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Author: Tanja Stadler

  • ORCiD: http://orcid.org/0000-0001-6431-535X
  • Most recently observed institution: ETH Zurich D-BSSE: Eidgenossische Technische Hochschule Zurich Department of Biosystems Science and Engineering

Rankings

  • All-time downloads: 148,373 (rank: 1,067 )
  • Categories:
    • bioinformatics: 2,880 (rank: 6,940 (tie) )
    • developmental biology: 561 (rank: 14,196 (tie) )
    • ecology: 264 (rank: 22,832 (tie) )
    • epidemiology: 106,396 (rank: 239 )
    • evolutionary biology: 15,485 (rank: 134 )
    • genetic and genomic medicine: 162 (rank: 18,612 (tie) )
    • genetics: 1,004 (rank: 20,079 (tie) )
    • genomics: 1,121 (rank: 27,516 (tie) )
    • health policy: 203 (rank: 2,248 (tie) )
    • immunology: 251 (rank: 44,138 (tie) )
    • infectious diseases: 12,941 (rank: 5,941 )
    • microbiology: 1,960 (rank: 11,627 (tie) )
    • paleontology: 627 (rank: 674 (tie) )
    • public and global health: 1,929 (rank: 3,703 (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 86,252 times
  • Download rankings, all-time:
    • Site-wide: 99
    • In epidemiology: 23
  • Year to date:
    • Site-wide: 956
  • Since beginning of last month:
    • Site-wide: 1,770

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

infectious diseases more details view paper
  • Downloaded 9,504 times
  • Download rankings, all-time:
    • Site-wide: 1,427
    • In infectious diseases: 442
  • Year to date:
    • Site-wide: 3,865
  • Since beginning of last month:
    • Site-wide: 19,186

Practical considerations for measuring the effective reproductive number, Rt

epidemiology more details view paper
  • Downloaded 8,923 times
  • Download rankings, all-time:
    • Site-wide: 1,560
    • In epidemiology: 204
  • Year to date:
    • Site-wide: 7,369
  • Since beginning of last month:
    • Site-wide: 13,668

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

epidemiology more details view paper
  • Downloaded 3,850 times
  • Download rankings, all-time:
    • Site-wide: 4,938
    • In epidemiology: 475
  • Year to date:
    • Site-wide: 6,996
  • Since beginning of last month:
    • Site-wide: 35,349

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

infectious diseases more details view paper
  • Downloaded 2,138 times
  • Download rankings, all-time:
    • Site-wide: 11,818
    • In infectious diseases: 1,714
  • Year to date:
    • Site-wide: 114,401
  • Since beginning of last month:
    • Site-wide: 113,778

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

public and global health more details view paper
  • Downloaded 2,044 times
  • Download rankings, all-time:
    • Site-wide: 12,598
    • In public and global health: 343
  • Year to date:
    • Site-wide: 4,745
  • Since beginning of last month:
    • Site-wide: 43,587

Joint inference of species histories and gene flow

evolutionary biology more details view paper
  • Downloaded 1,733 times
  • Download rankings, all-time:
    • Site-wide: 16,210
    • In evolutionary biology: 462
  • Year to date:
    • Site-wide: 18,282
  • Since beginning of last month:
    • Site-wide: 21,047

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

epidemiology more details view paper
  • Downloaded 1,722 times
  • Download rankings, all-time:
    • Site-wide: 16,365
    • In epidemiology: 1,123
  • Year to date:
    • Site-wide: 11,026
  • Since beginning of last month:
    • Site-wide: 180,376

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

evolutionary biology more details view paper
  • Downloaded 1,639 times
  • Download rankings, all-time:
    • Site-wide: 17,702
    • In evolutionary biology: 513
  • Year to date:
    • Site-wide: 69,941
  • Since beginning of last month:
    • Site-wide: 16,549

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

evolutionary biology more details view paper
  • Downloaded 1,563 times
  • Download rankings, all-time:
    • Site-wide: 19,045
    • In evolutionary biology: 558
  • Year to date:
    • Site-wide: 112,676
  • Since beginning of last month:
    • Site-wide: 51,506

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

evolutionary biology more details view paper
  • Downloaded 1,515 times
  • Download rankings, all-time:
    • Site-wide: 20,011
    • In evolutionary biology: 594
  • Year to date:
    • Site-wide: 101,951
  • Since beginning of last month:
    • Site-wide: 100,950

Estimating epidemic incidence and prevalence from genomic data

epidemiology more details view paper
  • Downloaded 1,511 times
  • Download rankings, all-time:
    • Site-wide: 20,100
    • In epidemiology: 1,294
  • Year to date:
    • Site-wide: 133,964
  • Since beginning of last month:
    • Site-wide: 80,078

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

epidemiology more details view paper
  • Downloaded 1,232 times
  • Download rankings, all-time:
    • Site-wide: 27,841
    • In epidemiology: 1,623
  • Year to date:
    • Site-wide: 72,827
  • Since beginning of last month:
    • Site-wide: 41,922

Within-patient genetic diversity of SARS-CoV-2

genomics more details view paper
  • Downloaded 1,189 times
  • Download rankings, all-time:
    • Site-wide: 29,420
    • In genomics: 2,549
  • Year to date:
    • Site-wide: 78,691
  • Since beginning of last month:
    • Site-wide: 29,061

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

epidemiology more details view paper
  • Downloaded 1,142 times
  • Download rankings, all-time:
    • Site-wide: 31,368
    • In epidemiology: 1,758
  • Year to date:
    • Site-wide: 160,073
  • Since beginning of last month:
    • Site-wide: 46,600

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 1,065 times
  • Download rankings, all-time:
    • Site-wide: 34,894
    • In microbiology: 1,948
  • Year to date:
    • Site-wide: 110,244
  • Since beginning of last month:
    • Site-wide: None

The heritability of pathogen traits - definitions and estimators

genetics more details view paper
  • Downloaded 1,024 times
  • Download rankings, all-time:
    • Site-wide: 37,071
    • In genetics: 1,438
  • Year to date:
    • Site-wide: 155,797
  • Since beginning of last month:
    • Site-wide: 131,635

The Structured Coalescent and its Approximations

evolutionary biology more details view paper
  • Downloaded 985 times
  • Download rankings, all-time:
    • Site-wide: 39,353
    • In evolutionary biology: 1,492
  • Year to date:
    • Site-wide: 173,455
  • Since beginning of last month:
    • Site-wide: 80,996

Bayesian Inference of Species Networks from Multilocus Sequence Data

evolutionary biology more details view paper
  • Downloaded 981 times
  • Download rankings, all-time:
    • Site-wide: 39,604
    • In evolutionary biology: 1,525
  • Year to date:
    • Site-wide: 170,167
  • Since beginning of last month:
    • Site-wide: 32,913

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

evolutionary biology more details view paper
  • Downloaded 943 times
  • Download rankings, all-time:
    • Site-wide: 42,087
    • In evolutionary biology: 1,671
  • Year to date:
    • Site-wide: 133,749
  • Since beginning of last month:
    • Site-wide: 74,789

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

microbiology more details view paper
  • Downloaded 940 times
  • Download rankings, all-time:
    • Site-wide: 42,268
    • In microbiology: 2,398
  • Year to date:
    • Site-wide: 148,968
  • Since beginning of last month:
    • Site-wide: 165,693

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

bioinformatics more details view paper
  • Downloaded 923 times
  • Download rankings, all-time:
    • Site-wide: 43,484
    • In bioinformatics: 4,429
  • Year to date:
    • Site-wide: 99,837
  • Since beginning of last month:
    • Site-wide: 85,256

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

evolutionary biology more details view paper
  • Downloaded 879 times
  • Download rankings, all-time:
    • Site-wide: 46,852
    • In evolutionary biology: 1,897
  • Year to date:
    • Site-wide: 68,449
  • Since beginning of last month:
    • Site-wide: 158,738

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

epidemiology more details view paper
  • Downloaded 744 times
  • Download rankings, all-time:
    • Site-wide: 60,093
    • In epidemiology: 2,946
  • Year to date:
    • Site-wide: 71,152
  • Since beginning of last month:
    • Site-wide: 143,925

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

infectious diseases more details view paper
  • Downloaded 673 times
  • Download rankings, all-time:
    • Site-wide: 69,204
    • In infectious diseases: 4,341
  • Year to date:
    • Site-wide: 88,061
  • Since beginning of last month:
    • Site-wide: 150,000

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

evolutionary biology more details view paper
  • Downloaded 671 times
  • Download rankings, all-time:
    • Site-wide: 69,559
    • In evolutionary biology: 3,023
  • Year to date:
    • Site-wide: 127,035
  • Since beginning of last month:
    • Site-wide: 82,801

TiDeTree: A Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data

developmental biology more details view paper
  • Downloaded 661 times
  • Download rankings, all-time:
    • Site-wide: 71,012
    • In developmental biology: 2,034
  • Year to date:
    • Site-wide: 6,857
  • Since beginning of last month:
    • Site-wide: 26,591

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

paleontology more details view paper
  • Downloaded 642 times
  • Download rankings, all-time:
    • Site-wide: 73,823
    • In paleontology: 131
  • Year to date:
    • Site-wide: 201,594
  • Since beginning of last month:
    • Site-wide: 132,778

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

evolutionary biology more details view paper
  • Downloaded 619 times
  • Download rankings, all-time:
    • Site-wide: 77,480
    • In evolutionary biology: 3,408
  • Year to date:
    • Site-wide: 161,959
  • Since beginning of last month:
    • Site-wide: 84,449

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

evolutionary biology more details view paper
  • Downloaded 575 times
  • Download rankings, all-time:
    • Site-wide: 84,971
    • In evolutionary biology: 3,947
  • Year to date:
    • Site-wide: 126,957
  • Since beginning of last month:
    • Site-wide: 51,470

SARS-CoV-2 vaccine Alpha and Delta variant breakthrough infections are rare and mild, but happen relative early after vaccination

infectious diseases more details view paper
  • Downloaded 564 times
  • Download rankings, all-time:
    • Site-wide: 87,106
    • In infectious diseases: 4,900
  • Year to date:
    • Site-wide: 26,156
  • Since beginning of last month:
    • Site-wide: 95,066

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

evolutionary biology more details view paper
  • Downloaded 556 times
  • Download rankings, all-time:
    • Site-wide: 88,666
    • In evolutionary biology: 3,966
  • Year to date:
    • Site-wide: 200,288
  • Since beginning of last month:
    • Site-wide: 125,046

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

evolutionary biology more details view paper
  • Downloaded 547 times
  • Download rankings, all-time:
    • Site-wide: 90,361
    • In evolutionary biology: 4,113
  • Year to date:
    • Site-wide: 183,275
  • Since beginning of last month:
    • Site-wide: 80,954

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

evolutionary biology more details view paper
  • Downloaded 542 times
  • Download rankings, all-time:
    • Site-wide: 91,251
    • In evolutionary biology: 4,283
  • Year to date:
    • Site-wide: 87,670
  • Since beginning of last month:
    • Site-wide: 42,515

Phylodynamic model adequacy using posterior predictive simulations

bioinformatics more details view paper
  • Downloaded 539 times
  • Download rankings, all-time:
    • Site-wide: 91,975
    • In bioinformatics: 7,907
  • Year to date:
    • Site-wide: 196,329
  • Since beginning of last month:
    • Site-wide: 78,864

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

evolutionary biology more details view paper
  • Downloaded 530 times
  • Download rankings, all-time:
    • Site-wide: 93,776
    • In evolutionary biology: 4,249
  • Year to date:
    • Site-wide: 190,080
  • Since beginning of last month:
    • Site-wide: 61,776

Phylodynamics on local sexual contact networks

epidemiology more details view paper
  • Downloaded 520 times
  • Download rankings, all-time:
    • Site-wide: 96,014
    • In epidemiology: 4,081
  • Year to date:
    • Site-wide: 207,525
  • Since beginning of last month:
    • Site-wide: 101,344

The probability distribution of the reconstructed phylogenetic tree with occurrence data

evolutionary biology more details view paper
  • Downloaded 505 times
  • Download rankings, all-time:
    • Site-wide: 99,230
    • In evolutionary biology: 4,457
  • Year to date:
    • Site-wide: 195,963
  • Since beginning of last month:
    • Site-wide: 152,847

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

epidemiology more details view paper
  • Downloaded 488 times
  • Download rankings, all-time:
    • Site-wide: 103,149
    • In epidemiology: 4,983
  • Year to date:
    • Site-wide: 48,516
  • 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 479 times
  • Download rankings, all-time:
    • Site-wide: 105,244
    • In bioinformatics: 8,773
  • Year to date:
    • Site-wide: 194,804
  • Since beginning of last month:
    • Site-wide: 127,124

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

epidemiology more details view paper
  • Downloaded 479 times
  • Download rankings, all-time:
    • Site-wide: 105,261
    • In epidemiology: 4,464
  • Year to date:
    • Site-wide: 166,540
  • Since beginning of last month:
    • Site-wide: 75,812

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

bioinformatics more details view paper
  • Downloaded 476 times
  • Download rankings, all-time:
    • Site-wide: 105,861
    • In bioinformatics: 8,902
  • Year to date:
    • Site-wide: 121,533
  • Since beginning of last month:
    • Site-wide: 165,983

Tuberculosis outbreak investigation using phylodynamic analysis

epidemiology more details view paper
  • Downloaded 440 times
  • Download rankings, all-time:
    • Site-wide: 114,611
    • In epidemiology: 4,738
  • Year to date:
    • Site-wide: 207,900
  • Since beginning of last month:
    • Site-wide: 154,072

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

evolutionary biology more details view paper
  • Downloaded 415 times
  • Download rankings, all-time:
    • Site-wide: 121,063
    • In evolutionary biology: 5,420
  • Year to date:
    • Site-wide: 209,131
  • Since beginning of last month:
    • Site-wide: 167,363

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

evolutionary biology more details view paper
  • Downloaded 392 times
  • Download rankings, all-time:
    • Site-wide: 127,441
    • In evolutionary biology: 5,802
  • Year to date:
    • Site-wide: 146,429
  • Since beginning of last month:
    • Site-wide: 128,505

SARS-CoV-2 in schools: genome analysis shows that concurrent cases in the second and third wave were often unconnected

infectious diseases more details view paper
  • Downloaded 334 times
  • Download rankings, all-time:
    • Site-wide: 144,638
    • In infectious diseases: 6,687
  • Year to date:
    • Site-wide: 21,139
  • Since beginning of last month:
    • Site-wide: 98,317

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

bioinformatics more details view paper
  • Downloaded 332 times
  • Download rankings, all-time:
    • Site-wide: 145,319
    • In bioinformatics: 11,323
  • Year to date:
    • Site-wide: 96,029
  • Since beginning of last month:
    • Site-wide: 65,571

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

evolutionary biology more details view paper
  • Downloaded 312 times
  • Download rankings, all-time:
    • Site-wide: 151,151
    • In evolutionary biology: 6,786
  • Year to date:
    • Site-wide: 163,628
  • Since beginning of last month:
    • Site-wide: 135,847

The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies

bioinformatics more details view paper
  • Downloaded 292 times
  • Download rankings, all-time:
    • Site-wide: 156,949
    • In bioinformatics: 12,017
  • Year to date:
    • Site-wide: 73,893
  • Since beginning of last month:
    • Site-wide: 117,805

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus H5N8 in Europe

ecology more details view paper
  • Downloaded 284 times
  • Download rankings, all-time:
    • Site-wide: 159,565
    • In ecology: 4,946
  • Year to date:
    • Site-wide: 62,472
  • Since beginning of last month:
    • Site-wide: 97,417

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

immunology more details view paper
  • Downloaded 271 times
  • Download rankings, all-time:
    • Site-wide: 163,325
    • In immunology: 4,984
  • Year to date:
    • Site-wide: 188,156
  • Since beginning of last month:
    • Site-wide: 106,006

The methodologies to assess the effects of non-pharmaceutical interventions during COVID-19: a systematic review

health policy more details view paper
  • Downloaded 264 times
  • Download rankings, all-time:
    • Site-wide: 165,320
    • In health policy: 438
  • Year to date:
    • Site-wide: 30,529
  • Since beginning of last month:
    • Site-wide: 21,970

A phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits

genetic and genomic medicine more details view paper
  • Downloaded 175 times
  • Download rankings, all-time:
    • Site-wide: 187,841
    • In genetic and genomic medicine: 1,332
  • Year to date:
    • Site-wide: 122,378
  • Since beginning of last month:
    • Site-wide: None

estimateR: An R package to estimate and monitor the effective reproductive number

epidemiology more details view paper
  • Downloaded 173 times
  • Download rankings, all-time:
    • Site-wide: 188,211
    • In epidemiology: 7,568
  • Year to date:
    • Site-wide: 55,088
  • Since beginning of last month:
    • Site-wide: 19,790

Robust phylodynamic analysis of genetic sequencing data from structured populations

evolutionary biology more details view paper
  • Downloaded 108 times
  • Download rankings, all-time:
    • Site-wide: 200,002
    • In evolutionary biology: 8,592
  • Year to date:
    • Site-wide: 89,342
  • Since beginning of last month:
    • Site-wide: 173,552

Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania

infectious diseases more details view paper
  • Downloaded 74 times
  • Download rankings, all-time:
    • Site-wide: 205,232
    • In infectious diseases: None
  • Year to date:
    • Site-wide: 123,275
  • Since beginning of last month:
    • Site-wide: 10,964

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