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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...-type-specific transcriptomic and epigenetic changes associated with aging in 88 the substantia nigra, we profiled this brain region in mice at four different age stages: 2 months 89 (adolescent), 6 months (mature adult), 12 months (middle-aged), and 18 months (old) using 10x 90 Genomics Chromium Multiome (Fig. 1A). We...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...using epigenomic profiling using Illumina Infinium microarrays involved 32,851 participants (Min et al. 2021), compared to the UK Biobank's exome sequencing of 454,787 individuals (Backman et al. 2021) and whole- sequencing of 150,119 individuals (Halldorsson et al. 2022).Whole- bisulfite sequencing...
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Method: QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
- Xiaoyu Song,
- Yuqing Shang,
- Michelle E. Ehrlich,
- Panos Roussos,
- Guo-Cheng Yuan,
- and Pei Wang
Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
...Foundation for Statistical Computing, Vienna. https://www.R-project.org/. ↵Shao X, Liao J, Li C, Lu X, Cheng J, Fan X. 2021. CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice. Brief Bioinform 22: bbaa269. doi...
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Method: Unveiling the functional fate of duplicated genes through expression profiling and structural analysis
- Alex Warwick Vesztrocy,
- Natasha Glover,
- Paul D. Thomas,
- Christophe Dessimoz,
- and Irene Julca
Genome Res. October 2025 35: 2273-2284; Published in Advance August 14, 2025, doi:10.1101/gr.280166.124
...and no significant phenotype in mutants (Li et al. 2007; Yoshihara and Spalding 2017; Waite and Dardick 2024). Similarly, studies in knockout mice suggest that Becn1 and Becn2 (Supplemental Fig. S13G) have distinct functions in regulating autophagosome formation and mitophagy (Galluzzi and Kroemer 2013; Quiles et al...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
....5%–56%) increase in the dnSNV rate with ART compared with naturally conceived mice (P = 0.017). Analysis of the dnSNV mutation spectrum identifies signatures attributable to germline DNA repair activity but reveals no differentially enriched signatures between cohorts. We observe no enrichment of dn...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
.... The fundamental tasks are to classify or group sequencing reads into distinct genomic bins, each representing a different taxon (e.g., species or strain) within a metagenomic sample (taxonomic binning), and to identify the taxa present while estimating their relative abundances in the sample (taxonomic profiling...
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Research: Optical genome mapping identifies rare structural variants in neural tube defects
- Nikhil S. Sahajpal,
- Jane Dean,
- Benjamin Hilton,
- Timothy Fee,
- Cindy Skinner,
- Alex Hastie,
- Barbara R. DuPont,
- Alka Chaubey,
- Michael J. Friez,
- and Roger E. Stevenson
Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
...associated with NTDs in mouse have been identified in association with NTDs. Six of these genes are being proposed as human NTD-associated genes for the first time, with strong or moderate evidence for pathogenicity.Four cases carried deletions of genes associated with NTDs in mice (FOXD4, RBBP4, TGIF1...
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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
.... Our analytical approaches shed light to the transcriptome profiling and isoform discovery at the single-cell level, which can be applied to human samples, propelling isoform-focused research of aging and disease context.MethodsSampling and animal proceduresAll mice were handled in accordance...
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Method: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
- Chen Li,
- Sijie Chen,
- Yixin Chen,
- Haiyang Bian,
- Minsheng Hao,
- Lei Wei,
- and Xuegong Zhang
Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
...is selected based on both expected alterations and directing scores with a same quantile threshold and is ranked by directing scores.TFcomb outperforms baseline methods in identifying individual reprogramming TFsTo the best of our knowledge, there is not a quantitative benchmark of individual reprogramming TF...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...to be a highly effective and reproducible method for capturing the binding of protein complexes or TFs (e.g., NF-kB and STAT3) and identifying genomic targets for protein–DNA binding with high signal-to-noise ratios (SNRs) (Nowak et al. 2005; Tian et al. 2012).Moreover, effective chromatin solubilization is also...

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