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SCARABEE SIGNED

Scalable inference algorithms for Bayesian evolutionary epidemiology

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EC-Contrib. €

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Project "SCARABEE" data sheet

The following table provides information about the project.

Coordinator
UNIVERSITETET I OSLO 

Organization address
address: PROBLEMVEIEN 5-7
city: OSLO
postcode: 313
website: www.uio.no

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 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.

# participants  country  role  EC contrib. [€] 
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
List of publications.
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, María 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, Joaquín 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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