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SCARABEE SIGNED

Scalable inference algorithms for Bayesian evolutionary epidemiology

Total Cost €

EC-Contrib. €

Partnership

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SCARABEE project word cloud

Explore the words cloud of the SCARABEE project. It provides you a very rough idea of what is the project "SCARABEE" about.

microbes cope infectious publicly genome bayesian evolutionary machine technologies epidemiology transmission published unprecedented centres microbial made benchmark computational intractable demonstrated gives algorithms leaps enormous packages epidemiologists human answer complexity mechanisms disease community giant burden developers discovery highlight causal health biological evolution pnas promise microbiologists leap pathogens questions discoveries pose multitude spread causing epistasis opportunity pathogen scalable learning wealth statistical genomics threat close leverage models inference breakthroughs considerably designed advances fulfil scarabee nature data free nor ranking central big benefit software combined sequencing science size journals combination simultaneously reducing

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 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.	NO (OSLO)	coordinator	2˙499˙961.00

Map

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

List of 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 SÃ¡nchez-BusÃ³, 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 SÃ¡nchez-BusÃ³, 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 TodoroviÄ‡, 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 birthâ€“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 MÃ©ric, 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 JosÃ© Arredondo, Benjamin Strope, Hackwon Do, Muthiah Kumaraswami, Jaana Vuopio, Kirsi GrÃ¶ndahl-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 MÃ©ric, 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 KangasrÃ¤Ã¤siÃ¶, Kusti SkytÃ©n, Marko JÃ¤rvenpÃ¤Ã¤, 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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