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Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2.
- Published in:
- Molecular Biology & Evolution, 2021, v. 38, n. 7, p. 2818, doi. 10.1093/molbev/msab072
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- Publication type:
- Article
Natural selection favoring more transmissible HIV detected in United States molecular transmission network.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-13723-z
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- Publication type:
- Article
Social and Genetic Networks of HIV-1 Transmission in New York City.
- Published in:
- PLoS Pathogens, 2017, v. 13, n. 1, p. 1, doi. 10.1371/journal.ppat.1006000
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- Publication type:
- Article
Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment.
- Published in:
- PLoS Computational Biology, 2021, v. 17, n. 9, p. 1, doi. 10.1371/journal.pcbi.1009336
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- Publication type:
- Article
AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters.
- Published in:
- Frontiers in Bioinformatics, 2024, p. 1, doi. 10.3389/fbinf.2024.1400003
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- Publication type:
- Article
ESTIMATING DIVERSIFICATION RATES: HOW USEFUL ARE DIVERGENCE TIMES?
- Published in:
- Evolution, 2011, v. 65, n. 2, p. 309, doi. 10.1111/j.1558-5646.2010.01159.x
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- Publication type:
- Article
Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype.
- Published in:
- Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.602296
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- Publication type:
- Article
When pigs fly: the avian origin of a ‘swine flu’.
- Published in:
- 2009
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- Publication type:
- Other
Phylogeographic analysis reveals an ancient East African origin of human herpes simplex virus 2 dispersal out-of-Africa.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33214-y
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- Publication type:
- Article
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31247-x
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- Publication type:
- Article
Increasing Capacity to Detect Clusters of Rapid HIV Transmission in Varied Populations—United States.
- Published in:
- Viruses (1999-4915), 2021, v. 13, n. 4, p. 577, doi. 10.3390/v13040577
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- Publication type:
- Article
Establishing a framework towards monitoring HCV microelimination among men who have sex with men living with HIV in Germany: A modeling analysis.
- Published in:
- PLoS ONE, 2022, v. 17, n. 5, p. 1, doi. 10.1371/journal.pone.0267853
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- Publication type:
- Article
HIV Migration Between Blood and Cerebrospinal Fluid or Semen Over Time.
- Published in:
- Journal of Infectious Diseases, 2014, v. 209, n. 10, p. 1642, doi. 10.1093/infdis/jit678
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- Publication type:
- Article
The Global Transmission Network of HIV-1.
- Published in:
- Journal of Infectious Diseases, 2014, v. 209, n. 2, p. 304, doi. 10.1093/infdis/jit524
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- Publication type:
- Article
Phylogenetic Relatedness of HIV-1 Donor and Recipient Populations.
- Published in:
- 2013
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- Publication type:
- Letter
A Challenge to the Ancient Origin of SIVagm Based on African Green Monkey Mitochondrial Genomes.
- Published in:
- PLoS Pathogens, 2007, v. 3, n. 7, p. e95, doi. 10.1371/journal.ppat.0030095
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- Publication type:
- Article
Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2.
- Published in:
- PLoS Computational Biology, 2009, v. 5, n. 5, p. 1, doi. 10.1371/journal.pcbi.1000377
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- Publication type:
- Article
StrainHub: a phylogenetic tool to construct pathogen transmission networks.
- Published in:
- Bioinformatics, 2020, v. 36, n. 3, p. 945, doi. 10.1093/bioinformatics/btz646
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- Publication type:
- Article
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences.
- Published in:
- Bioinformatics, 2019, v. 35, n. 11, p. 1852, doi. 10.1093/bioinformatics/bty921
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- Publication type:
- Article
Detecting Individual Sites Subject to Episodic Diversifying Selection.
- Published in:
- PLoS Genetics, 2012, v. 8, n. 7, p. 1, doi. 10.1371/journal.pgen.1002764
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- Publication type:
- Article
Author Correction: Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021.
- Published in:
- 2023
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- Publication type:
- Correction Notice
Impact of molecular sequence data completeness on HIV cluster detection and a network science approach to enhance detection.
- Published in:
- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-21924-8
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- Publication type:
- Article
Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021.
- Published in:
- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-19414-y
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- Publication type:
- Article
HIV co‐infection is associated with increased transmission risk in patients with chronic hepatitis C virus.
- Published in:
- Journal of Viral Hepatitis, 2019, v. 26, n. 11, p. 1351, doi. 10.1111/jvh.13160
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- Publication type:
- Article
Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York.
- Published in:
- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25168-4
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- Publication type:
- Article
The Relationship Between the Human Immunodeficiency Virus-1 Transmission Network and the HIV Care Continuum in Los Angeles County.
- Published in:
- Clinical Infectious Diseases, 2020, v. 71, n. 9, p. e384, doi. 10.1093/cid/ciaa114
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- Publication type:
- Article
A Glimpse Into the Origins of Genetic Diversity in the Severe Acute Respiratory Syndrome Coronavirus 2.
- Published in:
- 2020
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- Publication type:
- Editorial
Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021.
- Published in:
- Journal of Infectious Diseases, 2022, v. 226, n. 12, p. 2142, doi. 10.1093/infdis/jiac265
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- Publication type:
- Article
Addressing Ethical Challenges in US-Based HIV Phylogenetic Research.
- Published in:
- 2020
- By:
- Publication type:
- journal article
Growth of HIV-1 Molecular Transmission Clusters in New York City.
- Published in:
- 2018
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- Publication type:
- journal article
Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis.
- Published in:
- Journal of Infectious Diseases, 2015, v. 212, n. 6, p. 990, doi. 10.1093/infdis/jiv149
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- Publication type:
- Article
The role of socio-economic disparities in the relative success and persistence of SARS-CoV-2 variants in New York City in early 2021.
- Published in:
- PLoS Pathogens, 2024, v. 20, n. 6, p. 1, doi. 10.1371/journal.ppat.1012288
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- Publication type:
- Article
Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling.
- Published in:
- Virus Evolution, 2023, v. 9, n. 2, p. 1, doi. 10.1093/ve/vead069
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- Publication type:
- Article
Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage.
- Published in:
- Virus Evolution, 2019, v. 5, n. 2, p. N.PAG, doi. 10.1093/ve/vez041
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- Publication type:
- Article
Maintenance and reappearance of extremely divergent intra-host HIV-1 variants.
- Published in:
- Virus Evolution, 2018, v. 4, n. 2, p. 1, doi. 10.1093/ve/vey030
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- Publication type:
- Article
Interplay Between Geography and HIV Transmission Clusters in Los Angeles County.
- Published in:
- Open Forum Infectious Diseases, 2021, v. 8, n. 6, p. 1, doi. 10.1093/ofid/ofab211
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- Publication type:
- Article
Using HIV Networks to Inform Real Time Prevention Interventions.
- Published in:
- PLoS ONE, 2014, v. 9, n. 6, p. 1, doi. 10.1371/journal.pone.0098443
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- Publication type:
- Article
Using HIV Transmission Networks to Investigate Community Effects in HIV Prevention Trials.
- Published in:
- PLoS ONE, 2011, v. 6, n. 11, p. 1, doi. 10.1371/journal.pone.0027775
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- Publication type:
- Article
The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates.
- Published in:
- PLoS ONE, 2010, v. 5, n. 6, p. 1, doi. 10.1371/journal.pone.0011184
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- Publication type:
- Article
Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020.
- Published in:
- BMC Infectious Diseases, 2023, v. 23, n. 1, p. 1, doi. 10.1186/s12879-023-08423-5
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- Publication type:
- Article
Author Correction: Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context.
- Published in:
- 2021
- By:
- Publication type:
- Correction Notice
Author Correction: Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context.
- Published in:
- 2021
- By:
- Publication type:
- Correction Notice
Author Correction: Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context.
- Published in:
- 2021
- By:
- Publication type:
- Correction Notice
Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species.
- Published in:
- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2013, v. 7, n. 6, p. 1080, doi. 10.1038/ismej.2013.3
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- Publication type:
- Article
Relaxed Molecular Clocks, the Bias–Variance Trade-off, and the Quality of Phylogenetic Inference.
- Published in:
- Systematic Biology, 2010, v. 59, n. 1, p. 1, doi. 10.1093/sysbio/syp072
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- Publication type:
- Article
HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens.
- Published in:
- Molecular Biology & Evolution, 2018, v. 35, n. 7, p. 1812, doi. 10.1093/molbev/msy016
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- Publication type:
- Article
Gene-Wide Identification of Episodic Selection.
- Published in:
- Molecular Biology & Evolution, 2015, v. 32, n. 5, p. 1365, doi. 10.1093/molbev/msv035
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- Publication type:
- Article
Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection.
- Published in:
- Molecular Biology & Evolution, 2015, v. 32, n. 5, p. 1342, doi. 10.1093/molbev/msv022
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- Publication type:
- Article
RELAX: Detecting Relaxed Selection in a Phylogenetic Framework.
- Published in:
- Molecular Biology & Evolution, 2015, v. 32, n. 3, p. 820, doi. 10.1093/molbev/msu400
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- Publication type:
- Article
Evolutionary Origins of Human Herpes Simplex Viruses 1 and 2.
- Published in:
- Molecular Biology & Evolution, 2014, v. 31, n. 9, p. 2356, doi. 10.1093/molbev/msu185
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- Publication type:
- Article