Searching journal content for articles similar to Barrio-Hernandez et al. 30 (1): 127.

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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. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...(PD) is a prevalent neurodegenerative disorder predominantly affecting individuals over 60. Its motor symptoms stem from the deterioration of dopaminergic neurons within the substantia nigra. Despite aging being a significant risk factor, the specific mechanisms linking aging and PD pathology remain...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...cell-types, reveals lineage and stage-specific 17 IPA signatures, with lymphoid cells exhibiting higher IPA site usage than myeloid cells. Temporal 18 profiling during megakaryocyte differentiation uncovers dynamic, gene-specific IPA regulation 19 linked to functional pathways including peroxisomal...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...k-mer cross-species profiling reveals taxon-specific TE expansions accompanied 1 by KZFP co-option and functional impacts in ruminants 2 3 Pengju Zhao1,2*, Jiayi He1,2, Chen Peng1,2, Yuelang Zhang1,2, Chong Wang1,2, 4 Dongyou Yu1,2, Lingzhao Fang3*, Zhengguang Wang1,2* 5 6 1Hainan Institute...
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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
...al. 2022; Zheng et al. 2022). Therefore, to reveal the structure and function of microbial communities, we need to estimate their composition and abundance at finest resolution possible, that is, not only at the level of species, but also at the level of strains.For this study, we define a “strain...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
.... Finally, we determine cell-type-specific replication timing profiles, integrating our in vivo data sets with published data using cultured cell lines. Our results reveal that GSC-like cells display a distinct replication program, compared with somatic lineages, that aligns with chromatin state differences...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...(K27me3 LADs) in purple, Cluster 1 (K9me3 LADs) in blue, Cluster 2 (K9me2 LADs) in gold.Chromatin profiles across LADs in each cluster revealed stark differences in both the overall abundance of histone PTMs and their pattern over the LAD (Fig. 3C,D). As expected, H3K9ac and H3K27ac are highly...
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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
...had highly reproducible SNRs across six of the seven samples, and the variability observed in the remaining sample was within the expected range of experimental variability (Fig. 3A–C). To further assess antibody performance, we profiled signal enrichment around transcription start sites (TSSs...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...-kB in three mammalian lineages. Our comparative analyses of RELA binding, together with epigenetic and transcriptional profiles, revealed conserved and lineage-specific TE subfamilies that are likely to participate in mammalian NF-kB regulatory networks. Given the active enhancer features and proximity...
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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...more general single-cell genotypes and mutation models remains a research question.Applying ScisTree2 in studies of cancer biology and stem cell biologyInference of the cell lineage tree is very relevant to single-cell cancer genomics. For example, finding clonal populations is a common problem...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...2021). The same research group utilized LARRY in another study to explore clonal trajectories of adult HSCs during long-term bone marrow reconstitution (Rodriguez-Fraticelli et al. 2020). Their findings revealed the existing of an intrinsic molecular signature that characterizes functional long...
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