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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
...-Cas9 RE deletionsPaired sgRNAs (5′- and 3′-sgRNAs) were designed to target both ends of selected candidate REs in the human DNAJC9 locus to create a deletion. sgRNA with on-target high predicted cleavage and a low number of off-targets was carefully selected using the UCSC Genome Browser (hg38) (Perez...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...; slightly altered for exposition) were automatically generated by OMKar. The karyograms displayed show the “segment view” for easier referencing. Panels C and F describe the SV interpretation process after path decomposition, with black brackets indicating concordant blocks, red indicating deletion blocks...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...protein-coding gene sets. To define CGC1 genomic coordinates for sequences that either are shared with N2 (Supplemental Data File 10) or are unique to CGC1 (Supplemental Data File 11) to which genes or transcripts could be assigned, we aligned the two assemblies and identified uniquely aligned blocks...
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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
...↵Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, et al. 2002. The Generic Genome Browser: a building block for a model organism system database. Genome Res 12: 1599–1610. doi:10.1101/gr.403602 ↵Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfig...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...(Peaston et al. 2004; Pi et al. 2004; Rebollo et al. 2012; Erwin et al. 2014; Friedli and Trono 2015; Garcia-Perez et al. 2016; Thompson et al. 2016; Chuong et al. 2017; Huang et al. 2017). Genome-wide studies demonstrate that a significant portion of transcription factor (TF)-binding sites is derived from...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...In a new window Figure 2. Phasing accuracy and inversion analysis of trio-based and trio-free assemblies. (A) Phasing accuracy of PGAS (trio-free) assemblies with respect to trio-based phasing. (B) Haplotype assignment of 1-Mbp-sized blocks (left from ideogram, H1; right from ideogram, H2) to either...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...significance thresholds based on permutation analyses. (B,C) Increased expansion propensity is associated with the B haplotype at the Chr 13 QTL. Each point represents one strain. We used SNP haplotype blocks to assign each strain as harboring either the B (red) or D (blue) haplotype at this locus. The y...
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Method: The multicomparative 2-n-way genome suite
- Gennady Churakov,
- Fengjun Zhang,
- Norbert Grundmann,
- Wojciech Makalowski,
- Angela Noll,
- Liliya Doronina,
- and Jürgen Schmitz
Genome Res. October 2020 30: 1508-1516; Published in Advance July 29, 2020, doi:10.1101/gr.262261.120
..., the Santa Cruz Genomics Institute at the University of California Santa Cruz (UCSC) published their first graphical Genome Browser (Kent et al. 2002), which has become a comprehensive visual representation of the prevailing vertebrate assemblies (https://.ucsc.edu). Building on the Santa Cruz Genome Browser...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...libraries for each synteny block, based on previously selected NLE-informative chromosomes (Fig. 1A). In this way, we generated high-coverage and directional files for each human–gibbon synteny block that were BED-formatted into a unique composite file, and uploaded it as a custom track on UCSC Genome...
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Resource: Recompleting the Caenorhabditis elegans genome
- Jun Yoshimura,
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Idan Gabdank,
- Lamia Wahba,
- Cheryl L. Smith,
- Mark L. Edgley,
- Ann E. Rougvie,
- Andrew Z. Fire,
- Shinichi Morishita,
- and Erich M. Schwarz
Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
...as Supplemental Data File S1). For large-scale structural comparisons of the N2 reference assembly versus our final VC2010 assembly, we used the version of N2 from WormBase release WS220 (Lee et al. 2018). This has the advantage of being a highly used version that is available in the UCSC Genome Browser (where...
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