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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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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
...comparative assembly hubs using UCSC Genome Browser's framework. It uses snake track to show multiple query assemblies aligned to a target assembly, and annotations mapped to query assemblies can also be displayed with an automatic “liftOver.” JBrowse2 implemented linear synteny view to support cross...
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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
...-mediated repression allows activation of ERV enhancers upon entry into meiosis. This regulatory feature is observed for independently evolved KZFPs and ERVs in mice and humans, suggesting evolutionary conservation in mammals. Further, we show that KZFP-targeted ERVs are underrepresented on the sex chromosomes...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...of capturing large numbers of transcripts is the effect it may have on visualizing genomic data. Genome browsers such as Ensembl (Martin et al. 2023) and UCSC (Nassar et al. 2023) are frequently the primary access point for interrogating the intersection between genomic data and reference annotation, including...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...with estimates of evolutionary conservation deduced from whole- alignments between human and 99 other vertebrates, available as phastCons scores through the UCSC Genome Browser (Supplemental Methods; Siepel and Haussler 2005; Siepel et al. 2005). Overall, the two measures agree very well (Fig. 4C). For instance...
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RESOURCE: The Human Genome Browser at UCSC
- W. James Kent,
- Charles W. Sugnet,
- Terrence S. Furey,
- Krishna M. Roskin,
- Tom H. Pringle,
- Alan M. Zahler,
- and and David Haussler
Genome Res. June 1, 2002 12: 996-1006; Published in Advance May 16, 2002, doi:10.1101/gr.229102
.... A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu . This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...vertebrate sequenced.Transposon analysisMouse (mm39) and chimpanzee (panTro6) repeatmasked tracks were downloaded from UCSC Genome Browser's Table Browser function with the following parameters: “Table Browser → Repeats → Table “rmsk” → All fields from selected table → repeat-table.tsv.” The table...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...IslandExt, and GeneHancer tracks from the UCSC Genome Browser, respectively. In each case, the right panel shows a scatter plot of the average diploid STR genotypes (x-axis) and methylation β-values (y-axis) of the strongest associated (by P-value).To further characterize mSTRs, we investigated the properties...
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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: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
...al. 2004; Dubchak et al. 2009); MULTIZ for the UCSC Genome Browser (Miller et al. 2007; Meyer et al. 2013), and Pecan and EPO for the Ensembl Browser (Paten et al. 2008, 2009; Flicek et al. 2013). In addition, we tested a fairly broad set of standalone WGA tools, including progressiveMauve (Darling...
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