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Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49591-5
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- Article
Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork.
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- NPJ Vaccines, 2024, v. 9, n. 1, p. 1, doi. 10.1038/s41541-024-00879-z
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- Article
Estimating between-country migration in pneumococcal populations.
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- G3: Genes | Genomes | Genetics, 2024, v. 14, n. 6, p. 1, doi. 10.1093/g3journal/jkae058
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- Article
Detecting co-selection through excess linkage disequilibrium in bacterial genomes.
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- NAR Genomics & Bioinformatics, 2024, v. 6, n. 2, p. 1, doi. 10.1093/nargab/lqae061
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- Article
Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells.
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- Frontiers in Cellular & Infection Microbiology, 2024, p. 1, doi. 10.3389/fcimb.2024.1326730
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- Article
Sequentially Guided MCMC Proposals for Synthetic Likelihoods and Correlated Synthetic Likelihoods.
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- Bayesian Analysis, 2023, v. 18, n. 4, p. 1099, doi. 10.1214/22-BA1305
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- Article
Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract.
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- PLoS Biology, 2023, v. 21, n. 10, p. 1, doi. 10.1371/journal.pbio.3002329
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Mge-cluster: a reference-free approach for typing bacterial plasmids.
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- NAR Genomics & Bioinformatics, 2023, v. 5, n. 3, p. 1, doi. 10.1093/nargab/lqad066
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- Article
ABC of the future.
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- International Statistical Review, 2023, v. 91, n. 2, p. 243, doi. 10.1111/insr.12522
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A conversation with Elja Arjas (Helsinki, November 2021 and March 2022).
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- Scandinavian Journal of Statistics, 2023, v. 50, n. 1, p. 3, doi. 10.1111/sjos.12612
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- Article
Identification of multiplicatively acting modulatory mutational signatures in cancer.
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- BMC Bioinformatics, 2022, v. 22, n. 10, p. 1, doi. 10.1186/s12859-022-05060-8
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- Article
Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales.
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- Virus Evolution, 2022, v. 8, n. 2, p. 1, doi. 10.1093/ve/veac108
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Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae.
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- NAR Genomics & Bioinformatics, 2022, v. 4, n. 1, p. 1, doi. 10.1093/nargab/lqac011
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- Article
Likelihood-Free Inference by Ratio Estimation.
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- Bayesian Analysis, 2022, v. 17, n. 1, p. 1, doi. 10.1214/20-BA1238
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- Article
Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment.
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- Molecular Biology & Evolution, 2022, v. 39, n. 1, p. 1, doi. 10.1093/molbev/msab306
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- Article
Population analysis of Legionella pneumophila reveals a basis for resistance to complement-mediated killing.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-27478-z
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- Article
high-throughput multiplexing and selection strategy to complete bacterial genomes.
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- GigaScience, 2021, v. 10, n. 12, p. 1, doi. 10.1093/gigascience/giab079
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ON THE JENSEN-SHANNON DIVERGENCE AND THE VARIATION DISTANCE FOR CATEGORICAL PROBABILITY DISTRIBUTIONS.
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- Kybernetika, 2021, v. 57, n. 6, p. 879, doi. 10.14736/kyb-2021-6-0879
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- Article
Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages.
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- PLoS Genetics, 2021, v. 17, n. 9, p. 1, doi. 10.1371/journal.pgen.1009829
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- Article
Adaptive Approximate Bayesian Computation Tolerance Selection.
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- Bayesian Analysis, 2021, v. 16, n. 2, p. 397, doi. 10.1214/20-BA1211
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- Article
The global dissemination of hospital clones of Enterococcus faecium.
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- Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00868-0
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- Article
Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting.
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- BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04079-7
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Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli.
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- 2021
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- Correction Notice
Genome evolution and the emergence of pathogenicity in avian Escherichia coli.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-20988-w
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- Article
Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae.
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- G3: Genes | Genomes | Genetics, 2021, v. 11, n. 2, p. 1, doi. 10.1093/g3journal/jkab019
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Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals.
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- Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-020-00825-3
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- Article
Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.
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- PLoS Biology, 2020, v. 18, n. 10, p. 1, doi. 10.1371/journal.pbio.3000878
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- Article
Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies.
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- BMC Genomics, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s12864-020-06990-4
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Producing polished prokaryotic pangenomes with the Panaroo pipeline.
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- Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02090-4
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- Article
Genomic signatures of domestication in Old World camels.
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- Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-1039-5
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- Article
gplas: a comprehensive tool for plasmid analysis using short-read graphs.
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- Bioinformatics, 2020, v. 36, n. 12, p. 3874, doi. 10.1093/bioinformatics/btaa233
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- Article
Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen.
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- Molecular Biology & Evolution, 2020, v. 37, n. 2, p. 417, doi. 10.1093/molbev/msz225
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- Article
Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.
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- 2019
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- Correction Notice
Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.
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- Frontiers in Microbiology, 2019, v. 10, p. 1, doi. 10.3389/fmicb.2019.02360
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- Article
Genome-wide epistasis and co-selection study using mutual information.
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- Nucleic Acids Research, 2019, v. 47, n. 18, p. e112, doi. 10.1093/nar/gkz656
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- Article
Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species.
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- Environmental Microbiology, 2019, v. 21, n. 8, p. 3046, doi. 10.1111/1462-2920.14702
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- Article
Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary.
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- Molecular Ecology Resources, 2019, v. 19, n. 4, p. 1015, doi. 10.1111/1755-0998.13020
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- Article
Fast hierarchical Bayesian analysis of population structure.
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- Nucleic Acids Research, 2019, v. 47, n. 11, p. 5539, doi. 10.1093/nar/gkz361
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- Article
Patterns of cross‐resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials.
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- Evolutionary Applications, 2019, v. 12, n. 5, p. 878, doi. 10.1111/eva.12762
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- Article
Bayesian inference of atomistic structure in functional materials.
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- NPJ Computational Materials, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1038/s41524-019-0175-2
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- Article
The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease.
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- Clinical Infectious Diseases, 2019, v. 68, n. 1, p. 61, doi. 10.1093/cid/ciy417
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- Article
pyseer: a comprehensive tool for microbial pangenome-wide association studies.
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- Bioinformatics, 2018, v. 34, n. 24, p. 4310, doi. 10.1093/bioinformatics/bty539
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- Article
ELFI: Engine for Likelihood-Free Inference.
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- Journal of Machine Learning Research, 2018, v. 19, n. 1-26, p. 1
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- Article
Bacmeta: simulator for genomic evolution in bacterial metapopulations.
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- Bioinformatics, 2018, v. 34, n. 13, p. 2308, doi. 10.1093/bioinformatics/bty093
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- Article
Kpax3: Bayesian bi-clustering of large sequence datasets.
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- Bioinformatics, 2018, v. 34, n. 12, p. 2132, doi. 10.1093/bioinformatics/bty056
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- Article
Weak Epistasis May Drive Adaptation in Recombining Bacteria.
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- Genetics, 2018, v. 208, n. 3, p. 1247, doi. 10.1534/genetics.117.300662
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- Article
Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism.
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- Genome Biology & Evolution, 2018, v. 10, n. 3, p. 763, doi. 10.1093/gbe/evy026
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Progression and mortality of interstitial lung disease in mixed connective tissue disease: a long-term observational nationwide cohort study.
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- Rheumatology, 2018, v. 57, n. 2, p. 255, doi. 10.1093/rheumatology/kex077
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- Article
Disease evolution in mixed connective tissue disease: results from a long-term nationwide prospective cohort study.
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- Arthritis Research & Therapy, 2017, v. 19, p. 1, doi. 10.1186/s13075-017-1494-7
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- Article
Marginal Pseudo-Likelihood Learning of Discrete Markov Network Structures.
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- Bayesian Analysis, 2017, v. 12, n. 4, p. 1195, doi. 10.1214/16-BA1032
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- Article