Discover the SIB Remarkable Outputs 2021

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.

  • APSiC: a robust statistical framework for discovery of novel cancer genes 

    Groups involved: Oncogenomics, Bern and Computational Biology Group, Basel 
    Related resources: Portal, GitHub 
    What the committee said about the work: “This new algorithm enables the identification of new cancer-related genes even with data from few samples, showcasing on the APSiC portal its application to a real-world oncology datas

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  • BUSCO: assessing genomic data quality and beyond 

    Group involved: Computational Evolutionary Genomics, Geneva 
    Related resources: Current Protocols paper, Molecular Biology & Evolution paper, SwissOrthology 
    What the committee said about the work: “2021 showcased the maturation of this widely-used software with a step change in usability, speed, taxonomic breadth, and variety of applications in genomics, metagenomics, phylogenomics, and beyond.” 

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  • CoV-Spectrum: In-depth analysis of new SARS-CoV-2 variants

     Group involved: Computational Evolution, Zurich, Basel 
    Related resources: paper, GitHub 
    What the committee said about the work: “CoV-Spectrum responds to urgent needs to track known and identify new variants of concern. It highlights the importance of data sharing and is remarkable in how it scales with the volumes of data.” 

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  • Inferring positive selection on enhancers reveals a regulatory basis for the developmental hourglass model 

    Group involved: Evolutionary Bioinformatics, Lausanne 
    Related resources: GitHub 
    What the committee said about the work: “This work elegantly shows the utility of a novel method to detect positive selection in non-coding DNA regions, and applying it to better understand the hourglass pattern of animal evolution.” 

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  • LHC-MR: A powerful method for estimating causal effects of risk factors on complex human traits 

    Group involved: Statistical Genetics, Lausanne 
    Related resources: GitHub 
    What the committee said about the work: “This outstanding work substantially extends a widely applied statistical method, enabling estimation of bi-directional causal effects, direct heritabilities, and confounder effects.” 

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  • Mass spectra-based machine learning to predict antimicrobial resistance 

    Group involved: Machine Learning and Computational Biology Lab, Zurich, Basel 
    Related resources: GitHub, ETH Zurich news, in silico talk 
    What the committee said about the work: “Exploiting a unique and content-rich data source, this ML-based approach to deliver robust predictions represents an important new tool for accelerating and improving resistance testing in the clinic.” 

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  • Multidisciplinary approaches to trace the archaeal origins of gamete fusion

    Group involved: Computational Evolutionary Biology and Genomics, Lausanne
    Related resources: Quanta Magazine Article
    What the committee said about the work: “This discovery, using homology searches, solving the protein structure, and performing functional assays, is a major contribution to understanding the evolution of sexual reproduction.”

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  • Nextclade: Clade assignment, mutation calling and quality control for viral genomes

    Group involved: Microbial Evolution, Basel
    Related resources: GitHub, paper
    What the committee said about the work: “Nextclade has demonstrated its impact in an impressive way during the pandemic, with user-friendly tools for informative analysis of sequencing data from SARS-CoV-2 and seasonal influenza viruses.”

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  • Public engagement with science through: In the Light of Evolution

    Groups involved: Swiss-Prot, Geneva, and Laboratory of Computational Evolutionary Biology, Lausanne, and Training, Lausanne
    Related resources: News release, OhMyGenes
    What the committee said about the work: “This innovative outreach project for engaging the public on the topic of species evolution is very well conceived and executed. It is didactic and fun, with already a significant impact in classrooms.”

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  • SwissDrugDesign in 2021: a freely accessible web-based in silico drug design environment

    Group involved: Molecular Modelling Group, Lausanne
    Related resources: SwissBioisostere paper, SwissSimilarity paper
    What the committee said about the work: “The ecosystem of original, reliable, and user-friendly tools in the SwissDrugDesign suite is truly impressive, exemplified by the recent rebuilding of the SwissBioisostere and SwissSimilarity portals.”

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