Adrian Altenhoff
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Explore the profile of Adrian Altenhoff including associated specialties, affiliations and a list of published articles.
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14
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548
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Recent Articles
1.
Altenhoff A, Nevers Y, Tran V, Jyothi D, Martin M, Cosentino S, et al.
NAR Genom Bioinform
. 2024 Dec;
6(4):lqae167.
PMID: 39664814
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...
2.
Nevers Y, Warwick Vesztrocy A, Rossier V, Train C, Altenhoff A, Dessimoz C, et al.
Nat Biotechnol
. 2024 Feb;
43(1):124-133.
PMID: 38383603
In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a...
3.
Dylus D, Altenhoff A, Majidian S, Sedlazeck F, Dessimoz C
Nat Biotechnol
. 2023 Apr;
42(1):139-147.
PMID: 37081138
Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large...
4.
Dylus D, Altenhoff A, Majidian S, Sedlazeck F, Dessimoz C
bioRxiv
. 2022 Dec;
PMID: 36561179
The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and...
5.
Nevers Y, Jones T, Jyothi D, Yates B, Ferret M, Portell-Silva L, et al.
Nucleic Acids Res
. 2022 May;
50(W1):W623-W632.
PMID: 35552456
The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing...
6.
Zhou N, Jiang Y, Bergquist T, Lee A, Kacsoh B, Crocker A, et al.
Genome Biol
. 2019 Nov;
20(1):244.
PMID: 31744546
Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the...
7.
Kaleb K, Warwick Vesztrocy A, Altenhoff A, Dessimoz C
F1000Res
. 2019 Apr;
8:42.
PMID: 31001419
The Orthologous Matrix (OMA) is a well-established resource to identify orthologs among many genomes. Here, we present two recent additions to its programmatic interface, namely a REST API, and user-friendly...
8.
Glover N, Altenhoff A, Dessimoz C
PeerJ
. 2019 Jan;
6:e6231.
PMID: 30648004
In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species:...
9.
Train C, Pignatelli M, Altenhoff A, Dessimoz C
Bioinformatics
. 2018 Dec;
35(14):2504-2506.
PMID: 30508066
Summary: The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative...
10.
Pilizota I, Train C, Altenhoff A, Redestig H, Dessimoz C
Bioinformatics
. 2018 Sep;
35(7):1159-1166.
PMID: 30184069
Motivation: As the time and cost of sequencing decrease, the number of available genomes and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene annotations varies considerably...