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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
...Loss of multilevel 3D organization during breast cancer progression Roberto Rossini1, Saleh Oshaghi1, Maxim Nekrasov2, Aurélie Bellanger3, Renae Domaschenz2, Yasmin Dijkwel2, Mohamed Abdelhalim3, Rahul Agrawal3,4, Marit Ledsaak3,4, Philippe Collas3,5, Ragnhild Eskeland3,4, David Tremethick2...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...non-human species. For each human sSNV, SynMall provides multilevel annotations that combine American College of Medical Genetics and Genomics (ACMG)–aligned variant interpretation information, such as allele frequencies and functional effects, with more than 100 descriptors at the DNA, RNA...
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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
...Problem. arXiv:1906.01227 [cs.LG]. http://arxiv.org/abs/1906.01227 ↵Karypis G, Kumar V. 1998. A fast and high quality multilevel scheme for partitioning irregular graphs. SIAM J Sci Comput 20: 359–392. doi:10.1137/S1064827595287997 ↵Kingma DP, Ba J. 2014. Adam: a method for stochastic optimization. ar...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
...earlier in this paper.STMSC enhances domain identification by capturing multilevel biological heterogeneity, thereby revealing subtle biological texturesAccurately identifying and characterizing small spatial domains is critical in the study of biological tissue microstructures (Kalita-de Croft et al...
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Methods: Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
- Carmen G. Moles,
- Pedro Mendes,
- and Julio R. Banga
Genome Res. November 2003 13: 2467-2474; Published in Advance January 1, 2003, doi:10.1101/gr.1262503
...their bound constraints, therefore we have slightly modified the code for that purpose. uES The unconstrained Evolution Strategy (uES) is a (µ, λ)-ES evolutionary optimization algorithm (based on Schwefel 1995 ) for problems only constrained by bounds on the decision variables. SRES The Evolution Strategy...
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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
...of each species tree were estimated with GLOOME (Cohen and Pupko 2010), using as inputs the gene presence/absence matrices previously generated by Roary and the species trees. The parameter configuration file was set to optimize the likelihood of the observed phyletic profiles under a evolution model...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...-rich euchromatin. SatDNAs in (peri)centromeric heterochromatin have a long history of investigation, including many plant and animal species, and studies have suggested a role of satDNA in chromatin packaging, centromere formation/maintenance, and centromere evolution (Blattes et al. 2006; Melters et al. 2013...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...al. 2022). As a result, DNA lineage barcoding has been widely used in studies focused on cell differentiation and evolution (Naik et al. 2014; Biddy et al. 2018; Rodriguez-Fraticelli et al. 2018; Weinreb et al. 2020), cell heterogeneity and cell fate during drug resistance (Nguyen et al. 2014b; Bhang...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
...cannot generally distinguish between different allelic copies, and most previous studies infer an average chromatin architecture that incorporates the diploid without considering possible differences between homologs (Li et al. 2021). Variability in multilevel chromatin architecture between homologs...
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Method: Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries
- Matthew Wiens,
- Hossein Farahani,
- R. Wilder Scott,
- T. Michael Underhill,
- and Ali Bashashati
Genome Res. August 2024 34: 1196-1210; Published in Advance August 15, 2024, doi:10.1101/gr.277066.122
...Caller, and SAMtools perform well on both scRNA-seq and scATAC-seq, with small differences such that it is difficult to say which one is best. Depending on whether precision or recall is more important and depending on which modality is used, Strelka or SAMtools might give optimal performance. There appear to be trade...

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