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  • PL 68 (Pietari Kalmin katu 5)

    00014

    Finland

  • Finland

20022020
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Publications 2002 2020

2020

High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study

Pensar, J., Xu, Y., Puranen, S., Pesonen, M., Kabashima, Y. & Corander, J., 2020, In : Computational Statistics & Data Analysis. 141, p. 62-76 15 p.

Research output: Contribution to journalArticleScientificpeer-review

2019

A Logical Approach to Context-Specific Independence

Corander, J., Hyttinen, A., Kontinen, J., Pensar, J. & Väänänen, J., Sep 2019, In : Annals of Pure and Applied Logic. 170, 9, p. 975-992 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Bayesian inference of atomistic structure in functional materials

Todorovic, M., Gutmann, M. U., Corander, J. & Rinke, P., 18 Mar 2019, In : Npj computational materials. 5, 7 p., 35.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

McNally, A., Kallonen, T., Connor, C., Abudahab, K., Aanensen, D. M., Horner, C., Peacock, S. J., Parkhill, J., Croucher, N. J. & Corander, J., 30 Apr 2019, In : mBio. 10, 2, p. e00644-19

Research output: Contribution to journalArticleScientificpeer-review

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Fast and flexible bacterial genomic epidemiology with PopPUNK

Lees, J. A., Harris, S. R., Tonkin-Hill, G., Gladstone, R. A., Lo, S. W., Weiser, J. N., Corander, J., Bentley, S. D. & Croucher, N. J., Feb 2019, In : Genome Research. 29, 2, p. 304-316 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Fast hierarchical Bayesian analysis of population structure

Tonkin-Hill, G., Lees, J. A., Bentley, S. D., Frost, S. D. W. & Corander, J., 20 Jun 2019, In : Nucleic Acids Research. 47, 11, p. 5539-5549 11 p.

Research output: Contribution to journalArticleScientificpeer-review

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Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 648

Schaufler, K., Semmler, T., Wieler, L. H., Trott, D. J., Pitout, J., Peirano, G., Bonnedahl, J., Dolejska, M., Literak, I., Fuchs, S., Ahmed, N., Grobbel, M., Torres, C., McNally, A., Pickard, D., Ewers, C., Croucher, N. J., Corander, J. & Guenther, S., Jun 2019, In : Antimicrobial Agents and Chemotherapy. 63, 6, 12 p., e00243-19.

Research output: Contribution to journalArticleScientificpeer-review

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

Chiner-Oms, Á., Sánchez-Busó, L., Corander, J., Gagneux, S., Harris, S. R., Young, D., González-Candelas, F. & Comas, I., Jun 2019, In : Science Advances. 5, 6, 14 p., 3307.

Research output: Contribution to journalArticleScientificpeer-review

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Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary

Elbers, J. P., Rogers, M. F., Perelman, P. L., Proskuryakova, A. A., Serdyukova, N. A., Johnson, W. E., Horin, P., Corander, J., Murphy, D. & Burger, P. A., Jul 2019, In : Molecular Ecology Resources. 19, 4, p. 1015-1026 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis

Kachroo, P., Eraso, J. M., Beres, S. B., Olsen, R. J., Zhu, L., Nasser, W., Bernard, P. E., Cantu, C. C., Saavedra, M. O., Arredondo, M. J., Strope, B., Do, H., Kumaraswami, M., Vuopio, J., Gröndahl-Yli-Hannuksela, K., Kristinsson, K. G., Gottfredsson, M., Pesonen, M., Pensar, J., Davenport, E. R. & 11 othersClark, A. G., Corander, J., Caugant, D. A., Gaini, S., Magnussen, M. D., Kubiak, S. L., Nguyen, H. A. T., Long, S. W., Porter, A. R., DeLeo, F. R. & Musser, J. M., Mar 2019, In : Nature Genetics. 51, 3, p. 548-563 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Machine learning accelerated likelihood-free event reconstruction in dark matter direct detection

Simola, U., Pelssers, B., Barge, D., Conrad, J. & Corander, J., 6 Mar 2019, In : Journal of Instrumentation. 14, 28 p., 03004.

Research output: Contribution to journalArticleScientificpeer-review

Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence (vol 12, pg 2518, 2018)

Smet, A., Yahara, K., Rossi, M., Tay, A., Backert, S., Ensser, A., Fox, J. G., Flahou, B., Ducatelle, R., Haesebrouck, F. & Corander, J., Jul 2019, In : ISME Journal. 13, 7, p. 1890-1890 1 p.

Research output: Contribution to journalArticleScientificpeer-review

PANINI: Pangenome Neighbour Identification for Bacterial Populations

Abudahab, K., Prada, J. M., Yang, Z., Bentley, S. D., Croucher, N. J., Corander, J. & Aanensen, D. M., Apr 2019, In : Microbial Genomics. 5, 4, 10 p., 000220.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Patterns of cross-resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials

Colclough, A., Corander, J., Sheppard, S. K., Bayliss, S. C. & Vos, M., Jun 2019, In : Evolutionary Applications. 12, 5, p. 878-887 10 p.

Research output: Contribution to journalArticleScientificpeer-review

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rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree

Wailan, A. M., Coll, F., Heinz, E., Tonkin-Hill, G., Corander, J., Feasey, N. A. & Thomson, N. R., Apr 2019, In : Microbial Genomics. 5, 4, 9 p., 000264.

Research output: Contribution to journalArticleScientificpeer-review

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The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease

Cremers, A. J. H., Mobegi, F. M., van der Gaast-de Jongh, C., van Weert, M., van Opzeeland, F. J., Vehkala, M., Knol, M. J., Bootsma, H. J., Välimaki, N., Croucher, N. J., Meis, J. F., Bentley, S., van Hijum, S. A. F. T., Corander, J., Zomer, A. L., Ferwerda, G. & de Jonge, M. I., 1 Jan 2019, In : Clinical Infectious Diseases. 68, 1, p. 61-69 9 p.

Research output: Contribution to journalArticleScientificpeer-review

2018

Bacmeta: simulator for genomic evolution in bacterial metapopulations

Sipola, A., Marttinen, P. & Corander, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. 2308-2310 3 p.

Research output: Contribution to journalArticleScientificpeer-review

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Convergent amino acid signatures in polyphyletic Campylobacter jejuni subpopulations suggest human niche tropism

Méric, G., McNally, A., Pessia, A., Mourkas, E., Pascoe, B., Mageiros, L., Vehkala, M. E., Corander, J. I. & Shepard, S. K., 1 Mar 2018, In : Genome Biology and Evolution. 10, 3, p. 763-774 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

Méric, G., Mageiros, L., Pensar, J., Laabei, M., Yahara, K., Pascoe, B., Kittiwan, N., Tadee, P., Post, V., Lamble, S., Bowden, R., Bray, J. E., Morgenstern, M., Jolley, K. A., Maiden, M. C. J., Feil, E. J., Didelot, X., Miragaia, M., de Lencastre, H., Moriarty, T. F. & 5 othersRohde, H., Massey, R., Mack, D., Corander, J. & Sheppard, S. K., 28 Nov 2018, In : Nature Communications. 9, 11 p., 5034.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs

Flahou, B., Rossi, M., Bakker, J., Langermans, J. A. M., Heuvelman, E., Solnick, J. V., Martin, M. E., O'Rourke, J., Le Duc Ngoan, Xuan Hoa, N., Nakamura, M., Overby, A., Matsui, H., Ota, H., Matsumoto, T., Foss, D. L., Kopta, L. A., Omotosho, O., Franciosini, M. P., Proietti, P. C. & 13 othersGuo, A., Liu, H., Borilova, G., Bracarense, A. P., Linden, S. K., De Bruyckere, S., Zhang, G., De Witte, C., Smet, A., Pasmans, F., Ducatelle, R., Corander, J. & Haesebrouck, F., Jan 2018, In : ISME Journal. 12, 1, p. 77-86 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Exact Bayesian learning of Partition Directed Acyclic Graphs

Pensar, J., Kohonen, J. & Corander, J. I., 27 Jul 2018, In : Journal of Physics : Conference Series. 1036, 12 p., 012017.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Gene exchange drives the ecological success of a multi-host bacterial pathogen

Richardson, E. J., Bacigalupe, R., Harrison, E. M., Weinert, L. A., Lycett, S., Vrieling, M., Robb, K., Hoskisson, P. A., Holden, M. T. G., Feil, E. J., Paterson, G. K., Tong, S. Y. C., Shittu, A., van Wamel, W., Aanensen, D. M., Parkhill, J., Peacock, S. J., Corander, J., Holmes, M. & Fitzgerald, J. R., Sep 2018, In : Nature Ecology & Evolution. 2, 9, p. 1468-1478 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Identification of a Novel Genomic Island Associated with vanD-Type Vancomycin Resistance in Six Dutch Vancomycin-Resistant Enterococcus faecium Isolates

Top, J., Sinnige, J. C., Brouwer, E. C., Werner, G., Corander, J., Severin, J. A., Jansen, R., Bathoorn, E., Bonten, M. J. M., Rossen, J. W. A. & Willems, R. J. L., Mar 2018, In : Antimicrobial Agents and Chemotherapy. 62, 3, 7 p., e01793-17.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Identifying Bacterial Strains from Sequencing Data

Mäklin, T., Corander, J. & Honkela, A., 2018, Data Mining for Systems Biology: Methods and Protocols. Mamitsuka, H. (ed.). 2 ed. New York, NY: Humana press, p. 1-7 7 p. (Methods in Molecular Biology; vol. 1807).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Inverse finite-size scaling for high-dimensional significance analysis

Xu, Y., Puranen, S., Corander, J. & Kabashima, Y., 6 Jun 2018, In : Physical Review E. 97, 6, 9 p., 062112.

Research output: Contribution to journalArticleScientificpeer-review

Kpax3: Bayesian bi-clustering of large sequence datasets

Pessia, A. & Corander, J., 15 Jun 2018, In : Bioinformatics. 34, 12, p. 2132-2133 2 p.

Research output: Contribution to journalArticleScientificpeer-review

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Likelihood-free inference via classification

Gutmann, M. U., Dutta, R., Kaski, S. & Corander, J., Mar 2018, In : Statistics and Computing. 28, 2, p. 411-425 15 p.

Research output: Contribution to journalArticleScientificpeer-review

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Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence

Smet, A., Yahara, K., Rossi, M., Tay, A., Backert, S., Armin, E., Fox, J. G., Flahou, B., Ducatelle, R., Haesebrouck, F. & Corander, J., 25 Jun 2018, In : ISME Journal. 12, 10, p. 2518-2531 14 p.

Research output: Contribution to journalArticleScientificpeer-review

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

Arredondo-Alonso, S., Rogers, M. R. C., Braat, J. C., Verschuuren, T. D., Top, J., Corander, J., Willems, R. J. L. & Schürch, A. C., 1 Nov 2018, In : Microbial Genomics. 4, 11, 15 p., 000224.

Research output: Contribution to journalArticleScientificpeer-review

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pyseer: a comprehensive tool for microbial pangenome-wide association studies

Lees, J. A., Galardini, M., Bentley, S. D., Weiser, J. N. & Corander, J., 15 Dec 2018, In : Bioinformatics. 34, 24, p. 4310-4312 3 p.

Research output: Contribution to journalArticleScientificpeer-review

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Structure Learning for Bayesian Networks over Labeled DAGs

Hyttinen, A., Pensar, J., Kontinen, J. & Corander, J., 2018, Proceedings of the Ninth International Conference on Probabilistic Graphical Models. PMLR, Vol. 72. p. 133-144 12 p. (Proceedings of Machine Learning Research; vol. 72).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

SuperDCA for genome-wide epistasis analysis

Puranen, S., Pesonen, M., Pensar, J., Xu, Y. Y., Lees, J. A., Bentley, S. D., Croucher, N. J. & Corander, J., Jun 2018, In : Microbial Genomics. 4, 6, 12 p., 000184.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract

Lin, X. B., Wang, T., Stothard, P., Corander, J., Wang, J., Baines, J. F., Knowles, S. C. L., Baltrunaité, L., Tasseva, G., Schmaltz, R., Tollenaar, S., Cody, L. A., Grenier, T., Wu, W., Ramer-Tait, A. E. & Walter, J., 16 Jul 2018, In : ISME Journal. 12, 11, p. 2770-2784 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Weak Epistasis May Drive Adaptation in Recombining Bacteria

Arnold, B. J., Gutmann, M. U., Grad, Y. H., Sheppard, S. K., Corander, J., Lipsitch, M. & Hanage, W. P., Mar 2018, In : Genetics. 208, 3, p. 1247-1260 14 p.

Research output: Contribution to journalArticleScientificpeer-review

2017

A Bayesian Decision-Support Tool for Child Sexual Abuse Assessment and Investigation

Tadei, A., Pensar, J., Corander, J., Finnilä, K., Santtila, P. & Antfolk, J., 21 Sep 2017, In : Sexual Abuse. p. 1-23 23 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Asymptotic Analysis of Rayleigh Product Channels: A Free Probability Approach

Zheng, Z., Wei, L., Speicher, R., Muller, R. R., Hämäläinen, J. & Corander, J., Mar 2017, In : IEEE Transactions on Information Theory. 63, 3, p. 1731-1745 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Bayesian inference of physiologically meaningful parameters from body sway measurements

Tietavainen, A., Gutmann, M. U., Keski-Vakkuri, E., Corander, J. & Haeggstrom, E., 19 Jun 2017, In : Scientific Reports. 7, 14 p., 3771.

Research output: Contribution to journalArticleScientificpeer-review

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Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

Mostowy, R., Croucher, N. J., Andam, C. P., Corander, J., Hanage, W. P. & Marttinen, P., May 2017, In : Molecular Biology and Evolution. 34, 5, p. 1167-1182 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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Frequency-dependent selection in vaccine-associated pneumococcal population dynamics

Corander, J., Fraser, C., Gutmann, M. U., Arnold, B., Hanage, W. P., Bentley, S. D., Lipsitch, M. & Croucher, N. J., Dec 2017, In : Nature Ecology & Evolution. 1, 12, p. 1950-1960 11 p.

Research output: Contribution to journalArticleScientificpeer-review

From Random Matrix Theory to Coding Theory: Volume of a Metric Ball in Unitary Group

Wei, L., Pitaval, R-A., Corander, J. & Tirkkonen, O., May 2017, In : IEEE Transactions on Information Theory. 63, 5, p. 2814-2821 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Fundamentals and Recent Developments in Approximate Bayesian Computation

Lintusaari, J., Gutmann, M. U., Dutta, R., Kaski, S. & Corander, J., Jan 2017, In : Systematic Biology. 66, 1, p. E66-E82 17 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Genetic effects on life-history traits in the Glanville fritillary butterfly

Duplouy, A., Wong, S. C., Corander, J., Lehtonen, R. & Hanski, I., 25 May 2017, In : PeerJ. 5, 23 p., 3371.

Research output: Contribution to journalArticleScientificpeer-review

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Genomic Epidemiology of Penicillin Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States

Andam, C. P., Mitchell, P. K., Callendrello, A., Chang, Q., Corander, J., Chaguza, C., McGee, L., Beall, B. W. & Hanage, W. P., Apr 2017, In : Journal of Clinical Microbiology. 55, 4, p. 1104-1115 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Global and regional dissemination and evolution of Burkholderia pseudomallei

Chewapreecha, C., Holden, M. T. G., Vehkala, M., Välimäki, N., Yang, Z., Harris, S. R., Mather, A. E., Tuanyok, A., De Smet, B., Le Hello, S., Bizet, C., Mayo, M., Wuthiekanun, V., Limmathurotsakul, D., Phetsouvanh, R., Spratt, B. G., Corander, J., Keim, P., Dougan, G., Dance, D. A. B. & 3 othersCurrie, B. J., Parkhill, J. & Peacock, S. J., Apr 2017, In : Nature Reviews, Microbiology. 2, 4, 8 p., 16263.

Research output: Contribution to journalArticleScientificpeer-review

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Skwark, M. J., Croucher, N. J., Puranen, S., Chewapreecha, C., Pesonen, M., Xu, Y. Y., Turner, P., Harris, S. R., Beres, S. B., Musser, J. M., Parkhill, J., Bentley, S. D., Aurell, E. & Corander, J., Feb 2017, In : PLoS Genetics. 13, 2, 24 p., 1006508.

Research output: Contribution to journalArticleScientificpeer-review

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Layered adaptive importance sampling

Martino, L., Elvira, V., Luengo, D. & Corander, J., May 2017, In : Statistics and Computing. 27, 3, p. 599-623 25 p.

Research output: Contribution to journalArticleScientificpeer-review

Learning discrete decomposable graphical models via constraint optimization

Janhunen, T., Gebser, M., Rintanen, J., Nyman, H., Pensar, J. & Corander, J., Jan 2017, In : Statistics and Computing. 27, 1, p. 115-130 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Learning Gaussian graphical models with fractional marginal pseudo-likelihood

Leppä-Aho, J., Pensar, J., Roos, T. T. & Corander, J., 11 Jan 2017, In : International Journal of Approximate Reasoning. 83, p. 21-42 22 p.

Research output: Contribution to journalArticleScientificpeer-review

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Marginal Pseudo-Likelihood Learning of Discrete Markov Network Structures

Pensar, J., Nyman, H., Niiranen, J. & Corander, J., Dec 2017, In : Bayesian analysis. 12, 4, p. 1195-1215 21 p.

Research output: Contribution to journalArticleScientificpeer-review

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Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels

Mohandesan, E., Fitak, R. R., Corander, J., Yadamsuren, A., Chuluunbat, B., Abdelhadi, O., Raziq, A., Nagy, P., Stalder, G., Walzer, C., Faye, B. & Burger, P. A., 30 Aug 2017, In : Scientific Reports. 7, 12 p., 9970.

Research output: Contribution to journalArticleScientificpeer-review

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