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Literature DB >> 26367542

Devising a Consensus Framework for Validation of Novel Human Coding Loci.

Elspeth A Bruford¹, Lydie Lane², Jennifer Harrow³.

Abstract

A report on the Wellcome Trust retreat on devising a consensus framework for the validation of novel human protein coding loci, held in Hinxton, U.K., May 11-13, 2015.

Entities: Chemical Disease Gene Species

Keywords: long noncoding RNA; proteogenomics; ribosome profiling; small ORF; transcriptomics

Mesh：

Substances：

Year: 2015 PMID： 26367542 PMCID： PMC4765950 DOI： 10.1021/acs.jproteome.5b00688

Source DB: PubMed Journal: J Proteome Res ISSN： 1535-3893 Impact factor: 4.466

24 in total

1. Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.

Authors: Michael B Clark; Tim R Mercer; Giovanni Bussotti; Tommaso Leonardi; Katelin R Haynes; Joanna Crawford; Marion E Brunck; Kim-Anh Lê Cao; Gethin P Thomas; Wendy Y Chen; Ryan J Taft; Lars K Nielsen; Anton J Enright; John S Mattick; Marcel E Dinger
Journal: Nat Methods Date: 2015-03-09 Impact factor: 28.547

2. Mass-spectrometry-based draft of the human proteome.

Authors: Mathias Wilhelm; Judith Schlegl; Hannes Hahne; Amin Moghaddas Gholami; Marcus Lieberenz; Mikhail M Savitski; Emanuel Ziegler; Lars Butzmann; Siegfried Gessulat; Harald Marx; Toby Mathieson; Simone Lemeer; Karsten Schnatbaum; Ulf Reimer; Holger Wenschuh; Martin Mollenhauer; Julia Slotta-Huspenina; Joos-Hendrik Boese; Marcus Bantscheff; Anja Gerstmair; Franz Faerber; Bernhard Kuster
Journal: Nature Date: 2014-05-29 Impact factor: 49.962

3. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.

Authors: Mitchell Guttman; Pamela Russell; Nicholas T Ingolia; Jonathan S Weissman; Eric S Lander
Journal: Cell Date: 2013-06-27 Impact factor: 41.582

4. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

Authors: Markus Brosch; Gary I Saunders; Adam Frankish; Mark O Collins; Lu Yu; James Wright; Ruth Verstraten; David J Adams; Jennifer Harrow; Jyoti S Choudhary; Tim Hubbard
Journal: Genome Res Date: 2011-04-01 Impact factor: 9.043

5. IMGT®, the international ImMunoGeneTics information system® 25 years on.

Authors: Marie-Paule Lefranc; Véronique Giudicelli; Patrice Duroux; Joumana Jabado-Michaloud; Géraldine Folch; Safa Aouinti; Emilie Carillon; Hugo Duvergey; Amélie Houles; Typhaine Paysan-Lafosse; Saida Hadi-Saljoqi; Souphatta Sasorith; Gérard Lefranc; Sofia Kossida
Journal: Nucleic Acids Res Date: 2014-11-05 Impact factor: 19.160

6. The neXtProt knowledgebase on human proteins: current status.

Authors: Pascale Gaudet; Pierre-André Michel; Monique Zahn-Zabal; Isabelle Cusin; Paula D Duek; Olivier Evalet; Alain Gateau; Anne Gleizes; Mario Pereira; Daniel Teixeira; Ying Zhang; Lydie Lane; Amos Bairoch
Journal: Nucleic Acids Res Date: 2015-01 Impact factor: 16.971

7. An update on LNCipedia: a database for annotated human lncRNA sequences.

Authors: Pieter-Jan Volders; Kenneth Verheggen; Gerben Menschaert; Klaas Vandepoele; Lennart Martens; Jo Vandesompele; Pieter Mestdagh
Journal: Nucleic Acids Res Date: 2014-11-05 Impact factor: 16.971

8. Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq.

Authors: Julie L Aspden; Ying Chen Eyre-Walker; Rose J Phillips; Unum Amin; Muhammad Ali S Mumtaz; Michele Brocard; Juan-Pablo Couso
Journal: Elife Date: 2014-08-21 Impact factor: 8.140

9. Current status and new features of the Consensus Coding Sequence database.

Authors: Catherine M Farrell; Nuala A O'Leary; Rachel A Harte; Jane E Loveland; Laurens G Wilming; Craig Wallin; Mark Diekhans; Daniel Barrell; Stephen M J Searle; Bronwen Aken; Susan M Hiatt; Adam Frankish; Marie-Marthe Suner; Bhanu Rajput; Charles A Steward; Garth R Brown; Ruth Bennett; Michael Murphy; Wendy Wu; Mike P Kay; Jennifer Hart; Jeena Rajan; Janet Weber; Catherine Snow; Lillian D Riddick; Toby Hunt; David Webb; Mark Thomas; Pamela Tamez; Sanjida H Rangwala; Kelly M McGarvey; Shashikant Pujar; Andrei Shkeda; Jonathan M Mudge; Jose M Gonzalez; James G R Gilbert; Stephen J Trevanion; Robert Baertsch; Jennifer L Harrow; Tim Hubbard; James M Ostell; David Haussler; Kim D Pruitt
Journal: Nucleic Acids Res Date: 2013-11-11 Impact factor: 16.971

10. Analyzing the first drafts of the human proteome.

Authors: Iakes Ezkurdia; Jesús Vázquez; Alfonso Valencia; Michael Tress
Journal: J Proteome Res Date: 2014-07-16 Impact factor: 4.466

9 in total

Review 1. Towards a complete map of the human long non-coding RNA transcriptome.

Authors: Barbara Uszczynska-Ratajczak; Julien Lagarde; Adam Frankish; Roderic Guigó; Rory Johnson
Journal: Nat Rev Genet Date: 2018-09 Impact factor: 53.242

2. A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome.

Authors: Thierry Bertomeu; Jasmin Coulombe-Huntington; Andrew Chatr-Aryamontri; Karine G Bourdages; Etienne Coyaud; Brian Raught; Yu Xia; Mike Tyers
Journal: Mol Cell Biol Date: 2017-12-13 Impact factor: 4.272

Devising a Consensus Framework for Validation of Novel Human Coding Loci.

1. Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.

2. Mass-spectrometry-based draft of the human proteome.

3. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.

4. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

5. IMGT®, the international ImMunoGeneTics information system® 25 years on.

6. The neXtProt knowledgebase on human proteins: current status.

7. An update on LNCipedia: a database for annotated human lncRNA sequences.

8. Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq.

9. Current status and new features of the Consensus Coding Sequence database.

10. Analyzing the first drafts of the human proteome.

Review 1. Towards a complete map of the human long non-coding RNA transcriptome.

2. A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome.

Review 3. Mouse models of Down syndrome: gene content and consequences.

4. PepPSy: a web server to prioritize gene products in experimental and biocuration workflows.

5. The UniProtKB guide to the human proteome.

Review 6. Last rolls of the yoyo: Assessing the human canonical protein count.

7. Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

8. Loose ends: almost one in five human genes still have unresolved coding status.

9. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes.