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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
...and resources mentioned are provided in the Supplemental Documents.Scalable contextual features capture discriminative latent patternsCompared to the annotation module, the feature module enables flexible exploration of sSNV-related features at varying lengths. It integrates 39 DNA-level, 19 RNA-level, and 52...
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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
...(NGI) in Stockholm (NGI-S) and Uppsala (NGI-U). After fragmenting to 350-bp inserts and library preparation, DNA samples underwent WGS on the Illumina HiSeq X platform using v2.5 chemistry (Ameur et al. 2017). The 1000 individuals included in the data set all passed QC. The original mappings were...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...of repeats is tandem repeats (TRs), which are DNA sequences characterized by the contiguous repetition of at least one nucleotide, accounting for ∼6%–8% of the human (Cui et al. 2024; English et al. 2024; Rajan-Babu et al. 2024). TRs are broadly classified based on the size of their repetitive motif: TRs...
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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
...regions remain highly conserved, our analysis uncovers a significant proportion of SV sequences as transposable element (TE) insertions, especially DNA, LINE, and LTR TEs. These findings underscore that the cichlid is shaped both by small-nucleotide mutations and large, TE-derived sequence alterations...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
..., such as enhancers and promoters (Wray 2007; Fairfax et al. 2012; Chen et al. 2016; Cannavò et al. 2017; Abramov et al. 2021; Floc'hlay et al. 2021). However, establishing a mechanistic link between DNA sequence variation and TF binding remains challenging (Deplancke et al. 2016). Sequence variation that disrupts...
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Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
.... This results in a C-to-T mutation in cDNA. C-to-T mutations detected by RNA sequencing are indicative of m6A RNA modifications. (B, left) Immunofluorescence (IF) of HEK293T cells transfected with Apobec1-Yth-HA-Egfp (Yth-HA-E) or Egfp-Apobec1-Yth-HA (E-YTH-HA). Scale bar, 20 μm. Representative images are shown...
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Resource: Mitochondrial DNA variation across 56,434 individuals in gnomAD
- Kristen M. Laricchia,
- Nicole J. Lake,
- Nicholas A. Watts,
- Megan Shand,
- Andrea Haessly,
- Laura Gauthier,
- David Benjamin,
- Eric Banks,
- Jose Soto,
- Kiran Garimella,
- James Emery,
- Genome Aggregation Database Consortium,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Grace Tiao,
- Monkol Lek,
- Vamsi K. Mootha,
- and Sarah E. Calvo
Genome Res. March 2022 32: 569-582; Published in Advance January 24, 2022, doi:10.1101/gr.276013.121
...make it difficult to call heteroplasmic variants (Bolze et al. 2020). The first three mtDNA databases report only homoplasmic variants.The Genome Aggregation Database is a widely used resource of human genomic variation developed by an international consortium which has aggregated whole- sequence (WGS...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...these questions, we first analyzed two independent data sets comprising PCR-free whole- sequencing (WGS) and -wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using Hip...
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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...of the variation in the transition bias among various animal mitochondrial DNA. Gene 355: 58–66. doi:10.1016/j.gene.2005.05.019 ↵Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57: 289–300. doi:10.1111/j.2517-6161.1995.tb...
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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
...Biosciences (PacBio) HiFi and ultralong Oxford Nanopore Technologies (ONT), are both more expensive and more demanding of DNA quantity and quality. Numerous tools have been developed to detect SVs using paired-end short reads over the past decade. There are primarily three strategies used in popular...

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