Staying abreast of the latest advances and bright ideas emerging in a field as diverse as bioinformatics is challenging. To provide the global bioinformatics community with a shortlist of achievements of the year by SIB Scientists that are particularly deserving attention, here are the SIB Remarkable Outputs of 2021, selected by the Award Committee. From new algorithms to detect disease-related genes, to exploring the origins of sexual reproduction, discover these publications, software tools, databases and outreach projects.
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CoalRe: A Framework for phylogenetic inference on reassortment networks
Group involved: Computational Evolution, Zurich
Related resources: PNAS paper ; in silico talk; tutorial
What the committee said about the work: "Analyzing evolution in the presence of recombination and reassortment is one of the major open problems in phylogenetics. This is an original contribution to a very challenging computational problem."
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Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Group involved: Laboratory of Protein Design and Immunoengineering, Lausanne
Related resources: tutorial; in depth review
What the committee said about the work: "A very nice approach to capitalize on machine learning to analyze protein structures.The bioinformatics approach developed is innovative and essential to developing effective therapeutics."
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Enzyme annotation in UniProtKB using Rhea
Group involved: Swiss-Prot, Geneva
Related resources: talk at the SIB Days 2020
What the committee said about the work: "The shift from Enzyme Commission numbers to Rhea reactions is a huge step forward. There is little doubt that this will facilitate reuse and computational analysis of metabolic pathways and other reaction-based bioinformatics."
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Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles
Groups involved: Evolutionary-Functional Genomics, Lausanne & Evolutionary Bioinformatics, Lausanne & Computational Evolutionary Genomics, Geneva
Related resources: in silico talk
What the committee said about the work: "The authors have put together an impressive arsenal of resources and competences: an example of what computational biology can achieve. The method is very well explained and easy to follow."
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LEMMI: A continuous benchmarking platform for metagenomics classifiers
Group involved: Computational Evolutionary Genomics, Geneva
Related resources: Genome Research paper; preprint; webpage
What the committee said about the work: "The tool may become a great asset to microbial research. It allows to close the gap of metagenomic classifier benchmarks by offering a flexible, standardized framework."
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Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes
Group involved: Computational Cancer Biology, Lausanne
Related resources:
- Web application of MixMHC2pred
- Executables (from the two tools developed for this project): MoDec and MixMHC2pred
- News coverage: University of Lausanne release; Ludwig cancer research release; Nature News & ViewsWhat the committee said about the work: "This is an impressive contribution of a well thought out computational biology "driving" the biology. Substantial efforts went into benchmarking, the code is available and well documented, and the work is also provided as a web service."
The yearly SIB Remarkable Outputs focus on the achievements of the community of SIB Members, and are thus complementary to the SIB Awards, which are taking place every two years and single out scientists and resources at the national and international levels (meet the 2019 laureates).
