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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
..., UCell, and JASMINE—across nine healthy and cancer scRNA-seq data sets demonstrates their insufficiency in fulfilling this requirement. To address this limitation, we present Adjusted Neighborhood Scoring (ANS), a deterministic algorithm with enhanced control gene selection that significantly improves...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...University, Qingdao 266101, China; 310K Genomics Technology Co., Ltd., Shanghai 200233, China; 4Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China ↵5 These authors contributed equally to this work. Corresponding author: wshi...
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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...sequences. Zielezinski et al. (2017) demonstrated the effectiveness of alignment-free, k-mer-based methods for uncovering conserved genomic motifs and analyzing sequence similarity, whereas Fan et al. (2015) explored k-mers in comparative genomics, showing how they can approximate phylogenetic relationships...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...variations among TUGs, TNGs, and TDGs from ST to GR, suggesting a potential impact of THCs on gene transcriptional activity (Fig. 6B,C).View larger version: In this window In a new window Figure 6. THC unveils genomic dynamics during cellular differentiation. (A) Distribution of THCs of 1013 eligible genes...
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Method: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
- Da-Inn Lee and
- Sushmita Roy
Genome Res. May 2025 35: 1179-1193; Published in Advance March 20, 2025, doi:10.1101/gr.279930.124
...), disease (Lupiáñez et al. 2016), and evolutionary contexts (McCord 2017; Eres et al. 2019). High-throughput chromosomal conformation capture (Hi-C) technologies enable the study of 3D organization by experimentally measuring the tendency of genomic regions to spatially interact with one another (Mumbach et...
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Research: Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids
- Tülay Karakulak,
- Natalia Zajac,
- Hella Anna Bolck,
- Anna Bratus-Neuenschwander,
- Qin Zhang,
- Weihong Qi,
- Debleena Basu,
- Tamara Carrasco Oltra,
- Hubert Rehrauer,
- Christian von Mering,
- Holger Moch,
- and Abdullah Kahraman
Genome Res. April 2025 35: 698-711; Published in Advance March 19, 2025, doi:10.1101/gr.279345.124
...of Zurich, 8057 Zurich, Switzerland; 2Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, 8091 Zurich, Switzerland; 3Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; 4Functional Genomics Center Zurich, ETH, 8057 Zurich, Switzerland; 5Centre...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
...to an increasingly female-biased sex ratio. This almost deterministic genomic response to sociality may explain why social spider lineages do not persist. What causes species extinction is not clear, but either could be selfish meiotic drive eliminating the production of males or could be an inability to retain...
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Method: Inferring ancestry with the hierarchical soft clustering approach tangleGen
- Klara Elisabeth Burger,
- Solveig Klepper,
- Ulrike von Luxburg,
- and Franz Baumdicker
Genome Res. December 2024 34: 2244-2255; Published in Advance October 21, 2024, doi:10.1101/gr.279399.124
...of explainability, as it allows identifying the single-nucleotide polymorphisms that are responsible for the clustering structure. We demonstrate the capabilities and benefits of tangleGen for the inference of ancestral relationships, using both simulated data and data from the 1000 Genomes Project...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...with five-digit alleles, seven-digit alleles were further identified using IPD-KIR genomic sequences. However, when a CDS-only full allele (five-digit) aligned with variations, a further investigation was conducted to ascertain if the observed variations led to amino acid changes. Variations that altered...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...-read and long-read WGS data generated by the 1kGP and the Human Genome Structural Variation Consortium (HGSVC) (Ebert et al. 2021; Byrska-Bishop et al. 2022), in which 96.0% of the SVs overlapped either a short-read or long-read variant in the matched (Supplemental Table S6). We observed differences in number...

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