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Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

https://doi.org/https://doi.org/10.1073

Qiao, Qin; Edger, Patrick; Xue, Li; Qiong, La; Lu, Jie; Zhang, Yichen; Cao, Qiang; Yocca, Alan; Platts, Adrian; Knapp, Steven; et al (November 2021, Proceedings of the National Academy of Sciences of the United States of America)
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iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

https://doi.org/10.1016/j.softx.2020.100462

Renaud, Nicolas; Jung, Yong; Honavar, Vasant; Geng, Cunliang; Bonvin, Alexandre M.J.J.; Xue, Li C. (January 2020, SoftwareX)

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iScore: A novel graph kernel-based function for scoring protein-protein docking models

https://doi.org/10.1093/bioinformatics/btz496

Geng, Cunliang; Jung, Yong; Renaud, Nicolas; Honavar, Vasant; Bonvin, Alexandre M; Xue, Li C; Valencia, Alfonso (June 2019, Bioinformatics)

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microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

https://doi.org/10.1038/s41564-023-01575-9

Zuffa, Simone; Schmid, Robin; Bauermeister, Anelize; P. Gomes, Paulo Wender; Caraballo-Rodriguez, Andres M.; El Abiead, Yasin; Aron, Allegra T.; Gentry, Emily C.; Zemlin, Jasmine; Meehan, Michael J.; et al (February 2024, Nature Microbiology)

Abstract microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms’ role in ecology and human health.
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

https://doi.org/10.1002/prot.25838

Lensink, Marc F.; Brysbaert, Guillaume; Nadzirin, Nurul; Velankar, Sameer; Chaleil, Raphaël A.; Gerguri, Tereza; Bates, Paul A.; Laine, Elodie; Carbone, Alessandra; Grudinin, Sergei; et al (August 2019, Proteins: Structure, Function, and Bioinformatics)

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