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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...their relevant context would improve our ability for direct assessment of disease-associated variation. Profiling of allelic transcription factor (TF) activity across multiple cell and tissue types has shown that both genomic and tissue contexts modulate the penetrance of noncoding variants (Halow et al. 2021...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cisregulatory modules acting during vertebrate organogenesis Daniela M. Riley,1,7 Randa Elsayed,1,7 Mark D. Walsh,2,7 Simaran Johal,2 Ying Lin,3,4 Harry Walton,1 Till Bretschneider,5 Sascha Ott,1...
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Method: Minimizing reference bias with an imputed personalized reference
- Kavya Vaddadi,
- Mao-Jan Lin,
- Sina Majidian,
- Taher Mun,
- and Ben Langmead
Genome Res. March 5, 2026 gr.280989.125; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
...further by using a personalized reference, e.g. a diploid human reference constructed to match a donor individual’s alleles. We present a new impute-first alignment framework that combines elements of genotype imputation and read alignment. We first genotype the individual using a subsample of the input...
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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...in the manifestation of the disease in individuals carrying likely pathogenic rare coding variants.Incomplete penetrance represents a complex phenomenon whereby the presence of a pathogenic variant in the results in a disease phenotype in some but not all individuals that carry the variant (Vogt 1926; Cooper et al...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...for detailed observation of cellular and molecular changes during disease progression, enabling identification of precise therapeutic targets to inform drug development.Although ADNC stages do not capture longitudinal progression within individuals, we still observed clear cell type–specific transcriptional...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...impacts and evolutionary patterns over time remain elusive in humans owing to the technical and ethical complexities of functional studies. Integrating gene age dating with Mendelian disease phenotyping, we reveal a gradual rise in disease gene proportion as gene age increases. Logistic regression...
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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 the individual Seq1 and Seq2 data sets, excluding the requirement that dnSNVs are confirmed by both sequence batches (Supplemental Tables S3, S4).De novo mutation rate estimation and analysis of mutation spectrumTo assess differences in de novo mutation counts between cohorts, we fit a generalized linear model...
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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
...of fragmentation in de novo assembly persists, unless different types of data and manual curation are used, leading to a slower, more expensive assembly. For more information about the computational methods for assembly, readers can refer to Garg (2021) and Garg et al. (2022).Recently, a tremendous achievement has...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...cell population, enabling a more rapid and robust immune response.Sequencing immune-gene transcripts of individuals within a population reveals allelic diversity and allows comparison between immune responses to pathogenic antagonists, cancer, and autoimmune diseases (Boyd et al. 2010; Rodriguez et al...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...).ResultsMNase-seq profiling reveals -wide chromatin changes in genetic perturbation experimentsTo investigate chromatin changes in response to the deletion of individual transcriptional regulators, we profiled -wide chromatin occupancy in 201 yeast knockout strains (Supplemental Fig. S1; Giaever et al. 2002; Giaever...

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