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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...relies on sequence information to infer evolutionary relationships between genes or proteins. In contrast, protein structural information has long been overlooked, although structures are more conserved and closely linked to the functions than the sequences. To address this gap, we conducted a proteome...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...of nematodes is believed to date back to ∼650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry–based proteomics and machine...
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Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
- Siwei Chen,
- Yuan Liu,
- Yingying Zhang,
- Shayne D. Wierbowski,
- Steven M. Lipkin,
- Xiaomu Wei,
- and Haiyuan Yu
Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
...by hotspot mutations at the full proteome scale. Furthermore, by constructing a hotspot-affected network that connects all hotspot-affected interactions throughout the whole-human interactome, we uncover -wide relationships among hotspots and implicate novel cancer proteins that do not harbor hotspot...
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Resource: The developmental proteome of Drosophila melanogaster
- Nuria Casas-Vila,
- Alina Bluhm,
- Sergi Sayols,
- Nadja Dinges,
- Mario Dejung,
- Tina Altenhein,
- Dennis Kappei,
- Benjamin Altenhein,
- Jean-Yves Roignant,
- and Falk Butter
Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
...Nuria Casas-Vila,1,8 Alina Bluhm,1,8 Sergi Sayols,2,8 Nadja Dinges,3 Mario Dejung,4 Tina Altenhein,5 Dennis Kappei,6 Benjamin Altenhein,5,7 Jean-Yves Roignant,3 and Falk Butter1 1Quantitative Proteomics, Institute of Molecular Biology, 55128Mainz, Germany; 2Bioinformatics Core Facility, Institute...
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Resource: The mRNA-bound proteome of the early fly embryo
- Hans-Hermann Wessels,
- Koshi Imami,
- Alexander G. Baltz,
- Marcin Kolinski,
- Anastasia Beldovskaya,
- Matthias Selbach,
- Stephen Small,
- Uwe Ohler,
- and Markus Landthaler
Genome Res. July 2016 26: 1000-1009; Published in Advance April 28, 2016, doi:10.1101/gr.200386.115
...) and X490 (bottom) embryos. Proteins with at least two unique peptides and greater than 10-fold intensity in oligo(dT) pull-downs from crosslinked embryos compared to oligo(dT) precipitates from noncrosslinked embryos are considered as enriched and part of the early fly RNA-bound proteome (black). Common...
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Research: Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
- Yamile Marquez,
- Markus Höpfler,
- Zahra Ayatollahi,
- Andrea Barta,
- and Maria Kalyna
Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
..., Austria Alternative splicing (AS) diversifies transcriptomes and proteomes and is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events in Arabidopsis, we found unusual AS events inside annotated protein-coding exons. Here, we also...
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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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Resource: The Proteome Folding Project: Proteome-scale prediction of structure and function
- Kevin Drew,
- Patrick Winters,
- Glenn L. Butterfoss,
- Viktors Berstis,
- Keith Uplinger,
- Jonathan Armstrong,
- Michael Riffle,
- Erik Schweighofer,
- Bill Bovermann,
- David R. Goodlett,
- Trisha N. Davis,
- Dennis Shasha,
- Lars Malmström,
- and Richard Bonneau
Genome Res. November 2011 21: 1981-1994; Published in Advance August 8, 2011, doi:10.1101/gr.121475.111
...The Proteome Folding Project: Proteome-scale prediction of structure and function Kevin Drew 1 , Patrick Winters 1 , Glenn L. Butterfoss 1 , Viktors Berstis 2 , Keith Uplinger 2 , Jonathan Armstrong 2 , Michael Riffle 3...
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Method: Proteome-wide discovery of mislocated proteins in cancer
- KiYoung Lee,
- Kyunghee Byun,
- Wonpyo Hong,
- Han-Yu Chuang,
- Chan-Gi Pack,
- Enkhjargal Bayarsaikhan,
- Sun Ha Paek,
- Hyosil Kim,
- Hye Young Shin,
- Trey Ideker,
- and Bonghee Lee
Genome Res. August 2013 23: 1283-1294; Published in Advance May 14, 2013, doi:10.1101/gr.155499.113
...Proteome-wide discovery of mislocated proteins in cancer KiYoung Lee 1 , 2 , 8 , 9 , Kyunghee Byun 3 , 4 , 8 , Wonpyo Hong 1 , 2 , Han-Yu Chuang 5 , Chan-Gi Pack 6 , Enkhjargal Bayarsaikhan 3 , Sun Ha Paek 7...
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Research: Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models
- Nadine Borchert,
- Christoph Dieterich,
- Karsten Krug,
- Wolfgang Schütz,
- Stephan Jung,
- Alfred Nordheim,
- Ralf J. Sommer,
- and Boris Macek
Genome Res. June 2010 20: 837-846; Published in Advance March 17, 2010, doi:10.1101/gr.103119.109
...Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models Nadine Borchert 1 , 5 , Christoph Dieterich 1 , 2 , 5 , Karsten Krug 3 , 5 , Wolfgang Schütz 3 , Stephan Jung 3 , Alfred Nordheim...
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