Searching journal content for articles similar to Leonard et al. 34 (2): 300.

Displaying results 1-10 of 5991

For checked items

view abstracts
download to citation manager

Select this article
Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...associated with breast cancer risk (Helgadottir et al. 2021) and somatic variation in relapsed pediatric acute lymphoblastic leukemia (Sayyab et al. 2021).In this study, we aim to evaluate the improvement of mapping short-read WGS data to the new T2T-CHM13 reference compared to the reference s...
OPEN ACCESS ARTICLE
Select this article
Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., and contrast several metrics (including the LD structure and the SNP entropy) of the simulated sequences with that of real sequences as a genotype simulation quality assessment.MethodsVariational autoencodersRepresentation learning, also known as feature learning, attempts to recover a compact set of so...
OPEN ACCESS ARTICLE
Select this article
Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...Lake Malawi cichlid pan graph reveals extensive structural variation driven by transposable elements Fu Xiang Quah1,2, Miguel Vasconcelos Almeida1, Moritz Blumer2, Chengwei Ulrika Yuan1,2, Bettina Fischer2, Kirsten See1, Ben Jackson2, Richard Zatha3, Bosco Rusuwa3, George F. Turner4, M. Emília...
OPEN ACCESS ARTICLE
Select this article
Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
- Wei-Hao Lee,
- Lechuan Li,
- Ruth Dannenfelser,
- and Vicky Yao
Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
...the data into “guided” components (directly linked to provided labels such as batch or phenotypic condition), as well as an “unguided” component that captures shared residual variation (Fig. 1B; Methods). This dual strategy enables ALPINE to not only reconstruct the original data accurately but also...
Select this article
Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
..., spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream of the KIT gene has been proposed...
Select this article
Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...within reads (Narzisi and Schatz 2015; Mousavi et al. 2019), affecting mappability to a reference . Some SRS STR genotyping tools can estimate larger-than-read-length allele sizes (Dolzhenko et al. 2017; Dolzhenko et al. 2019; Mousavi et al. 2019) but cannot capture variation in motif structure nor...
Select this article
Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...and updates structured knowledge from recent literature. Beyond human data, SynMall incorporates sSNVs from non-human species: (1) it collects vertebrate sSNVs from multiple sources and maps them onto the human via MSA; (2) it also integrates genotype–phenotype associations for sSNVs from economically...
Select this article
Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...that structural variations (SVs), including large (>30-bp) deletions (DELs), insertions (INSs), duplications (DUPs), inversions (INVs), and translocations (TRAs) (Feuk et al. 2006), greatly contribute to crop phenotypic diversity and selection for physiological and morphological phenotypes (Alonge et al. 2020; Li...
Select this article
Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...flexible penalization based on the number of edges found in the network, which aids in the identification of a network structure that improves the discovery of true gene-gene interactions while reducing false positives (Huang et al. 2020). Here, we focus on improving the statistical power of network...
OPEN ACCESS ARTICLE
Select this article
Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...with hundreds of species and tens of thousands of genes. ERC2.0 improves upon previous iterations of ERC in algorithm speed, normalizing for heteroskedasticity, and normalizing correlations via Fisher transformations. These improvements have resulted in greater statistical power to predict biological function...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Leonard et al. 34 (2): 300.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: