JOURNAL ARTICLES
PREPRINTS
Stamouli S, Beber ME, Normark T, Christensen II TA, Andersson-Li L, Borry M, Jamy M, nf-core community, Fellows Yates JA. nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. Available on the BioRxiv, https://www.biorxiv.org/content/10.1101/2023.10.20.563221v1.full
Velsko IM, Fagernäs Z, Tromp M, Bedford S, Buckley HR, Clark G, Dudgeon J, Flexner J, Leal-Tamarii A, Lewis CM, Matisoo-Smith E, Nägele K, Ozga AT, Rohrlach AB, Posth C, Shing R, Spriggs M, Willie E, Valentin Frédérique, Warinner C. Exploring archaeogenetic studies of dental calculus to shed light on past human migrations in Oceania. Available on BioRxiv, https://doi.org/10.1101/2023.10.18.563027
Bartholdy BP, Velsko IM, Gur-Arieh S, Fagernäs Z, Warinner C, Henry AG. Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus. Available on BioRxiv, https://doi.org/10.1101/2023.05.23.541904
PUBLISHED ARTICLES
Bayarsaikhan J, Turbat T, Bayandelger C, Tuvshinjargal T, Wang J, Chechushkov I, Uetsuki M, Isahaya N, Hudson M, Miller D, Shiraishi N, Li Y, Zhang C, Eregzen G, Caspari G, López Calle P, Conver JL, Hodgins G, Richter KK, Warinner C, Taylor WTT*. Early saddle and stirrup technology in East Asia: new discoveries from Urd Ulaan Uneet Cave, western Mongolia. Antiquity, https://doi.org/10.15184/aqy.2023.172.
Wegner CE, Stahl R, Velsko I, Hübner A, Warinner C, Lehmann R, Ritschel T, Totsche KU, Küsel K. (2023) A glimpse of the paleome in endolithic microbial communities. Microbiome 11(210), https://doi.org/10.1186/s40168-023-01647-2.
Borry M, Forsythe A, Andrades Valtueña A, Hübner A, Ibrahim A, Quagliariello A, White AE, Kocher A, Vågene A, Bartholdy BJ, Spurite D, Yaxal Ponce-Soto G, Neumann G, Huang I-T, Light I, Velsko IM, Jackson I, Frangenberg J, Serrano JG, Fumey J, Özdogan KT, Blevins KE, Daly KG, Lolopolo M, Moraitou M, Michel M, van Os M, Bravo-Lopez M, Sarhan MS, Dagtas ND, Oskolkov N, Smith OS, Lebrasseur O, Rozwalak P, Eisenhofer R, Wasef S, Ramachandran SL, Vanghi V, Warinner C*, Fellows Yates J*. (2023) Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000, https://f1000research.com/articles/12-926.
Velsko IM, Gallois S, Stahl R, Henry A, Warinner C*. (2023) High conservation of the dental plaque microbiome community across populations with differing subsistence strategies. Molecular Biology and Evolution, http://doi.org/10.1111/mec.16988
Klapper M, Hübner A, Ibrahim A, Borry M, Chowdhury S, Frangenberg J, Hänsch V, Herbst R, Suma H, Velsko IM, Wasmuth I, Fellows Yates JA, Zhang S, Al-Jammal WK, Bratovanov EV, Dahse HM, Horch T, Hertweck C, Gonzalez Morales MR, Straus LG, Vilotijevic I, Warinner C*, Stallforth P*. (2023) Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science 380: 619-624, www.science.org/doi/10.1126/science.adf5300
Lee JH, Miller BK, Bayarsaikhan J, Johannesson E, Ventresca Miller A, Warinner C*, Jeong C*. (2023) Genetic population structure of the Xiongnu Empire at imperial and local scales. Science Advances 9(15):eadf3904, www.science.org/doi/10.1126/sciadv.adf3904
Warinner C. (2022) An Archaeology of Microbes. Journal of Anthropological Research 108, https://www.journals.uchicago.edu/doi/10.1086/721976
Dimopouls EA, Carmagnini A, Velsko IM, Warinner C, Larson G, Frantz LA, Irving-Pease E. (2022) HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data. PLoS Computational Biology 18(9): e1010493, https://doi.org/10.1371/journal.pcbi.1010493
Moraitou M, Forsythe A, Fellows Yates JA, Brealey JC, Warinner C, Guschanski K. (2022) Dental calculus metagenomics suggest that ecology, not host phylogeny, shapes the oral microbiome in closely related species. Molecular Biology and Evolution, https://doi.org/10.1093/molbev/msac263
Paladugu R, Korzow-Richter K, Valente MJ, Gabriel S, Detry C, Warinner C, Barrocas Dias C. (2022) Your horse is a donkey! Identifying domesticated equids from Western Iberia using collagen fingerprinting. Journal of Archaeological Science 149:105696. https://doi.org/10.1016/j.jas.2022.105696
Velsko I, Semerau L, Inskip SA, García-Collado MI, Ziesemer K, Serrano Ruber M, Benítez de Lugo Enrich L, Molero-García JM, Gallego Valle D, Peña Ruiz AC, Salazar Garcia DC, Hoogland MLP, Warinner C*. (2022) Ancient dental calculus preserves signatures of biofilm succession and inter-individual variation independent of dental pathology. PNAS Nexus 1: 1-14. https://doi.org/10.1093/pnasnexus/pgac148
Austin RM, Zuckerman M, Honap TP, Lee H, Ward GK, Warinner C, Sankaranarayanan K, Hofman CA. (2022) Remembering St. Louis Individual: Structural violence and acute bacterial infections in a historical anatomical collection. Communications Biology 5:1050. https://doi.org/10.1038/s42003-022-03890-z
Warinner C, Richter K, Collins, M. (2022) Paleoproteomics. Chemical Reviews. DOI: 10.1021/acs.chemrev.1c00703
Borry M, Hübner A, Warinner C. (2022) sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files. Journal of Open Source Software (JOSS) 7(74), 4360. https://doi.org/10.21105/joss.04360
Richter K, Seabrook M, Codlin M, Warinner C*. (2022) A primer for ZooMS applications in archaeology. PNAS 119(20) e2109323119. https://www.pnas.org/doi/10.1073/pnas.2109323119
Reichhardt B, Abrahms-Kavunenko S. (2022) Plastic Purity and Sacred Dairy Microbes, Vitality and Standardisation in Mongolian Dairying. Copenhagen Journal of Asian Studies 40(1): 66-90. https://doi.org/10.22439/cjas.v40i1.6556
Andrades Valtueña A, Neumann GU, Spyrou MA, Musralina L, Aron F, Beisenov A, Belinskiy AB, Bos KI, Buzhilova A, Conrad M, Djansugurova LB, Dobes M, Ernée M, Fernández-eraso J, Frohlich B, Furmanek M, Haluszko A, Hansen S, Éadaoin Harney, Hiss AN, Hübner A, Key FM, Khussainova E, Kitov Y, Kitova AO, Knipper C, Kühnert D, Lalueza-Fox C, Littleton J, Massey K, Mittnik A, Mujika-Alustiza JA, Olalde I, Papac L, Penske S, Peska J, Pinhasi R, Reich D, Reinhold S, Stahl R, Stäuble H, Tukhbatova RI, Vasilyev S, Veselovskaya E, Warinner C, Stockhammer PW, Haak W*, Krause J*, Herbig A*. (2022) Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague. PNAS 119(17): e2116722119. https://doi.org/10.1073/pnas.2116722119
Scott A, Reinhold S, Hermes T, Kalmykov AA, Belinskiy A, Buzhilova A, Berezina N, Kantorovich AR, Maslov VE, Guliyev F, Lyonnet B, Gasimov P, Jalilov B, Eminli J, Iskandarov E, Hammer E, Nugent S, Hagan R, Majander K, Onkamo P, Nordqvist K, Shishlina N, Kaverzneva E, Korolev A, Khokhlov AA, Smolyaninov RV, Sharapova SV, Krause R, Karapetian M, Stolarczyk E, Krause J, Hansen S*, Haak W*, Warinner C*. (2022) Emergence and intensification of dairying in the Caucasus and Eurasian steppes. Nature Ecology and Evolution. doi: 10.1038/s41559-022-01701-6. See our companion blog post.
Fagernäs Z, Salazar-Garcia DC, Avilés Ferández A, Haber Uriarte M, Henry A, Lomba Maurandi J, Ozga A, Velsko IM, Warinner C*. (2022) Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation. FEMS Microbes 3: xtac006. See companion blog post.
Liu C, Witonsky D, Gosling A, Lee JH, Ringbauer H, Hagan R, Patel N, Stahl R, Novembre J, Aldenderfer M, Warinner C*, Di Rienzo A*, Jeong C*. (2022) Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors. Nature Communications 13:1203. https://doi.org/10.1038/s41467-022-28827-2
Der Sarkissian, C., Velsko, I.M., Fotakis, A.K., Vågene, Å.J., Hübner, A. and Fellows Yates, J.A. (2021) Ancient Metagenomic Studies: Considerations for the Wider Scientific Community. mSystems, 6(6), pp.e01315-21.
Zhang F, Chao N, Scott A, Fu Q, Bjorn R, Li W, Wei D, Wang W, Fan L, Abuduresule I, Hu X, Ruan Q, Niyazi A, Dong G, Cao P, Liu F, Dai Q, Feng X, Yang R, Tang Z, Ma P, Li C, Gao S, Xu Y, Wu S, Wen S, Zhu H, Zhou H, Roberts M, Kumar V, Krause J*, Warinner C*, Jeong C*, Cui Y*. (2021) The genomic origins of the Bronze Age Tarim mummies. Nature 599: 256–261. https://www.nature.com/articles/s41586-021-04052-7
Alpaslan-Roodenberg S, Anthony D, Babiker H, Bánffy E, Booth T, Capone P, Deshpande-Mukherjee A, Eisenmann S, Fehren-Schmitz L, Frachetti M, Fujita R, Frieman CJ, Fu Q, Gates Jr. HL, Gibbon V, Haak H, Hajdinjak M, Hofmann KP, Holguin B, Inomata T, Kanzawa-Kiriyama H, Keegan W, Kelso J, Krause J, Kumaresan G, Kusimba C, Kusimba S, Lalueza-Fox C, Llamas B, MacEachern S, Mallick S, Matsumura H, Morales-Arce AY, Motuzaite Matuzeviciute G, Mushrif-Tripathy V, Nakatsuka N, Nores R, Ogola C, Okumura M, Patterson N, Pinhasi R, Prasad SPR, Prendergast ME, Punzo JL, Reich R, Sawafuji R, Sawchuk E, Schiffels S, Sedig J, Shnaider S, Sirak K, Skoglund P, Slon V, Snow M, Soressi M, Spriggs M, Stockhammer PW, Szécsényi-Nagy A, Thangaraj K, Tiesler V, Tobler R, Wang CC, Warinner C, Yasawardene S, Zahir M. (2021) Ethics of DNA Research on Human Remains: Five Globally Applicable Guidelines. Nature, https://doi.org/10.1038/s41586-021-04008-x.
Hendy J, Rest M, Reichhardt B, Aldenderfer M, Warinner C. Cultures of Fermentation: Living with Microbes. Current Anthropology 62, supplement 24.
Reichhardt B, Enkh-Amgalan Z, Warinner C, Rest M. (2021) Photo Essay: Enduring Cycles – Documenting dairying in Mongolia and the Alps. In press at Current Anthropology 62, supplement 24.
Kocher A, Papac L, Barquera R, Key F, Spyrou MA, Hübler R, Prüfer K, Rohrlach AJ, Aron F, Stahl R, Wissgott A, Mittnik A, Feldman M, Neumann G, Villalba V, Majander K, Ghalichi A, Rivollat M, Penske S, Tukhbatova RI, Keller M, Musralin L, Nelson E, van de Loosdrecht M, Nägele K, Michel M, Ferraz da Silva T, Sabin S, Gretzinger J, Skourtanioti E, Parker C, Gnecchi Ruscone GA, Giffin K, Friederlich S, Meller H, Ernee M, Dobes M, Massy K, Skeates R, Erdal YS, Sayer D, Küßner M, Deguilloux MF, Mannerma K, Moiseyev V, Steiner H, Salazar-Garcia DC, Guevara E, Tung TA, Mannino M, Schimmernti V, Hallgren F, Kitov EP, Hernández-Zaragoza DI, Máquez-Morfín L, Rademaker K, Carmona Ballestero E, Harbeck M, Shishlina N, Kaverzneva E, Utrilla P, Lösch S, Shnayder S, Mazzarello V, Schultz M, Sperduit A, Semal P, Rottier S, Ramsl P, Van de Vijver K, Sagona C, Read C, Samashev Z, Beisenov AZ, Djansugurova LB, Khussainova E, Rojo-Guerra M, Tejedor-Rodriguez C, Garcia-Martinez de Lagran I. Aarcusa-Magallon H, Garrido-Pena R, Royo-Guillen JI, Roksandic M, Chinique de Armas Y, Hernandez Godoy ST, Kostka M, Kacki S, Saintot S, Baird D, Fernandez-Dominguez E, Veleminsky P, Limbursky P, Lefranc P, Binder D, Amkreutz L, Altena E, Llamas B, Alvarez CAlmet M, Krauß, Slavchv V, Rosenstock E, Francken M, Karapetian MK, Chaplygin MS, Kufterin VV, Khohlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Longova M, Danielisova A, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 374 (6565): 182-188.
Borry M, Hübner A, Rohrlach AB, Haak W, Warinner C. Pydamage: automated ancient damage identification and estimation for contigs in ancient DNA de Novo assembly. PeerJ 9:e11845. DOI: 10.7717/peerj.11845.
Jacobson DK, Moore KN, Gunderson CC, Rowland MR, Austin RM†, Honap T, Xu J, Warinner C, Sankaranarayanan K, Lewis C. Shifts in gut and vaginal microbiomes are associated with cancer recurrence time in women with ovarian cancer. PeerJ 9:e11574.
Wibowo MC, Yang Z, Tierney BT, Borry M, Huebner A, Barajas-Olmos F, Contreras-Cubas C, García-Ortiz H, Martínez-Hernández A, Luber JM, Kirstahler P, Blohm T, Zimmerman S, Smiley FE, Ballal SA, Pamp SJ, Reinhard K, Russ J, Orozco L, Warinner C, Snow M, LeBlanc S, Kostic AD. Reconstruction of ancient microbial genomes from the human gut. Nature. https://doi.org/10.1038/s41586-021-03532-0. See also the Nature News and Views article by Matthew Olm and Justin Sonnenburg about our research.
Fellows Yates J, Velsko I, Aron F, Hofman C, Austin R, Arthur J, Crevecoeur I, Dalén L, Gonzalez Morales M, Guschanski K, Henry AG, Humphrey LT, Mann AE, Nägele K, Parker CE, Posth C, Rougier H, Semal P, Stock J, Guy Strauss L, Weedman Arthur K, Wrangham R, Curtis M, Diez JC, Gibbon V, Menedez M, Peresani M, Roksandic M, Walker MJ, Power RC, Lewis CM, Sankaranarayan K, Salazar-Garcia DC, Krause J, Herbig A, Warinner C. The evolution and changing ecology of the African hominid oral microbiome. PNAS 118 (20) e2021655118. https://doi.org/10.1073/pnas.2021655118
Reichhardt B. (2021) Pastoral dairying in rural Mongolia: microbes as heritage. Archaeology of Food and Foodways 1(1): 85-102, DOI: 10.1558/aff.15577
Taylor W, Pruvost M, Posth C, Rendu W, Krajcarz M, Brancaleoni G, Spengler R, Hermes T, Schiavinato S, Hodgins G, Stahl R, Abdykanova A, Saltanat A, Fedorowicz S, Orlando L, Douka K, Krivoshapkin A, Jeong C, Warinner C, Shnaider S. (2021) Evidence for the early dispersal of Near Eastern domesticates into high mountain Central Asia. Nature Human Behavior.
Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. 2021. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9:e10947. DOI: 10.7717/peerj.10947.
Orlando L, Allaby R, Skoglund P, Sarkissian C, Stockhammer PW, Avila M, Fu Q, Krause J, Willerslev E, Stone A, Warinner C. (2021) Ancient DNA analysis. Nature Reviews Methods Primers 1:14. https://doi.org/10.1038/ s43586-020-00011-0. Also available via ReadCube. Related PrimeView Highlights.
Rampelli S, Turroni S, Mallol C, Hernandez C, Galván B, Sistiaga A, Biagi E, Astolfi A, Brigidi P, Benazzi S, Lewis CM, Warinner C, Hofman CA, Schnorr SL, Candela M (2021) Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. Communications Biology 4:169. https://doi.org/10.1038/s42003-021-01689-y. See also companion blog post by SL Schnorr.
Bleasdale M, Richter KK, Janzen A, Brown S, Scott A, Zech J, Wilkin S, Wang K, Schiffels S, Desideri J, Besse M, Reinold J, Saad M, Babiker H, Power RC, Ndiema E, Ogola C, Manthi FK, Zahir M, Petraglia M, Trachsel C, Nanni P, Grossmann J, Hendy J, Crowther A, Roberts P, Goldstein ST, Boivin N (2021) Ancient proteins provide evidence of dairy consumption in eastern Africa. Nature Communications, 12(1), pp.1-11.
Fellows Yates J, Andrades Valtueña A, Vägene AJ, Cribdon B, Velsko IM, Borry M, Bravo-López MJ, Fernandez-Guerra A, Green EJ, Ramachandran SL, Heintzman PD, Spyrou MA, Hübner A, Gancz AS, Hider J, Allshouse AF, Warinner C (2021) Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Nature Scientific Data 8(31).
Scott AS, Power RC, Altmann-Wendling V, Artzy M, Martin MAS, Eisenmann S, Hagan R, Salazar-Garcia DC, Salmon Y, Yegorov D, Milevski I, Finkelstein I, Stockhammer PW, Warinner C (2020) Evidence for long-distance trade in exotic foods and spices from South Asia to the Near East in the 2nd millennium BCE. Proceedings of the National Academy of Sciences USA 118 (2) e2014956117. https://doi.org/10.1073/pnas.2014956117.
Nielsen RL, Helenius M, Garcia S, Roager HM, Aytan D, Hansen LBS, Lind MV, Vogt J, Dalgaard M, Dahl MI, Jensen CB, Muktupavela R, Warinner C, Appel V, Gøbel R, Vestergaard H, Hansen Torben, Kristiansen K, Pedersen SB, Petersen TN, Lauritzen L, Licht TR, Pedersen O, Gupta R. (2020) Data integration for prediction of weight loss in dietary cross-over studies. Scientific Reports 76097. https://doi.org/10.1038/s41598-020-76097-z
Jeong C, Wang K, Wilkin S, Taylor WTT, Miller BK, Bemmann JH, Stahl R, Chiovelli C, Knolle F, Ulziibayar S, Khatanbaatar D, Erdenebaatar D, Erdenebat U, Ochir A, Ankhsanaa G, Vanchigdash C, Ochir B, Munkhbayar C, Tumen D, Kovalev A, Kradin N, Bazarov BA, Miyagashev DA, Konovalov PB, Zhambaltarova E, Ventresca Miller A, Haak W, Schiffels S, Krause J, Boivin N, Myagmar E, Hendy J, Warinner C. (2020) A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe. Cell 183, 1-15. Article translation in Mongolian: Евразийн Зүүн тал нутаг дахь 6000 жилийн динамик генетик түүх
Skourtanioti E, Erdal YS, Frangipane M, Balossi Restelli F, Yener A, Pinnock F, Matthiae P, Özbal R, Schoop U, Guliyev F, Akhundof T, Lyonnet B, Hammer EL, Nugent SE, Burri M, Neumann G, Penske S, Ingman T, Akar M, Shafiq R, Palumbi G, Eisenmann S, d’Andrea M, Schachner A, Warinner C, Jeong C, Stockhammer P, Haak W, Krause J. (2020) Genomic history of Neolithic to Bronze Age Anatolia, Northern Levant and South Caucasus. Cell 181:1158-1175.
Fagernäs Z, Garcia Collado MI, Hendy J, Hofman C, Speller C, Velsko I, Warinner C. (2020) A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus. Journal of Archaeological Science 118:105135. https://doi.org/10.1016/j.jas.2020.105135
Borry M, Cordova B, Perri A, Wibowo MC, Ko WTJ, Yu J, Kagone TS, Meda N, Carabin H, Jacobson D, Honap T, Reinhard K, Lewis CM, Kostic A, Jeong C, Herbig A, Hübner A, Warinner C. (2020) CoproID predicts the source of coprolites and paleofeces using microbiome composition and endogenous DNA content. PeerJ 8:e9001. doi: 10.7717/peerj.9001.
Wilkin S, Ventresca Miller A, Taylor WTT, Miller BK, Hagan RW, Bleasdale M, Scott A, Gankhuyg S, Ramsøe A, Trachsel C, Nanni P, Grossmann J, Orlando L, Horton M, Stockhammer P, Myagmar E, Boivin N, Warinner C, Hendy J. (2020) Dairy pastoralism sustained Eastern Eurasian steppe populations for 5000 years. Nature Ecology and Evolution 4:346-355. https://doi.org/10.1038/s41559-020-1120-y. Article translation in Mongolian: Сүү, цагаан идээ голлосон мал аж ахуй Зүүн Евразийн тал нутгийн ард түмний амь зуулгыг 5000 жилийн турш залгуулжээ
Honap T, Sankaranarayanan K, Schnorr SL, Ozga AT, Warinner C, Lewis C. (2020) Biogeographic study of human gut associated crAssphage suggests impacts from industrialization and recent expansion. PLoS ONE, https://doi.org/10.1371/journal.pone.0226930
Hagan RW, Hofman CA, Hübner A, Reinhard K, Schnorr S, Lewis CM, Sankaranarayanan K, Warinner C*. (2020) Comparison of extraction methods for recovering ancient microbial DNA from paleofeces. American Journal of Physical Anthropology, doi: 10.1002/ajpa.2397B.
Huebler R, Key FM, Warinner C, Bos KI, Krause J, Herbig A. (2019) HOPS: Automated detection and authentication of pathogen DNA in archaeological remains. Genome Biology 20: 280.
Geber J, Tromp M, Scott A, Bouwman A, Nanni P, Grossmann J, Hendy J, Warinner C. (2019) Relief food subsistence revealed by microparticle and proteomics analyses of dental calculus from victims of the Great Irish Famine. Proceedings of the National Academy of Sciences USA. DOI: 10.1073/pnas.1908839116.
Borry, Maxime (2019). Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification. Journal of Open Source Software 4(41):1540. DOI: 10.21105.joss/01540
Aronsen GP, Fehren-Schmitz L, Krigbaum J, Kamenov GD, Conlogue G, Warinner C, Ozga A, Sankaranarayanan K, Griego A, DeLuca DW, Eckels HT, Byczkiewicz R, Grurich T, Pellatier N, Brownlee S, Marichal A, Williamson K, Tonoike Y, Bellantoni NF. (2019) The dead shall be raised: Multidisciplinary analysis of 19thcentury human skeletons reveals complexity in New Haven Connecticut immigrant socioeconomic history and identity. PLoS ONE 14(9): e0219279. DOI: 10.1371/journal.pone.0219279.
Hernández-Hernández O, Hernández-Zaragoza DI, Barquera R, Warinner C, López Gil C, Arrieta-Bolaños E, Clayton S, Bravo-Acevedo A, Ramos-de la Cruz F, Méndez-Mani P, Pavón-Vargas M, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. (2019) Genetic diversity of HLA system in two populations from Oaxaca, Mexico: Oaxaca City and rural Oaxaca. Human Immunology, in press. DOI: 10.1016/j.humimm.2019.07.278
Jillian A. Swift, Michael Bunce, Joe Dortch, Kristina Douglass, J. Tyler Faith, James A. Fellows Yates, Judith Field, Simon G. Haberle, Eileen Jacob, Chris N. Johnson, Emily Lindsey, Eline D. Lorenzen, Julien Louys, Gifford Miller, Alexis M. Mychajliw, Viviane Slon, Natalia A. Villavicencio, Michael R. Waters, Frido Welker, Rachel Wood, Michael Petraglia, Nicole Boivin, and Patrick Roberts (2019), Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene. BioScience, DOI: 10.1093/biosci/biz105.
Velsko IM, Fellows-Yates JA, Aron F, Hagen RW, Frantz LAF, Loe L, Rodriguez Martinez JB, Chaves E, Gosden C, Larson G, Warinner C*. (2019) Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage. Microbiome 7:102. DOI: 10.1186/s40168-019-0717-3
Hofman CA, Warinner C*. (2019) Ancient DNA 101: An introductory guide in the era of high-throughput sequencing. SAA Record 19(1): 18-25.
Radini A, Tromp M, Beach A, Tong E, Speller C, McCormick M, Dudgeon JV, Collins MJ, Rühli F, Kröger R, Warinner C*. (2019) Medieval women’s early involvement in manuscript production suggested by lapis lazuli identification in dental calculus. Science Advances 5, eaau7126. DOI: 10.1126/sciadv.aau7126.
Ziesemer KA, Ramos-Madrigal J, Mann AE, Brandt B, Sankaranarayanan K, Ozga A, Hoogland M, Salazar Garcia D, Frohlich B, Milner G, Aldenderfer M, Lewis CM, Hofman C, Warinner C, Schroeder H*. (2018) The efficacy of whole human genome and high-throughput sequencing on ancient dental calculus. American Journal of Physical Anthropology. DOI: 10.1002/ajpa.23763.
Jeong C, Wilkin S, Amgalantugs T, Bouwman A, Taylor W, Bromage S, Tsolmon S, Hagan R, Trachsel C, Grossman J, Littleton J, Makarewicz C, Krigbaum J, Burri M, Irmer F, Scott A, Davaasambuu G, Wright J, Myagmar E, Boivin N, Robbeets M, Rühli F, Krause J, Frohlich B, Hendy J, Warinner C*. (2018) Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe. Proceedings of the National Academy of Sciences USA 115(48): E11248-E11255. DOI: 10.1073/pnas.1813608115.
Lindo J, Haas R, Hofman C, Apata M, Moraga M, Verdugo R, Watson JT, Llave CV, Witonsky D, Vargas Pacheco E, Villena M, Soria R, Beall C, Warinner C, Novembre J, Aldenderfer M, Di Rienzo A. (2018) The genetic prehistory of the Andean highlands 7,000 years BP through European contact. Science Advances 4(11): eaau4921. DOI: 10.1126/sciadv.aau4921.
Velsko IM, Frantz LAF, Herbig A, Larson G, Warinner C*. (2018) Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research. mSystems 3:e00080-18. DOI: 10.1128/mSystems.00080-18.
Hendy J, Warinner C, Barnes I, Bouwman A, Collins M, Fiddyment S, Fischer R, Hagan R, Hofman CA, Holst M, Chaves E, Klaus L, Larson G, Mackie M, McGrath K, Mundorff A, Radini A, Rao H, Trachsel C, Velsko I, Speller C. (2018) Proteomic evidence of dietary sources in ancient dental calculus. Proceedings of the Royal Society B 285: 20180977. DOI: 10.1098/rspb.2018.0977.
Mann AE, Sabin S, Ziesemer KA, Vågene Å, Schroeder H, Ozga A, Sankaranarayanan K, Hofman CA, Fellows-Yates J, Salazar Garcia D, Frohlich B, Aldenderfer M, Hoogland M, Read C, Krause J, Hofman C, Bos K, Warinner C*. (2018) Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports 8:9822.
Martínez Tuñón A, Robles García NM, Clark D, Warinner C, Tuross N. (2018) Clandestine pulque production during the sixteenth century in the Tlacolula Valley, Oaxaca, Mexico. Mexicon 40(2):52-59.
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov A, Chen Y, Dorrestein PC, Dunn RR, Fahimpour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholz P, Humphrey G, Huttenhower C, Jackson MA, Kelley ST, Knights D, Ladau J, Leach J, Melnik A, Metcalf JL, Montassier E, Navas-Molina J, Peddada S, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Spector T, Thackray VG, Thompson LR, Vasquez-Baeza Y, Wischmeyer P, Wolfe E, The American Gut Consortium, Knight R. (2018) American Gut: an Open Platform for Citizen-Science Microbiome Research. mSystems 3(3): e00031-18. DOI: 10.1128/mSystems.00031-18
Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ. (2018) A guide to ancient protein studies. Nature Ecology and Evolution. DOI: 10.1038/s41559-018-0510-x
Vågene AJ, Campana MG, Robles García N, Warinner C, Spyrou MA, Andrades Valtueña A, Huson D, Tuross N, Herbig A, Bos KI, Krause J. (2018) Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico. Nature Ecology and Evolution 1-9, doi:10.1038/s41559-017-0446-6.
Morales-Arce AY*, Hofman CA, Duggan A, Benfer A, Katzenberg MA, McCafferty G, Warinner C*. (2017) Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico. Scientific Reports 7, 18100. DOI:10.1038/s41598-017-18356-0
Warinner C, Hendy J. (2017) Ancient cultures: The archaeology of dairy and the enduring legacy of ‘heirloom’ microbes. Mælkeritidende 21:10-11.
Velsko IM, Overmyer KA, Speller C, Loe L, Sankaranarayanan K, Collins M, Lewis CM, Bautista Rodriguez J, Chaves E, Coon JJ, Larson G, Warinner C*. (2017) The dental calculus metabolome in modern and historic samples. Metabolomics 13:134
Warinner C, Herbig A, Mann AE, Fellows Yates JA, Weiss CL, Burbano HA, Orlando L, Krause J. (2017) A robust framework for microbial archaeology. Annu. Rev. Genom. Hum. Genet. 18:321-356.
Velsko I, Warinner C*. (2017) Bioarchaeology of the human microbiome. Bioarchaeology International 1(1-2):86-99. See also open access version.
Bouwman A, Shved N, Akgül G, Rühli F, Warinner C*. (2017) Ancient DNA investigation of a medieval German cemetery confirms long-term stability of CCR5-∆32 allele frequencies in Central Europe. Human Biology 89(2).
Olsen K, White CD, Longstaffe FJ, Rühli FJ, Warinner C, and Salazar-Garcia DC. (2017) Isotopic anthropology of rural German medieval diet: intra- and inter-population variability. Archaeological and Anthropological Sciences, in press. doi:10.1007/s12520-016-0432-y
Schnorr S, Sankaranarayanan K, Lewis CM, Warinner C*. (2016) Insights into human evolution from ancient and contemporary microbiome studies. Current Opinion in Genetics and Development 41:14-26.
Warinner C. (2016) Dental calculus and the evolution of the human oral microbiome. California Dental Association Journal 44(7):411-420.
Jeong C, Ozga AT, Witonsky D, Malmstrom H, Edlund H, Hofman CA, Hagan RW, Jakobsson M, Lewis CM, Aldenderfer M, Di Rienzo A, Warinner C*. (2016) Long-term genetic stability and a high altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. Proceedings of the National Academy of Sciences USA 113(27):7485-7490.
Olsen K, White CD, Longstaffe FJ, Rühli FJ, Warinner C, and Salazar-Garcia DC. (2016) Isotopic anthropology of rural German medieval diet: intra- and inter-population variability. Archaeological and Anthropological Sciences, doi:10.1007/s12520-016-0432-y
Ozga AT, Nieves-Colón MA, Honap T, Sankaranarayanan K, Hofman C, Milner G, Lewis CM, Stone AC, Warinner C*. (2016) Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. American Journal of Physical Anthropology 160:220-228.
Sankaranarayanan K, Ozga AT, Warinner C, Tito RY, Obregon-Tito AJ, Xu J, Gaffney PM, Jervis L, Cox D, Stephens L, Foster M, Tallbull G, Spicer P, Lewis CM. (2015) Gut microbiome diversity among Cheyenne & Arapaho Individuals in Western Oklahoma. Current Biology, doi: http://dx.doi.org/10.1016/j.cub.2015.10.060.
Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar Garcia DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C*. (2015) Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Scientific Reports 5, 16498. doi: 10.1038/srep16498.
Warinner C, Lewis CM. (2015) Microbiome and health in past and present human populations. American Anthropologist 117(4): 740-741, doi:10.1111/aman.12367.
Obregon-Tito A, Tito R, Metcalf J, Sankaranarayanan K, Clemente J, Ursell L, Xu Z, Van Treuren W, Knight R, Gaffney P, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga A, Lewis CM. (2015) Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications 6, 6505.
Warinner C, Speller C, Collins MJ, Lewis CM* (2015) Ancient Human Microbiomes. Journal of Human Evolution 79, 125-136. http://dx.doi.org/10.1016/j.jhevol.2014.10.016
Warinner C*, Speller C, Collins MJ (2014) A New Era in Paleomicrobiology: Prospects for Ancient Dental Calculus as a Long-Term Record of the Human Oral Microbiome. Philosophical Transactions of the Royal Society B 370: 20130376. http://dx.doi.org/10.1098/rstb.2013.0376
Warinner C*, Hendy J, Speller C, Cappellini E, Fischer R, Trachsel C, Arneborg J, Lynnerup N, Craig OE, Swallow DM, Fotakis A, Christensen RJ, Olsen J, Liebert A, Montalva N, Fiddyment S, Mackie M, Canci A, Bouwman A, Rühli F, Gilbert MTP, Collins MJ* (2014) Direct Evidence of Milk Consumption from Ancient Human Dental Calculus. Scientific Reports 4, 7104. doi:10.1038/srep07104.
Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, The Scientists for Advancement of Microbiome Research, White O (2014). Advancing the Microbiome Research Community. Cell 159(2):227-230.
Natallia Shved, Cordula Haas, Christina Papageorgopoulou, Guelfirde Akguel, Katja Paulsen, Abigail Bouwman, Christina Warinner, Frank Rühli (2014) Post Mortem DNA Degradation of Human Tissue Experimentally Mummified in Salt. PLoS ONE 9(10): e110753. doi:10.1371/journal.pone.0110753.
Warinner C*, Rodrigues JFM, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-García DC, Eppler E, Seiler R, Hansen L, Samaniego Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup C, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis, Jr. CM, Collins MJ, Gilbert MTP, Rühli F, Cappellini E* (2014). Pathogens and host immunity in the ancient human oral cavity. Nature Genetics 46(4):336-344. doi:10.1038/ng.2906.
Kruettli A, Bouwman A, Akguel G, Della Casa P, Ruehli F, Warinner C* (2014). Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval Central Europe. PLoS ONE 9(1), e86251.
Guedes J, Carrasco D, Flad R, Fosse E, Herzfeld M, Lamberg-Karlovsky K, Lewis C, Liebmann M, Meadow R, Patterson N, Price M, Reiches M, Richardson S, Shattuck-Heidorn H, Ur J, Urton G, Warinner C. 2013. Is poverty in our genes? A reply to Ashraf and Galor. Current Anthropology 54(1): 71-79. For links to media coverage, click here.
Warinner C, Robles García N, and Tuross N. 2013. Maize, beans and the floral isotopic diversity of highland Oaxaca, Mexico. Journal of Archaeological Science 40(2):868-873.
Warinner C*, Robles García N, Spores R, Tuross N. 2012. Disease, demography, and diet in early colonial New Spain: Investigation of a 16th century Mixtec epidemic cemetery at Teposcolula Yucundaa. 2012. Latin American Antiquity 23(4):467-489.
Warinner C,* d’Alpoim Guedes J, and Goode D. 2011. Paleobot.org: Establishing open-access online reference collections for archaeobotanical research. Vegetation History and Archaeobotany 20(3):241-244.
Warinner C* and Tuross N. 2010. Tissue isotopic enrichment associated with growth depression in a pig: implications for archaeology and ecology. American Journal of Physical Anthropology 141:486-493.
Warinner C* and Tuross N. 2009. Alkaline cooking and stable isotope diet-tissue discrimination in swine: archaeological implications. Journal of Archaeological Science 36(8):1690-1697.
Tuross N,* Warinner C, Kirsanow K and Kester C. 2008. Organic Oxygen and Hydrogen Isotopes in a Porcine Controlled Dietary Study. Rapid Communications in Mass Spectrometry 22(11):1741-1745.
BOOKS
Marston JM, d’Alpoim Guedes J, Warinner C, eds. Method and Theory in Paleoethnobotany. University Press of Colorado, 2014. Available for order here.
Houston S, Brittenham C, Mesick C, Tokovinine A, and Warinner C. Veiled Brightness: A History of Ancient Maya Color. Austin: University of Texas Press, 2009. Available for order here.
Warinner C. Life and Death at Teposcolula Yucundaa: Mortuary, Archaeogenetic, and Isotopic Investigations of the Early Colonial Period in Mexico. PhD Dissertation, Harvard University, 2010.
BOOK CHAPTERS
Fagernäs Z, Warinner C. “Dental calculus.” In: Pollard M, Makarewicz C, and Armitage, R, eds., Handbook of Archaeological Sciences, 2nd Edition. John Wiley & Sons, Ltd, 2023. ISBN: 9781119592044. https://doi.org/10.1002/9781119592112.
Smith T, Warinner C. (2022) Developmental, evolutionary, and behavioral perspectives on oral health. In: Plomp K, Roberts C, Elton S, Bentley G, eds., Evolving Health: Paleopathology and Evolutionary Medicine, Oxford University Press, https://academic.oup.com/book/43111/chapter/361608086
Hendy, J., Rest, M., & Warinner, C. (2021). The Origins of Yoghurt Microbes. In The Book of Fermentology (1st ed.). NC State University Libraries. NC State University Libraries. https://doi.org/10.52750/605475
Hendy, J., Rest, M., and Warinner, C. (2021). “The Ancient History of Yoghurt.” In The Book of Fermentology (1st ed.). NC State University Libraries. https://doi.org/10.52750/679579
Hendy, J., Rest, M., and Warinner, C. (2022). “The Modern History of Yoghurt.” In The Book of Fermentology (1st ed.). NC State University Libraries. https://doi.org/https://doi.org/10.52750/679579
Warinner C, Ozga A, Radini A, Sankaranarayanan K, Lewis CM. (2019) “Genetic and microscopic analysis of human dental calculus from Swift Water Place, Alaska,” in Anderson D, Anderson W, eds., Life at Swift Water Place, Alaska, at the Threshold of European Contact. University of Alaska Press.
Warinner C and d’Alpoim Guedes J. Digitizing the archaeobotanical record. In: Marston JM, d’Alpoim Guedes J, Warinner C, eds. Method and Theory in Paleoethnobotany. University Press of Colorado Boulder, 2014. Available for order here.
Warinner C. From the ground up: Advances in stable isotope-based paleodietary inference. Marston JM, d’Alpoim Guedes J, Warinner C, eds. Method and Theory in Paleoethnobotany. University Press of Colorado, Boulder, 2014.
Marston, JM, d’Alpoim Guedes J, and Warinner C. “Paleoethnobotanical Method and Theory in the 21st Century,” in Marston JM, d’Alpoim Guedes J, and Warinner C, eds. Method and Theory in Paleoethnobotany. University Press of Colorado, Boulder, 2014.
Warinner C and Tuross N. (2015) “Ancient DNA and Stable Isotope Analysis of the Teposcolula Grand Plaza Cemetery,” in Nelly Robles-García, ed. Yucundaa: La ciudad mixteca Yucundaa-Pueblo Viejo de Teposcolula y su transformación prehispánica-colonial. Vol. 2. Instituto Nacional de Antropología e Historia.
Tuross N, Warinner C, and Robles Garcia N. (2015) “Evidence for Mixtec/Dominican Interaction from the Radiocarbon Dates at Yucundaa (Pueblo Viejo de Teposcolula),” in Nelly Robles-García, ed. Yucundaa: La ciudad mixteca Yucundaa-Pueblo Viejo de Teposcolula y su transformación prehispánica-colonial. Vol. 2. Instituto Nacional de Antropología e Historia.