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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
...of how animals fight 32 infections. 33 Key words 34 Drosophila immunity/Immune-responsive enhancer/STARR-seq 35 36 Running Title 37 Genome-wide survey of fly immune enhancers 38 39 Introduction 40 When encountering pathogenic microbes, animals must regulate an effective immune response 41 to survive...
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Method: De novo reconstruction of satellite repeat units from sequence data
- Yujie Zhang,
- Justin Chu,
- Haoyu Cheng,
- and Heng Li
Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
...in this article, we will call “ABCD” in this example as a 4-monomer HOR unit to avoid confusion.In the human , the active centromeric regions that centromeric proteins bind to are primarily composed of alpha HORs (αHORs; Altemose et al. 2022). Conversely, though, not all αHORs are present in the active regions...
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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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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
...oligonucleotides by infusion cloning into the BsmBI site in two separate Lenti-multi-CRISPR plasmids. All plasmids were fully sequenced by Oxford Nanopore Technologies (Eurofins Genomics) and the sequences manually verified.A total of 600,000 C1 cells were seeded per six wells in DMEM/F12 supplemented media...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...27-mer tandem repeat regions. Self-to-self dot plot of 12 prominent tandem repeat genomic regions sharing a common 27-mer repeat unit. For example, the top row shows a 21,489 nt genomic region of CHROMOSOME_V (1,221,871–1,243,359) on the + (Watson) strand. Dots represent perfect matches of length 54...
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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
...305-0074, Japan; 2Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Corresponding authors: skato@riken.jp, mohkuma@riken.jpAbstractGenome sequences provide fundamental information for both basic and applied life sciences. Whole...
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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
...Illumina short-reads data to assemble the A. avenae . We assessed the ploidy of A. avenae and confirmed it to be diploid (Supplemental Fig. S2A). The haploid size was estimated to be ∼173 Mb (Supplemental Fig. S2B). Furthermore, k-mer–based analyses revealed a high level of genomic heterozygosity (∼6...
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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
...in our lab that were used to generate HiFi data). We adapted the idea developed by McKay et al. (2015) for estimating copy numbers. Briefly, we masked the entire histone locus in the iso-1 HiFi assembly, introduced only a single copy of the histone unit as a separate contig, and mapped Illumina data...
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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: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...Geometric deep learning framework for de novo assembly Lovro Vrček1,2, Xavier Bresson3, Thomas Laurent4, Martin Schmitz1,3, Kenji Kawaguchi3 and Mile Šikić1,2 1Genome Institute of Singapore, A*STAR, Singapore 138672; 2Faculty of Electrical Engineering and Computing, University of Zagreb, 10000...

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