ortholog conjecture", or standard model of…”
Get full text

Inferring Orthology and Paralogy by Altenhoff, Adrian M, Glover, Natasha M, Dessimoz, Christophe

“…The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most…”
Get more information

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces by Altenhoff, Adrian M, Glover, Natasha M, Train, Clément-Marie, Kaleb, Klara, Warwick Vesztrocy, Alex, Dylus, David, de Farias, Tarcisio M, Zile, Karina, Stevenson, Charles, Long, Jiao, Redestig, Henning, Gonnet, Gaston H, Dessimoz, Christophe

“…Abstract The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent…”
Get full text

OMA standalone: orthology inference among public and custom genomes and transcriptomes by Altenhoff, Adrian M, Levy, Jeremy, Zarowiecki, Magdalena, Tomiczek, Bartłomiej, Warwick Vesztrocy, Alex, Dalquen, Daniel A, Müller, Steven, Telford, Maximilian J, Glover, Natasha M, Dylus, David, Dessimoz, Christophe

“…Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many…”
Get full text

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements by Altenhoff, Adrian M, Škunca, Nives, Glover, Natasha, Train, Clément-Marie, Sueki, Anna, Piližota, Ivana, Gori, Kevin, Tomiczek, Bartlomiej, Müller, Steven, Redestig, Henning, Gonnet, Gaston H, Dessimoz, Christophe

“…The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e…”
Get full text

OMAMO: orthology-based alternative model organism selection by Nicheperovich, Alina, Altenhoff, Adrian M, Dessimoz, Christophe, Majidian, Sina

“…The conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding of human biology…”
Get full text

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference by Train, Clément-Marie, Glover, Natasha M, Gonnet, Gaston H, Altenhoff, Adrian M, Dessimoz, Christophe

“…Accurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous…”
Get full text

Quality of computationally inferred gene ontology annotations by Skunca, Nives, Altenhoff, Adrian, Dessimoz, Christophe

“…Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e…”
Get full text

iHam and pyHam: visualizing and processing hierarchical orthologous groups by Train, Clément-Marie, Pignatelli, Miguel, Altenhoff, Adrian, Dessimoz, Christophe

“…Abstract Summary The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of…”
Get full text

Standardized benchmarking in the quest for orthologs by Altenhoff, Adrian M, Boeckmann, Brigitte, Capella-Gutierrez, Salvador, Dalquen, Daniel A, DeLuca, Todd, Forslund, Kristoffer, Huerta-Cepas, Jaime, Linard, Benjamin, Pereira, Cécile, Pryszcz, Leszek P, Schreiber, Fabian, da Silva, Alan Sousa, Szklarczyk, Damian, Train, Clément-Marie, Bork, Peer, Lecompte, Odile, von Mering, Christian, Xenarios, Ioannis, Sjölander, Kimmen, Jensen, Lars Juhl, Martin, Maria J, Muffato, Matthieu, Gabaldón, Toni, Lewis, Suzanna E, Thomas, Paul D, Sonnhammer, Erik, Dessimoz, Christophe

“…Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary…”
Get full text

OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem by Altenhoff, Adrian M, Warwick Vesztrocy, Alex, Bernard, Charles, Train, Clement-Marie, Nicheperovich, Alina, Prieto Baños, Silvia, Julca, Irene, Moi, David, Nevers, Yannis, Majidian, Sina, Dessimoz, Christophe, Glover, Natasha M

“…Abstract In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and…”
Get full text

The Quest for Orthologs benchmark service and consensus calls in 2020 by Altenhoff, Adrian M, Garrayo-Ventas, Javier, Cosentino, Salvatore, Emms, David, Glover, Natasha M, Hernández-Plaza, Ana, Nevers, Yannis, Sundesha, Vicky, Szklarczyk, Damian, Fernández, José M, Codó, Laia, for Orthologs Consortium, the Quest, Gelpi, Josep Ll, Huerta-Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martin, Maria J, Capella-Gutierrez, Salvador, Thomas, Paul D, Sonnhammer, Erik, Dessimoz, Christophe

“…Abstract The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many…”
Get full text

The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study by Dalquen, Daniel A, Altenhoff, Adrian M, Gonnet, Gaston H, Dessimoz, Christophe

“…The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally…”
Get full text

OMA 2011: orthology inference among 1000 complete genomes by Altenhoff, Adrian M, Schneider, Adrian, Gonnet, Gaston H, Dessimoz, Christophe

“…OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th…”
Get full text

DrosOMA: the Drosophila Orthologous Matrix browser [version 2; peer review: 4 approved] by Thiébaut, Antonin, Altenhoff, Adrian M., Campli, Giulia, Glover, Natasha, Dessimoz, Christophe, Waterhouse, Robert M.

“…Background Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene…”
Get full text

DrosOMA: the Drosophila Orthologous Matrix browser [version 1; peer review: 1 approved, 1 approved with reservations] by Thiébaut, Antonin, Altenhoff, Adrian M., Campli, Giulia, Glover, Natasha, Dessimoz, Christophe, Waterhouse, Robert M.

“…Background: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and…”
Get full text

Inferring orthology and paralogy by Altenhoff, Adrian M, Dessimoz, Christophe

“…The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most…”
Get more information