How to Validate a Bayesian Evolutionary Model.

Authors: Mendes, Fábio K¹ (AUTHOR), Bouckaert, Remco² (AUTHOR), Carvalho, Luiz M³ (AUTHOR), Drummond, Alexei J⁴ (AUTHOR)

Source: Systematic Biology. Jan2025, Vol. 74 Issue 1, p158-175. 18p.

Subject Terms: *SOFTWARE validation, *STATISTICAL software, *LIFE sciences, *COMPUTATIONAL biology, *EVOLUTIONARY models

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

Authors: Ogilvie, Huw A, Mendes, Fábio K, Vaughan, Timothy G, Matzke, Nicholas J, Stadler, Tanja, Welch, David, Drummond, Alexei J

Source: Systematic biology. 71(1):208-220

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100142918089.0x000001&indx=1&recIds=ETOCvdc_100142918089.0x000001

PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models.

Authors: Mendes, Fábio K¹ (AUTHOR) fmendes@lsu.edu, Landis, Michael J² (AUTHOR)

Source: Systematic Biology. Nov2024, Vol. 73 Issue 6, p1051-1060. 10p.

Subject Terms: *EVOLUTIONARY models, *STATISTICAL learning, *PYTHON programming language, *TEACHING models, *SIMULATION methods & models

The perils of intralocus recombination for inferences of molecular convergence

Authors: Mendes, Fábio K., Livera, Andrew P., Hahn, Matthew W.

Source: Philosophical Transactions: Biological Sciences, 2019 Jul . 374(1777), 1-9.

Access URL: https://www.jstor.org/stable/26675067

A multi‐platform package for the analysis of intra‐ and interspecific trait evolution

Authors: Gaboriau, Théo, Mendes, Fábio K., Joly, Simon, Silvestro, Daniele, Salamin, Nicolas, Price, Samantha

Source: Methods in ecology and evolution. 11(11):1439-1447

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100109067264.0x000001&indx=1&recIds=ETOCvdc_100109067264.0x000001

Why Concatenation Fails Near the Anomaly Zone

Authors: Mendes, Fábio K., Hahn, Matthew W.

Source: Systematic Biology, 2018 Jan 01. 67(1), 158-169.

Access URL: https://www.jstor.org/stable/26581924

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales.

Authors: Ogilvie, Huw A¹ (AUTHOR) huw.a.ogilvie@rice.edu, Mendes, Fábio K^2,3 (AUTHOR) huw.a.ogilvie@rice.edu, Vaughan, Timothy G^4,5 (AUTHOR), Matzke, Nicholas J^2,3 (AUTHOR), Stadler, Tanja^4,5 (AUTHOR), Welch, David^2,6 (AUTHOR), Drummond, Alexei J^2,3,6 (AUTHOR)

Source: Systematic Biology. Jan2022, Vol. 71 Issue 1, p208-220. 13p.

Subject Terms: *MOLECULAR orientation, *MORPHOLOGY, *EVOLUTIONARY models, *FOSSILIZATION, *MOLECULES, *MOLECULAR clock, *SEQUENCE alignment

Gene Tree Discordance Causes Apparent Substitution Rate Variation

Authors: Mendes, Fábio K., Hahn, Matthew W.

Source: Systematic Biology, 2016 Jul 01. 65(4), 711-721.

Access URL: http://www.jstor.org/stable/44028788

Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters.

Authors: Zhang, Rong¹, Drummond, Alexei J^2,3, Mendes, Fábio K⁴, f.mendes@wustl.edu

Source: Systematic Biology; Jan2024, Vol. 73 Issue 1, p102-124, 23p

Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations

Authors: Douglas, Jordan, Mendes, Fábio K, Bouckaert, Remco, Xie, Dong, Jiménez-Silva, Cinthy L, Swanepoel, Christiaan, de Ligt, Joep, Ren, Xiaoyun, Storey, Matt, Hadfield, James, Simpson, Colin R, Geoghegan, Jemma L, Drummond, Alexei J, Welch, David

Source: Virus evolution. 7(2)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100142929863.0x000001&indx=1&recIds=ETOCvdc_100142929863.0x000001

LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses.

Authors: Drummond, Alexei J., Chen, Kylie, Mendes, Fábio K., Xie, Dong

Source: PLoS Computational Biology; 7/18/2023, Vol. 19 Issue 7, p1-16, 16p, 1 Diagram, 1 Chart, 3 Graphs

Subject Terms: GRAPHICAL user interfaces, PHYLOGENETIC models, SOFTWARE compatibility

Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps.

Authors: Schrider, Daniel R.¹, dan.schrider@rutgers.edu, Mendes, Fábio K., Hahn, Matthew W.^2,3, Kern, Andrew D.^1,4

Source: Genetics; May2015, Vol. 200 Issue 1, p267-284, 31p

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand.

Authors: Geoghegan, Jemma L., Ren, Xiaoyun, Storey, Matthew, Hadfield, James, Jelley, Lauren, Jefferies, Sarah, Sherwood, Jill, Paine, Shevaun, Huang, Sue, Douglas, Jordan, Mendes, Fábio K., Sporle, Andrew, Baker, Michael G., Murdoch, David R., French, Nigel, Simpson, Colin R., Welch, David, Drummond, Alexei J., Holmes, Edward C., Duchêne, Sebastián

Source: Nature Communications; 12/11/2020, Vol. 11 Issue 1, p1-7, 7p

Subject Terms: SARS-CoV-2, NUCLEOTIDE sequencing, INFECTIOUS disease transmission, COVID-19, EPIDEMIOLOGY, PUBLIC health surveillance

Geographic Terms: NEW Zealand

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

Authors: Bouckaert, Remco, Vaughan, Timothy G., Barido-Sottani, Joëlle, Duchêne, Sebastián, Fourment, Mathieu, Gavryushkina, Alexandra, Heled, Joseph, Jones, Graham, Kühnert, Denise, De Maio, Nicola, Matschiner, Michael, Mendes, Fábio K., Müller, Nicola F., Ogilvie, Huw A., du Plessis, Louis, Popinga, Alex, Rambaut, Andrew, Rasmussen, David, Siveroni, Igor, Suchard, Marc A.

Source: PLoS Computational Biology; 4/8/2019, Vol. 15 Issue 4, p1-28, 28p, 3 Diagrams, 1 Chart, 3 Graphs

Subject Terms: BAYESIAN analysis, COMPUTER software, PHYLOGENY, ROBUST statistics, BIOGEOGRAPHY, EVOLUTIONARY theories

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CAFE 5 models variation in evolutionary rates among gene families.

Authors: Mendes, Fábio K^1,2 (AUTHOR), Vanderpool, Dan¹ (AUTHOR) danvand@indiana.edu, Fulton, Ben^1,3 (AUTHOR), Hahn, Matthew W^1,4 (AUTHOR)

Source: Bioinformatics. Dec2020, Vol. 36 Issue 22/23, p5516-5518. 3p.

Subject Terms: *EVOLUTIONARY models, *GENE families, *GENES, *INTERNET servers, *SOURCE code, *INTEGRATED software

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