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Method: Assessment of megabase-scale somatic copy number variation using single-cell sequencing
- Kristin A. Knouse,
- Jie Wu,
- and Angelika Amon
Genome Res. March 2016 26: 376-384; Published in Advance January 15, 2016, doi:10.1101/gr.198937.115
...Assessment of megabase-scale somatic copy number variation using single-cell sequencing Kristin A. Knouse 1 , 2 , Jie Wu 3 and Angelika Amon 1 1Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical...
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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...affected by partial BTA4 mono- or trisomy resulted in imputation and phasing errors, which explains why this sire had the lowest LD max value among confirmed IR carriers. The deletions of several megabases associated with t(24;29)-der 29 and t(3;8) also caused local phasing and imputation errors because...
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Method: Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line
- Patrick Essletzbichler,
- Tomasz Konopka,
- Federica Santoro,
- Doris Chen,
- Bianca V. Gapp,
- Robert Kralovics,
- Thijn R. Brummelkamp,
- Sebastian M.B. Nijman,
- and Tilmann Bürckstümmer
Genome Res. December 2014 24: 2059-2065; Published in Advance November 4, 2014, doi:10.1101/gr.177220.114
...Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line Patrick Essletzbichler 1 , Tomasz Konopka 2 , Federica Santoro 1 , 4 , Doris Chen 2 , Bianca V. Gapp 2 , Robert Kralovics 2...
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Method: Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes
- Yinxiu Zhan,
- Luca Mariani,
- Iros Barozzi,
- Edda G. Schulz,
- Nils Blüthgen,
- Michael Stadler,
- Guido Tiana,
- and Luca Giorgetti
Genome Res. March 2017 27: 479-490; Published in Advance January 5, 2017, doi:10.1101/gr.212803.116
...themselves, and if so, why those properties emerge at this particular folding scale.A comprehensive analysis that considers all previously identified topological levels simultaneously and compares them to one another in terms of their functional and physical properties is currently lacking. A small number...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...Table S8). On average, the uninterrupted TfSat01 arrays within the multi-megabase regions have a median length of 11.8 kb (Fig. 2B). Although the number of mapped TfSat01 arrays varies up to 6.4-fold between different chromosomes, the median length of uninterrupted arrays remains rather consistent...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...fossils,” which are characterized by low speciation rates and morphological change over long time scales (Darwin 1859; Stanley 1975; Eldredge and Stanley 1984; Schopf 1984; Casane and Laurenti 2013; Bennett et al. 2018; Lidgard and Love 2018, 2023; Turner 2019), may exhibit slow rates of nucleotide...
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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...features of mammalian interphase folding at the megabase scale (McCord et al. 2020). First, boundaries partition chromosomes into a series of topologically associating domains (TADs), appearing as squares of enriched contact frequency on the Hi-C maps. Boundaries between adjacent TADs are largely specified...
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Methods: Two-parameter characterization of chromosome-scale recombination rate
- Wentian Li and
- Jan Freudenberg
Genome Res. December 2009 19: 2300-2307; Published in Advance September 14, 2009, doi:10.1101/gr.092676.109
...11030, USA Abstract The genome-wide recombination rate (RR) of a species is often described by one parameter, the ratio between total genetic map length ( G ) and physical map length ( P ), measured in centimorgans per megabase (cM/Mb). The value of this parameter varies greatly between...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...et al. 2021). The name of the CENH3-occupied sequences (CEN178) is written alongside in blue. A scale bar is provided indicating physical distance (megabases). (E) Representing monocentric retrotransposon architecture, a physical map of Triticum monococcum Chromosome 2A is shown (Ahmed et al. 2023...
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LETTER: The scale of mutational variation in the murid genome
- Daniel J. Gaffney and
- Peter D. Keightley
Genome Res. August 2005 15: 1086-1094; Published in Advance July 15, 2005, doi:10.1101/gr.3895005
...“hotspots” also occur in murids, the lack of an observed relationship may be explained, in part, by this effect. For example, if recombination rates vary over scales of kilobases, as opposed to megabases, then any relationship between mutation and recombination may be obscured by averaging rates over large...

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