Searching journal content for articles similar to Kaessmann et al. 12 (11): 1642.

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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...effectively. Moreover, ScPGE greatly reduces computational demands for modeling by using discrete cCREs instead of the entire genomic region flanking target genes, facilitating rapid training and deployment for new cell types. To quantify its computational demand, we systematically evaluated the model...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...explosion: Given that each human typically contains 40,000 to 200,000 variants at <0.5% minor allele frequency (MAF) (The 1000 Genomes Project Consortium 2015), an analysis of all possible rare variant pairs yields between 8 billion to nearly 20 trillion combinations per individual, necessitating a priori...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...in inbred mouse s (Garretson et al. 2025).The biological mechanisms underlying the elevated rate of dnSNVs in ART-derived mice remain unclear. Known mutational processes often leave distinct genomic signatures, including signatures attributable to oncogenic processes (Alexandrov et al. 2020) and germline...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...DongAhn Yoo1, Katherine M. Munson1 and Evan E. Eichler1,2 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA; 2Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA Corresponding author: ee3@uw...
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Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
- Wei-Hao Lee,
- Lechuan Li,
- Ruth Dannenfelser,
- and Vicky Yao
Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
...extract meaningful condition-associated genes, remove batch-associated signatures, and use the unguided components to build a low-dimensional embedding of any remaining variation. In single-cell data sets, the unguided components will typically capture the condition- and batch-agnostic cell-type variation...
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Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
...impacts when used with non-human species. Here, we use bovine s to assess the limits of using human –trained variant callers, including the allele frequency channel (DV-AF) and joint-caller DeepTrio (DT). Our novel approach, TrioTrain, automates extending DV for diploid species lacking Genome...
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Method: Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq
- Yike Xie,
- Abbas Habibalahi,
- Ayad G. Anwer,
- Kanu Wahi,
- Jacqueline Bailey,
- Francis Lin,
- Catherine Gatt,
- Emma M.V. Johansson,
- Tatyana Chtanova,
- Jeff Holst,
- Ewa Goldys,
- and Fabio Zanini
Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
...Unit, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales 2033, Australia; 6UNSW Cellular Genomics Futures Institute, UNSW Sydney, Sydney, New South Wales 2052, Australia; 7Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney...
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Method: Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
- Ziyan Rao,
- Min Zhang,
- Shaodong Huang,
- Chenyang Wu,
- Yuheng Zhou,
- Weijie Zhang,
- Xia Lin,
- and Dongyu Zhao
Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124
...underscore the significance of the CDTs combined with expression and interaction as an effective signature for the discovery of cancer driver lncRNAs.DiscussionlncRNAs can create an additional regulatory dimension superimposed over the genomic and epigenomic programs by interacting with DNAs, RNAs...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
.... Mitchell4, Jason E. Fish6,7,15 and Michael D. Wilson1,2 1Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3K3, Canada; 2Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 0A4, Canada; 3Institut de Pharmacologie Moléculaire et Cellulaire, Université...
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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA; 3McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA ↵4 These authors contributed equally to this work. Corresponding...
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