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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...in eight families (6%), where variants in BRCA1, PALB2, and ATM created intronic pseudoexons that were spliced into transcripts, resulting in premature truncations (Gulsuner et al. 2024). Overall, the elucidation of the inheritance patterns of previously hidden variations promises to enhance genetic...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...as macrosynteny, is seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern of evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, we reconstruct the chromosomal evolutionary history of five...
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Research: Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures
- Jiseon Lim,
- Wonjoo Kim,
- Jun Kim,
- and Junho Lee
Genome Res. November 2023 33: 1947-1957; Published in Advance November 2, 2023, doi:10.1101/gr.278124.123
...Biology and Genetics, Seoul National University, Seoul 08826, South Korea; 3Research Institute of Basic Sciences, Seoul National University, Seoul 08826, South Korea; 4Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134...
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Resource: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium
Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
...data on depth of sequence read coverage in 300-bp genomic windows. We excluded windows with a high rate of ambiguous read mapping, leaving 77% (177 Mbp) of genomic windows accessible to CNV calling. For each individual mosquito, we fitted a hidden Markov model (HMM) to windowed depth of coverage values...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...of cell fates from single-cell snapshots. However, the study suggested that scRNA-seq fails to capture the heritable properties that guide fate determination, where additional studies such as chromatin accessibility or proteomics information may help to identify the hidden information (VanHorn and Morris...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
...in mouse available in the Mouse Genome Informatics (MGI) database (Table 6; Supplemental Table 5; Bult et al. 2008). We excluded nine comparisons from the analysis because transcripts from these loci were expressed in a nonspatially restricted manner in zebrafish or mouse, and we could not exclude...
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Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...to examine and compare the dynamic of RTEs in their multiple brain regions. With rapid advancements in single-cell sequencing technology and analytical tools, investigating loci-specific RTE expression dynamics holds great promise for unveiling the hidden roles of RTEs in neurodegenerative diseases. Although...

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