Searching journal content for articles similar to Elsik et al. 16 (11): 1329.

Displaying results 1-10 of 465

For checked items

view abstracts
download to citation manager

Select this article
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
...-length transcripts. Using these technologies, researchers have reported tens of thousands of novel transcripts, even in well-annotated s, while developing new algorithms and experimental approaches to handle the noisy data. The Long-read RNA-seq Genome Annotation Assessment Project community effort benchmarked LRS...
OPEN ACCESS ARTICLE
Select this article
Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...-alone methods. Several tools, such as AUGUSTUS (Stanke and Waack 2003; Stanke et al. 2006) and SNAP (Korf 2004), and popular annotation pipelines, like BRAKER (Stanke et al. 2008; Hoff et al. 2019) and MAKER (Campbell et al. 2014) have successfully implemented this strategy. Moreover, although the majority of s...
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
...the information of gene and exon boundaries in annotations to enumerate candidate isoforms, and it uses a modified LASSO procedure to select isoforms. CIDANE also uses the LASSO regression in its first phase, and then it uses a delayed column generation technique in its second phase to check if new isoforms...
Select this article
Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
- German Nudelman,
- Antonio Frasca,
- Brandon Kent,
- Kirsten C. Sadler,
- Stuart C. Sealfon,
- Martin J. Walsh,
- and Elena Zaslavsky
Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
...similar isoforms of annotated genes, long-read sequencing has become an important tool in the efforts to improve the transcriptome and annotation of several organisms (Sharon et al. 2013; Kim et al. 2014; Thomas et al. 2014; Gordon et al. 2015; Abdel-Ghany et al. 2016; Wang et al. 2016b).In this study, we...
Select this article
Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
.... 1F,I) with deeper conservation in sncRNAs andmRNAs (coding sequences [CDS]). CRSs regions are mostly intronic or intergenic (Fig. 1D; annotation sources are listed in Supplemental Material) and are enriched for small ncRNAs (sncRNAs; including 230 precursor-microRNAs and 199 snoRNAs) and UTRs (Fig...
OPEN ACCESS ARTICLE
Select this article
Method: Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
- Xiaohan Yang,
- Timothy J. Tschaplinski,
- Gregory B. Hurst,
- Sara Jawdy,
- Paul E. Abraham,
- Patricia K. Lankford,
- Rachel M. Adams,
- Manesh B. Shah,
- Robert L. Hettich,
- Erika Lindquist,
- Udaya C. Kalluri,
- Lee E. Gunter,
- Christa Pennacchio,
- and Gerald A. Tuskan
Genome Res. April 2011 21: 634-641; Published in Advance March 2, 2011, doi:10.1101/gr.109280.110
...a potential improvement in small protein annotation in Populus. Some small proteins have been reported to be involved in cellto-cell communications in plants. For example, a small protein of 94 aa called CAPRICE (CPC) is a transcription factor involved in intercellular signal transduction associated with root...
OPEN ACCESS ARTICLE
Select this article
Methods: Improving gene annotation using peptide mass spectrometry
- Stephen Tanner,
- Zhouxin Shen,
- Julio Ng,
- Liliana Florea,
- Roderic Guigó,
- Steven P. Briggs,
- and Vineet Bafna
Genome Res. February 2007 17: 231-239; Published in Advance December 22, 2006, doi:10.1101/gr.5646507
...of tremendous recent advances in computational gene finding, comprehensive annotation remains a challenge. Peptide mass spectrometry is a powerful tool for researching the dynamic proteome and suggests an attractive approach to discover and validate protein-coding genes. We present algorithms to construct...
Select this article
RESOURCE: Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
- Melody S. Clark,
- Yvonne J.K. Edwards,
- Dan Peterson,
- Sandra W. Clifton,
- Amanda J. Thompson,
- Masahide Sasaki,
- Yutaka Suzuki,
- Kiyoshi Kikuchi,
- Shugo Watabe,
- Koichi Kawakami,
- Sumio Sugano,
- Greg Elgar,
- and Stephen L. Johnson
Genome Res. December 2003 13: 2747-2753; Published in Advance January 1, 2003, doi:10.1101/gr.1691503
..., N., Saito, R., Suzuki, H., et al. 2002 . Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420 : 563 -573. ↵ Parsons, J.D. 1995 . Improved tools for DNA comparison and clustering. Comput. Appl. Biosci. 11 : 603 -613. ↵ Parsons, J.D., Brenner, S...
Select this article
Methods: Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
- Nitin Gupta,
- Stephen Tanner,
- Navdeep Jaitly,
- Joshua N. Adkins,
- Mary Lipton,
- Robert Edwards,
- Margaret Romine,
- Andrei Osterman,
- Vineet Bafna,
- Richard D. Smith,
- and Pavel A. Pevzner
Genome Res. September 2007 17: 1362-1377; Published in Advance August 9, 2007, doi:10.1101/gr.6427907
...therefore argue that MS studies are necessary to complement the existing gene prediction tools by accurate annotations of NME and many other post-translational modifications. In this work we exploit a data set containing 14.5 million tandem mass spectra for S. oneidensis . These data include samples from 17...
Select this article
Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
- Antonio Nappi,
- Liubov Shilova,
- Theofanis Karaletsos,
- Na Cai,
- and Francesco Paolo Casale
Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
...All experiments were conducted using the UKB cohort (Bycroft et al. 2018) based on the latest whole-exome sequencing (WES) release. Individual and variant quality control (QC) followed the protocols from Genebass (Karczewski et al. 2022). Variant annotation was performed using the pipeline described in Clarke et...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Elsik et al. 16 (11): 1329.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: