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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
...sections describe the main modules of SynMall in greater detail.View larger version: In this window In a new window Figure 1. Architecture of the SynMall database and its annotation-based analyses. (A) An overview of SynMall, including integrated resources for both human and non-human sSNVs. (B) Syn...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...phenotypic differences between breeds. Collectively, our work provides a road map for performing constraint-based analysis of genetic variation in other domesticated species with similar genomic resources, such as cattle, swine, and horses.ResultsA framework for evaluating gene sequence constraint metrics...
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Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
- Xiran Liu,
- Lorin Crawford,
- and Sohini Ramachandran
Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
..., or nonprioritized—among multiple traits based on their regularized effects. Clustering applied to our neural network shrinkage results also produces consistently higher precision and recall for distinguishing gene-level associations in simulations. We demonstrate the application of ML-MAGES on association analyses...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...window Figure 1. Species selection for comparative genomic analyses of mammalian diet. The carnivory score represents the proportion of the diet composed of animal-based food items for each species, as listed in EltonTraits (Wilman et al. 2014). This score was used as input in our RERconverge analyses...
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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...-MS guarantees accurate quantification, it is resource-intensive and time-consuming and, most importantly, fails to provide transcript-specific insights. Alternatively, antibody-based approaches, including the methylated RNA immunoprecipitation followed by sequencing (MeRIP-Seq), have garnered attention...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...Pan-based inference using integer programming Ghanshyam Chandra1, Md Helal Hossen2, Stephan Scholz3,4, Alexander T. Dilthey3,4, Daniel Gibney2 and Chirag Jain1 1Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India; 2Department of Computer...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...(Fig. 5C).Facilitating broad uptake of HGDP + 1kGP as a public resource via development of detailed tutorialsIn an effort to increase accessibility of this data set, we have made publicly available tutorials of our analyses implemented primarily in Hail (https://hail.is). Hail is an open source, Python-based...
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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
....kivisild@kuleuven.beAbstractGenotype imputation from low-pass sequencing data presents unique opportunities for genomic analyses but comes with specific challenges. In this study, we explore the impact of quality filters on genetic ancestry and Polygenic Score (PGS) estimation after imputing 32,769 low-pass -wide sequences (LPS) from...
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Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...” (Tabula Muris Senis) data, we identified tissue-level transcriptomic aging programs for more than 20 murine tissues and created a multitissue resource of mouse quantitative aging-associated genes. We observe that SCALE correlates well with other age indicators, such as the accumulation of somatic...
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Resource: A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
- Jane Hawkey,
- Ben Vezina,
- Jonathan M. Monk,
- Louise M. Judd,
- Taylor Harshegyi,
- Sebastián López-Fernández,
- Carla Rodrigues,
- Sylvain Brisse,
- Kathryn E. Holt,
- and Kelly L. Wyres
Genome Res. May 2022 32: 1004-1014; Published in Advance March 11, 2022, doi:10.1101/gr.276289.121
...the importance of selecting a diverse range of strains when exploring KpSC metabolism. This diverse set of highly accurate GEMs could be used to inform novel drug design, enhance genomic analyses, and identify novel virulence and resistance determinants. We envisage that these 37 curated strain-specific GEMs...
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