publication . Article . 2017

Emerging concepts of data integration in pathogen phylodynamics

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe;
Open Access English
  • Published: 01 Jan 2017
Abstract
Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise in...
Subjects
free text keywords: Genetics, Ecology, Evolution, Behavior and Systematics, Data integration, computer.software_genre, computer, Pathogen, Virology, Zoology, Evolutionary biology, Biology, Virus diseases, Biological evolution, Phylogenetics, Viral phylodynamics, The following are online-only papers that are freely available as part of Issue 66(1) online.
Funded by
EC| VIROGENESIS
Project
VIROGENESIS
Virus discovery and epidemic tracing from high throughput metagenomic sequencing
  • Funder: European Commission (EC)
  • Project Code: 634650
  • Funding stream: H2020 | RIA
,
NIH| BAYESIAN MODELING AND DATA INTEGRATION IN INFECTIOUS DISEASE PHYLODYNAMICS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI107034-05
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
EC| PREDEMICS
Project
PREDEMICS
Preparedness, Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidisciplinary Approaches
  • Funder: European Commission (EC)
  • Project Code: 278433
  • Funding stream: FP7 | SP1 | HEALTH
,
NIH| Genomics, GPUs, and Next Generation Computational Statistics
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG006139-06
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
EC| VIRALPHYLOGEOGRAPHY
Project
VIRALPHYLOGEOGRAPHY
Evolutionary reconstruction of viral spread in time and space
  • Funder: European Commission (EC)
  • Project Code: 260864
  • Funding stream: FP7 | SP2 | ERC
157 references, page 1 of 11

Alizon S.Fraser C.2013.Within-host and between-host evolutionary rates across the HIV-1 genome.Retrovirology 10:49.23639104 [OpenAIRE] [PubMed]

Alizon S.von Wyl V.Stadler T.Kouyos R.D.Yerly S.Hirschel B.Boni J.Shah C.Klimkait T.Furrer H.Rauch A.Vernazza P.L.Bernasconi E.Battegay M.Bürgisser P.Telenti A.Günthard H.F.Bonhoeffer S.the Swiss Cohort Study.2 Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load.PLoS Path.6:e1001123.

Ayres D.L.Darling A.Zwickl D.J.Beerli P.Holder M.T.Lewis P.O.Huelsenbeck J.P.Ronquist F.Swofford D.L.Cummings M.P.Rambaut A.Suchard M.A.2 BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.Syst. Biol.61:170–173.21963610 [OpenAIRE] [PubMed]

Baele G.Lemey P.2 Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency.Bioinformatics 29:1970–1979.23766415 [PubMed]

Bahl J.Nelson M.I.Chan K.H.Chen R.Vijaykrishna D.Halpin R.A.Stockwell T.B.Lin X.Wentworth D.E.Ghedin E.Guan Y.Peiris J.S.M Riley S.Rambaut A.Holmes E.C.Smith G.J.D.2 Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans.Proc. Natl. Acad. Sci. USA 108:19359–19364.

Baize S.Pannetier D.Oestereich L.Rieger T.Koivogui L.Magassouba N.Soropogui B.Sow M.S.Keïta S.De Clerck H.Tiffany A.Dominguez G.Loua M.TraoréA.KoliéM.Malano E.R.Heleze E.Bocquin A.Mély S.Raoul H.Caro V.Cadar D.Gabriel M.Pahlmann M.Tappe D.Schmidt-Chanasit J.Impouma B.Diallo A.K.Formenty P.Van Herp M.Günther S.2 Emergence of Zaire ebola virus disease in Guinea.N. Engl. J. Med.371:1418–1425.24738640 [OpenAIRE] [PubMed]

Barton N.H.Etheridge A.M.Véber A.2 Modelling evolution in a spatial continuum.J. Stat. Mech.P01002.

Bedford T.Riley S.Barr I.G.Broor S.Chadha M.Cox N.J.Daniels R.S.Gunasekaran C.P.Hurt A.C.Kelso A.Klimov A.Lewis N.S.Li X.McCauley J.W.Odagiri T.Potdar V.Rambaut A.Shu Y.Skepner E.Smith D.J.Suchard M.A.Tashiro M.Wang D.Xu X.Lemey P.Russell C.A.2015.Global circulation patterns of seasonal influenza viruses vary with antigenic drift.Nature 523:217–220.26053121 [OpenAIRE] [PubMed]

Bedford T.Suchard M.A.Lemey P.Dudas G.Gregory V.Hay A.J.McCauley J.W.Russell C.A.Smith D.J.Rambaut A.2014.Integrating influenza antigenic dynamics with molecular evolution.eLife 3:e01914.24497547 [OpenAIRE] [PubMed]

Bennett S.N.Drummond A.J.Kapan D.D.Suchard M.A.MuñozJordán J.L.Pybus O.G.Holmes E.C.Gubler D.J.2010.Epidemic dynamics revealed in Dengue evolution.Mol. Biol. Evol.27:811–818.19965886 [OpenAIRE] [PubMed]

Biek R.Henderson J.C.Waller L.A.Rupprecht C.E.Real L.A.2007.A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus.Proc. Natl. Acad. Sci. USA 104:7993–7998.17470818 [OpenAIRE] [PubMed]

Bielejec F.Baele G.Vrancken B.Suchard M.A.Rambaut A.Lemey P.2016.Spread3: Interactive visualization of spatiotemporal history and trait evolutionary processes.Mol. Biol. Evol. [OpenAIRE]

Bloomquist E.W.Lemey P.Suchard M.A.2010.Three roads diverged? Routes to phylogeographic inference.Trends Ecol. Evol.25:626–632.20863591 [OpenAIRE] [PubMed]

Bloomquist E.W.Suchard M.A.2010.Unifying vertical and nonvertical evolution: a stochastic arg-based framework.Syst. Biol.59:27–41.20525618 [OpenAIRE] [PubMed]

Bouckaert R.Lemey P.Dunn M.Greenhill S.J.Alekseyenko A.V.Drummond A.J.Gray R.D.Suchard M.A.Atkinson Q.D.2012.Mapping the origins and expansion of the indo-european language family.Science 337:957–960.22923579 [OpenAIRE] [PubMed]

157 references, page 1 of 11
Abstract
Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise in...
Subjects
free text keywords: Genetics, Ecology, Evolution, Behavior and Systematics, Data integration, computer.software_genre, computer, Pathogen, Virology, Zoology, Evolutionary biology, Biology, Virus diseases, Biological evolution, Phylogenetics, Viral phylodynamics, The following are online-only papers that are freely available as part of Issue 66(1) online.
Funded by
EC| VIROGENESIS
Project
VIROGENESIS
Virus discovery and epidemic tracing from high throughput metagenomic sequencing
  • Funder: European Commission (EC)
  • Project Code: 634650
  • Funding stream: H2020 | RIA
,
NIH| BAYESIAN MODELING AND DATA INTEGRATION IN INFECTIOUS DISEASE PHYLODYNAMICS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AI107034-05
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
EC| PREDEMICS
Project
PREDEMICS
Preparedness, Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidisciplinary Approaches
  • Funder: European Commission (EC)
  • Project Code: 278433
  • Funding stream: FP7 | SP1 | HEALTH
,
NIH| Genomics, GPUs, and Next Generation Computational Statistics
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG006139-06
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
EC| VIRALPHYLOGEOGRAPHY
Project
VIRALPHYLOGEOGRAPHY
Evolutionary reconstruction of viral spread in time and space
  • Funder: European Commission (EC)
  • Project Code: 260864
  • Funding stream: FP7 | SP2 | ERC
157 references, page 1 of 11

Alizon S.Fraser C.2013.Within-host and between-host evolutionary rates across the HIV-1 genome.Retrovirology 10:49.23639104 [OpenAIRE] [PubMed]

Alizon S.von Wyl V.Stadler T.Kouyos R.D.Yerly S.Hirschel B.Boni J.Shah C.Klimkait T.Furrer H.Rauch A.Vernazza P.L.Bernasconi E.Battegay M.Bürgisser P.Telenti A.Günthard H.F.Bonhoeffer S.the Swiss Cohort Study.2 Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load.PLoS Path.6:e1001123.

Ayres D.L.Darling A.Zwickl D.J.Beerli P.Holder M.T.Lewis P.O.Huelsenbeck J.P.Ronquist F.Swofford D.L.Cummings M.P.Rambaut A.Suchard M.A.2 BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.Syst. Biol.61:170–173.21963610 [OpenAIRE] [PubMed]

Baele G.Lemey P.2 Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency.Bioinformatics 29:1970–1979.23766415 [PubMed]

Bahl J.Nelson M.I.Chan K.H.Chen R.Vijaykrishna D.Halpin R.A.Stockwell T.B.Lin X.Wentworth D.E.Ghedin E.Guan Y.Peiris J.S.M Riley S.Rambaut A.Holmes E.C.Smith G.J.D.2 Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans.Proc. Natl. Acad. Sci. USA 108:19359–19364.

Baize S.Pannetier D.Oestereich L.Rieger T.Koivogui L.Magassouba N.Soropogui B.Sow M.S.Keïta S.De Clerck H.Tiffany A.Dominguez G.Loua M.TraoréA.KoliéM.Malano E.R.Heleze E.Bocquin A.Mély S.Raoul H.Caro V.Cadar D.Gabriel M.Pahlmann M.Tappe D.Schmidt-Chanasit J.Impouma B.Diallo A.K.Formenty P.Van Herp M.Günther S.2 Emergence of Zaire ebola virus disease in Guinea.N. Engl. J. Med.371:1418–1425.24738640 [OpenAIRE] [PubMed]

Barton N.H.Etheridge A.M.Véber A.2 Modelling evolution in a spatial continuum.J. Stat. Mech.P01002.

Bedford T.Riley S.Barr I.G.Broor S.Chadha M.Cox N.J.Daniels R.S.Gunasekaran C.P.Hurt A.C.Kelso A.Klimov A.Lewis N.S.Li X.McCauley J.W.Odagiri T.Potdar V.Rambaut A.Shu Y.Skepner E.Smith D.J.Suchard M.A.Tashiro M.Wang D.Xu X.Lemey P.Russell C.A.2015.Global circulation patterns of seasonal influenza viruses vary with antigenic drift.Nature 523:217–220.26053121 [OpenAIRE] [PubMed]

Bedford T.Suchard M.A.Lemey P.Dudas G.Gregory V.Hay A.J.McCauley J.W.Russell C.A.Smith D.J.Rambaut A.2014.Integrating influenza antigenic dynamics with molecular evolution.eLife 3:e01914.24497547 [OpenAIRE] [PubMed]

Bennett S.N.Drummond A.J.Kapan D.D.Suchard M.A.MuñozJordán J.L.Pybus O.G.Holmes E.C.Gubler D.J.2010.Epidemic dynamics revealed in Dengue evolution.Mol. Biol. Evol.27:811–818.19965886 [OpenAIRE] [PubMed]

Biek R.Henderson J.C.Waller L.A.Rupprecht C.E.Real L.A.2007.A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus.Proc. Natl. Acad. Sci. USA 104:7993–7998.17470818 [OpenAIRE] [PubMed]

Bielejec F.Baele G.Vrancken B.Suchard M.A.Rambaut A.Lemey P.2016.Spread3: Interactive visualization of spatiotemporal history and trait evolutionary processes.Mol. Biol. Evol. [OpenAIRE]

Bloomquist E.W.Lemey P.Suchard M.A.2010.Three roads diverged? Routes to phylogeographic inference.Trends Ecol. Evol.25:626–632.20863591 [OpenAIRE] [PubMed]

Bloomquist E.W.Suchard M.A.2010.Unifying vertical and nonvertical evolution: a stochastic arg-based framework.Syst. Biol.59:27–41.20525618 [OpenAIRE] [PubMed]

Bouckaert R.Lemey P.Dunn M.Greenhill S.J.Alekseyenko A.V.Drummond A.J.Gray R.D.Suchard M.A.Atkinson Q.D.2012.Mapping the origins and expansion of the indo-european language family.Science 337:957–960.22923579 [OpenAIRE] [PubMed]

157 references, page 1 of 11
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publication . Article . 2017

Emerging concepts of data integration in pathogen phylodynamics

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe;