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Author: Jukka Corander

Rankings

  • All-time downloads: 45,029 (rank: 4,454 )
  • Categories:
    • bioinformatics: 8,635 (rank: 1,319 )
    • epidemiology: 434 (rank: 22,314 (tie) )
    • evolutionary biology: 4,696 (rank: 837 )
    • genetic and genomic medicine: 360 (rank: 10,139 (tie) )
    • genetics: 1,524 (rank: 13,025 (tie) )
    • genomics: 18,176 (rank: 818 )
    • microbiology: 11,204 (rank: 1,619 )

Downloads per author, site-wide

Preprints

Antimicrobial exposure in sexual networks drives divergent evolution in modern gonococci

genomics more details view paper
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    • Site-wide: 1,928
    • In genomics: 152
  • Year to date:
    • Site-wide: 83,350
  • Since beginning of last month:
    • Site-wide: 69,724

High-resolution sweep metagenomics using fast probabilistic inference

bioinformatics more details view paper
  • Downloaded 2,841 times
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    • Site-wide: 5,907
    • In bioinformatics: 586
  • Year to date:
    • Site-wide: 81,662
  • Since beginning of last month:
    • Site-wide: 39,141

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

genomics more details view paper
  • Downloaded 2,207 times
  • Download rankings, all-time:
    • Site-wide: 8,600
    • In genomics: 862
  • Year to date:
    • Site-wide: 115,905
  • Since beginning of last month:
    • Site-wide: 107,891

Efficient inference of recent and ancestral recombination within bacterial populations

bioinformatics more details view paper
  • Downloaded 1,953 times
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    • Site-wide: 10,292
    • In bioinformatics: 1,167
  • Year to date:
    • Site-wide: 79,357
  • Since beginning of last month:
    • Site-wide: 129,769

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

microbiology more details view paper
  • Downloaded 1,813 times
  • Download rankings, all-time:
    • Site-wide: 11,500
    • In microbiology: 672
  • Year to date:
    • Site-wide: 77,712
  • Since beginning of last month:
    • Site-wide: 97,028

Fast and flexible bacterial genomic epidemiology with PopPUNK

genomics more details view paper
  • Downloaded 1,662 times
  • Download rankings, all-time:
    • Site-wide: 13,082
    • In genomics: 1,308
  • Year to date:
    • Site-wide: 83,348
  • Since beginning of last month:
    • Site-wide: 129,915

Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

genomics more details view paper
  • Downloaded 1,482 times
  • Download rankings, all-time:
    • Site-wide: 15,651
    • In genomics: 1,530
  • Year to date:
    • Site-wide: 78,659
  • Since beginning of last month:
    • Site-wide: 154,265

Predicting evolution using frequency-dependent selection in bacterial populations

evolutionary biology more details view paper
  • Downloaded 1,337 times
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    • Site-wide: 18,313
    • In evolutionary biology: 620
  • Year to date:
    • Site-wide: 76,245
  • Since beginning of last month:
    • Site-wide: 82,832

Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli

microbiology more details view paper
  • Downloaded 1,259 times
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    • Site-wide: 20,046
    • In microbiology: 1,169
  • Year to date:
    • Site-wide: 133,585
  • Since beginning of last month:
    • Site-wide: 122,850

PANINI: Pangenome Neighbor Identification for Bacterial Populations

microbiology more details view paper
  • Downloaded 1,202 times
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    • Site-wide: 21,534
    • In microbiology: 1,252
  • Year to date:
    • Site-wide: 107,416
  • Since beginning of last month:
    • Site-wide: 37,331

Improved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions

microbiology more details view paper
  • Downloaded 1,159 times
  • Download rankings, all-time:
    • Site-wide: 22,736
    • In microbiology: 1,320
  • Year to date:
    • Site-wide: 33,641
  • Since beginning of last month:
    • Site-wide: 38,548

Genome-wide epistasis and co-selection study using mutual information

genomics more details view paper
  • Downloaded 1,103 times
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    • Site-wide: 24,508
    • In genomics: 2,242
  • Year to date:
    • Site-wide: 133,577
  • Since beginning of last month:
    • Site-wide: 144,133

Fast Hierarchical Bayesian Analysis of Population Structure

genomics more details view paper
  • Downloaded 1,071 times
  • Download rankings, all-time:
    • Site-wide: 25,658
    • In genomics: 2,317
  • Year to date:
    • Site-wide: 117,218
  • Since beginning of last month:
    • Site-wide: 135,469

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

bioinformatics more details view paper
  • Downloaded 968 times
  • Download rankings, all-time:
    • Site-wide: 29,811
    • In bioinformatics: 3,310
  • Year to date:
    • Site-wide: 128,032
  • Since beginning of last month:
    • Site-wide: 158,151

A comprehensive and high-quality collection of E. coli genomes and their genes

genomics more details view paper
  • Downloaded 874 times
  • Download rankings, all-time:
    • Site-wide: 34,606
    • In genomics: 2,901
  • Year to date:
    • Site-wide: 35,291
  • Since beginning of last month:
    • Site-wide: 40,733

Resolving outbreak dynamics using Approximate Bayesian Computation for stochastic birth-death models

bioinformatics more details view paper
  • Downloaded 870 times
  • Download rankings, all-time:
    • Site-wide: 34,834
    • In bioinformatics: 3,772
  • Year to date:
    • Site-wide: 137,244
  • Since beginning of last month:
    • Site-wide: 125,681

Genomic Epidemiology with Mixed Samples

bioinformatics more details view paper
  • Downloaded 853 times
  • Download rankings, all-time:
    • Site-wide: 35,838
    • In bioinformatics: 3,862
  • Year to date:
    • Site-wide: 23,204
  • Since beginning of last month:
    • Site-wide: 20,416

Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen

evolutionary biology more details view paper
  • Downloaded 811 times
  • Download rankings, all-time:
    • Site-wide: 38,561
    • In evolutionary biology: 1,716
  • Year to date:
    • Site-wide: 157,078
  • Since beginning of last month:
    • Site-wide: 158,900

Genomic determinants of sympatric speciation of the Mycobacterium tuberculosis complex across evolutionary timescales.

evolutionary biology more details view paper
  • Downloaded 806 times
  • Download rankings, all-time:
    • Site-wide: 38,928
    • In evolutionary biology: 1,737
  • Year to date:
    • Site-wide: 147,831
  • Since beginning of last month:
    • Site-wide: 157,308

The impact of host metapopulation structure on the population genetics of colonizing bacteria

genetics more details view paper
  • Downloaded 771 times
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    • Site-wide: 41,469
    • In genetics: 1,794
  • Year to date:
    • Site-wide: 131,679
  • Since beginning of last month:
    • Site-wide: 118,998

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

genetics more details view paper
  • Downloaded 753 times
  • Download rankings, all-time:
    • Site-wide: 42,928
    • In genetics: 1,859
  • Year to date:
    • Site-wide: 158,641
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    • Site-wide: 144,572

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions

microbiology more details view paper
  • Downloaded 747 times
  • Download rankings, all-time:
    • Site-wide: 43,366
    • In microbiology: 2,594
  • Year to date:
    • Site-wide: 78,041
  • Since beginning of last month:
    • Site-wide: 135,237

SuperDCA for genome-wide epistasis analysis

genomics more details view paper
  • Downloaded 716 times
  • Download rankings, all-time:
    • Site-wide: 46,058
    • In genomics: 3,566
  • Year to date:
    • Site-wide: 144,034
  • Since beginning of last month:
    • Site-wide: 107,750

One Health or Three? Transmission modelling of Klebsiella isolates reveals ecological barriers to transmission between humans, animals and the environment

microbiology more details view paper
  • Downloaded 683 times
  • Download rankings, all-time:
    • Site-wide: 49,194
    • In microbiology: 2,973
  • Year to date:
    • Site-wide: 9,591
  • Since beginning of last month:
    • Site-wide: 6,909

Co-evolutionary signals from Burkholderia pseudomallei genomics identify its survival strategies and highlight improving environmental health as prevention policy

microbiology more details view paper
  • Downloaded 656 times
  • Download rankings, all-time:
    • Site-wide: 51,897
    • In microbiology: 3,173
  • Year to date:
    • Site-wide: 16,845
  • Since beginning of last month:
    • Site-wide: 2,271

The contribution of genetic variation of Streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease

microbiology more details view paper
  • Downloaded 641 times
  • Download rankings, all-time:
    • Site-wide: 53,528
    • In microbiology: 3,299
  • Year to date:
    • Site-wide: 77,554
  • Since beginning of last month:
    • Site-wide: 51,151

Different evolutionary trends form the twilight zone of the bacterial pan-genome

genomics more details view paper
  • Downloaded 635 times
  • Download rankings, all-time:
    • Site-wide: 54,293
    • In genomics: 4,048
  • Year to date:
    • Site-wide: 10,804
  • Since beginning of last month:
    • Site-wide: 44,602

A high-throughput multiplexing and selection strategy to complete bacterial genomes

microbiology more details view paper
  • Downloaded 614 times
  • Download rankings, all-time:
    • Site-wide: 56,782
    • In microbiology: 3,524
  • Year to date:
    • Site-wide: 11,409
  • Since beginning of last month:
    • Site-wide: 18,637

On the identifiability of transmission dynamic models for infectious diseases

bioinformatics more details view paper
  • Downloaded 606 times
  • Download rankings, all-time:
    • Site-wide: 57,711
    • In bioinformatics: 5,699
  • Year to date:
    • Site-wide: 156,281
  • Since beginning of last month:
    • Site-wide: 157,854

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

genomics more details view paper
  • Downloaded 554 times
  • Download rankings, all-time:
    • Site-wide: 64,408
    • In genomics: 4,581
  • Year to date:
    • Site-wide: 128,894
  • Since beginning of last month:
    • Site-wide: 125,094

gplas: a comprehensive tool for plasmid analysis using short-read graphs

bioinformatics more details view paper
  • Downloaded 544 times
  • Download rankings, all-time:
    • Site-wide: 65,968
    • In bioinformatics: 6,309
  • Year to date:
    • Site-wide: 113,473
  • Since beginning of last month:
    • Site-wide: 102,042

Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis

microbiology more details view paper
  • Downloaded 543 times
  • Download rankings, all-time:
    • Site-wide: 66,097
    • In microbiology: 4,207
  • Year to date:
    • Site-wide: 141,234
  • Since beginning of last month:
    • Site-wide: 92,846

Designing ecologically-optimised vaccines using population genomics

evolutionary biology more details view paper
  • Downloaded 522 times
  • Download rankings, all-time:
    • Site-wide: 69,263
    • In evolutionary biology: 3,460
  • Year to date:
    • Site-wide: 133,339
  • Since beginning of last month:
    • Site-wide: 99,054

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

genomics more details view paper
  • Downloaded 515 times
  • Download rankings, all-time:
    • Site-wide: 70,419
    • In genomics: 4,849
  • Year to date:
    • Site-wide: 23,186
  • Since beginning of last month:
    • Site-wide: 119,879

Bacmeta: simulation for genomic evolution in bacterial metapopulations

genomics more details view paper
  • Downloaded 499 times
  • Download rankings, all-time:
    • Site-wide: 72,910
    • In genomics: 4,957
  • Year to date:
    • Site-wide: 161,568
  • Since beginning of last month:
    • Site-wide: 152,391

Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion

microbiology more details view paper
  • Downloaded 471 times
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    • Site-wide: 77,796
    • In microbiology: 5,134
  • Year to date:
    • Site-wide: 134,491
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    • Site-wide: 56,860

The effect of recombination on the evolution of a population of Neisseria meningitidis

evolutionary biology more details view paper
  • Downloaded 442 times
  • Download rankings, all-time:
    • Site-wide: 83,290
    • In evolutionary biology: 4,198
  • Year to date:
    • Site-wide: 59,820
  • Since beginning of last month:
    • Site-wide: 111,434

Transcriptome remodeling contributes to epidemic disease caused by the human pathogen Streptococcus pyogenes

evolutionary biology more details view paper
  • Downloaded 441 times
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    • Site-wide: 83,487
    • In evolutionary biology: 4,213
  • Year to date:
    • Site-wide: 154,858
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    • Site-wide: 158,241

Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data

epidemiology more details view paper
  • Downloaded 434 times
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    • Site-wide: 84,784
    • In epidemiology: 3,668
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    • Site-wide: 110,478
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    • Site-wide: 92,719

Cross-species evolutionary rewiring in the enteric bacterium Campylobacter

microbiology more details view paper
  • Downloaded 403 times
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    • Site-wide: 91,120
    • In microbiology: 6,179
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    • Site-wide: 21,844
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Population analysis of Legionella pneumophila reveals the basis of resistance to complement-mediated killing

microbiology more details view paper
  • Downloaded 369 times
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    • Site-wide: 98,792
    • In microbiology: 6,805
  • Year to date:
    • Site-wide: 58,217
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Mode and dynamics of vanA-type vancomycin-resistancedissemination in Dutch hospitals

genetic and genomic medicine more details view paper
  • Downloaded 360 times
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    • Site-wide: 100,931
    • In genetic and genomic medicine: 537
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    • Site-wide: 106,234
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    • Site-wide: 140,239

The binding mechanism of Streptococcus suis accessory virulence factor and adhesin SadP to globotetraosylceramide

microbiology more details view paper
  • Downloaded 359 times
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    • Site-wide: 101,193
    • In microbiology: 7,013
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    • Site-wide: 74,248
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    • Site-wide: 61,757

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

evolutionary biology more details view paper
  • Downloaded 337 times
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    • Site-wide: 106,631
    • In evolutionary biology: 5,323
  • Year to date:
    • Site-wide: 135,307
  • Since beginning of last month:
    • Site-wide: 153,148

Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.

microbiology more details view paper
  • Downloaded 285 times
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    • Site-wide: 119,963
    • In microbiology: 8,603
  • Year to date:
    • Site-wide: 153,659
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    • Site-wide: 135,535

Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation

genomics more details view paper
  • Downloaded 220 times
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    • Site-wide: 136,753
    • In genomics: 7,261
  • Year to date:
    • Site-wide: 50,857
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    • Site-wide: 4,113

Genome-wide association, prediction and heritability in bacteria

genomics more details view paper
  • Downloaded 174 times
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    • Site-wide: 147,736
    • In genomics: 7,563
  • Year to date:
    • Site-wide: 67,407
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    • Site-wide: 6,048

Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen Enterococcus faecium

genomics more details view paper
  • Downloaded 124 times
  • Download rankings, all-time:
    • Site-wide: 156,534
    • In genomics: 7,801
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    • Site-wide: 160,010
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    • Site-wide: 149,127

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