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Resource: Incorporating RNA-seq data into the zebrafish Ensembl genebuild
- John E. Collins,
- Simon White,
- Stephen M.J. Searle,
- and Derek L. Stemple
Genome Res. October 2012 22: 2067-2078; Published in Advance July 12, 2012, doi:10.1101/gr.137901.112
...Incorporating RNA-seq data into the zebrafish Ensembl genebuild John E. Collins 1 , Simon White , Stephen M.J. Searle and Derek L. Stemple Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA...
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ENSEMBL Special: The Ensembl Analysis Pipeline
- Simon C. Potter,
- Laura Clarke,
- Val Curwen,
- Stephen Keenan,
- Emmanuel Mongin,
- Stephen M.J. Searle,
- Arne Stabenau,
- Roy Storey,
- and Michele Clamp
Genome Res. May 2004 14: 934-941; doi:10.1101/gr.1859804
...: 541 -550. ↵ Stabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M., and Birney, E. 2004 . The Ensembl core software libraries. Genome Res. (this issue). ↵ Wan, H. and Wootton, J.C. 2000 . A global compositional complexity measure for biological sequences: AT-rich and GC-rich s encode less...
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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
...., and Clamp, M. 2004 . The Otter annotation system. Genome Res. (this issue). ↵ Stabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M., and Birney, E. 2004 . The Ensembl core software libraries. Genome Res. (this issue). ↵ Stalker, J., Gibbins, B., Meidl, P., Smith, J., Spooner, W., Hotz, H...
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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...no competing interests.AcknowledgmentsWe thank the Crick Genomics STP for sequencing the libraries. We also thank the members of the van Werven lab for the critical reading of the manuscript. This work was supported by the Francis Crick Institute (CC2043), which receives its core funding from Cancer Research...
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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
...CE, using RNA-seq data sourced from Zhou et al. (2023). Each transcript was assigned an AED score, reflecting the proportion of the transcript overlapped by a StringTie model from each of the three RNA-seq libraries.Paralog and ortholog counts were generated from Ensembl Compara (build 111) (for details...
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ENSEMBL Special: The Ensembl Automatic Gene Annotation System
- Val Curwen,
- Eduardo Eyras,
- T. Daniel Andrews,
- Laura Clarke,
- Emmanuel Mongin,
- Steven M.J. Searle,
- and Michele Clamp
Genome Res. May 2004 14: 942-950; doi:10.1101/gr.1858004
...protein, cDNA, and EST sequences. The gene-building system rests on top of the core Ensembl (MySQL) database schema and Perl Application Programming Interface (API), and the data generated are accessible through the Ensembl genome browser ( http://www.ensembl.org ). To date, the Ensembl predicted gene...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...-Mulia and Gilbert 2016b; Vouzas and Gilbert 2023). One limitation is the lack of methods enabling the simultaneous measurement of RT and gene expression from the same samples. Although multiple RT profiling methods exist at the ensemble population level (Marchal et al. 2018; Hulke et al. 2020; Rivera-Mulia et al...
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ENSEMBL Special: The Ensembl Web Site: Mechanics of a Genome Browser
- James Stalker,
- Brian Gibbins,
- Patrick Meidl,
- James Smith,
- William Spooner,
- Hans-Rudolf Hotz,
- and Antony V. Cox
Genome Res. May 2004 14: 951-955; doi:10.1101/gr.1863004
..., C., Proctor, G., Clamp, M., and Birney, E. 2004 . The Ensembl core software libraries. Genome Res. (this issue). ↵ Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., et al. 2002 . The Generic Genome Browser: A building block...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...-life + interaction to evaluate the relative impact of transcript half-life compared with the transcript abundance based on levels from the total RNA libraries. All statistical analyses and figures were done using R (v4.2.1) (R Core Team 2004). Functional annotation was performed with WebGestalt 2024 (Elizarraras et...
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Research: Core promoter T-blocks correlate with gene expression levels in C. elegans
- Vladislav Grishkevich,
- Tamar Hashimshony,
- and Itai Yanai
Genome Res. May 2011 21: 707-717; Published in Advance March 2, 2011, doi:10.1101/gr.113381.110
...and intron, 39 UTR, and the 39 adjacent and 39 distal end regions, the T-block and A-block frequency is shown for different expression groups as in Figure 4. The 39UTR and core promoter are T-rich, while exons are A-rich. For each region, 100 bpwere selected as the core promoter. Ensembl annotation was used...

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