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Author: Tanja Stadler

Rankings

  • All-time downloads: 128,596 (rank: 795 )
  • Categories:
    • bioinformatics: 2,119 (rank: 7,628 (tie) )
    • epidemiology: 98,607 (rank: 145 )
    • evolutionary biology: 13,199 (rank: 123 )
    • genetics: 937 (rank: 17,302 (tie) )
    • genomics: 931 (rank: 25,236 (tie) )
    • immunology: 180 (rank: 33,598 (tie) )
    • infectious diseases: 9,734 (rank: 5,343 )
    • microbiology: 1,716 (rank: 9,548 (tie) )
    • paleontology: 594 (rank: 481 (tie) )
    • public and global health: 579 (rank: 6,222 (tie) )

Downloads per author, site-wide

Preprints

Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

epidemiology more details view paper
  • Downloaded 81,832 times
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    • Site-wide: 67
    • In epidemiology: 14
  • Year to date:
    • Site-wide: 157
  • Since beginning of last month:
    • Site-wide: 1,107

Practical considerations for measuring the effective reproductive number, Rt

epidemiology more details view paper
  • Downloaded 7,926 times
  • Download rankings, all-time:
    • Site-wide: 1,271
    • In epidemiology: 159
  • Year to date:
    • Site-wide: 2,244
  • Since beginning of last month:
    • Site-wide: 13,755

Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples

infectious diseases more details view paper
  • Downloaded 7,741 times
  • Download rankings, all-time:
    • Site-wide: 1,312
    • In infectious diseases: 377
  • Year to date:
    • Site-wide: 252
  • Since beginning of last month:
    • Site-wide: 6,450

Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2

epidemiology more details view paper
  • Downloaded 2,701 times
  • Download rankings, all-time:
    • Site-wide: 5,604
    • In epidemiology: 498
  • Year to date:
    • Site-wide: 1,471
  • Since beginning of last month:
    • Site-wide: 9,855

The origin and early spread of SARS-CoV-2 in Europe

infectious diseases more details view paper
  • Downloaded 1,984 times
  • Download rankings, all-time:
    • Site-wide: 8,856
    • In infectious diseases: 1,270
  • Year to date:
    • Site-wide: 31,902
  • Since beginning of last month:
    • Site-wide: 102,683

Estimating epidemic incidence and prevalence from genomic data

epidemiology more details view paper
  • Downloaded 1,403 times
  • Download rankings, all-time:
    • Site-wide: 14,770
    • In epidemiology: 1,005
  • Year to date:
    • Site-wide: 68,396
  • Since beginning of last month:
    • Site-wide: 58,961

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

evolutionary biology more details view paper
  • Downloaded 1,381 times
  • Download rankings, all-time:
    • Site-wide: 15,120
    • In evolutionary biology: 517
  • Year to date:
    • Site-wide: 20,284
  • Since beginning of last month:
    • Site-wide: 29,590

Fast and Robust Inference of Phylogenetic Ornstein-Uhlenbeck Models Using Parallel Likelihood Calculation

evolutionary biology more details view paper
  • Downloaded 1,379 times
  • Download rankings, all-time:
    • Site-wide: 15,156
    • In evolutionary biology: 518
  • Year to date:
    • Site-wide: 25,839
  • Since beginning of last month:
    • Site-wide: 67,705

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

evolutionary biology more details view paper
  • Downloaded 1,369 times
  • Download rankings, all-time:
    • Site-wide: 15,336
    • In evolutionary biology: 525
  • Year to date:
    • Site-wide: 52,549
  • Since beginning of last month:
    • Site-wide: 82,192

Joint inference of species histories and gene flow

evolutionary biology more details view paper
  • Downloaded 1,182 times
  • Download rankings, all-time:
    • Site-wide: 19,072
    • In evolutionary biology: 689
  • Year to date:
    • Site-wide: 16,680
  • Since beginning of last month:
    • Site-wide: None

The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology

epidemiology more details view paper
  • Downloaded 1,052 times
  • Download rankings, all-time:
    • Site-wide: 22,660
    • In epidemiology: 1,346
  • Year to date:
    • Site-wide: 100,549
  • Since beginning of last month:
    • Site-wide: 75,200

Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland

epidemiology more details view paper
  • Downloaded 1,025 times
  • Download rankings, all-time:
    • Site-wide: 23,518
    • In epidemiology: 1,384
  • Year to date:
    • Site-wide: 3,007
  • Since beginning of last month:
    • Site-wide: 51,921

Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data

epidemiology more details view paper
  • Downloaded 977 times
  • Download rankings, all-time:
    • Site-wide: 25,242
    • In epidemiology: 1,453
  • Year to date:
    • Site-wide: 20,704
  • Since beginning of last month:
    • Site-wide: 28,420

The heritability of pathogen traits - definitions and estimators

genetics more details view paper
  • Downloaded 937 times
  • Download rankings, all-time:
    • Site-wide: 26,848
    • In genetics: 1,231
  • Year to date:
    • Site-wide: 101,600
  • Since beginning of last month:
    • Site-wide: 73,231

Within-patient genetic diversity of SARS-CoV-2

genomics more details view paper
  • Downloaded 931 times
  • Download rankings, all-time:
    • Site-wide: 27,067
    • In genomics: 2,468
  • Year to date:
    • Site-wide: 11,402
  • Since beginning of last month:
    • Site-wide: 44,687

Bayesian Inference of Species Networks from Multilocus Sequence Data

evolutionary biology more details view paper
  • Downloaded 912 times
  • Download rankings, all-time:
    • Site-wide: 27,820
    • In evolutionary biology: 1,193
  • Year to date:
    • Site-wide: 119,502
  • Since beginning of last month:
    • Site-wide: None

The Structured Coalescent and its Approximations

evolutionary biology more details view paper
  • Downloaded 905 times
  • Download rankings, all-time:
    • Site-wide: 28,161
    • In evolutionary biology: 1,213
  • Year to date:
    • Site-wide: 107,246
  • Since beginning of last month:
    • Site-wide: None

Clinical extended-spectrum beta-lactamase antibiotic resistance plasmids have diverse transfer rates and can spread in the absence of antibiotic selection

microbiology more details view paper
  • Downloaded 902 times
  • Download rankings, all-time:
    • Site-wide: 28,285
    • In microbiology: 1,690
  • Year to date:
    • Site-wide: 41,777
  • Since beginning of last month:
    • Site-wide: 2,903

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

microbiology more details view paper
  • Downloaded 814 times
  • Download rankings, all-time:
    • Site-wide: 32,681
    • In microbiology: 1,971
  • Year to date:
    • Site-wide: 90,915
  • Since beginning of last month:
    • Site-wide: 30,420

A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates

evolutionary biology more details view paper
  • Downloaded 813 times
  • Download rankings, all-time:
    • Site-wide: 32,722
    • In evolutionary biology: 1,477
  • Year to date:
    • Site-wide: 93,082
  • Since beginning of last month:
    • Site-wide: None

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

bioinformatics more details view paper
  • Downloaded 781 times
  • Download rankings, all-time:
    • Site-wide: 34,670
    • In bioinformatics: 3,824
  • Year to date:
    • Site-wide: 63,988
  • Since beginning of last month:
    • Site-wide: 91,176

Improved multi-type birth-death phylodynamic inference in BEAST 2

evolutionary biology more details view paper
  • Downloaded 617 times
  • Download rankings, all-time:
    • Site-wide: 47,336
    • In evolutionary biology: 2,344
  • Year to date:
    • Site-wide: 39,199
  • Since beginning of last month:
    • Site-wide: 62,315

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process

paleontology more details view paper
  • Downloaded 594 times
  • Download rankings, all-time:
    • Site-wide: 49,623
    • In paleontology: 97
  • Year to date:
    • Site-wide: 150,974
  • Since beginning of last month:
    • Site-wide: 61,356

Wastewater-based estimation of the effective reproductive number of SARS-CoV-2

public and global health more details view paper
  • Downloaded 579 times
  • Download rankings, all-time:
    • Site-wide: 51,368
    • In public and global health: 771
  • Year to date:
    • Site-wide: 6,878
  • Since beginning of last month:
    • Site-wide: 16,776

Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models

evolutionary biology more details view paper
  • Downloaded 564 times
  • Download rankings, all-time:
    • Site-wide: 53,059
    • In evolutionary biology: 2,704
  • Year to date:
    • Site-wide: 137,143
  • Since beginning of last month:
    • Site-wide: None

Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

evolutionary biology more details view paper
  • Downloaded 539 times
  • Download rankings, all-time:
    • Site-wide: 55,985
    • In evolutionary biology: 2,891
  • Year to date:
    • Site-wide: 116,039
  • Since beginning of last month:
    • Site-wide: 57,917

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

evolutionary biology more details view paper
  • Downloaded 499 times
  • Download rankings, all-time:
    • Site-wide: 61,170
    • In evolutionary biology: 3,186
  • Year to date:
    • Site-wide: 151,926
  • Since beginning of last month:
    • Site-wide: None

MASCOT: Parameter and state inference under the marginal structured coalescent approximation

evolutionary biology more details view paper
  • Downloaded 487 times
  • Download rankings, all-time:
    • Site-wide: 62,815
    • In evolutionary biology: 3,274
  • Year to date:
    • Site-wide: 148,102
  • Since beginning of last month:
    • Site-wide: None

Phylodynamic model adequacy using posterior predictive simulations

bioinformatics more details view paper
  • Downloaded 481 times
  • Download rankings, all-time:
    • Site-wide: 63,654
    • In bioinformatics: 6,252
  • Year to date:
    • Site-wide: 127,141
  • Since beginning of last month:
    • Site-wide: 56,290

Parallel Likelihood Calculation for Phylogenetic Comparative Models: the SPLITT C++ Library

evolutionary biology more details view paper
  • Downloaded 479 times
  • Download rankings, all-time:
    • Site-wide: 64,017
    • In evolutionary biology: 3,332
  • Year to date:
    • Site-wide: 117,127
  • Since beginning of last month:
    • Site-wide: None

Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data

epidemiology more details view paper
  • Downloaded 470 times
  • Download rankings, all-time:
    • Site-wide: 65,327
    • In epidemiology: 2,876
  • Year to date:
    • Site-wide: 32,780
  • Since beginning of last month:
    • Site-wide: 48,979

Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

evolutionary biology more details view paper
  • Downloaded 466 times
  • Download rankings, all-time:
    • Site-wide: 65,990
    • In evolutionary biology: 3,447
  • Year to date:
    • Site-wide: 132,605
  • Since beginning of last month:
    • Site-wide: 66,593

Phylodynamics on local sexual contact networks

epidemiology more details view paper
  • Downloaded 457 times
  • Download rankings, all-time:
    • Site-wide: 67,330
    • In epidemiology: 2,950
  • Year to date:
    • Site-wide: 144,631
  • Since beginning of last month:
    • Site-wide: 32,813

The probability distribution of the reconstructed phylogenetic tree with occurrence data

evolutionary biology more details view paper
  • Downloaded 450 times
  • Download rankings, all-time:
    • Site-wide: 68,461
    • In evolutionary biology: 3,565
  • Year to date:
    • Site-wide: 103,048
  • Since beginning of last month:
    • Site-wide: None

Accurate detection of HIV transmission clusters from phylogenetic trees using a multi-state birth-death model

bioinformatics more details view paper
  • Downloaded 421 times
  • Download rankings, all-time:
    • Site-wide: 73,196
    • In bioinformatics: 6,896
  • Year to date:
    • Site-wide: 149,203
  • Since beginning of last month:
    • Site-wide: None

External introductions helped drive and sustain the high incidence of HIV-1 in rural KwaZulu-Natal, South Africa

epidemiology more details view paper
  • Downloaded 387 times
  • Download rankings, all-time:
    • Site-wide: 79,349
    • In epidemiology: 3,373
  • Year to date:
    • Site-wide: 119,569
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    • Site-wide: None

Tuberculosis outbreak investigation using phylodynamic analysis

epidemiology more details view paper
  • Downloaded 377 times
  • Download rankings, all-time:
    • Site-wide: 81,282
    • In epidemiology: 3,442
  • Year to date:
    • Site-wide: 147,993
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    • Site-wide: None

Ignoring fossil age uncertainty leads to inaccurate topology and divergence times in time calibrated tree inference

evolutionary biology more details view paper
  • Downloaded 366 times
  • Download rankings, all-time:
    • Site-wide: 83,346
    • In evolutionary biology: 4,343
  • Year to date:
    • Site-wide: 93,907
  • Since beginning of last month:
    • Site-wide: 94,437

A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

evolutionary biology more details view paper
  • Downloaded 355 times
  • Download rankings, all-time:
    • Site-wide: 85,620
    • In evolutionary biology: 4,457
  • Year to date:
    • Site-wide: 32,430
  • Since beginning of last month:
    • Site-wide: 107,812

The influence of the phylogenetic inference pipeline on murine antibody repertoire sequencing data following viral infection

bioinformatics more details view paper
  • Downloaded 323 times
  • Download rankings, all-time:
    • Site-wide: 92,433
    • In bioinformatics: 8,165
  • Year to date:
    • Site-wide: 87,927
  • Since beginning of last month:
    • Site-wide: 97,346

The ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data

evolutionary biology more details view paper
  • Downloaded 269 times
  • Download rankings, all-time:
    • Site-wide: 104,769
    • In evolutionary biology: 5,356
  • Year to date:
    • Site-wide: 139,697
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    • Site-wide: None

Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection

immunology more details view paper
  • Downloaded 180 times
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    • Site-wide: 126,753
    • In immunology: 3,704
  • Year to date:
    • Site-wide: 139,882
  • Since beginning of last month:
    • Site-wide: 97,365

Joint inference of migration and reassortment patterns for viruses with segment genomes

evolutionary biology more details view paper
  • Downloaded 167 times
  • Download rankings, all-time:
    • Site-wide: 129,722
    • In evolutionary biology: 6,446
  • Year to date:
    • Site-wide: 37,352
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    • Site-wide: None

Estimating disease spread using structured coalescent andbirth-death models: A quantitative comparison

bioinformatics more details view paper
  • Downloaded 113 times
  • Download rankings, all-time:
    • Site-wide: 141,418
    • In bioinformatics: 10,961
  • Year to date:
    • Site-wide: 75,450
  • Since beginning of last month:
    • Site-wide: 98,680

DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2

infectious diseases more details view paper
  • Downloaded 9 times
  • Download rankings, all-time:
    • Site-wide: 152,683
    • In infectious diseases: 5,961
  • Year to date:
    • Site-wide: 152,570
  • Since beginning of last month:
    • Site-wide: 8,672

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