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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
...to annotate samples based on cell-type composition. By comparing aggregation strategies, we find that regressing confounders within studies and prioritizing larger studies optimizes network reconstruction. We apply these findings to infer three consensus networks (universal, cancer, noncancer) and 27 context...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...no additional processing steps and thus facilitating its integration into existing genomic diagnostic workflows. Ongoing improvements in accuracy, throughput, and cost reduction further broaden LRS's applications across model and nonmodel organisms. With decreasing costs, LRS is now practical for generating...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
..., Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, Hainan 7 572000, China. 8 2College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, 9 China. 10 3Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, 11 Denmark. 12 13 Email addresses: 14 Pengju Zhao...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...regions in model organisms that combine data and predictions: The best-known (and available via many integrator tools) is ReMap (Hammal et al. 2022), but an interesting alternative is CistromeDB (Zheng et al. 2019). There are also time-honored genomic resources for specific model organisms...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...the transition and emission probabilities are based on a previously defined model for structured populations with migration and recombination (Steinrücken et al. 2013). After decoding, the probability that a target haplotype is introgressed is computed, resulting in a set of introgressed tracts per target...
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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
..., Washington 98195, USA; 19Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut 06030-6403, USA Corresponding author: mindyshi@temple.eduAbstractThe human is packaged within a three-dimensional (3D) nucleus and organized into structural units known as compartments, topologically...
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Research: A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
- Xuelei Dai,
- Peipei Bian,
- Dexiang Hu,
- Funong Luo,
- Yongzhen Huang,
- Shaohua Jiao,
- Xihong Wang,
- Mian Gong,
- Ran Li,
- Yudong Cai,
- Jiayue Wen,
- Qimeng Yang,
- Weidong Deng,
- Hojjat Asadollahpour Nanaei,
- Yu Wang,
- Fei Wang,
- Zijing Zhang,
- Benjamin D. Rosen,
- Rasmus Heller,
- and Yu Jiang
Genome Res. August 2023 33: 1284-1298; Published in Advance September 15, 2023, doi:10.1101/gr.277481.122
....In the present study, we generated high-quality partially phased s for 10 representative Chinese indicine cattle breeds across southern China, with the aim of identifying the genomic landscape of non-Hereford sequence. By taking advantage of these partially phased assemblies, we comprehensively assessed...
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Method: Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
...Institut Jules Bordet, Université Libre de Bruxelles, 1000 Brussels, Belgium ↵13 These authors contributed equally to this work. Corresponding author: stein.aerts@kuleuven.vib.beAbstractDeciphering the genomic regulatory code of enhancers is a key challenge in biology because this code underlies cellular...
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Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
- Mayank Murali,
- Jamie Saquing,
- Senbao Lu,
- Ziyang Gao,
- Emily F. Watts,
- Ben Jordan,
- Zachary Peters Wakefield,
- Ana Fiszbein,
- David R. Cooper,
- Peter J. Castaldi,
- Dmitry Korkin,
- and Gloria M. Sheynkman
Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
...Health Genomics, University of Virginia, Charlottesville, Virginia 22903, USA; 11UVA Cancer Center, University of Virginia, Charlottesville, Virginia 22903, USA Corresponding author: gs9yr@virginia.eduAbstractLong-read RNA-seq has shed light on transcriptomic complexity, but questions remain about...
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Research: Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells
- Bingxiang Xu,
- Xiaomeng Gao,
- Xiaoli Li,
- Yan Jia,
- Feifei Li,
- and Zhihua Zhang
Genome Res. July 2022 32: 1285-1297; Published in Advance July 14, 2022, doi:10.1101/gr.276554.122
...Bingxiang Xu1,2,3,6, Xiaomeng Gao1,2,6, Xiaoli Li1,2,4, Yan Jia1, Feifei Li1,5 and Zhihua Zhang1,2 1Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Chaoyang District, Beijing 100101, China; 2School of Life Science, University of Chinese...

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