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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
...the genomic outcomes of CRI-SPA-Map engineering, we whole- sequenced 185 555 CRI-SPA-Map isolates (typically four local and two distal isolates; Supplemental Table S2) 186 created from the 92 YKO strains. We analyzed genotype calls at 8,257 high-quality variants 187 across the (7,954 SNVs and 303 indels...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...) (Braasch et al. 2016). Whole- and gene synteny maps show that Chromosomes 14 and 17 in the L. oculatus (Braasch et al. 2016) are fused in A. spatula and L. osseus (Fig. 1A; Supplemental Fig. S1F). Through sequencing depth analysis, we confirmed the accuracy of the identified chromosome fusion events...
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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
...variable, locus-specific recombination costs based on known recombination rates (Petes 2001). However, recombination maps analogous to those used on linear reference s are not yet available for pan graphs.Next, we consider the complexity of path inference problem. We show that the problem is NP-hard, even...
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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
...that genetic risk for brain disorders resides within brain-enriched regulatory regions, maps of regulatory elements in brain-relevant cell types are of substantial value. We utilized a large-scale CapSTARR-seq approach to validate putative enhancer regions and characterize the noncoding genomic landscape of ph...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...; Kvon et al. 2014). 130 Previous work has finely mapped the time-course of transcriptional regulation of immune genes 131 in the first 24 hrs of Imd stimulation in whole adult flies (Schlamp et al. 2021) and clustered the 132 genes by their expression timing. We found IMD enhancers for just under half...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...progressionTo map differences in long-range contacts in our progression model, we searched for any A/B-compartment switching, a property reported to be implicated in breast cancer (Barutcu et al. 2015). Most of the (2124 Mbp; ∼78%) remains in the same compartment across stages (Fig. 1B). However...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...and haplotag the BAM file. All commands are given in the Supplemental Code. De novo assembly was performed using Hifiasm (0.23.0–h5ca1c30_0) (Cheng et al. 2021), and SVs were called using SVIM-asm (v1.0.3) (Supplemental Code; Heller and Vingron 2021).Optical Genome MappingOptical Genome Mapping (OGM...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...-reserved 3D architecture of A. avenae. (A) Hi-C heat map of two haplotype sets of A. avenae; from top to bottom are nine pairs of homologous chromosomes 1–9. (B) Circos plot (Krzywinski et al. 2009) of A. avenae haplotype-resolved T2T genomic features. I: The collinearity between two sets of haplotypes; II...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...-chromatin configuration, and transcriptional activation. Mapping these physical properties and biochemical activities, through profiling chromatin accessibility and active transcription, is a key tool for understanding the logic and mechanisms of transcription and its regulation. However, the relationship between...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...on the array (Dover et al. 1993; Elder and Turner 1995; Lower et al. 2018). Untangling patterns of concerted evolution on tandem arrays experiencing different forces requires a comprehensive map of genetic variation spanning such clusters.The cluster of highly conserved histone genes on Chromosome arm 2L...
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