Jukka Corander

• Štrumbelj, Erik; Bouchard-Côté, Alexandre; Corander, Jukka; Gelman, Andrew; Rue, Håvard & Murray, Lawrence [Show all 9 contributors for this article] (2024). Past, Present and Future of Software for Bayesian Inference. Statistical Science. ISSN 0883-4237. 39(1), p. 46–61. doi: 10.1214/23-STS907.
• Paganini, Julian A.; Kerkvliet, Jesse J.; Vader, Lisa; Plantinga, Nienke L.; Meneses, Rodrigo & Corander, Jukka [Show all 9 contributors for this article] (2024). PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli. Microbial Genomics. ISSN 2057-5858. 10(2). doi: 10.1099/mgen.0.001193.
• Pöntinen, Anna Kaarina; Gladstone, Rebecca Ashley; Pesonen, Henri; Pesonen, Maiju; Cleon, Francois Pierre Alexandre & Parcell, Benjamin J [Show all 14 contributors for this article] (2024). Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study. Lancet Microbe. ISSN 2666-5247. 5(2), p. e142–e150. doi: 10.1016/S2666-5247(23)00292-6.
• pesonen, maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka; Johannessen, Mona & Hanssen, Anne-Merethe Christiansen (2024). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Frontiers in Cellular and Infection Microbiology. ISSN 2235-2988. 14. doi: 10.3389/fcimb.2024.1326730.
• Picchini, Umberto; Simola, Umberto & Corander, Jukka (2023). Sequentially Guided MCMC Proposals for Synthetic Likelihoods and Correlated Synthetic Likelihoods. Bayesian Analysis. ISSN 1936-0975. 18(4), p. 1099–1129. doi: 10.1214/22-BA1305.
• Chaguza, Chrispin; Pöntinen, Anna Kaarina; Top, Janetta; Alonso, Sergio Arredondo; Freitas, Ana R. & Novais, Carla [Show all 12 contributors for this article] (2023). The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection. Microbiology spectrum. ISSN 2165-0497. 11(6). doi: 10.1128/spectrum.00201-23. Full text in Research Archive
• Pereira, Ana P.; Antunes, Patrícia; Bierge, Paula; Willems, Rob J.L.; Corander, Jukka & Coque, Teresa M. [Show all 10 contributors for this article] (2023). Unraveling Enterococcus susceptibility to quaternary ammonium compounds: genes, phenotypes, and the impact of environmental conditions. Microbiology spectrum. ISSN 2165-0497. 11(5). doi: 10.1128/spectrum.02324-23. Full text in Research Archive
• Calland, Jessica Kate; Haukka, Kaisa; Kpordze, Stephen W; Brusah, Atanyiwoen; Corbella, Marta & Merla, Cristina [Show all 13 contributors for this article] (2023). Population structure and antimicrobial resistance among Klebsiella isolates sampled from human, animal, and environmental sources in Ghana: a cross-sectional genomic One Health study. Lancet Microbe. ISSN 2666-5247. 4(11), p. e943–e952. doi: 10.1016/S2666-5247(23)00208-2. Full text in Research Archive
• Connor, Christopher H.; Zucoloto, Amanda Z.; Munnoch, John T.; Yu, Ian-Ling; Corander, Jukka & Hoskisson, Paul A. [Show all 8 contributors for this article] (2023). Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract. PLoS Biology. ISSN 1544-9173. 21(10). doi: 10.1371/journal.pbio.3002329. Full text in Research Archive
• Alonso, Sergio Arredondo; Gladstone, Rebecca Ashley; Pöntinen, Anna Kaarina; Gama, João Alves; Schürch, Anita C. & Lanza, Val F. [Show all 10 contributors for this article] (2023). Mge-cluster: a reference-free approach for typing bacterial plasmids. NAR Genomics and Bioinformatics. ISSN 2631-9268. 5(3). doi: 10.1093/nargab/lqad066. Full text in Research Archive
• Alonso, Sergio Arredondo; Blundell-Hunter, George; Fu, Zuyi; Gladstone, Rebecca Ashley; Fillol-Salom, Alfred & Loraine, Jessica [Show all 25 contributors for this article] (2023). Evolutionary and functional history of the Escherichia coli K1 capsule. Nature Communications. ISSN 2041-1723. 14(1). doi: 10.1038/s41467-023-39052-w. Full text in Research Archive
• Petazzoni, Greta; Bellinzona, Greta; Merla, Cristina; Corbella, Marta; Monzillo, Vincenzina & Samuelsen, Ørjan [Show all 10 contributors for this article] (2023). The COVID-19 Pandemic Sparked off a Large-Scale Outbreak of Carbapenem-Resistant Acinetobacter baumannii from the Endemic Strains at an Italian Hospital. Microbiology spectrum. ISSN 2165-0497. 11(2). doi: 10.1128/spectrum.04505-22. Full text in Research Archive
• Snaith, Ann E.; Dunn, Steven J.; Moran, Robert A.; Newton, Paul N.; Dance, David A. B. & Davong, Viengmon [Show all 10 contributors for this article] (2023). The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. Microbial Genomics. ISSN 2057-5858. 9(5). doi: 10.1099/mgen.0.001000. Full text in Research Archive
• Tonkin-Hill, Gerry; Corander, Jukka & Parkhill, Julian (2023). Challenges in prokaryote pangenomics. Microbial Genomics. ISSN 2057-5858. 9(5). doi: 10.1099/mgen.0.001021. Full text in Research Archive
• Tonkin-Hill, Gerry; Gladstone, Rebecca Ashley; Pöntinen, Anna Kaarina; Alonso, Sergio Arredondo; Bentley, Stephen D. & Corander, Jukka (2023). Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe. Genome Research. ISSN 1088-9051. 33(1), p. 129–140. doi: 10.1101/gr.277340.122. Full text in Research Archive
• Mai, The Tien; Lees, John A; Gladstone, Rebecca Ashley & Corander, Jukka (2023). Inferring the heritability of bacterial traits in the era of machine learning. Bioinformatics Advances. ISSN 2635-0041. 3(1). doi: 10.1093/bioadv/vbad027. Full text in Research Archive
• Rebelo, Andreia; Duarte, Bárbara; Ferreira, Carolina; Mourão, Joana; Ribeiro, Sofia & Freitas, Ana R. [Show all 12 contributors for this article] (2023). Enterococcus spp. from chicken meat collected 20 years apart overcome multiple stresses occurring in the poultry production chain: Antibiotics, copper and acids. International journal of food microbiology. ISSN 0168-1605. 384. doi: 10.1016/j.ijfoodmicro.2022.109981. Full text in Research Archive
• Yang, Zhirong; Chen, Yuwei; Sedov, Denis; Kaski, Samuel & Corander, Jukka (2023). Stochastic Cluster Embedding. Statistics and computing. ISSN 0960-3174. 33(12). doi: 10.1007/s11222-022-10186-z. Full text in Research Archive
• Li, Nien-Kung; Corander, Jukka; Grad, Yonatan H. & Chang, Hsiao-Han (2022). Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales. Virus Evolution. ISSN 2057-1577. 8(2). doi: 10.1093/ve/veac108.
• Kičiatovas, Dovydas; Guo, Qingli; Kailas, Miika; Pesonen, Henri; Corander, Jukka & Kaski, Samuel [Show all 8 contributors for this article] (2022). Identification of multiplicatively acting modulatory mutational signatures in cancer. BMC Bioinformatics. ISSN 1471-2105. 23. doi: 10.1186/s12859-022-05060-8. Full text in Research Archive
• Mäklin, Tommi; Thorpe, Harry Arthur Frank Wright; Pöntinen, Anna Kaarina; Gladstone, Rebecca Ashley; Shao, Yan & Pesonen, Maiju [Show all 12 contributors for this article] (2022). Strong pathogen competition in neonatal gut colonisation. Nature Communications. ISSN 2041-1723. 13(1). doi: 10.1038/s41467-022-35178-5. Full text in Research Archive Show summary

  Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.

• Thorpe, Harry Arthur Frank Wright; Booton, Ross; Kallonen, Teemu; Gibbon, Marjorie J.; Couto, Natacha & Passet, Virginie [Show all 21 contributors for this article] (2022). A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nature Microbiology. ISSN 2058-5276. 7, p. 2054–2067. doi: 10.1038/s41564-022-01263-0. Full text in Research Archive
• Corander, Jukka; Hanage, William P & Pensar, Johan (2022). Causal discovery for the microbiome. Lancet Microbe. ISSN 2666-5247. 3(11), p. e881–e887. doi: 10.1016/S2666-5247(22)00186-0. Full text in Research Archive Show summary

  Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch's classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere.

• Simola, U.; Bonfanti, A.; Dumusque, X.; Cisewski-Kehe, J.; Kaski, S. & Corander, Jukka (2022). Accounting for stellar activity signals in radial-velocity data by using change point detection techniques. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 664. doi: 10.1051/0004-6361/202142941. Full text in Research Archive Show summary

  Context. Active regions on the photosphere of a star have been the major obstacle for detecting Earth-like exoplanets using the radial velocity (RV) method. A commonly employed solution for addressing stellar activity is to assume a linear relationship between the RV observations and the activity indicators along the entire time series, and then remove the estimated contribution of activity from the variation in RV data (overall correction method). However, since active regions evolve on the photosphere over time, correlations between the RV observations and the activity indicators will correspondingly be anisotropic. Aims. We present an approach that recognizes the RV locations where the correlations between the RV and the activity indicators significantly change in order to better account for variations in RV caused by stellar activity. Methods. The proposed approach uses a general family of statistical breakpoint methods, often referred to as change point detection (CPD) algorithms; several implementations of which are available in R and python. A thorough comparison is made between the breakpoint-based approach and the overall correction method. To ensure wide representativity, we use measurements from real stars that have different levels of stellar activity and whose spectra have different signal-to-noise ratios. Results. When the corrections for stellar activity are applied separately to each temporal segment identified by the breakpoint method, the corresponding residuals in the RV time series are typically much smaller than those obtained by the overall correction method. Consequently, the generalized Lomb–Scargle periodogram contains a smaller number of peaks caused by active regions. The CPD algorithm is particularly effective when focusing on active stars with long time series, such as α Cen B. In that case, we demonstrate that the breakpoint method improves the detection limit of exoplanets by 74% on average with respect to the overall correction method. Conclusions. CPD algorithms provide a useful statistical framework for estimating the presence of change points in a time series. Since the process underlying the RV measurements generates anisotropic data by its intrinsic properties, it is natural to use CPD to obtain cleaner signals from RV data. We anticipate that the improved exoplanet detection limit may lead to a widespread adoption of such an approach. Our test on the HD 192310 planetary system is encouraging, as we confirm the presence of the two hosted exoplanets and we determine orbital parameters consistent with the literature, also providing much more precise estimates for HD 192310 c. Key words: techniques: radial velocities / methods: data analysis / stars: activity / planetary systems

• Pesonen, Henri; Simola, Umberto; Kohn Luque, Alvaro; Vuollekoski, Henri; Lai, Xiaoran & Frigessi, Arnoldo [Show all 11 contributors for this article] (2022). ABC of the future. International Statistical Review. ISSN 0306-7734. doi: 10.1111/insr.12522. Full text in Research Archive
• Tonkin-Hill, Gerry; Ling, Clare; Chaguza, Chrispin; Salter, Susannah J.; Hinfonthong, Pattaraporn & Nikolaou, Elissavet [Show all 15 contributors for this article] (2022). Pneumococcal within-host diversity during colonization, transmission and treatment. Nature Microbiology. ISSN 2058-5276. 7(11), p. 1791–1804. doi: 10.1038/s41564-022-01238-1. Full text in Research Archive Show summary

  Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child’s life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.

• Pereira, Ana P.; Antunes, Patrícia; Willems, Rob; Corander, Jukka; Coque, Teresa M. & Peixe, Luísa [Show all 8 contributors for this article] (2022). Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans. Microbiology spectrum. ISSN 2165-0497. 10(4). doi: 10.1128/spectrum.01176-22. Full text in Research Archive Show summary

  Chlorhexidine (CHX) is widely used to control the spread of pathogens (e.g., human/animal clinical settings, ambulatory care, food industry). Enterococcus faecalis, a major nosocomial pathogen, is broadly distributed in diverse hosts and environments facilitating its exposure to CHX over the years. Nevertheless, CHX activity against E. faecalis is understudied. Our goal was to assess CHX activity and the variability of ChlR-EfrEF proteins (associated with CHX tolerance) among 673 field isolates and 1,784 E. faecalis genomes from the PATRIC database from different sources, time spans, clonal lineages, and antibiotic-resistance profiles. The CHX MIC (MICCHX) and minimum bactericidal concentration (MBCCHX) against E. faecalis presented normal distributions (0.5 to 64 mg/L). However, more CHX-tolerant isolates were detected in the food chain and recent human infections, suggesting an adaptability of E. faecalis populations in settings where CHX is heavily used. Heterogeneity in ChlR-EfrEF sequences was identified, with isolates harboring incomplete ChlR-EfrEF proteins, particularly the EfrE identified in the ST40 clonal lineage, showing low MICCHX (≤1mg/L). Distinct ST40-E. faecalis subpopulations carrying truncated and nontruncated EfrE were detected, with the former being predominant in human isolates. This study provides a new insight about CHX susceptibility and ChlR-EfrEF variability within diverse E. faecalis populations. The MICCHX/MBCCHX of more tolerant E. faecalis (MICCHX = 8 mg/L; MBCCHX = 64 mg/L) remain lower than in-use concentrations of CHX (≥500 mg/L). However, increased CHX use, combined with concentration gradients occurring in diverse environments, potentially selecting multidrug-resistant strains with different CHX susceptibilities, signals the importance of monitoring the trends of E. faecalis CHX tolerance within a One Health approach. IMPORTANCE Chlorhexidine (CHX) is a disinfectant and antiseptic used since the 1950s and included in the World Health Organization’s list of essential medicines. It has been widely applied in hospitals, the community, the food industry, animal husbandry and pets. CHX tolerance in Enterococcus faecalis, a ubiquitous bacterium and one of the leading causes of human hospital-acquired infections, remains underexplored. Our study provides novel and comprehensive insights about CHX susceptibility within the E. faecalis population structure context, revealing more CHX-tolerant subpopulations from the food chain and recent human infections. We further show a detailed analysis of the genetic diversity of the efrEF operon (previously associated with E. faecalis CHX tolerance) and its correlation with CHX phenotypes. The recent strains with a higher tolerance to CHX and the multiple sources where bacteria are exposed to this biocide alert us to the need for the continuous monitoring of E. faecalis adaptation toward CHX tolerance within a One Health approach.

• Lees, John A.; Tonkin-Hill, Gerry; Yang, Zhirong & Corander, Jukka (2022). Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation. Philosophical Transactions of the Royal Society of London. Biological Sciences. ISSN 0962-8436. 377(1861). doi: 10.1098/rstb.2021.0237. Full text in Research Archive Show summary

  In less than a decade, population genomics of microbes has progressed fromthe effort of sequencing dozens of strains to thousands, or even tens of thou-sands of strains in a single study. There are now hundreds of thousands ofgenomes available even for a single bacterial species, and the number of gen-omes is expected to continue to increase at an accelerated pace given theadvances in sequencing technology and widespread genomic surveillanceinitiatives. This explosion of data calls for innovative methods to enablerapid exploration of the structure of a population based on different datamodalities, such as multiple sequence alignments, assemblies and estimatesof gene content across different genomes. Here, we present Mandrake, anefficient implementation of a dimensional reduction method tailored forthe needs of large-scale population genomics. Mandrake is capable of visua-lizing population structure from millions of whole genomes, and weillustrate its usefulness with several datasets representing major pathogens.Our method is freely available both as an analysis pipeline (https://github.com/johnlees/mandrake) and as a browser-based interactive application(https://gtonkinhill.github.io/mandrake-web/).This article is part of a discussion meeting issue‘Genomic populationstructures of microbial pathogens’.1. IntroductionAdvances in DNA sequencing technology have recently made whole-genomesequencing both affordable and scalable enough for routine use in pathogensurveillance by research organizations and public health agencies around theworld [1,2]. A striking example of this is genomic surveillance of the SARS-CoV-2 virus for which over one million genome sequences became availablein just 15 months after its initial discovery [3]. To shed light on population geno-mic data at this scale calls for new tools that can be used for rapid exploration ofthe structure among the samples, with particular emphasis on detecting clustersof similar sequences [4,5]. In this paper, we explore and extend a class ofmethods that aims to reduce the dimensionality of such data to only two dimen-sions, in a manner that supports ready visualization and identification ofclusters.© 2022 The Authors. Published by the Royal Society under the terms of the Creative Commons AttributionLicense http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the originalauthor and source are credited.

• Aushev, Alexander; Pesonen, Henri Eerikki; Heinonen, Markus; Corander, Jukka & Kaski, Samuel (2022). Likelihood-free inference with deep Gaussian processes. Computational Statistics & Data Analysis. ISSN 0167-9473. 174. doi: 10.1016/j.csda.2022.107529. Full text in Research Archive
• van Hal, Sebastiaan J; Willems, Rob J L; Gouliouris, Theodore; Ballard, Susan A; Coque, Teresa M & Hammerum, Anette M [Show all 16 contributors for this article] (2022). The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis. Lancet Microbe. ISSN 2666-5247. 3(2), p. e133–e141. doi: 10.1016/S2666-5247(21)00236-6. Full text in Research Archive Show summary

  Background The genomic relationships among Enterococcus faecium isolates are the subject of ongoing research that seeks to clarify the origins of observed lineages and the extent of horizontal gene transfer between them, and to robustly identify links between genotypes and phenotypes. E faecium is considered to form distinct groups—A and B—corresponding to isolates derived from patients who were hospitalised (A) and isolates from humans in the community (B). The additional separation of A into the so-called clades A1 and A2 remains an area of uncertainty. We aimed to investigate the relationships between A1 and non-A1 groups and explore the potential role of non-A1 isolates in shaping the population structure of hospital E faecium. Methods We collected short-read sequence data from invited groups that had previously published E faecium genome data. This hospital-based isolate collection could be separated into three groups (or clades, A1, A2, and B) by augmenting the study genomes with published sequences derived from human samples representing the previously defined genomic clusters. We performed phylogenetic analyses, by constructing maximum-likelihood phylogenetic trees, and identified historical recombination events. We assessed the pan-genome, did resistome analysis, and examined the genomic data to identify mobile genetic elements. Each genome underwent chromosome painting by use of ChromoPainter within FineSTRUCTURE software to assess ancestry and identify hybrid groups. We further assessed highly admixed regions to infer recombination directionality. Findings We assembled a collection of 1095 hospital E faecium sequences from 34 countries, further augmented by 33 published sequences. 997 (88%) of 1128 genomes clustered as A1, 92 (8%) as A2, and 39 (4%) as B. We showed that A1 probably emerged as a clone from within A2 and that, because of ongoing gene flow, hospital isolates currently identified as A2 represent a genetic continuum between A1 and community E faecium. This interchange of genetic material between isolates from different groups results in the emergence of hybrid genomes between clusters. Of the 1128 genomes, 49 (4%) hybrid genomes were identified: 33 previously labelled as A2 and 16 previously labelled as A1. These interactions were fuelled by a directional pattern of recombination mediated by mobile genetic elements. By contrast, the contribution of B group genetic material to A1 was limited to a few small regions of the genome and appeared to be driven by genomic sweep events. Interpretation A2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect of E faecium could benefit from strategies to reduce these genomic interactions, such as a focus on reducing the acquisition of hospital A1 strains by patients entering the hospital.

• Mallawaarachchi, Sudaraka; Tonkin-Hill, Gerry; Croucher, Nicholas J.; Turner, Paul; Speed, Doug & Corander, Jukka [Show all 7 contributors for this article] (2022). Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae. NAR Genomics and Bioinformatics. ISSN 2631-9268. 4(1). doi: 10.1093/nargab/lqac011. Full text in Research Archive Show summary

  Whole-genome sequencing has facilitated genome-wide analyses of association, prediction and heritability in many organisms. However, such analyses in bacteria are still in their infancy, being limited by difficulties including genome plasticity and strong population structure. Here we propose a suite of methods including linear mixed models, elastic net and LD-score regression, adapted to bacterial traits using innovations such as frequency-based allele coding, both insertion/deletion and nucleotide testing and heritability partitioning. We compare and validate our methods against the current state-of-art using simulations, and analyse three phenotypes of the major human pathogen Streptococcus pneumoniae, including the first analyses of minimum inhibitory concentrations (MIC) for penicillin and ceftriaxone. We show that the MIC traits are highly heritable with high prediction accuracy, explained by many genetic associations under good population structure control. In ceftriaxone MIC, this is surprising because none of the isolates are resistant as per the inhibition zone criteria. We estimate that half of the heritability of penicillin MIC is explained by a known drug-resistance region, which also contributes a quarter of the ceftriaxone MIC heritability. For the within-host carriage duration phenotype, no associations were observed, but the moderate heritability and prediction accuracy indicate a moderately polygenic trait.

• Corander, Jukka; Remes, Ulpu Maria Vilhelmiina & Koski, Timo (2021). On the Jensen-Shannon divergence and the variation distance for categorical probability distributions. Kybernetika (Praha). ISSN 0023-5954. 57(6), p. 879–907. doi: 10.14736/kyb-2021-6-0879.
• Gladstone, Rebecca Ashley; Siira, Lotta; Brynildsrud, Ola Brønstad; Vestrheim, Didrik Frimann; Turner, Paul & Clarke, S.C. [Show all 21 contributors for this article] (2021). International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease. Vaccine. ISSN 0264-410X. 40(7), p. 1054–1060. doi: 10.1016/j.vaccine.2021.10.046. Full text in Research Archive Show summary

  Background: Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them. Methods: Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating. Results: Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0-2 SNPs) with the common ancestor dated around 2017. Conclusion: The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

• Mäklin, Tommi; Kallonen, Teemu; David, Sophia; Boinett, Christine J.; Pascoe, Ben & Meric, Guillaume [Show all 13 contributors for this article] (2021). High-resolution sweep metagenomics using fast probabilistic inference [version 1; peer review: 1 approved, 1 approved with reservations]. Wellcome Open Research. ISSN 2398-502X. 5(14). doi: 10.12688/WELLCOMEOPENRES.15639.2. Full text in Research Archive
• Biffignandi, Gherard Batisti; Gibbon, Marjorie J.; Corbella, Marta; Thorpe, Harry Arthur Frank Wright; Merla, Cristina & Castelli, Michele [Show all 13 contributors for this article] (2021). Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae. G3: Genes, Genomes, Genetics. ISSN 2160-1836. 11(2). doi: 10.1093/g3journal/jkab019. Full text in Research Archive
• Horesh, Gal; Blackwell, Grace A.; Tonkin-Hill, Gerry; Corander, Jukka; Heinz, Eva & Thomson, Nicholas R. (2021). A comprehensive and high-quality collection of escherichia coli genomes and their genes. Microbial Genomics. ISSN 2057-5858. 7(2), p. 1–15. doi: 10.1099/mgen.0.000499. Full text in Research Archive
• Wee, Bryan A.; Alves, Joana; Lindsay, Diane S. J.; Klatt, Ann-Brit; Sargison, Fiona A. & Cameron, Ross L. [Show all 13 contributors for this article] (2021). Population analysis of Legionella pneumophila reveals a basis for resistance to complement-mediated killing. Nature Communications. ISSN 2041-1723. 12(1). doi: 10.1038/s41467-021-27478-z. Full text in Research Archive
• Horesh, Gal; Taylor-Brown, Alyce; McGimpsey, Stephanie; Lassalle, Florent; Corander, Jukka & Heinz, Eva [Show all 7 contributors for this article] (2021). Different evolutionary trends form the twilight zone of the bacterial pan-genome. Microbial Genomics. ISSN 2057-5858. 7(9). doi: 10.1099/MGEN.0.000670. Full text in Research Archive
• Gibbon, Marjorie J.; Couto, Natacha; David, Sophia; Barden, Ruth; Standerwick, Richard & Jagadeesan, Kishore Kumar [Show all 17 contributors for this article] (2021). A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England. Microbial Genomics. ISSN 2057-5858. 7(3). doi: 10.1099/mgen.0.000509. Full text in Research Archive
• Kantele, Anu; Kuenzli, Esther; Dunn, Steven; Dance, David A.B.; Newton, Paul N. & Davong, Viengmon [Show all 14 contributors for this article] (2021). Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study. Lancet Microbe. ISSN 2666-5247. 2(4), p. e151–e158. doi: 10.1016/S2666-5247(20)30224-X. Full text in Research Archive
• Alonso, Sergio Arredondo; Pöntinen, Anna Kaarina; Cleon, Francois Pierre Alexandre; Gladstone, Rebecca Ashley; Schürch, Anita C. & Johnsen, Pål Jarle [Show all 8 contributors for this article] (2021). A high-throughput multiplexing and selection strategy to complete bacterial genomes. GigaScience. ISSN 2047-217X. 10(12), p. 1–13. doi: 10.1093/gigascience/giab079. Full text in Research Archive
• Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin & Mäkinen, Veli [Show all 9 contributors for this article] (2021). Bacterial genomic epidemiology with mixed samples. Microbial Genomics. ISSN 2057-5858. 7(11), p. 1–18. doi: 10.1099/MGEN.0.000691. Full text in Research Archive
• Chewapreecha, Claire; Pensar, Johan; Chattagul, Supaksorn; Pesonen, Maiju; Sangphukieo, Apiwat & Boonklang, Phumrapee [Show all 18 contributors for this article] (2021). Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 39(1). doi: 10.1093/molbev/msab306. Full text in Research Archive
• Suotsalo, Kimmo; Xu, Yingying; Corander, Jukka & Pensar, Johan (2021). High-dimensional structure learning of sparse vector autoregressive models using fractional marginal pseudo-likelihood. Statistics and computing. ISSN 0960-3174. 31(73). doi: 10.1007/s11222-021-10049-z. Full text in Research Archive
• Pöntinen, Anna Kaarina; Top, Janetta; Alonso, Sergio Arredondo; Tonkin-Hill, Gerry; Freitas, Ana R. & Novais, Carla [Show all 21 contributors for this article] (2021). Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nature Communications. ISSN 2041-1723. 12. doi: 10.1038/s41467-021-21749-5. Full text in Research Archive
• Calland, Jessica K.; Pascoe, Ben; Bayliss, Sion; Mourkas, Evangelos; Berthenet, Elvire & Thorpe, Harry Arthur Frank Wright [Show all 12 contributors for this article] (2021). Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages. PLoS Genetics. ISSN 1553-7390. 17(9). doi: 10.1371/journal.pgen.1009829. Full text in Research Archive
• MacAlasdair, Neil; Pesonen, Maiju; Brynildsrud, Ola Brønstad; Eldholm, Vegard; Kristiansen, Paul Arne & Corander, Jukka [Show all 8 contributors for this article] (2021). The effect of recombination on the evolution of a population of Neisseria meningitidis. Genome Research. ISSN 1088-9051. 31(7), p. 1258–1268. doi: 10.1101/gr.264465.120. Full text in Research Archive
• Mageiros, Leonardos; Meric, Guillaume; Bayliss, Sion; Pensar, Johan; Pascoe, Ben & Mourkas, Evangelos [Show all 19 contributors for this article] (2021). Genome evolution and the emergence of pathogenicity in avian Escherichia coli. Nature Communications. ISSN 2041-1723. 12(1). doi: 10.1038/s41467-021-20988-w. Full text in Research Archive
• van Hal, Sebastiaan J.; Willems, Rob J.L.; Gouliouris, Theodore; Ballard, Susan A.; Coque, Teresa M. & Hammerum, Anette M. [Show all 21 contributors for this article] (2021). The global dissemination of hospital clones of Enterococcus faecium. Genome Medicine. ISSN 1756-994X. 13(52). doi: 10.1186/s13073-021-00868-0. Full text in Research Archive
• Gladstone, Rebecca Ashley; McNally, Alan; Pöntinen, Anna Kaarina; Tonkin-Hill, Gerry; Lees, John A. & Skytén, Kusti Onni [Show all 29 contributors for this article] (2021). Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study. Lancet Microbe. ISSN 2666-5247. 2(7), p. e331–e341. doi: 10.1016/S2666-5247(21)00031-8. Full text in Research Archive Show summary

  Background The clonal diversity underpinning trends in multidrug resistant Escherichia coli causing bloodstream infections remains uncertain. We aimed to determine the contribution of individual clones to resistance over time, using large-scale genomics-based molecular epidemiology. Methods This was a longitudinal, E coli population, genomic, cohort study that sampled isolates from 22 512 E coli bloodstream infections included in the Norwegian surveillance programme on resistant microbes (NORM) from 2002 to 2017. 15 of 22 laboratories were able to share their isolates, and the first 22·5% of isolates from each year were requested. We used whole genome sequencing to infer the population structure (PopPUNK), and we investigated the clade composition of the dominant multidrug resistant clonal complex (CC)131 using genetic markers previously reported for sequence type (ST)131, effective population size (BEAST), and presence of determinants of antimicrobial resistance (ARIBA, PointFinder, and ResFinder databases) over time. We compared these features between the 2002–10 and 2011–17 time periods. We also compared our results with those of a longitudinal study from the UK done between 2001 and 2011. Findings Of the 3500 isolates requested from the participating laboratories, 3397 (97·1%) were received, of which 3254 (95·8%) were successfully sequenced and included in the analysis. A significant increase in the number of multidrug resistant CC131 isolates from 71 (5·6%) of 1277 in 2002–10 to 207 (10·5%) of 1977 in 2011–17 (p<0·0001), was the largest clonal expansion. CC131 was the most common clone in extended-spectrum β-lactamase (ESBL)-positive isolates (75 [58·6%] of 128) and fluoroquinolone non-susceptible isolates (148 [39·2%] of 378). Within CC131, clade A increased in prevalence from 2002, whereas the global multidrug resistant clade C2 was not observed until 2007. Multiple de-novo acquisitions of both blaCTX-M ESBL-encoding genes in clades A and C1 and gain of phenotypic fluoroquinolone non-susceptibility across the clade A phylogeny were observed. We estimated that exponential increases in the effective population sizes of clades A, C1, and C2 occurred in the mid-2000s, and in clade B a decade earlier. The rate of increase in the estimated effective population size of clade A (Ne=3147) was nearly ten-times that of C2 (Ne=345), with clade A over-represented in Norwegian CC131 isolates (75 [27·0%] of 278) compared with the UK study (8 [5·4%] of 147 isolates). Interpretation The early and sustained establishment of predominantly antimicrobial susceptible CC131 clade A isolates, relative to multidrug resistant clade C2 isolates, suggests that resistance is not necessary for clonal success. However, even in the low antibiotic use setting of Norway, resistance to important antimicrobial classes has rapidly been selected for in CC131 clade A isolates. This study shows the importance of genomic surveillance in uncovering the complex ecology underlying multidrug resistance dissemination and competition, which have implications for the design of strategies and interventions to control the spread of high-risk multidrug resistant clones.

• Alonso, Sergio Arredondo; Top, Janetta; Corander, Jukka; Willems, Rob J. L. & Schürch, Anita C. (2021). Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals. Genome Medicine. ISSN 1756-994X. 13(1), p. 1–18. doi: 10.1186/s13073-020-00825-3. Full text in Research Archive
• Mai, The Tien; Turner, Paul & Corander, Jukka (2021). Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting. BMC Bioinformatics. ISSN 1471-2105. 22(1). doi: 10.1186/s12859-021-04079-7. Full text in Research Archive
• Harrow, Gabrielle L.; Lees, John A.; Hanage, William P.; Lipsitch, Marc; Corander, Jukka & Colijn, Caroline [Show all 7 contributors for this article] (2021). Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. The ISME Journal. ISSN 1751-7362. 15, p. 1523–1538. doi: 10.1038/s41396-020-00867-w. Full text in Research Archive
• Mai, The Tien; Rønneberg, Leiv; Zhao, Zhi; Zucknick, Manuela & Corander, Jukka (2020). Learning Cancer Drug Sensitivities in Large-Scale Screens from Multi-omics Data with Local Low-Rank Structure. Lecture Notes in Computer Science (LNCS). ISSN 0302-9743. 12313, p. 67–79. doi: 10.1007/978-3-030-63061-4_7.
• Lees, J.A.; Mai, The Tien & Corander, Jukka (2020). Improved prediction of bacterial genotype-phenotype associations using interpretable pangenome-spanning regressions. mBio. ISSN 2161-2129. 11. doi: 10.1128/mBio.01344-20.
• Aalto-Araneda, Mariella; Pöntinen, Anna; Pesonen, Maiju; Corander, Jukka; Markkula, Annukka & Tasara, Taurai [Show all 8 contributors for this article] (2020). Strain Variability of Listeria monocytogenes under NaCl Stress Elucidated by a High-Throughput Microbial Growth Data Assembly and Analysis Protocol. Applied and Environmental Microbiology. ISSN 0099-2240. 86(6). doi: 10.1128/AEM.02378-19.
• Top, Janetta; Arredondo-Alonso, Sergio; Schürch, Anita C.; Puranen, Santeri; Pesonen, Maiju & Pensar, Johan [Show all 8 contributors for this article] (2020). Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium. Microbial Genomics. ISSN 2057-5858. 6(12), p. 1–8. doi: 10.1099/mgen.0.000488. Full text in Research Archive
• Tonkin-Hill, Gerry; MacAlasdair, Neil; Ruis, Christopher; Weimann, Aaron; Horesh, Gal & Lees, John A. [Show all 14 contributors for this article] (2020). Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biology. ISSN 1465-6906. 21, p. 1–21. doi: 10.1186/s13059-020-02090-4. Full text in Research Archive
• Azarian, Taj; Martinez, Pamela P.; Arnold, Brian; Qiu, Xueting; Grant, Lindsay R. & Corander, Jukka [Show all 16 contributors for this article] (2020). Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS Biology. ISSN 1544-9173. 18(10). doi: 10.1371/journal.pbio.3000878. Full text in Research Archive
• Arredondo-Alonso, Sergio; Top, Janetta; McNally, Alan; Puranen, Santeri; Pesonen, Maiju & Pensar, Johan [Show all 14 contributors for this article] (2020). Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium. mBio. ISSN 2161-2129. 11(1). doi: 10.1128/mBio.03284-19. Full text in Research Archive
• Colijn, Caroline; Corander, Jukka & Croucher, Nicholas J. (2020). Designing ecologically optimized pneumococcal vaccines using population genomics. Nature Microbiology. ISSN 2058-5276. 5(3), p. 473–485. doi: 10.1038/s41564-019-0651-y.
• Arnold, Brian; Sohail, Mashaal; Wadsworth, Crista; Corander, Jukka; Hanage, William P. & Sunyaev, Shamil R. [Show all 7 contributors for this article] (2020). Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 37(2), p. 417–428. doi: 10.1093/molbev/msz225.
• Pensar, Johan; Xu, Yingying; Puranen, Juha Santeri; Pesonen, Maiju; Kabashima, Yoshiyuki & Corander, Jukka (2020). High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study. Computational Statistics & Data Analysis. ISSN 0167-9473. 141, p. 62–76. doi: 10.1016/j.csda.2019.06.012. Full text in Research Archive
• Schaufler, Katharina; Semmler, Torsten; Wieler, Lothar H.; Trott, Darren J.; Pitout, Johann & Peirano, Gisele [Show all 19 contributors for this article] (2019). Genomic and functional analysis of emerging virulent and multidrug-resistant Escherichia coli lineage sequence type 648. Antimicrobial Agents and Chemotherapy. ISSN 0066-4804. 63:e00243-19(6), p. 1–12. doi: 10.1128/AAC.00243-19.
• Elbers, Jean P; Rogers, Mark F; Perelman, Polina L; Proskuryakova, Anastasia A; Serdyukova, Natalia A & Johnson, Warren E. [Show all 10 contributors for this article] (2019). Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary. Molecular Ecology Resources. ISSN 1755-098X. 19(4), p. 1015–1026. doi: 10.1111/1755-0998.13020. Full text in Research Archive
• Léon-Sampedro, Ricardo; del Campo, Rosa; Rodriguez-Baños, Mercedes; Lanza, Val F.; Pozuelo, María José & Francés-Cuesta, Carlos [Show all 15 contributors for this article] (2019). Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environmental Microbiology. ISSN 1462-2912. 21(8), p. 3046–3062. doi: 10.1111/1462-2920.14702.
• Lintusaari, Jarno; Blomstedt, Paul; Rose, Brittany; Sivula, Tuomas; Gutmann, Michael U. & Kaski, Samuel [Show all 7 contributors for this article] (2019). Resolving outbreak dynamics using approximate bayesian computation for stochastic birth-death models. Wellcome Open Research. ISSN 2398-502X. 4(14). doi: 10.12688/wellcomeopenres.15048.2. Full text in Research Archive
• Pensar, Johan; Puranen, Santeri; Arnold, Brian; MacAlasdair, Neil; Kuronen, Juri & Tonkin-Hill, Gerry [Show all 17 contributors for this article] (2019). Genome-wide epistasis and co-selection study using mutual information. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(18), p. 1–14. doi: 10.1093/nar/gkz656. Full text in Research Archive
• Merla, Cristina; Rodrigues, Carla; Passet, Virginie; Corbella, Marta; Thorpe, Harry A & Kallonen, Teemu [Show all 13 contributors for this article] (2019). Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov. Frontiers in Microbiology. ISSN 1664-302X. 10(2360), p. 1–9. doi: 10.3389/fmicb.2019.02360. Full text in Research Archive
• Tonkin-Hill, Gerry; Lees, John A; Bentley, Stephen D; Frost, Simon DW & Corander, Jukka (2019). Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(11), p. 5539–5549. doi: 10.1093/nar/gkz361. Full text in Research Archive
• Sanchez-Buso, Leonor; Golparian, Daniel; Corander, Jukka; Grad, Yonatan H.; Ohnishi, Makoto & Flemming, Rebecca [Show all 10 contributors for this article] (2019). The impact of antimicrobials on gonococcal evolution. Nature Microbiology. ISSN 2058-5276. doi: 10.1038/s41564-019-0501-y.
• Lu, Yao; Corander, Jukka & Yang, Zhirong (2019). Doubly Stochastic Neighbor Embedding on Spheres. Pattern Recognition Letters. ISSN 0167-8655. 128, p. 100–106. doi: 10.1016/j.patrec.2019.08.026. Full text in Research Archive
• Chiner-Oms, Álvaro; Sanchez-Buso, Leonor; Corander, Jukka; Gagneux, Sébastien; Harris, Simon R & Young, D [Show all 8 contributors for this article] (2019). Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. Science Advances. ISSN 2375-2548. 5(6). doi: 10.1126/sciadv.aaw3307. Full text in Research Archive
• Corander, Jukka; Hyttinen, Antti; Kontinen, Juha; Pensar, Johan & Väänänen, Jouko (2019). A logical approach to context-specific independence. Annals of Pure and Applied Logic. ISSN 0168-0072. 170(9), p. 975–992. doi: 10.1016/j.apal.2019.04.004.
• Gladstone, Rebecca A; Lo, Stephanie W; Lees, John A; Croucher, Nicholas J.; van Tonder, Andries J. & Corander, Jukka [Show all 26 contributors for this article] (2019). International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine. ISSN 2352-3964. 43, p. 338–346. doi: 10.1016/j.ebiom.2019.04.021. Full text in Research Archive
• Gouliouris, Theodore; Raven, Kathy E; Moradigaravand, Danesh; Ludden, Catherine; Coll, Francesc & Blane, Beth [Show all 13 contributors for this article] (2019). Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment. Genome Research. ISSN 1088-9051. 29(4), p. 626–634. doi: 10.1101/gr.232629.117. Full text in Research Archive
• Cremers, Amelieke J. H.; Mobegi, Fredrick M.; Van Der Gaast-De Jongh, Christa; Van Weert, Michelle; Van Opzeeland, Fred J. & Vehkala, Minna [Show all 17 contributors for this article] (2019). The contribution of genetic variation of streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease. Clinical Infectious Diseases. ISSN 1058-4838. 68(1), p. 61–69. doi: 10.1093/cid/ciy417.
• Lees, John A; Harris, Simon R; Tonkin-Hill, Gerry; Gladstone, Rebecca A; Lo, Stephanie W & Weiser, Jeffrey N [Show all 9 contributors for this article] (2019). Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Research. ISSN 1088-9051. 29(2), p. 304–316. doi: 10.1101/gr.241455.118. Full text in Research Archive

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• Bastakoti, Srijana; Pesonen, Maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka & Johannessen, Mona Susan [Show all 7 contributors for this article] (2023). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells.
• Bastakoti, Srijana; Pesonen, Maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka & Johannessen, Mona Susan [Show all 7 contributors for this article] (2023). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells.
• Bastakoti, Srijana; Pesonen, maiju; Ajayi, Clément; Julin, Kjersti; Johannessen, Mona Susan & Corander, Jukka [Show all 7 contributors for this article] (2023). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells.
• Hanssen, Anne-Merethe Christiansen; Ajayi, Clément; Johannessen, Mona Susan; Julin, Kjersti; Pesonen, Maiju & Corander, Jukka [Show all 7 contributors for this article] (2023). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells.
• Angchagun, Kesorn; Boonklang, Phumrapee; Chomkatekaew, Chalita; Pakdeerat, Sukritpong; Wongsuwan, Gumphol & Amornchai, Premjit [Show all 25 contributors for this article] (2023). BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection. Wellcome Open Research. ISSN 2398-502X. 8. doi: 10.12688/wellcomeopenres.19809.2.
• Ross, Theodor Anton; Pöntinen, Anna Kaarina; Janice, Jessin ; Holsbø, Einar; Corander, Jukka & Hegstad, Kristin [Show all 7 contributors for this article] (2022). Leveraging machine learning for finding novel putative virulence factors in Enterococcus faecium.
• Järvenpää, Marko Juhani & Corander, Jukka (2022). On predictive inference for intractable models via approximate Bayesian computation. Statistics and computing. ISSN 0960-3174. 33(2). doi: 10.1007/s11222-022-10163-6.
• Corander, Jukka (2022). A conversation with Elja Arjas (Helsinki, November 2021 and March 2022). Scandinavian Journal of Statistics. ISSN 0303-6898. doi: 10.1111/sjos.12612. Full text in Research Archive
• Congo-Ouedraogo, M.; Poncin, T.; Sangaré, L.; Mérimèche, M.; Braille, A. & Jacquier, H. [Show all 13 contributors for this article] (2022). Genomic and antimicrobial resistance analyses of Neisseria gonorrhoeae isolates, Burkina Faso, 2018–2019. Journal of the European Academy of Dermatology and Venereology. ISSN 0926-9959. doi: 10.1111/jdv.18037.
• Kloos, Julia Maria; Jänisch, Lea; Pöntinen, Anna Kaarina; Samuelsen, Ørjan; Johnsen, Pål Jarle & Corander, Jukka [Show all 7 contributors for this article] (2022). Different metabolic proficiency among dominant ExPEC lineages.
• Gladstone, Rebecca Ashley; McNally, Alan; Johnsen, Pål Jarle; Samuelsen, Ørjan & Corander, Jukka (2021). Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection – Authors’ reply. Lancet Microbe. ISSN 2666-5247. 2(10). doi: 10.1016/S2666-5247(21)00176-2.
• Mageiros, Leonardos; Meric, Guillaume; Bayliss, Sion; Pensar, Johan; Pascoe, Ben & Mourkas, Evangelos [Show all 19 contributors for this article] (2021). Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli (Nature Communications, (2021), 12, 1, (765), 10.1038/s41467-021-20988-w). Nature Communications. ISSN 2041-1723. 12(1). doi: 10.1038/s41467-021-22238-5.
• Corander, Jukka (2020). New Pathogenesis Mechanisms and Translational Leads Identified by Multidimensional Analysis of Necrotizing Myositis in Primates. mBio. ISSN 2161-2129. doi: 10.1128/mBio.03363-19.
• Corander, Jukka (2020). PYLFIRE: Python implementation of likelihood-free inference by ratio estimation. Wellcome Open Research. ISSN 2398-502X. doi: 10.12688/wellcomeopenres.15583.1.
• Corander, Jukka (2020). gplas: a comprehensive tool for plasmid analysis using short-read graphs. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btaa233.
• Corander, Jukka (2020). Genomic signatures of domestication in Old World camels. Communications Biology. ISSN 2399-3642. doi: 10.1038/s42003-020-1039-5.
• Corander, Jukka (2020). Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies. BMC Genomics. ISSN 1471-2164. doi: 10.1186/s12864-020-06990-4.
• Corander, Jukka (2020). The binding mechanism of the virulence factor Streptococcus suis adhesin P subtype to globotetraosylceramide is associated with systemic disease. Journal of Biological Chemistry. ISSN 0021-9258. doi: 10.1074/jbc.RA120.014818.
• Corander, Jukka (2020). Likelihood-free inference by ratio estimation. Bayesian Analysis. ISSN 1936-0975. doi: 10.1214/20-BA1238.
• Corander, Jukka (2020). Adaptive Approximate Bayesian Computation tolerance selection. Bayesian Analysis. ISSN 1936-0975. doi: 10.1214/20-BA1211.
• Corander, Jukka (2020). Improved prediction of bacterial genotype-phenotype associations using interpretable pangenome-spanning regressions. mBio. ISSN 2161-2129. doi: 10.1128/mBio.01344-20.
• Arredondo-Alonso, Sergio; Rogers, Malbert R.C.; Braat, Johanna C.; Verschuuren, Tess D.; Top, Janetta & Corander, Jukka [Show all 8 contributors for this article] (2019). Corrigendum: Mlplasmids: A user-friendly tool to predict plasmid-and chromosome-derived sequences for single species, (Microbial Genomics), (2018), 4, 10.1099/mgen.0.000224. Microbial Genomics. ISSN 2057-5858. 5(1). doi: 10.1099/mgen.0.000249.

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