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Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- Arkarachai Fungtammasan,
- Erin Walsh,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- and Kateryna D. Makova
Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
...histone modification sites, nuclear lamina binding sites, and microRNA occurrence), DNA replication (replication timing and replication origin density), recombination and mutation (recombination rates and evolutionarily breakpoint regions), and DNA sequence/structure (direct and inverted repeats, triplex...
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LETTER: Retroelement Distributions in the Human Genome: Variations Associated With Age and Proximity to Genes
- Patrik Medstrand,
- Louie N. van de Lagemaat,
- and Dixie L. Mager
Genome Res. October 1, 2002 12: 1483-1495; doi:10.1101/gr.388902
..., for the SINE (Alu and MIR) elements, densities within genes are close to that predicted or are overrepresented based on average GC content of gene regions (Fig. 3 A,B,D). In contrast, L1 elements and all six LTR classes, particularly those in the same transcriptional direction, are underrepresented within...
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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
...and the aggressive phenotype observed in the patient. Further investigation of the tandem duplication mechanism revealed microhomology regions at both proximal and distal breakpoints within Alu elements, which were codirectionally aligned with the transcriptional direction of PALB2, suggesting the role of repetitive...
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...on familial genotyping or direct read-based phasing if possible.With significantly longer read lengths, LRS outperforms SRS in read-based phasing, increasing phase block N50s (largest haplotype block length such that 50% of all heterozygous sites are contained in haplotype blocks of equal or greater size...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...and adjacent nontumor tissues, potentially exerting a direct influence on genes integral to normal hepatic function, including TCP10L and EVA1C. A possible explanation is that these somatic SVs may arise from premalignant intermediate state cells or tumor cells within the adjacent nontumor tissues (Aran et al...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...recombination and nucleotide composition is GC-biased gene conversion (gBGC), that is, the fixation bias favoring “strong” (G and C) over “weak” alleles (A and T) during recombination (Duret and Galtier 2009). This process mimics directional selection and can alter nucleotide composition between regions...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...et al. 2023), are capable of quantitatively estimating the modification level of each site based on nucleotide deletion signatures.In addition to these antibody and chemical-based detection methods, nanopore direct sequencing of full-length native RNA molecules is increasingly receiving attention...
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LETTER: Alu-Containing Exons are Alternatively Spliced
- Rotem Sorek,
- Gil Ast,
- and Dan Graur
Genome Res. July 1, 2002 12: 1060-1067; doi:10.1101/gr.229302
...: Optical Technologies and Informatics, Proc SPIE , eds Bittner M.L. , Chen Y. , Dorsel A.N. , Dougherty E.D. ( SPIE , Bellingham, WA ), 4266 : 86 – 95 . ↵ Stenger J.E. , Lobachev K.S. , Gordenin D. , Darden T.A. , Jurka J. , Resnick M.A. ( 2001 ) Biased distribution of inverted and direct Alus in the human...
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LETTER: Low copy repeats mediate distal chromosome 22q11.2 deletions: Sequence analysis predicts breakpoint mechanisms
- Tamim H. Shaikh,
- Ronald J. O’Connor,
- Mary Ella Pierpont,
- James McGrath,
- April M. Hacker,
- Manjunath Nimmakayalu,
- Elizabeth Geiger,
- Beverly S. Emanuel,
- and Sulagna C. Saitta
Genome Res. April 2007 17: 482-491; Published in Advance March 9, 2007, doi:10.1101/gr.5986507
.... ↵ Stenger, J.E. , Lobachev, K.S. , Gordenin, D. , Darden, T.A. , Jurka, J. , Resnick, M.A. ( 2001 ) Biased distribution of inverted and direct Alus in the human : Implications for insertion, exclusion, and stability . Genome Res. 11 : 12 – 27 . ↵ Urban, A.E. , Korbel, J.O. , Selzer, R. , Richmond, T...
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Letter: Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
- Jesse D. Hollister and
- Brandon S. Gaut
Genome Res. August 2009 19: 1419-1428; Published in Advance May 28, 2009, doi:10.1101/gr.091678.109
...) subsets. There was a higher percentage of polymorphic insertions in the uTE sample (53%) than the mTE sample (44%), but the excess was not significant (FET P = 0.15). The presence and direction of selection acting on a class of mutations is commonly inferred by comparing the SFS to a (presumably) neutral...

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