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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
...and Jonas Paulsen1 1Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway; 2Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia; 3...
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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
...that gars have lower TE copy numbers and a much lower degree of TE activity than other representative vertebrates (Fig. 3). Together with our inference that gars have the lowest rates of global genomic nucleotide substitution across all vertebrates (Brownstein et al. 2024) and have highly conserved synteny...
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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
.... OMKar integrates structural variants (SVs) and copy number (CN) variants into a breakpoint graph representation. It re-estimates CNs using integer linear programming to enforce CN balance and then identifies constrained Eulerian paths corresponding to full chromosome structures. OMKar is evaluated on 38...
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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
...variants, which constitute the primary data used for inferring cell lineage trees. The primary class of genomic variants studied in this paper is the single nucleotide variant (SNV). We do not consider more complex variants such as copy number variations (CNVs) for cell lineage tree inference (see...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...sizes for reliable GCN inference. recount3, a data set with 316,443 processed human RNA-seq samples, provides an opportunity to improve network reconstruction. However, GCN inference from public data is challenged by confounders and inconsistent labeling. To address this, we develop a pipeline...
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Method: Bayesian inference of sample-specific coexpression networks
- Enakshi Saha,
- Viola Fanfani,
- Panagiotis Mandros,
- Marouen Ben Guebila,
- Jonas Fischer,
- Katherine H. Shutta,
- Dawn L. DeMeo,
- Camila M. Lopes-Ramos,
- and John Quackenbush
Genome Res. September 2024 34: 1397-1410; Published in Advance August 12, 2024, doi:10.1101/gr.279117.124
...equally to this work. Corresponding author: johnq@hsph.harvard.eduAbstractGene regulatory networks (GRNs) are effective tools for inferring complex interactions between molecules that regulate biological processes and hence can provide insights into drivers of biological systems. Inferring coexpression...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...Ran Zhang1,2, Chengxiang Qiu1, Galina N. Filippova3, Gang Li1,2, Jay Shendure1,4,5,6,7, Jean-Philippe Vert8, Xinxian Deng3, William Stafford Noble1,9 and Christine M. Disteche3,10 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 2eScience Institute...
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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
..., Bengio Y, Bresson X. 2023. Benchmarking graph neural networks. J Mach Learn Res 24: 1–48. ↵Edmonds J, Johnson EL. 2003. Matching: a well-solved class of integer linear programs. In Combinatorial optimization—Eureka, you Shrink!, Lecture notes in computer science (ed. Jünger M, Reinelt G), pp. 27...
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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
..., Stanford University, Stanford, California 94305, USA; 2MiLaboratories Incorporated, San Francisco, California 94114, USA; 3Unit of Animal Genomics, WELBIO, GIGA-R and Faculty of Veterinary Medicine, University of Liège (B34), 4000 Liège, Belgium; 4Department of Biochemistry and Molecular Genetics...
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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
...follow the original strand choice of the C. elegans N2 assembly (The C. elegans Sequencing Consortium 1998). We drew dot plots between sequences of two chromosomes or chromosome sets with GenomeMatcher 3.0.6 (Ohtsubo et al. 2008) using the NUCmer program in MUMmer 4.0.0rc1 (Kurtz et al. 2004); we drew...
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