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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...that deletion cassette replacement introduced short donor 25 DNA tracts of variable length, resulting in a finely recombined mapping population. Using only 26 the known location of the gene deletions, which marks where donor DNA is introduced, we 27 identify a 6.5 kb-region shaping yeast growth. We further...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...were functionally annotated by mapping them to in-house profiles of the Clusters of Orthologous Genes (COG) database (2020 release) (Galperin et al. 2021) with HMMER v3.1b2 (e-value < 0.001; http://hmmer.org). The 26 major prokaryotic functional categories defined in the COG database were assigned...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...of Chromosome 8 and restore euploidy in cells derived from an individual with a complex rearrangement of Chromosome 8p. Transcriptomic analysis revealed 361 differentially expressed genes between the proband and the euploid revertant, highlighting genes both within and outside the 8p region that may contribute...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...et al. 2009) was used to extract uniquely mapped reads and remove PCR duplicates. mosdepth (Pedersen and Quinlan 2018) was used to calculate read coverage along the (parameters: -t 3 -n ‐‐fast-mode ‐‐by 250,000).Gene density, GC content, nucleotide diversityThe gene density of each chromosome...
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Research: Most chromatin interactions are not in linkage disequilibrium
- Sean Whalen and
- Katherine S. Pollard
Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
...to single nucleotide polymorphisms (SNPs) can impact gene function by altering exonic sequence or by changing gene regulation. Recent studies estimate that 93% of disease-associated variants are in noncoding DNA (Welter et al. 2014) and 60% of causal variants map to regulatory elements (Farh et al. 2015...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...variants and their mechanisms of action in relevant biological systems at scale. The identification of functional variants relative to proxy variants in high linkage disequilibrium (LD) presents an additional challenge. Recent studies have begun to map molecular quantitative trait loci (molQTLs) for gene...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD; r2 > 0.4) (Pers et al. 2015; Ghasemi et al. 2021) were also intersected against the panel design, showing a total of 460 unique GWAS and ∼30,000 total linked SNPs intersecting. The functionality of these putative enhancers was further confirmed...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
..., HRAS, MAP2K2, PTK6, RAC1, SDC4, TSC2, and SRC, among others, are connected with a large number (more than five) of genes and thus may play critical roles in this network (Supplemental Figs. S11–S13). Meanwhile, these cancer genes were also reported to be highly relative in colorectal cancer...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...and gene paralogs were grouped when they shared protein domains predicted to have equivalent functions because they belong to the same functional family in the CATH database (Sillitoe et al. 2015; Das et al. 2015b). These mutations can be mapped to a single 3D structural representative. Known functional...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...development of multiomicmethods provided tools for the assessment of cell identity and cell-to-cell heterogeneity. Multiomic, single-cell methods also inform on distinct aspects of the epi in parallel with gene expression (Cao et al. 2018; Zhu et al. 2019; Flynn et al. 2023). Approaches that map features of 3...
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