selected scholarly activity
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chapters
- Australia and Oceania. 191-210. 2021
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conferences
- Examining sampling strategies for archaeological dental calculus through the exploration of the regional variation of bacteria in the oral microbiome. American Journal of Physical Anthropology. 222-223. 2020
- PalaeoChip: An eDNA targeted enrichment approach for reconstructing human palaeoecoystems. American Journal of Physical Anthropology. 193-193. 2020
- Mitochondrial population dynamics in Black Death London. American Journal of Physical Anthropology. 142-142. 2018
- A mitochondrial DNA study of the Beothuk and Maritime Archaic, extinct aboriginal populations from Newfoundland and Labrador. American Journal of Physical Anthropology. 167-168. 2017
- Assessing Demographic Change From the Iron Age (7th-4th c.BCE) through the Roman Period (1st-3rd c.CE) in Southern Italy Using Isotope and Whole-Mitochondrial Genome Analysis. American Journal of Physical Anthropology. 172-172. 2017
- Molecular evidence for Plasmodium falciparum malaria in 1st-4th c. AD southern Italy. American Journal of Physical Anthropology. 275-276. 2017
- Ancient pathogen genomics: a strategy for the parallel detection of multiple pathogens in archaeological samples. American Journal of Physical Anthropology. 219-219. 2016
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journal articles
- The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.. Microbial Genomics. 10:001293. 2024
- In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences.. PLoS Computational Biology. 20:e1011539. 2024
- Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains. Nature Communications. 14:5475. 2023
- A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade. PLoS Pathogens. 19:e1011538-e1011538. 2023
- The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information. Microbial Genomics. 9:mgen000908. 2023
- Genomic data suggest parallel dental vestigialization within the xenarthran radiation. Peer Community Journal. 3. 2023
- Monkeypox in Montréal: Epidemiology, Phylogenomics, and Public Health Response to a Large North American Outbreak. ACP journal club. 176:67-76. 2023
- Genomic data suggest parallel dental vestigialization within the xenarthran radiation 2022
- Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis. International Journal of Paleopathology. 39:20-34. 2022
- Smallpox's antiquity in doubt. Journal of Roman Archaeology (JRA). 35:897-913. 2022
- A 16th century Escherichia coli draft genome associated with an opportunistic bile infection. Communications Biology. 5:599. 2022
- Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments. Current Biology. 32:851-860.e7. 2022
- SARS-CoV-2 infection and transmission in the North American deer mouse. Nature Communications. 12:3612. 2021
- Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set. Quaternary Research. 99:305-328. 2021
- Response to Brinkmann et al. “Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States”. Genome Biology. 21:287. 2020
- The origins and genomic diversity of American Civil War Era smallpox vaccine strains. Genome Biology. 21:175. 2020
- American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations. Nature Communications. 11:4048. 2020
- Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark. American Journal of Physical Anthropology. 169:240-252. 2019
- Dorset Pre-Inuit and Beothuk foodways in Newfoundland, ca. AD 500-1829. PLoS ONE. 14:e0210187-e0210187. 2019
- Ancient Roman mitochondrial genomes and isotopes reveal relationships and geographic origins at the local and pan-Mediterranean scales. Journal of Archaeological Science: Reports. 20:200-209. 2018
- Resolving the phylogenetic position of Darwin's extinct ground sloth ( Mylodon darwinii ) using mitogenomic and nuclear exon data. Proceedings of the Royal Society of London. Biological Sciences. 285:20180214-20180214. 2018
- The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data. Molecular Biology and Evolution (MBE). 35:871-886. 2018
- Correction: The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathogens. 14:e1006887-e1006887. 2018
- The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathogens. 14:e1006750-e1006750. 2018
- Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico. Scientific Reports. 7:18100. 2017
- Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada. Current Biology. 27:3149-3156.e11. 2017
- Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses. 9:276-276. 2017
- A molecular portrait of maternal sepsis from Byzantine Troy. eLife. 6:e20983. 2017
- Abstract. eLife. 6. 2017
- 17th Century Variola Virus Reveals the Recent History of Smallpox. Current Biology. 26:3407-3412. 2016
- Plasmodium falciparum malaria in 1 st –2 nd century CE southern Italy. Current Biology. 26:R1220-R1222. 2016
- Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biology. 16:224. 2015
- Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus). PLoS ONE. 10:e0134207-e0134207. 2015
- Recent developments in the genetic history of East Asia and Oceania. Current Opinion in Genetics and Development. 29:9-14. 2014
- Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology. 24:R1035-R1037. 2014
- Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion. American Journal of Human Genetics. 94:721-733. 2014
- A Highly Unstable Recent Mutation in Human mtDNA. American Journal of Human Genetics. 92:279-284. 2013
- Investigating the Prehistory of Tungusic Peoples of Siberia and the Amur-Ussuri Region with Complete mtDNA Genome Sequences and Y-chromosomal Markers. PLoS ONE. 8:e83570-e83570. 2013
- Coordination of cytochrome c oxidase gene expression in the remodelling of skeletal muscle. Journal of Experimental Biology. 214:1880-1887. 2011
- Phylogeographic genomics of mitochondrial DNA: Highly-resolved patterns of intraspecific evolution and a multi-species, microarray-based DNA sequencing strategy for biodiversity studies. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics. 3:1-11. 2008
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preprints
- In silicoanalyses identifies sequence contamination thresholds for Nanopore-generated SARS-CoV2 sequences 2023
- AncientClostridiumDNA and variants of tetanus neurotoxins associated with human archaeological remains 2022
- A 16th Century Escherichia Coli Draft Genome Associated with an Opportunistic Bile Infection 2022
- North American deer mice are susceptible to SARS-CoV-2 2020
- PalaeoChip Arctic1.0: An optimised eDNA targeted enrichment approach to reconstructing past environments 2019
- The gateway into Remote Oceania: new insights from genome-wide data 2017