selected scholarly activity
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chapters
- Past Plagues: On the Synergies of Genetic and Historical Interpretations of Infectious Disease 2022
- Ancient Pathogens Through Human History: A Paleogenomic Perspective. 115-138. 2018
- Migration. 191-+. 2011
- DNA. 241-245. 2007
- DNA. 241-245. 2001
- DNA from Amber Inclusions. 92-103. 1994
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DNA Chemical Instability
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conferences
- The effect of diet on the gut microbiome of humans and non-human primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY. 3-3. 2022
- 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
- Malaria in the rural hinterland of southern Italy: A multi-faceted anthropological and genomic perspective from Vagnari (1st-4th c. CE). American Journal of Physical Anthropology. 166-166. 2018
- 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
- Hunting for pathogens: ancient DNA and the historical record. American Journal of Physical Anthropology. 213-213. 2015
- Water isotopes of Ontario: investigating the applications of hydrogen and oxygen isotopes as geographical indicators. American Journal of Physical Anthropology. 188-188. 2013
- A draft genome of Yersinia pestis from victims of the Black Death. American Journal of Physical Anthropology. 103-104. 2012
- DNA, DINOSAURS, AND METAGENOMICS: A NEW TOOL FOR MASS IDENTIFICATION OF DNA FROM FOSSIL BONE. Journal of Vertebrate Paleontology. 185-185. 2011
- THE COMPLETE MITOGENOME OF THE COLUMBIAN MAMMOTH, WITH EVIDENCE FOR COLUMBIAN/WOOLLY MAMMOTH INTERBREEDING IN NORTH AMERICA. Journal of Vertebrate Paleontology. 149-149. 2011
- THE "TIME-DEPENDENCY OF MOLECULAR RATES OF EVOLUTION" REVISITED: HOW WELL-CALIBRATED PALEONTOLOGICAL EVIDENCE CAN CLEAR THE MESS IN THE BAYESIAN DEBATE GENERATED BY POORLY-CALIBRATED UNINFORMATIVE MOLECULAR DATA. Journal of Vertebrate Paleontology. 86A-86A. 2009
- Advances in molecular and phylogenetic studies of Xenarthra. Journal of Morphology. 1066-1066. 2007
- Mammoth metagenomics: New technologies, new insights, new possibilities. Journal of Vertebrate Paleontology. 110A-110A. 2006
- DNA from fossils: Lake embedded plant and sediment remains. Geochimica et Cosmochimica Acta. A346-A346. 2005
- Local Molecular Clocks in Three Nuclear Genes: Divergence Times for Rodents and Other Mammals and Incompatibility Among Fossil Calibrations. Journal of Molecular Evolution. S201-S213. 2003
- Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution. 261-275. 2003
- Search for geologically aged nucleic acids.. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. U934-U934. 2003
- The top 10 list: criteria of authenticity for DNA from ancient and forensic samples. International Congress Series. 575-579. 2003
- Preservation of DNA in the Fossil Record. ACS Symposium Series. 132-146. 1998
- Molecular preservation of insects entombed in amber.. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 40-GEOC. 1997
- Preservation of DNA in the fossil record.. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 56-GEOC. 1997
- Amino acids in the amber matrix and in entombed insects. ACS Symposium Series. 255-262. 1995
- AMINO-ACID RACEMIZATION AND THE PRESERVATION OF DNA IN INSECTS ENTOMBED IN AMBER. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 15-GEOC. 1994
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journal articles
- Permafrost microbial communities follow shifts in vegetation, soils, and megafauna extinctions in Late Pleistocene NW North America. Environmental DNA. 5:1759-1779. 2023
- Improving the extraction of ancient Yersinia pestis genomes from the dental pulp. iScience. 26:106787-106787. 2023
- Peste noire, sélection naturelle et susceptibilité aux maladies auto-immunes ou auto-inflammatoires. Medecine/sciences. 39:331-333. 2023
- Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark. Current Biology. 33:1147-1152.e5. 2023
- Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis. Communications Biology. 6:23. 2023
- Relict permafrost preserves megafauna, insects, pollen, soils and pore-ice isotopes of the mammoth steppe and its collapse in central Yukon. Quaternary Science Reviews. 299:107878-107878. 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
- Evolution of immune genes is associated with the Black Death. Nature. 611:312-319. 2022
- Probe design for simultaneous, targeted capture of diverse metagenomic targets. Cell Reports Methods. 2:100246-100246. 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
- Black Death Upon the land : 400 Years of Plague in Denmark. Current Biology. 2022
- Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nature Communications. 12:7120. 2021
- Probe design for simultaneous, targeted capture of diverse metagenomic targets. Cell Reports Methods. 1:100069-100069. 2021
- Correction for Finlay et al., The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome. Proceedings of the National Academy of Sciences of the United States of America. 118:e2102333118. 2021
- The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome. Proceedings of the National Academy of Sciences of the United States of America. 118:e2010217118. 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
- Acceleration of plague outbreaks in the second pandemic. Proceedings of the National Academy of Sciences of the United States of America. 117:27703-27711. 2020
- The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Current Biology. 30:R1215-R1231. 2020
- American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations. Nature Communications. 11:4048. 2020
- Fast I(n)dentification of Pathogens in Neonates (FINDPATH-N): protocol for a prospective pilot cohort study of next-generation sequencing for pathogen identification in neonates with suspected sepsis. BMJ Paediatrics Open. 4:e000651-e000651. 2020
- Rapid Design of a Bait Capture Platform for Culture- and Amplification-Free Next-Generation Sequencing of SARS-CoV-2 2020
- A Black Death mass grave at Thornton Abbey: the discovery and examination of a fourteenth-century rural catastrophe. Antiquity. 94:179-196. 2020
- Diverse Variola virus strains were widespread in Northern Europe in the Viking age. Science. 2020
- Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes. Antimicrobial Agents and Chemotherapy. 64:e01324-e01319. 2019
- The Justinianic Plague: An inconsequential pandemic?. Proceedings of the National Academy of Sciences of the United States of America. 116:25546-25554. 2019
- Shifting Climates, Foods, and Diseases: The Human Microbiome through Evolution. BioEssays. 41:e1900034. 2019
- Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths. Current Biology. 29:2031-2042.e6. 2019
- 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
- A phylogenomic framework and timescale for comparative studies of tunicates. Journal of Biology. 16:39. 2018
- Human ectoparasite transmission of the plague during the Second Pandemic is only weakly supported by proposed mathematical models. Proceedings of the National Academy of Sciences of the United States of America. 115:E7892-E7893. 2018
- 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
- Chitinase genes ( CHIA s) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals. Science Advances. 4:eaar6478. 2018
- A Single Amino Acid Change in the Response Regulator PhoP, Acquired during Yersinia pestis Evolution, Affects PhoP Target Gene Transcription and Polymyxin B Susceptibility. Journal of Bacteriology. 200:e00050-e00018. 2018
- A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Sciences of the United States of America. 115:E2566-E2574. 2018
- A multi-faceted anthropological and genomic approach to framing Plasmodium falciparum malaria in Imperial period central-southern Italy (1st–4th c. CE). Journal of Anthropological Archaeology. 49:210-224. 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
- Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus. Clinical and Vaccine Immunology. 2:e00511-e00517. 2017
- A phylogenomic framework and timescale for comparative studies of tunicates 2017
- ‘Written in Bone’: New Discoveries about the Lives and Burials of Four Roman Londoners. Britannia (Society for the Promotion of Roman Studies). 48:253-277. 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
- Molecular identification of paleofeces from Bechan Cave, southeastern Utah, USA. Quaternary International. 443:140-146. 2017
- Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus). PeerJ PrePrints. 2017
- The hidden anatomy of paranasal sinuses reveals biogeographically distinct morphotypes in the nine-banded armadillos (Dasypus novemcinctus). PeerJ PrePrints. 2017
- A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals. Current Biology. 27:958-967. 2017
- The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Scientific Reports. 7:44585. 2017
- A molecular portrait of maternal sepsis from Byzantine Troy. eLife. 6:e20983. 2017
- Abstract. eLife. 6. 2017
- Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genusDasypus). PeerJ. 5:e3650-e3650. 2017
- 17th Century Variola Virus Reveals the Recent History of Smallpox. Current Biology. 26:3407-3412. 2016
- Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation. BMC Ecology and Evolution. 16:230. 2016
- Plasmodium falciparum malaria in 1 st –2 nd century CE southern Italy. Current Biology. 26:R1220-R1222. 2016
- Estimation of Gene Insertion/Deletion Rates with Missing Data. Genetics. 204:513-529. 2016
- Genome-Wide Screening of Retroviral Envelope Genes in the Nine-Banded Armadillo (Dasypus novemcinctus, Xenarthra) Reveals an Unfixed Chimeric Endogenous Betaretrovirus Using the ASCT2 Receptor. Journal of Virology. 90:8132-8149. 2016
- Genetic structuring in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microsatellite loci. Genetica. 144:469-476. 2016
- Predicting biotic interactions and their variability in a changing environment. Biology Letters. 12:20151073-20151073. 2016
- Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans. Molecular Biology and Evolution (MBE). 33:621-642. 2016
- The phylogenetic affinities of the extinct glyptodonts. Current Biology. 26:R155-R156. 2016
- Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. eLife. 5:e12994. 2016
- ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Research (NAR). 44:D808-D818. 2016
- Thrice better than once: quality control guidelines to validate new mitogenomes. Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis. 27:449-454. 2016
- Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography, and Introgression. Frontiers in Ecology and Evolution. 4. 2016
- Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta. BMC Ecology and Evolution. 15:148. 2015
- Flawed evidence for convergent evolution of the circadianCLOCKgene in mole-rats 2015
- Surveying the Repair of Ancient DNA from Bones Via High-Throughput Sequencing. BioTechniques. 59:19-25. 2015
- Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth. Current Biology. 25:1395-1400. 2015
- Evolution of Proteasome Regulators in Eukaryotes. Genome Biology and Evolution. 7:1363-1379. 2015
- Correction to ‘Ancient DNA and the tropics: a rodent's tale’. Biology Letters. 11:20150111-20150111. 2015
- Naked but Not Hairless: The Pitfalls of Analyses of Molecular Adaptation Based on Few Genome Sequence Comparisons. Genome Biology and Evolution. 7:768-774. 2015
- Ancient human genomics: the methodology behind reconstructing evolutionary pathways. Journal of Human Evolution. 79:21-34. 2015
- Introduction to the Snowmastodon Project Special Volume The Snowmastodon Project. Quaternary Research. 82:473-476. 2014
- Yersinia pestis and the three plague pandemics–Authors' reply. The Lancet Infectious Diseases. 14:919-919. 2014
- Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Molecular Ecology Resources. 14:966-975. 2014
- Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Molecular Ecology Resources. 14:966-975. 2014
- OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals. Molecular Biology and Evolution (MBE). 31:1923-1928. 2014
- Ancient DNA and the tropics: a rodent's tale. Biology Letters. 10:20140224-20140224. 2014
- Ancient Whole Genome Enrichment Using Baits Built from Modern DNA. Molecular Biology and Evolution (MBE). 31:1292-1294. 2014
- Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis. The Lancet Infectious Diseases. 14:319-326. 2014
- Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array. Scientific Reports. 4:4245. 2014
- Convergence of gut microbiomes in myrmecophagous mammals. Molecular Ecology. 23:1301-1317. 2014
- Second-Pandemic Strain ofVibrio choleraefrom the Philadelphia Cholera Outbreak of 1849. New England Journal of Medicine. 370:334-340. 2014
- Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae). Molecular Phylogenetics and Evolution. 69:728-739. 2013
- Quantitative PCR as a Predictor of Aligned Ancient DNA Read Counts Following Targeted Enrichment. BioTechniques. 55:300-309. 2013
- Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small‐scale reproducibility. Molecular Ecology Resources. 13:798-810. 2013
- Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals. Molecular Biology and Evolution (MBE). 30:2134-2144. 2013
-
Evolutionary and mechanistic insights into substrate and product accommodation of
CTP :phosphocholine cytidylyltransferase fromP lasmodium falciparum. The FEBS Journal. 280:3132-3148. 2013 - Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes. Genome Biology and Evolution. 5:1185-1199. 2013
- Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). Journal of Biology. 10:65. 2012
- RUNX2 tandem repeats and the evolution of facial length in placental mammals. BMC Ecology and Evolution. 12:103. 2012
- JOINT RECONSTRUCTION OF DIVERGENCE TIMES AND LIFE-HISTORY EVOLUTION IN PLACENTAL MAMMALS USING A PHYLOGENETIC COVARIANCE MODEL. Evolution. 66:1773-1787. 2012
- Antibiotic resistance is ancient: implications for drug discovery. Trends in Microbiology. 20:157-159. 2012
- Evolutionary and Functional Analyses of the Interaction between the Myeloid Restriction Factor SAMHD1 and the Lentiviral Vpx Protein. Cell Host and Microbe. 11:205-217. 2012
- Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos. Molecular Phylogenetics and Evolution. 62:673-680. 2012
- Case Study: Ancient Sloth DNA Recovered from Hairs Preserved in Paleofeces. Methods in molecular biology (Clifton, N.J.). 840:51-56. 2012
- Extraction of DNA from Paleofeces. Methods in molecular biology (Clifton, N.J.). 840:37-42. 2012
- Fossil Rhabdoviral Sequences Integrated into Arthropod Genomes: Ontogeny, Evolution, and Potential Functionality. Molecular Biology and Evolution (MBE). 29:381-390. 2012
- Mylodon darwinii DNA sequences from ancient fecal hair shafts. Annals of Anatomy. 194:26-30. 2012
- Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. Comptes Rendus - Biologies. 335:32-50. 2012
- Yersinia pestis: New Evidence for an Old Infection. PLoS ONE. 7:e49803-e49803. 2012
- Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics. BMC Ecology and Evolution. 11:30. 2011
- Erratum: A draft genome of Yersinia pestis from victims of the Black Death. Nature. 480:278-278. 2011
- A draft genome of Yersinia pestis from victims of the Black Death. Nature. 478:506-510. 2011
- Diversification of Wolbachia Endosymbiont in the Culex pipiens Mosquito. Molecular Biology and Evolution (MBE). 28:2761-2772. 2011
- Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid ofYersinia pestisfrom victims of the Black Death. Proceedings of the National Academy of Sciences of the United States of America. 108:E746-E752. 2011
- Antibiotic resistance is ancient. Nature. 477:457-461. 2011
- Herald waves of cholera in nineteenth century London. Journal of the Royal Society Interface. 8:756-760. 2011
- Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae). Infection, Genetics and Evolution. 11:663-670. 2011
- Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome Biology. 12:R51-R51. 2011
- MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE. 6:e22594-e22594. 2011
- Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate. Science. 330:1381-1385. 2010
- Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA. PLoS ONE. 5:e13931-e13931. 2010
- Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates. Journal of Molecular Evolution. 71:153-167. 2010
- Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues. Analytical Biochemistry. 400:110-117. 2010
- Regional differences in bone collagen δ13C and δ15N of Pleistocene mammoths: Implications for paleoecology of the mammoth steppe. Palaeogeography, Palaeoclimatology, Palaeoecology. 286:88-96. 2010
- An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models. BMC Ecology and Evolution. 9:187. 2009
- Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny. BMC Genomics. 10:534. 2009
- A Quantitative Approach to Detect and Overcome PCR Inhibition in Ancient DNA Extracts. BioTechniques. 47:941-949. 2009
- Comment on “DNA from Pre-Clovis Human Coprolites in Oregon, North America”. Science. 325:148-148. 2009
- Response to Comment by Poinar et al . on “DNA from Pre-Clovis Human Coprolites in Oregon, North America”. Science. 325:148-148. 2009
- Time Dependency of Molecular Rates in Ancient DNA Data Sets, A Sampling Artifact?. Systematic Biology. 58:348-360. 2009
- New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic Acids Research (NAR). 37:3215-3229. 2009
- Estimating Maximum Likelihood Phylogenies with PhyML. Methods in molecular biology (Clifton, N.J.). 537:113-137. 2009
- IS LEPROSY SPREADING AMONG NINE-BANDED ARMADILLOS IN THE SOUTHEASTERN UNITED STATES?. Journal of Wildlife Diseases. 45:144-152. 2009
- PhyloExplorer: a web server to validate, explore and query phylogenetic trees. BMC Ecology and Evolution. 9:108-108. 2009
- Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts". Science. 322:857-857. 2008
- Additional molecular support for the new chordate phylogeny. Genesis. 46:592-604. 2008
- Out of America: Ancient DNA Evidence for a New World Origin of Late Quaternary Woolly Mammoths. Current Biology. 18:1320-1326. 2008
- Conserved Features and Evolutionary Shifts of the EDA Signaling Pathway Involved in Vertebrate Skin Appendage Development. Molecular Biology and Evolution (MBE). 25:912-928. 2008
- Retroposed Elements and Their Flanking Regions Resolve the Evolutionary History of Xenarthran Mammals (Armadillos, Anteaters, and Sloths). Molecular Biology and Evolution (MBE). 24:2573-2582. 2007
- Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland. Science. 317:111-114. 2007
- Plant DNA sequences from feces: potential means for assessing diets of wild primates. American Journal of Primatology. 69:699-705. 2007
- A preliminary analysis of the DNA and diet of the extinct Beothuk: A systematic approach to ancient human DNA. American Journal of Physical Anthropology. 132:594-604. 2007
- Molecular evidence for hybridisation between the two living species of South American ratites: potential conservation implications. Conservation Genetics. 8:503-507. 2007
- OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics. BMC Ecology and Evolution. 7:241-241. 2007
- Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research (NAR). 35:1-10. 2007
- Resolving the root of the avian mitogenomic tree by breaking up long branches. Molecular Phylogenetics and Evolution. 42:1-13. 2007
- Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature. 442:684-687. 2006
- Origine des vertébrés : la tunique fait-elle le moine ?. Medecine/sciences. 22:688-690. 2006
- Les datations moléculaires à l’heure de la génomique. Medecine/sciences. 22:374-380. 2006
- Phylogenomics: the beginning of incongruence?. Trends in Genetics. 22:225-231. 2006
- Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature. 439:965-968. 2006
- Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA. Science. 311:392-394. 2006
- Heterotachy and long-branch attraction in phylogenetics. BMC Ecology and Evolution. 5:50. 2005
- Phylogenomics. Annual Review of Ecology, Evolution, and Systematics. 36:541-562. 2005
- Long‐term survival of ancient DNA in Egypt: Response to Zink and Nerlich (2003). American Journal of Physical Anthropology. 128:110-114. 2005
- Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics. 6:361-375. 2005
- Osteocalcin protein sequences of Neanderthals and modern primates. Proceedings of the National Academy of Sciences of the United States of America. 102:4409-4413. 2005
- Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods. Systematic Biology. 54:66-76. 2005
- Relaxed Molecular Clock Provides Evidence for Long-Distance Dispersal of Nothofagus (Southern Beech). PLoS Biology. 3:e14-e14. 2005
- A novel method for collection and preservation of faeces for genetic studies. Molecular Ecology Resources. 4:761-764. 2004
- Genetic Analyses from Ancient DNA. Annual Review of Genetics. 38:645-679. 2004
- The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?. Proceedings of the National Academy of Sciences of the United States of America. 101:15386-15391. 2004
- Genome-Scale Phylogeny and the Detection of Systematic Biases. Molecular Biology and Evolution (MBE). 21:1455-1458. 2004
- Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends in Ecology and Evolution. 19:141-147. 2004
- Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Molecular Ecology. 13:321-335. 2004
- Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans.. BMC Ecology and Evolution. 4:11-11. 2004
- Army Ants Trapped by Their Evolutionary History. PLoS Biology. 1:e37-e37. 2003
- Comment on "Hexapod Origins: Monophyletic or Paraphyletic?". Science. 301:1482-1482. 2003
- Molecular caving. Current Biology. 13:R693-R695. 2003
- Nuclear Gene Sequences from a Late Pleistocene Sloth Coprolite. Current Biology. 13:1150-1152. 2003
- Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability. Molecular Biology and Evolution (MBE). 20:248-254. 2003
- Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting. Molecular Biology and Evolution (MBE). 19:1656-1671. 2002
- The Genetic Secrets Some Fossils Hold. Accounts of Chemical Research. 35:676-684. 2002
- Molecular analysis of a 11 700‐year‐old rodent midden from the Atacama Desert, Chile. Molecular Ecology. 11:913-924. 2002
- The evolution of armadillos, anteaters and sloths depicted by nuclear and mitochondrial phylogenies: implications for the status of the enigmatic fossil Eurotamandua. Proceedings of the Royal Society of London. Biological Sciences. 268:1605-1615. 2001
- Ancient DNA. Nature Reviews Genetics. 2:353-359. 2001
- Molecular Analyses of Oral Polio Vaccine Samples. Science. 292:743-744. 2001
- A molecular analysis of dietary diversity for three archaic Native Americans. Proceedings of the National Academy of Sciences of the United States of America. 98:4317-4322. 2001
- A molecular analysis of ground sloth diet through the last glaciation. Molecular Ecology. 9:1975-1984. 2000
- Ancient DNA: Do It Right or Not at All. Science. 289:1139-1139. 2000
- Preservation of DNA From Endangered Species. Science. 289:725-727. 2000
- Preservation of DNA from endangered species.. Science. 289:726. 2000
- DNA from fossils: the past and the future. Acta Paediatrica, International Journal of Paediatrics, Supplement. 88:133-140. 1999
- Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear and mitochondrial data confirm a founder effect in Dasypus novemcinctus (Xenarthra). Molecular Ecology. 8:1743-1748. 1999
- Protein preservation and DNA retrieval from ancient tissues. Proceedings of the National Academy of Sciences of the United States of America. 96:8426-8431. 1999
- Molecular Coproscopy: Dung and Diet of the Extinct Ground Sloth Nothrotheriops shastensis. Science. 281:402-406. 1998
- Chemical preservation of plants and insects in natural resins. Proceedings of the Royal Society of London. Biological Sciences. 265:641-647. 1998
- Neandertal Genetics. Science. 277:1021b-1025. 1997
- Neandertal Genetics. Science. 277:1021-1025. 1997
- “Colony Sequencing”: Direct Sequencing of Plasmid DNA from Bacterial Colonies. BioTechniques. 22:412-418. 1997
- Digital photogrammetric quantification of surface area and volume on scanning electron micrographs of frozen hydrated lung tissue. Scanning. 18:456-459. 1996
- Amino Acid Racemization and the Preservation of Ancient DNA. Science. 272:864-866. 1996
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preprints
- Reply to Barton et al: signatures of natural selection during the Black Death 2023
- A 16th Century Escherichia Coli Draft Genome Associated with an Opportunistic Bile Infection 2022
- Plagued by a cryptic clock: Insight and issues from the global phylogeny of Yersinia pestis 2021
- Probe Design for Simultaneous, Targeted Capture of Diverse Metagenomic Targets 2020
- PalaeoChip Arctic1.0: An optimised eDNA targeted enrichment approach to reconstructing past environments 2019
- Adaptation in a fibronectin binding autolysin ofStaphylococcus saprophyticus 2017
- Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus 2016