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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
...in this window to the enhancer. More restrictive enhancer-607 gene assignments were made by sorting genes into activity classes based on expression in the 608 RNA-seq data (expression threshold: TPM > 1). For each activity class, genes were matched to 609 the allowed set of enhancers by scanning 15 kb upstream...
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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
...), with names for selected genes. (Bottom) Virtual 4C track (see Methods) showing Hi-C contacts from MYC toward the Chromosome 10 region for 10A (blue), T1 (yellow), and C1 (green). (E) FISH image of the MYC gene (yellow) and the Chromosome 10 enhancer (blue; Chr 10 position 73,117,711–73,267,436) expected...
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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
...(Browne et al. 2002; Goyal et al. 2005; Banton and Tunnacliffe 2012). However, the absence of high-quality, chromosome-level assemblies has thus far restricted more detailed investigations into the underlying regulatory mechanisms. In recent years, more haplotype s have been analyzed which provide...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...-seq assemblers (Fig. 4). Globally, TOGA achieved greater reference protein coverage than Liftoff, and in vertebrates, TOGA achieved the highest reference protein coverage (H. sapiens) or was virtually tied with BRAKER3 (G. gallus) (Fig. 4). In vertebrates, the RNA-seq assemblers obtained slightly lower reference...
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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
...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...on microscopic chromosome examination, a complex and expertise-dependent process with megabase-scale resolution. Optical mapping (OGM) technology offers an efficient approach to detect large-scale genomic lesions. Here, we introduce OMKar, a computational method that generates virtual karyotypes from OGM data...
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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
...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...: jinulee@yonsei.ac.kr (J.L.) 26 27 Abstract 28 Homology-directed repair (HDR) enables precise editing; however, its 29 application in mammalian cells is limited by low efficiency due to competition from error-30 prone repair pathways and intrinsically restricted HDR activity. Existing HDR-31 enhancement...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
...for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA; 3Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA; 4Center for Biomolecular Condensates...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
.... 2001; The ENCODE Project Consortium 2004; McGarvey et al. 2015; Frankish et al. 2019). These reference annotations are absolutely essential for virtually all transcriptomics research and beyond, but they lack information on what tissues and cell types express what isoforms and at what level.A resource...
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