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Method: Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
- Ulrich Omasits,
- Maxime Quebatte,
- Daniel J. Stekhoven,
- Claudia Fortes,
- Bernd Roschitzki,
- Mark D. Robinson,
- Christoph Dehio,
- and Christian H. Ahrens
Genome Res. November 2013 23: 1916-1927; Published in Advance July 22, 2013, doi:10.1101/gr.151035.112
...Method Ulrich Omasits,1,2 Maxime Quebatte,3 Daniel J. Stekhoven,1 Claudia Fortes,4 Bernd Roschitzki,4 Mark D. Robinson,1,5 Christoph Dehio,3 and Christian H. Ahrens1,6,7 1Quantitative Model Organism Proteomics, Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; 2...
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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
...Discovery and annotation of small proteins using genomics, proteomics, and computational approaches Xiaohan Yang 1 , 2 , 6 , Timothy J. Tschaplinski 1 , 2 , Gregory B. Hurst 3 , Sara Jawdy 1 , 2 , Paul E. Abraham 2 , 4...
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Resource: De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
- Catherine Adamidi,
- Yongbo Wang,
- Dominic Gruen,
- Guido Mastrobuoni,
- Xintian You,
- Dominic Tolle,
- Matthias Dodt,
- Sebastian D. Mackowiak,
- Andreas Gogol-Doering,
- Pinar Oenal,
- Agnieszka Rybak,
- Eric Ross,
- Alejandro Sánchez Alvarado,
- Stefan Kempa,
- Christoph Dieterich,
- Nikolaus Rajewsky,
- and Wei Chen
Genome Res. July 2011 21: 1193-1200; Published in Advance May 2, 2011, doi:10.1101/gr.113779.110
...De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics Catherine Adamidi 1 , 3 , Yongbo Wang 1 , 3 , Dominic Gruen 1 , 3 , Guido Mastrobuoni 1 , 3 , Xintian You 1 , 3...
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Method: Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
- Markus Brosch,
- Gary I. Saunders,
- Adam Frankish,
- Mark O. Collins,
- Lu Yu,
- James Wright,
- Ruth Verstraten,
- David J. Adams,
- Jennifer Harrow,
- Jyoti S. Choudhary,
- and Tim Hubbard
Genome Res. May 2011 21: 756-767; Published in Advance April 1, 2011, doi:10.1101/gr.114272.110
...Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome Markus Brosch 1 , Gary I. Saunders 1 , Adam Frankish , Mark O. Collins , Lu Yu , James Wright...
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LETTER: The Comparative Proteomics of Ubiquitination in Mouse
- Colin A.M. Semple,
- RIKEN GER Group,
- and GSL Members
Genome Res. June 2003 13: 1389-1394; doi:10.1101/gr.980303
...The Comparative Proteomics of Ubiquitination in Mouse Colin A.M. Semple 1 , 5 , RIKEN GER Group 2 , and GSL Members 3 , 4 1 MRC Human Genetics Unit, Crewe Road, Edinburgh, EH4 2XU, UK 2 Laboratory for Genome Exploration Research...
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RESOURCE: Human ORFeome Version 1.1: A Platform for Reverse Proteomics
- Jean-François Rual,
- Tomoko Hirozane-Kishikawa,
- Tong Hao,
- Nicolas Bertin,
- Siming Li,
- Amélie Dricot,
- Ning Li,
- Jennifer Rosenberg,
- Philippe Lamesch,
- Pierre-Olivier Vidalain,
- Tracey R. Clingingsmith,
- James L. Hartley,
- Dominic Esposito,
- David Cheo,
- Troy Moore,
- Blake Simmons,
- Reynaldo Sequerra,
- Stephanie Bosak,
- Lynn Doucette-Stamm,
- Christian Le Peuch,
- Jean Vandenhaute,
- Michael E. Cusick,
- Joanna S. Albala,
- David E. Hill,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2128-2135; doi:10.1101/gr.2973604
...Human ORFeome Version 1.1: A Platform for Reverse Proteomics Jean-François Rual 1 , 2 , 9 , Tomoko Hirozane-Kishikawa 1 , 9 , Tong Hao 1 , 9 , Nicolas Bertin 1 , 3 , 9 , Siming Li 1 , 9 , Amélie Dricot 1 , Ning Li...
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Method: Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome
- Russell C. DeKelver,
- Vivian M. Choi,
- Erica A. Moehle,
- David E. Paschon,
- Dirk Hockemeyer,
- Sebastiaan H. Meijsing,
- Yasemin Sancak,
- Xiaoxia Cui,
- Eveline J. Steine,
- Jeffrey C. Miller,
- Phillip Tam,
- Victor V. Bartsevich,
- Xiangdong Meng,
- Igor Rupniewski,
- Sunita M. Gopalan,
- Helena C. Sun,
- Kathleen J. Pitz,
- Jeremy M. Rock,
- Lei Zhang,
- Gregory D. Davis,
- Edward J. Rebar,
- Iain M. Cheeseman,
- Keith R. Yamamoto,
- David M. Sabatini,
- Rudolf Jaenisch,
- Philip D. Gregory,
- and Fyodor D. Urnov
Genome Res. August 2010 20: 1133-1142; Published in Advance May 27, 2010, doi:10.1101/gr.106773.110
...Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome Russell C. DeKelver 1 , Vivian M. Choi 1 , Erica A. Moehle 1 , David E. Paschon 1...
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Letter: Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
- Monica A. Grobei,
- Ermir Qeli,
- Erich Brunner,
- Hubert Rehrauer,
- Runxuan Zhang,
- Bernd Roschitzki,
- Konrad Basler,
- Christian H. Ahrens,
- and Ueli Grossniklaus
Genome Res. October 2009 19: 1786-1800; Published in Advance June 22, 2009, doi:10.1101/gr.089060.108
...Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function Monica A. Grobei 1 , 2 , Ermir Qeli 1 , Erich Brunner 1 , Hubert Rehrauer 3 , Runxuan Zhang 1 , 6...
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Methods: Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
- Gennifer E. Merrihew,
- Colleen Davis,
- Brent Ewing,
- Gary Williams,
- Lukas Käll,
- Barbara E. Frewen,
- William Stafford Noble,
- Phil Green,
- James H. Thomas,
- and Michael J. MacCoss
Genome Res. October 2008 18: 1660-1669; Published in Advance July 24, 2008, doi:10.1101/gr.077644.108
...Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations Gennifer E. Merrihew 1 , Colleen Davis 1 , 2 , Brent Ewing 1 , 2 , Gary Williams 3 , Lukas Käll 1 , Barbara E. Frewen 1...
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METHODS: Identification of Novel Human Genes Evolutionarily Conserved in Caenorhabditis elegans by Comparative Proteomics
- Chun-Hung Lai,
- Chang-Yuan Chou,
- Lan-Yang Ch'ang,
- Chung-Shyan Liu,
- and Wen-chang Lin
Genome Res. May 1, 2000 10: 703-713; doi:10.1101/gr.10.5.703
...Identification of Novel Human Genes Evolutionarily Conserved in Caenorhabditis elegans by Comparative Proteomics Chun-Hung Lai 1 , Chang-Yuan Chou 1 , Lan-Yang Ch'ang 1 , Chung-Shyan Liu 2 , and Wen-chang Lin 1 , 3 1...

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