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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...relationships between 3D structure and oncogenic processes.The mammalian is folded into large-scale dynamic three-dimensional (3D) chromatin conformations that provide a framework for regulated gene expression. In the interphase nucleus, chromosomes exist as territories (Cremer and Cremer 2010; Rowley...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...3), mirroring previous large-scale observations using chicken WCP and BAC-FISH onto Apalone (O'Connor et al. 2018) and cDNA-FISH onto the Chinese softshell turtle Pelodiscus sinensis (Matsuda et al. 2005) (denoted Pelodiscus hereafter). This observation indicates that the fairly conserved karyotype...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...and assemble, and therefore, they are underrepresented or absent even in the best assemblies (for review, see Miga 2015; Lower et al. 2018). However, with the improvement of long-read sequencing technology, especially the Oxford Nanopore platform, it has recently been demonstrated that genomic loci made of sat...
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Resource: GenomeVIP: a cloud platform for genomic variant discovery and interpretation
- R. Jay Mashl,
- Adam D. Scott,
- Kuan-lin Huang,
- Matthew A. Wyczalkowski,
- Christopher J. Yoon,
- Beifang Niu,
- Erin DeNardo,
- Venkata D. Yellapantula,
- Robert E. Handsaker,
- Ken Chen,
- Daniel C. Koboldt,
- Kai Ye,
- David Fenyö,
- Benjamin J. Raphael,
- Michael C. Wendl,
- and Li Ding
Genome Res. August 2017 27: 1450-1459; Published in Advance May 18, 2017, doi:10.1101/gr.211656.116
...Cloud-generated calls were 99.0%–99.7% for SNVs and 88.5%–93.0% for indels, both of whose ranges are comparable to the results from GenomeVIP (Fig. 4F). Table 1. Examples of large-scale projects utilizing GenomeVIP Computational resources (CPU-h) Variants (millions) Project Samples VarScan2 GATK Strelka Pindel SNVs...
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RESOURCE: A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
- Daniel Blankenberg,
- James Taylor,
- Ian Schenck,
- Jianbin He,
- Yi Zhang,
- Matthew Ghent,
- Narayanan Veeraraghavan,
- Istvan Albert,
- Webb Miller,
- Kateryna D. Makova,
- Ross C. Hardison,
- and Anton Nekrutenko
Genome Res. June 2007 17: 960-964; doi:10.1101/gr.5578007
...: A platform for interactive large-scale analysis . Genome Res. 15 : 1451 – 1455 . ↵ Gibbs, R.A. , Weinstock, G.M. , Metzker, M.L. , Muzny, D.M. , Sodergren, E.J. , Scherer, S. , Scott, G. , Steffen, D. , Worley, K.C. , Burch, P.E. , et al. ( 2004 ) Genome sequence of the Brown Norway rat yields insights...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...methylation has substantially impacted the large-scale evolution of mammalian s. Spontaneous deamination elevates the mutation rate at methylated cytosines (Bird 1980). Consequently, germline DNA methylation profiles have shaped the CpG landscape of mammalian s (Cohen et al. 2011), resulting in the CpG island...
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Perspective: Biological data sciences in genome research
- Michael C. Schatz
Genome Res. October 2015 25: 1417-1422; doi:10.1101/gr.191684.115
...://cloud.google.com/ genomics/), and other commercial vendors are also emerging to help manage the deluge of data using commercial cloud platforms and are likely to play an increasingly important role in genomics in the future. The major technical reason this model will become more widespread is that at large scales...
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Method: Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium
- Cheng-Lin Frank Li,
- Balaji Santhanam,
- Amanda Nicole Webb,
- Blaž Zupan,
- and Gad Shaulsky
Genome Res. September 2016 26: 1268-1276; Published in Advance June 15, 2016, doi:10.1101/gr.205682.116
...DNAdamage and free radical production in epithelial cells. J Biol Chem 280: 21061–21066. HaeltermanNA, Jiang L, Li Y, Bayat V, Sandoval H, Ugur B, TanKL, Zhang K, Bei D, Xiong B, et al. 2014. Large-scale identification of chemically inducedmutations inDrosophilamelanogaster.Genome Res24: 1707–1718. Hirose S...
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Research: DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome
- Leslie Y. Beh,
- Manuel M. Müller,
- Tom W. Muir,
- Noam Kaplan,
- and Laura F. Landweber
Genome Res. November 2015 25: 1727-1738; Published in Advance September 1, 2015, doi:10.1101/gr.188516.114
..., such as transcription (Piña et al. 1990; Lam et al. 2008). In light of this, it is crucial to understand how nucleosomes are organized across the . Genome-wide nucleosome maps in major model organisms have revealed strikingly similar nucleosome patterns near gene starts, where a nucleosome-depleted region upstream...
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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
.... To illustrate the utility of STR-FM, we applied it to the completely sequenced human s from the Platinum Genomes Project (Ajay et al. 2011) and determined human -wide germline mutation rates at STRs. Results The STR-FM pipeline We designed the STR-FMpipeline as a collection of tools in Galaxy (Giardine et al...

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