SCARABEE SIGNED
Scalable inference algorithms for Bayesian evolutionary epidemiology
Total Cost €
0EC-Contrib. €
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Explore the words cloud of the SCARABEE project. It provides you a very rough idea of what is the project "SCARABEE" about.
Project "SCARABEE" data sheet
The following table provides information about the project.
| Coordinator |
UNIVERSITETET I OSLO
Organization address contact info |
| Coordinator Country | Norway [NO] |
| Total cost | 2˙499˙961 € |
| EC max contribution | 2˙499˙961 € (100%) |
| Programme |
1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC)) |
| Code Call | ERC-2016-ADG |
| Funding Scheme | ERC-ADG |
| Starting year | 2017 |
| Duration (year-month-day) | from 2017-08-01 to 2022-07-31 |
Partnership
Take a look of project's partnership.
| # | ||||
|---|---|---|---|---|
| 1 | UNIVERSITETET I OSLO | NO (OSLO) | coordinator | 2˙499˙961.00 |
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Project objective
Advances in sequencing technologies are currently providing an unprecedented opportunity to a detailed discovery of the mechanisms involved in the evolution and spread of microbes causing human infectious disease. Simultaneously the developers of statistical methods face an enormous challenge to cope with the wealth of data brought by this opportunity. We have very recently demonstrated the ability of our advanced computational approaches to deliver breakthroughs in understanding pathogen evolution and transmission in numerous highlight results published in Science, PNAS and top-ranking Nature journals. The rise of microbial Big Data gives a promise of a giant leap in making causal discoveries, however, the existing statistical methods are neither able to cope with the size and complexity of the emerging data sets nor designed to answer the novel biological questions they enable. To fulfil the promise of giant leaps SCARABEE will leverage scalable inference methods by a unique combination of machine learning algorithms and Bayesian statistical models for evolutionary epidemiology. We focus on central biological questions about adaptation, epistasis, genome evolution and transmission of microbes causing infectious disease. The Big Data combined with the novel inference methods will make it possible to answer a multitude of important questions that remain currently intractable. Through our close collaboration with the leading research centres in infectious disease epidemiology and genomics we expect the SCARABEE project to considerably advance understanding of the evolution and transmission of numerous pathogens that pose a major threat to human health, which will be important for reducing their disease burden in the future. Large-scale biological data will be used to benchmark the developed methods, which will be made publicly available as free software packages to benefit the wide community of microbiologists and infectious disease epidemiologists.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2019 |
U. Simola, B. Pelssers, D. Barge, J. Conrad, J. Corander Machine learning accelerated likelihood-free event reconstruction in dark matter direct detection published pages: P03004-P03004, ISSN: 1748-0221, DOI: 10.1088/1748-0221/14/03/P03004 |
Journal of Instrumentation 14/03 | 2020-03-05 |
| 2019 |
Leonor Sánchez-Busó, Daniel Golparian, Jukka Corander, Yonatan H. Grad, Makoto Ohnishi, Rebecca Flemming, Julian Parkhill, Stephen D. Bentley, Magnus Unemo, Simon R. Harris The impact of antimicrobials on gonococcal evolution published pages: 1941-1950, ISSN: 2058-5276, DOI: 10.1038/s41564-019-0501-y |
Nature Microbiology 4/11 | 2020-03-05 |
| 2019 |
Alan McNally, Teemu Kallonen, Christopher Connor, Khalil Abudahab, David M. Aanensen, Carolyne Horner, Sharon J. Peacock, Julian Parkhill, Nicholas J. Croucher, Jukka Corander Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection published pages: , ISSN: 2150-7511, DOI: 10.1128/mbio.00644-19 |
mBio 10/2 | 2020-03-05 |
| 2019 |
Johan Pensar, Santeri Puranen, Brian Arnold, Neil MacAlasdair, Juri Kuronen, Gerry Tonkin-Hill, Maiju Pesonen, Yingying Xu, Aleksi Sipola, Leonor Sánchez-Busó, John A Lees, Claire Chewapreecha, Stephen D Bentley, Simon R Harris, Julian Parkhill, Nicholas J Croucher, Jukka Corander Genome-wide epistasis and co-selection study using mutual information published pages: e112-e112, ISSN: 0305-1048, DOI: 10.1093/nar/gkz656 |
Nucleic Acids Research 47/18 | 2020-03-05 |
| 2019 |
Gerry Tonkin-Hill, John A Lees, Stephen D Bentley, Simon D W Frost, Jukka Corander Fast hierarchical Bayesian analysis of population structure published pages: 5539-5549, ISSN: 0305-1048, DOI: 10.1093/nar/gkz361 |
Nucleic Acids Research 47/11 | 2020-03-05 |
| 2020 |
Caroline Colijn, Jukka Corander, Nicholas J. Croucher Designing ecologically optimized pneumococcal vaccines using population genomics published pages: , ISSN: 2058-5276, DOI: 10.1038/s41564-019-0651-y |
Nature Microbiology | 2020-03-05 |
| 2019 |
Milica Todorović, Michael U. Gutmann, Jukka Corander, Patrick Rinke Bayesian inference of atomistic structure in functional materials published pages: , ISSN: 2057-3960, DOI: 10.1038/s41524-019-0175-2 |
npj Computational Materials 5/1 | 2020-02-28 |
| 2019 |
Jarno Lintusaari, Paul Blomstedt, Brittany Rose, Tuomas Sivula, Michael U. Gutmann, Samuel Kaski, Jukka Corander Resolving outbreak dynamics using approximate Bayesian computation for stochastic birth–death models published pages: 14, ISSN: 2398-502X, DOI: 10.12688/wellcomeopenres.15048.2 |
Wellcome Open Research 4 | 2020-02-28 |
| 2018 |
Gerry Tonkin-Hill, John A. Lees, Stephen D. Bentley, Simon D.W. Frost, Jukka Corander RhierBAPS: An R implementation of the population clustering algorithm hierBAPS published pages: 93, ISSN: 2398-502X, DOI: 10.12688/wellcomeopenres.14694.1 |
Wellcome Open Research 3 | 2020-02-28 |
| 2019 |
John A. Lees, Simon R. Harris, Gerry Tonkin-Hill, Rebecca A. Gladstone, Stephanie W. Lo, Jeffrey N. Weiser, Jukka Corander, Stephen D. Bentley, Nicholas J. Croucher Fast and flexible bacterial genomic epidemiology with PopPUNK published pages: 304-316, ISSN: 1088-9051, DOI: 10.1101/gr.241455.118 |
Genome Research 29/2 | 2019-04-18 |
| 2018 |
Guillaume Méric, Alan McNally, Alberto Pessia, Evangelos Mourkas, Ben Pascoe, Leonardos Mageiros, Minna Vehkala, Jukka Corander, Samuel K Sheppard Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism published pages: 763-774, ISSN: 1759-6653, DOI: 10.1093/gbe/evy026 |
Genome Biology and Evolution 10/3 | 2019-04-18 |
| 2018 |
Annemieke Smet, Koji Yahara, Mirko Rossi, Alfred Tay, Steffen Backert, Ensser Armin, James G. Fox, Bram Flahou, Richard Ducatelle, Freddy Haesebrouck, Jukka Corander Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence published pages: 2518-2531, ISSN: 1751-7362, DOI: 10.1038/s41396-018-0199-5 |
The ISME Journal 12/10 | 2019-04-18 |
| 2018 |
Santeri Puranen, Maiju Pesonen, Johan Pensar, Ying Ying Xu, John A. Lees, Stephen D. Bentley, Nicholas J. Croucher, Jukka Corander SuperDCA for genome-wide epistasis analysis published pages: , ISSN: 2057-5858, DOI: 10.1099/mgen.0.000184 |
Microbial Genomics 4/6 | 2019-04-18 |
| 2018 |
Yingying Xu, Santeri Puranen, Jukka Corander, Yoshiyuki Kabashima Inverse finite-size scaling for high-dimensional significance analysis published pages: , ISSN: 2470-0045, DOI: 10.1103/physreve.97.062112 |
Physical Review E 97/6 | 2019-04-18 |
| 2019 |
Priyanka Kachroo, Jesus M. Eraso, Stephen B. Beres, Randall J. Olsen, Luchang Zhu, Waleed Nasser, Paul E. Bernard, Concepcion C. Cantu, Matthew Ojeda Saavedra, MarÃa José Arredondo, Benjamin Strope, Hackwon Do, Muthiah Kumaraswami, Jaana Vuopio, Kirsi Gröndahl-Yli-Hannuksela, Karl G. Kristinsson, Magnus Gottfredsson, Maiju Pesonen, Johan Pensar, Emily R. Davenport, Andrew G. Clark, Jukka Corander, Dominique A. Caugant, Shahin Gaini, Marita Debess Magnussen, Samantha L. Kubiak, Hoang A. T. Nguyen, S. Wesley Long, Adeline R. Porter, Frank R. DeLeo, James M. Musser Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis published pages: 548-559, ISSN: 1061-4036, DOI: 10.1038/s41588-018-0343-1 |
Nature Genetics 51/3 | 2019-04-18 |
| 2018 |
Aleksi Sipola, Pekka Marttinen, Jukka Corander Bacmeta: simulator for genomic evolution in bacterial metapopulations published pages: 2308-2310, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty093 |
Bioinformatics 34/13 | 2019-04-18 |
| 2018 |
Emily J. Richardson, Rodrigo Bacigalupe, Ewan M. Harrison, Lucy A. Weinert, Samantha Lycett, Manouk Vrieling, Kirsty Robb, Paul A. Hoskisson, Matthew T. G. Holden, Edward J. Feil, Gavin K. Paterson, Steven Y. C. Tong, Adebayo Shittu, Willem van Wamel, David M. Aanensen, Julian Parkhill, Sharon J. Peacock, Jukka Corander, Mark Holmes, J. Ross Fitzgerald Gene exchange drives the ecological success of a multi-host bacterial pathogen published pages: 1468-1478, ISSN: 2397-334X, DOI: 10.1038/s41559-018-0617-0 |
Nature Ecology & Evolution 2/9 | 2019-04-18 |
| 2018 |
Brian J. Arnold, Michael U. Gutmann, Yonatan H. Grad, Samuel K. Sheppard, Jukka Corander, Marc Lipsitch, William P. Hanage Weak Epistasis May Drive Adaptation in Recombining Bacteria published pages: 1247-1260, ISSN: 0016-6731, DOI: 10.1534/genetics.117.300662 |
Genetics 208/3 | 2019-04-18 |
| 2018 |
John A Lees, Marco Galardini, Stephen D Bentley, Jeffrey N Weiser, Jukka Corander pyseer: a comprehensive tool for microbial pangenome-wide association studies published pages: 4310-4312, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty539 |
Bioinformatics 34/24 | 2019-04-18 |
| 2018 |
Khalil Abudahab, JoaquÃn M. Prada, Zhirong Yang, Stephen D. Bentley, Nicholas J. Croucher, Jukka Corander, David M. Aanensen PANINI: Pangenome Neighbour Identification for Bacterial Populations published pages: , ISSN: 2057-5858, DOI: 10.1099/mgen.0.000220 |
Microbial Genomics | 2019-04-18 |
| 2018 |
Guillaume Méric, Leonardos Mageiros, Johan Pensar, Maisem Laabei, Koji Yahara, Ben Pascoe, Nattinee Kittiwan, Phacharaporn Tadee, Virginia Post, Sarah Lamble, Rory Bowden, James E. Bray, Mario Morgenstern, Keith A. Jolley, Martin C. J. Maiden, Edward J. Feil, Xavier Didelot, Maria Miragaia, Herminia de Lencastre, T. Fintan Moriarty, Holger Rohde, Ruth Massey, Dietrich Mack, Jukka Corander, Samuel K. Sheppard Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-07368-7 |
Nature Communications 9/1 | 2019-04-18 |
| 2018 |
Jarno Lintusaari, Henri Vuollekoski, Antti Kangasrääsiö, Kusti Skytén, Marko Järvenpää, Pekka Marttinen, Michael U. Gutmann, Aki Vehtari, Jukka Corander, Samuel Kaski ELFI: Engine for Likelihood-Free Inference published pages: , ISSN: 1533-7928, DOI: |
Journal of Machine Learning Research | 2019-04-18 |
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