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Resource: Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome
- Kourosh Salehi-Ashtiani,
- Chenwei Lin,
- Tong Hao,
- Yun Shen,
- David Szeto,
- Xinping Yang,
- Lila Ghamsari,
- HanJoo Lee,
- Changyu Fan,
- Ryan R. Murray,
- Stuart Milstein,
- Nenad Svrzikapa,
- Michael E. Cusick,
- Frederick P. Roth,
- David E. Hill,
- and Marc Vidal
Genome Res. December 2009 19: 2334-2342; Published in Advance October 2, 2009, doi:10.1101/gr.098640.109
...RSTs can be readily assembled to generate full transcripts. For longer transcripts, the gaps of nonoverlapping 59 RSTs and 39 RSTs are filled by sequences from WormBase transcript models. Genome Research 2335 www..org Large-scale RACE of the C. elegans ORFeome Primer design and generation of RACE...
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RESOURCE: WormBase as an Integrated Platform for the C. elegans ORFeome
- Nansheng Chen,
- Daniel Lawson,
- Keith Bradnam,
- Todd W. Harris,
- and Lincoln D. Stein
Genome Res. October 15, 2004 14: 2155-2161; doi:10.1101/gr.2521304
...connection with the reagent-based resources at the ORFeome project Web site. Footnotes Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2521304. ↵ 3 Corresponding author. E-MAIL chenn@cshl.org ; FAX (516) 367-6851. Accepted April 16, 2004...
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LETTER: New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones
- Anita G. Fernandez,
- Kristin C. Gunsalus,
- Jerry Huang,
- Ling-Shiang Chuang,
- Nancy Ying,
- Hsiao-lan Liang,
- Caroline Tang,
- Aaron J. Schetter,
- Charles Zegar,
- Jean-François Rual,
- David E. Hill,
- Valerie Reinke,
- Marc Vidal,
- and Fabio Piano
Genome Res. February 2005 15: 250-259; doi:10.1101/gr.3194805
...Piano, F David E Hill Caroline Tang Fabio, Piano Jerry, Huang Nancy David Hill Kristin C V Reinke AG Fernandez C Zegar Zegar, C Schetter Aaron J. Charles Zegar 10.1101/gr.3194805 1088-9051 genome;15/2/250 New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones...
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PERSPECTIVE: ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List
- Michael A. Brasch,
- James L. Hartley,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2001-2009; doi:10.1101/gr.2769804
..., S., et al. 2002 . Structural genomics: A pipeline for providing structures for the biologist. Protein Sci. 11 : 723 -738. ↵ Chen, N., Lawson, D., Bradnam, K., Harris, T.W., and Stein, L.D. 2004 . WormBase as an integrated platform for the C. elegans ORFeome. Genome Res. (this issue). ↵ Cheo, D...
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Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
- Mayank Murali,
- Jamie Saquing,
- Senbao Lu,
- Ziyang Gao,
- Emily F. Watts,
- Ben Jordan,
- Zachary Peters Wakefield,
- Ana Fiszbein,
- David R. Cooper,
- Peter J. Castaldi,
- Dmitry Korkin,
- and Gloria M. Sheynkman
Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
...pipeline that compares related protein isoform sequences and, in the process, tracks simultaneously the changes at all three levels, to understand the impact of AS on transcriptome, ORFeome, and proteome diversity. Biosurfer computes details not immediately apparent from annotation files or manual...
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RESOURCE: High-Throughput Computational and Experimental Techniques in Structural Genomics
- Mark R. Chance,
- Andras Fiser,
- Andrej Sali,
- Ursula Pieper,
- Narayanan Eswar,
- Guiping Xu,
- J. Eduardo Fajardo,
- Thirumuruhan Radhakannan,
- and Nebojsa Marinkovic
Genome Res. October 15, 2004 14: 2145-2154; doi:10.1101/gr.2537904
...Consortium. In this report, we outline the progress of the Consortium in establishing its pipeline for structural genomics, and some of the experimental and bioinformatics efforts leading to structural annotation of proteins. The Consortium has established a pipeline for structural biology studies, automated...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
.... The study of individual protein structures is also well under way. A C. elegans structural genomics group has formed a high-throughput protein-to-structure pipeline ( Liu et al. 2005b ). They have determined the crystal structure of 78 proteins or protein fragments ( http...
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Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
- William K.M. Lai,
- Luca Mariani,
- Gerson Rothschild,
- Edwin R. Smith,
- Bryan J. Venters,
- Thomas R. Blanda,
- Prashant K. Kuntala,
- Kylie Bocklund,
- Joshua Mairose,
- Sarah N. Dweikat,
- Katelyn Mistretta,
- Matthew J. Rossi,
- Daniela James,
- James T. Anderson,
- Sabrina K. Phanor,
- Wanwei Zhang,
- Zibo Zhao,
- Avani P. Shah,
- Katherine Novitzky,
- Eileen McAnarney,
- Michael-C. Keogh,
- Ali Shilatifard,
- Uttiya Basu,
- Martha L. Bulyk,
- and B. Franklin Pugh
Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
...directly but only indirectly through other proteins (Wang et al. 2012; Mariani et al. 2017), including those that potentially form an undiscovered chromatin class (which would not be in our discovery pipeline). The enrichment of a noncognate motif suggests that the genomic occupancy of the ChIP-profiled ss...
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Research: Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
- Arttu Jolma,
- Jilin Zhang,
- Estefania Mondragón,
- Ekaterina Morgunova,
- Teemu Kivioja,
- Kaitlin U. Laverty,
- Yimeng Yin,
- Fangjie Zhu,
- Gleb Bourenkov,
- Quaid Morris,
- Timothy R. Hughes,
- Louis James Maher III,
- and Jussi Taipale
Genome Res. July 2020 30: 962-973; Published in Advance July 23, 2020, doi:10.1101/gr.258848.119
...and Biophysics, Karolinska Institutet, SE-171 77, Solna, Sweden; 2Department of Biochemistry and Molecular Biology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, Minnesota 55905, USA; 3Genome-Scale Biology Program, University of Helsinki, FI-00014...
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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...error rates and the relative lack of bioinformatics tools and analysis pipelines designed for long, error-rich reads.In this study, we have generated an atlas of postembryonic transcript structure using dRNA-seq to sequence RNA extracted from the major stages of the C. elegans developmental life cycle...
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