Searching journal content for articles similar to Curwen et al. 14 (5): 942.

Displaying results 1-10 of 216

For checked items

view abstracts
download to citation manager

Select this article
Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic s Tomáš Brůna1,4,5, Alexandre Lomsadze2,4 and Mark Borodovsky1,2,3 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; 2Wallace H. Coulter Department of Biomedical...
OPEN ACCESS ARTICLE
Select this article
Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
- Kuan-Hao Chao,
- Jakob M. Heinz,
- Celine Hoh,
- Alan Mao,
- Alaina Shumate,
- Mihaela Pertea,
- and Steven L. Salzberg
Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
...-centric algorithm considers both types of alignments, chooses optimal open reading frames, resolves overlapping gene loci, and finds additional gene copies when they exist. LiftOn can reliably transfer annotation between s representing members of the same species, as we demonstrate on human, mouse, honeybee, rice...
Select this article
Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
.... (Signal) Weighted harmonic mean of the observed/expected ratio and −log (FDR), (gene count) the number of proteins annotated with a particular term. The results highlight the genes as significant regulators associated with CD4 naive cells.In the case of CD4 naive T cells, a subset of T lymphocytes...
Select this article
Method: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
- Lars Gabriel,
- Tomáš Brůna,
- Katharina J. Hoff,
- Matthis Ebel,
- Alexandre Lomsadze,
- Mark Borodovsky,
- and Mario Stanke
Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
..., Borodovsky M. 2020. GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genom Bioinform 2: lqaa026. doi:10.1093/nargab/lqaa026 ↵Brůna T, Hoff KJ, Lomsadze A, Stanke M, Borodovsky M. 2021. BRAKER2: automatic eukaryotic annotation with GeneMark-EP+ and AUGUSTUS...
OPEN ACCESS ARTICLE
Select this article
Method: AIDE: annotation-assisted isoform discovery with high precision
- Wei Vivian Li,
- Shan Li,
- Xin Tong,
- Ling Deng,
- Hubing Shi,
- and Jingyi Jessica Li
Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119
...>95% of human isoforms are >300 bp, with a mean length of 1712 bp (GENCODE annotation, release 24) (Harrow et al. 2012). Hence, RNA-seq reads are short fragments of full-length isoforms. Since most isoforms of the same gene share some overlapping regions, many RNA-seq reads do not unequivocally map...
Select this article
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
...Sequencing Project (IRGSP), with an annotation set (gene models, gene, and protein sequences) released in 2005 (International Rice Genome Sequencing Project and Sasaki 2005). The IRGSP canonical reference (IRGSP RefSeq) is derived from the japonica variety Nipponbare, despite indica rice accounting...
OPEN ACCESS ARTICLE
Select this article
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
..., United Kingdom Abstract Ensembl gene annotation provides a comprehensive catalog of transcripts aligned to the reference sequence. It relies on publicly available species-specific and orthologous transcripts plus their inferred protein sequence. The accuracy of gene models is improved...
OPEN ACCESS ARTICLE
Select this article
Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
- Charlie George Barker,
- Eirini Petsalaki,
- Girolamo Giudice,
- Julia Sero,
- Emmanuel Nsa Ekpenyong,
- Chris Bakal,
- and Evangelia Petsalaki
Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
...Table S2.We used Enrichr and their suite of gene set libraries (Kuleshov et al. 2016) to functionally annotate and label some of the modules using enrichment of genes contained within them. We found that the “RAP1 signaling” module is also enriched for terms such as VEGF signaling and hemostasis...
OPEN ACCESS ARTICLE
Select this article
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
...in “annotation,” however, is beginning to expand, as other algorithms are developed and deployed. For example, Ensembl automatic annotation has begun to include pseudogenes and some RNA genes. For projects without existing high-quality annotation, Ensembl provides an automatic annotation. This process...
Select this article
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
...., Searle, S., and Clamp, M. 2004 . The Ensembl automatic gene annotation system. Genome Res. (this issue). ↵ Down, T.A. and Hubbard, T.J.P. 2002 . Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12 : 458 -461. ↵ Durbin, R. and Mieg, T. 1991 . A C...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Curwen et al. 14 (5): 942.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: