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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
...with comprehensive annotations and intuitive navigation, gained widespread popularity in the community (Kent et al. 2002; Lee et al. 2022). In addition to the UCSC Genome Browser, there are multiple other tools available to visualize s, each with its own advantages and focuses (e.g., Ensembl [Fernández...
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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
...by MSCI.MethodsSequence comparison of KZFPs among mammalian speciesThe identity scores of KZFPs were calculated using the BioMart web tool (https://www.ensembl.org/biomart/martview). We first organized the gene names of KZFPs in mice or humans as a gene list and then chose the data set “GRCm39” or “GRCh38...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...drift from population bottlenecks, as LD changes more quickly than site frequency patterns (Ferrer-Admetlla et al. 2014; Weigand and Leese 2018). Methods like iHES (Voight et al. 2006), XP-EHH (Sabeti et al. 2007), and REHH (Qanbari et al. 2010) look for long regions of homozygosity caused by selective...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...likelihood estimate is not in the confidence interval; ‐‐filter-regions: filtering sites in segmental duplication regions downloaded from UCSC Genome Browser (http://.ucsc.edu/); ‐‐gangstr-max-call-DP 1000 and ‐‐gangstr-min-call-DP 20: filtering calls with >1000× or <20× coverage; ‐‐min-locus-hwep 0...
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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
...structural variants (SVs; 50 bp < SV < 10 kbp) (Supplemental Fig. S12). To reduce the search space, we removed rare variants (non-major-allele fraction < 0.15) and variants only weakly associated with the expansion propensity phenotype (model P-value > 5 × 10−4). We used the Ensembl Variant Effect Predictor...
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Research: Broad domains of histone marks in the highly compact Paramecium macronuclear genome
- Franziska Drews,
- Abdulrahman Salhab,
- Sivarajan Karunanithi,
- Miriam Cheaib,
- Martin Jung,
- Marcel H. Schulz,
- and Martin Simon
Genome Res. April 2022 32: 710-725; Published in Advance March 9, 2022, doi:10.1101/gr.276126.121
..., Schizosaccharomyces pombe, Drosophila menlanogaster, Homo sapiens). A window of 300 kb is shown for each chromosome in a browser. (B) Summary of genomic features of the same organisms named in A. For details on collected data, see Methods. (C) Detection of histone modifications in vegetative Paramecium nuclei...
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Resource: JBrowse: A next-generation genome browser
- Mitchell E. Skinner,
- Andrew V. Uzilov,
- Lincoln D. Stein,
- Christopher J. Mungall,
- and Ian H. Holmes
Genome Res. September 2009 19: 1630-1638; Published in Advance July 1, 2009, doi:10.1101/gr.094607.109
...web site: Mechanics of a browser. Genome Res 14: 951–955. Stein L, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich J, Harris T, Arva A, et al. 2002. The generic browser: A building block for a model organism system database. Genome Res 12: 1599–1610. Tweedie S, Ashburner M, Falls K...
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ENSEMBL Special: An Overview of Ensembl
- Ewan Birney,
- T. Daniel Andrews,
- Paul Bevan,
- Mario Caccamo,
- Yuan Chen,
- Laura Clarke,
- Guy Coates,
- James Cuff,
- Val Curwen,
- Tim Cutts,
- Thomas Down,
- Eduardo Eyras,
- Xose M. Fernandez-Suarez,
- Paul Gane,
- Brian Gibbins,
- James Gilbert,
- Martin Hammond,
- Hans-Rudolf Hotz,
- Vivek Iyer,
- Kerstin Jekosch,
- Andreas Kahari,
- Arek Kasprzyk,
- Damian Keefe,
- Stephen Keenan,
- Heikki Lehvaslaiho,
- Graham McVicker,
- Craig Melsopp,
- Patrick Meidl,
- Emmanuel Mongin,
- Roger Pettett,
- Simon Potter,
- Glenn Proctor,
- Mark Rae,
- Steve Searle,
- Guy Slater,
- Damian Smedley,
- James Smith,
- Will Spooner,
- Arne Stabenau,
- James Stalker,
- Roy Storey,
- Abel Ureta-Vidal,
- K. Cara Woodwark,
- Graham Cameron,
- Richard Durbin,
- Anthony Cox,
- Tim Hubbard,
- and Michele Clamp
Genome Res. May 2004 14: 925-928; Published in Advance April 12, 2004, doi:10.1101/gr.1860604
...-R., and Cox, A.V. 2004 . The Ensembl web site—mechanics of a browser. Genome Res. (this issue). ↵ Stein, L.D. and Thierry-Mieg, J. 1998 . Scriptable access to the Caenorhabditis elegans sequence and other ACEDB databases. Genome Res. 8 : 1308 -1315. ↵ Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J...
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ENSEMBL Special: The Ensembl Core Software Libraries
- Arne Stabenau,
- Graham McVicker,
- Craig Melsopp,
- Glenn Proctor,
- Michele Clamp,
- and Ewan Birney
Genome Res. May 2004 14: 929-933; doi:10.1101/gr.1857204
...for Biotechnology Information. Nucleic Acids Res. 29 : 11 -16. WEB SITE REFERENCES ↵ http://www.ensembl.org/Docs/ensembl_tutorial.pdf ; Ensembl online tutorial document. The Ensembl Core Software Libraries Arne Stabenau 1 , Graham McVicker 1 , Craig Melsopp 1 , Glenn Proctor 1 , Michele Clamp 2 , and Ewan Birney 1...
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ENSEMBL Special: ESTGenes: Alternative Splicing From ESTs in Ensembl
- Eduardo Eyras,
- Mario Caccamo,
- Val Curwen,
- and Michele Clamp
Genome Res. May 2004 14: 976-987; doi:10.1101/gr.1862204
...and produce a minimal set of putative transcript variants that have nonequivalent splicing structure and are compatible with the EST evidence. The resulting transcripts produced from ESTs are the ESTGenes as shown in the Ensembl Web site ( www.ensembl.org ). The algorithm can be applied to ESTs, m...

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