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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...-10-62733394. 14 Email: huxx@cau.edu.cn. 15 Yuzhe Wang, State Key Laboratory of Animal Biotech Breeding, College of Biological 16 Sciences, China Agricultural University, Beijing, 100193, China. Phone +86-10-62731314. 17 Email: yuzhe891@cau.edu.cn. 18 19 Abstract 20 Predicting phenotypes from genomic mutations...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...; pentagons represent human genomic regions with HBV integration (colors indicate distinct chromosomes). The arrows mark the 3′-end. (D) Proportion of integration loci classified into the five categories depicted in panel C.Based on the mapping results of the chimeric reads, several patterns of HBV...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...-RNAs are produced from a variety of features, including hpRNAs and repetitive elementsThree genomic loci—F43E2.6, Y57G11C.1145, and mir-5592—accounted for ∼98% of 23H-RNA reads in our GFP::RDE-1 co-IP sRNA-seq libraries (Fig. 3A; Supplemental Table S1). F43E2.6, which is annotated as a coding gene but with no known...
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Research: Genome-wide oscillations in G + C density and sequence conservation
- Zarmik Moqtaderi,
- Susan Brown,
- and Welcome Bender
Genome Res. November 2021 31: 2050-2057; Published in Advance October 14, 2021, doi:10.1101/gr.274332.120
...and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations. Genome Res 27: 1988–2000. doi:10.1101/gr.219956.116 ↵Audit B, Vaillant C, Arnéodo A, d'Aubenton-Carafa Y, Thermes C. 2004. Wavelet analysis of DNA bending profiles reveals structural constraints...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...shown expression in the extraembryonic serosa and suggested functions in extraembryonic membrane patterning (Ferguson et al. 2014). It should also be noted that relatively few species were compared in these initial surveys owing to the lack of genomic data; hence, patterns of Shx gene evolution were...
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Research: Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
- Lisa Barros de Andrade e Sousa,
- Iris Jonkers,
- Laurène Syx,
- Ilona Dunkel,
- Julie Chaumeil,
- Christel Picard,
- Benjamin Foret,
- Chong-Jian Chen,
- John T. Lis,
- Edith Heard,
- Edda G. Schulz,
- and Annalisa Marsico
Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
...(Table 1; Supplemental Text S1). In addition, we included a series of genomic and structural features, such as gene density, the frequency of 3D chromatin interactions with different genomic elements, and the linear distance to other genomic features, such as the distance to the Xist locus, the next TAD...
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Research: Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism
- Dale J. Annear,
- Geert Vandeweyer,
- Alba Sanchis-Juan,
- F. Lucy Raymond,
- and R. Frank Kooy
Genome Res. November/December 2022 32: 1967-1980; Published in Advance November 9, 2022, doi:10.1101/gr.277011.122
...is known about whether the same inheritance and mutation patterns seen in the disease-associated CGG STRs are replicated among all or any of the other known CGG STRs spread throughout the human .In a previous study, we cataloged and categorized more than 6000 unique CGG STR loci across the human . The CGG...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...for each species partitioned according to their orthology profiles. A. florea possessed the greatest number of lineage-specific genes followed by A. mellifera.Genome-wide patterns of positive selectionTo identify positive selection that acted on protein-coding genes during the evolution of honey bees, we...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...loci. More recently, careful analysis and categorization of clinical manifestations served as essential tools in recent discoveries where the same expansion mutations occurring at different genomic loci all resulted in benign adult familial myoclonic epilepsy (BAFME), also known as familial adult...
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Method: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns
- Bowen Jin,
- John A. Capra,
- Penelope Benchek,
- Nicholas Wheeler,
- Adam C. Naj,
- Kara L. Hamilton-Nelson,
- John J. Farrell,
- Yuk Yee Leung,
- Brian Kunkle,
- Badri Vadarajan,
- Gerard D. Schellenberg,
- Richard Mayeux,
- Li-San Wang,
- Lindsay A. Farrer,
- Margaret A. Pericak-Vance,
- Eden R. Martin,
- Jonathan L. Haines,
- Dana C. Crawford,
- and William S. Bush
Genome Res. April 2022 32: 778-790; Published in Advance February 24, 2022, doi:10.1101/gr.276069.121
...context will improve rare variant association tests. Prior studies have shown that missense variants show nonrandom patterns in protein structures, such as cancer-associated hotspot regions with a high density of missense somatic mutations (Tokheim et al. 2016). Our group (Sivley et al. 2018) also found...
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