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
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
Burge K, Velsko IM, Salazar-García DC, Uriarte MH, Lomba Maurandi J, Warinner C. (2026) Comparing the performance of double-stranded and single-stranded DNA libraries for ancient oral microbiome reconstruction. Molecular Ecology Resources 26(7): e70201. https://doi.org/10.1111/1755-0998.70201.
Zeibig T, Spyrou MA, Kocher A, Gaul E, Abadie I, Aldenderfer MA, Barquera R, Beckett JF, Beisenov A, Belinski AB, Betancourt P, Boersma R, Carrion P, Childebayeva A, Cooper C, Cucca F, Djansugurova L, Ernée M, Fehren-Schmitz L, Ghalichi A, Gómez-Valdés JA, Gretzinger J, Vigil-Escalera Guirado A, Hansen L, Hansen S, Harvarti K, Hernandez-Zaragoza DI, Jankauskas R, Keller M, Khartanovich V, Kim D, Kinaston R, Kozakaitė J, Krausse DI, Küßner M, Lai L, Lösch S, Mannino M, Márquez-Morfín L, McGeorge PJP, Michel M, Moiseyev V, Moon H, Mötsch A, Musralina L, Myagmar E, Németh RE, Neumann GU, Olmo Enciso L, Papac L, Peltola S, Posth C, Powell A, Rathmann H, Di Salvo R, Samashev Z, Sayer D, Schimmenti V, Schmitt F, Sintes E, Terberger T, Tukhbatova R, Vågene AJ, Van de Vijver K, Villalba V, Jin Woo E, Ximenez T, McCormick M, Risch R, Reinhold S, Jeong C, Onkamo P, Warinner C, Bos K, Schiffels S, Mittnik A, Haak W, Herbig A, Krause J. (2026) Tracing the evolution and diversity of ancient human Parvovirus B19 across human history. Current Biology 36:1-16, https://doi.org/10.1016/j.cub.2026.08.032.
Alvarez Saravia D, Rosenbaum A, Straub D, Downie J, Lundin D, Borry M, Hübner A, Fedewa G, nf-core community, Uribe-Paredes R, Navarrete MA, Warinner C, Nahsen S, Yepes-García, Köhn L, Fellows Yates J. (2026) Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5. Bioinformatics 42(9): btag628, https://doi.org/10.1093/bioinformatics/btag628.
Velsko I, Hübner A, Fagernäs, Fellows Yates JA, Mann A, Hofman C, Ozga A, Lewis CM, Speller C, Fiddyment S, Francken M, Wahl J, Krause J Radini A, King T*, Warinner C*. The oral microbiome of King Richard III. American Journal of Biological Anthropology 191(1): e70350, https://doi.org/10.1002/ajpa.70350.
Nyambal T, Lkhamsuren K, Hübner A, Khuygaa S-O, Bromage S, Stahl R, Rest M, Reichhardt B, Battulga A, Odonchimed S, Dambadarjaa D, Tulgaa K, Warinner C, Tsolmon S. (2026) Distinctive Patterns of Gut Bifidobacterium Diversity in Mongolian Adults: Regional Variation and Dairy Intake Associations. Nutrients 18, 2816, https://doi.org/10.3390/nu18172816
Nyambal T, Hübner A, Lkhamsuren K, Khuygaa S-O, Stahl R, Gantumur A, Chimeddorj B, Dambadarjaa D, Tulgaa K, Warinner C, Tsolmon S*. (2026) Isolation and Preliminary Analysis of Bifidobacterium Strains from Fecal Samples of Mongolian Individuals: Bifidobacterium Diversity in Mongolian Gut. Central Asian Journal of Medical Sciences 12(2):24-36. https://doi.org/10.24079/CAJMS.2024.01.001
Fellows Yates J, Hübner A, Borry M, nf-core community, Warinner C. De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag. PLoS Computational Biology, 22(8): e1014591, https://doi.org/10.1371/journal.pcbi.1014591
Galtier A, Warinner C, Velsko IM*. (2026) Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed thorugh paleogenomics. Genome Biology and Evolution 18(6), https://doi.org/10.1093/gbe/evag136
Wasmuth I, Ibrahim A, Köhler P, Hovhannisyan H, Marcet-Houben M, Gabaldón T, Tsolmon S, Warinner C, Stallforth P. (2026) Cyclic Lipopeptide-Mediated Growth Promotion of Milk-Associated Candida zeylanoides. ISME 20(1):wrag033, https://doi.org/10.1093/ismejo/wrag033.
Beck J, Flad R, Alex B, Caramanica A, Costopoulos A, Kawa NC, Marwick B, Warinner C, Bardolph D, Borck L, Douglass K, Farahani A, Fitzpatrick M, Fogelin L, Heath-Stout LE, Hutson S, Magnani M, Magnani N, Mauricio AC, Overholtzer L, Rest M, Souleles DS, Verdun da Silva Carmo R. (2026) Changing the landscape of archaeological publishing. Current Anthropology 67(1): https://www.doi.org/10.1086/739789.
Herbst R, Ibrahim A, Hübner A, Knüpfer U, Regenstein L, Wiedemann C, Hellmich UA, Warinner C*, Stallforth P*. (2025) Actifensin evolution in the human oral cavity over the past 100,000 years. Journal of the American Chemical Society, https://doi.org/10.1021/jacs.5c14335.
Bandyopadhyay E, Witonsky D, Constanza de la Fuente Castro C, Pasupuleti N, Lee J, Shastry V, Sander N, Ahlawat B, Dwivedi A, Angmo T, Sharma A, Kaushik A, Moots HM†, Moreno-Mayar JV, Kumar S, Chandra Bhatt R, Bist Mengwal K, Chauhan H, Ganjoo RK, Mushrif-Tripathy V, Bihari Ota S, Warinner C, Aldenderfer M, Di Rienzo A, Jeong C, Singh Rawat N, Norbu T, Singh E, Nautiyal V, Raghavan M*, Rai N*. (2025) Dynamic human admixture histories over the last ~1,300 years at the northern Himalayan frontier. Science Advances 11, eadu9625, https://www.science.org/doi/epdf/10.1126/sciadv.adu9625
Gill H, Seidualy M, Lee J, Lee J, Moon H, Tashmanbetova Z, Walter A, Bianco R, Kiyasbek G, Hermes T, Krause J, Kurmangaliev A, Rakhmankulov M, Samashev Z, Aitkali A, Zhuniskhanov A, Zhabagin M*, Doumani Dupuy P*, Warinner C*, Jeong C*. (2025) Ancient genomes from eastern Kazakhstan reveal dynamic genetic legacy of Inner Eurasian hunter-gatherers. Science Advances 11, eadw8219. https://www.science.org/doi/epdf/10.1126/sciadv.adw8219
Lee J, Brosseder U, Moon H, Stahl R, Semerau L, Gantulga JO, Magail J, Bemmann J, Yeruul-Erdene C, Warinner C*, Jeong C*. (2025) Slab Grave expansion disrupted long co-existence of distinct Bronze Age herders in central Mongolia. Nature Communications 16:8420. https://doi.org/10.1038/s41467-025-63789-1.
De-Dios T, Bonucci B, Barbieri R, Kushniarevich A, D’Atanasio E, Dittmar, JM, Cessford C, Solnik A, Robb JE, Warinner C, Oras E, Scheib CL. (2025) Bone adhered sediments as a source of target and environmental DNA and proteins. Molecular Biology and Evolution 42: 1-19. https://doi.org/10.1093/molbev/msaf202
Light-Maka I, Hermes TR, Raffaela AB, Semerau L, Kosintsev P, Alekseeva V, Kim D, Hanage W, Herbig A, Jeong C, Warinner C*, Key F*. (2025) Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage. Cell 188:1-15. https://doi.org/10.1016/j.cell.2025.07.029
Dekker JAA, Peters C, Winter RM, Collins MJ, Dickinson MR, Harvey VL, Hill E, Nair B, Tsutaya T, Viñas-Caron LC, Warinner C, Welker F, Fagernäs Z. (2025) Open science, communication, and collaboration for the future of palaeoproteomics. Peer Community Journal 5(e77). https://doi.org/10.24072/pci.archaeo.100601
Wasmuth I, Warinner C, Stallforth P. (2025) Microbial dynamics and Pseudomonas natural product production in milk and dairy products. Natural Product Reports. https://doi.org/10.1039/d4np00074a.
Boldgiv B, Lkhagva A, Edwards S, Stenseth NC, Bayarsaikhan J, Altangerel D, Usukhjargal D, Dovchin B, Gombobaatar S, Batsaikhan N, Warinner C, Hart I, Galbreath K, Greiman SE, Malaney J, Murdoch JD, McLean B, DeWitte S, Manzitto-Tripp E, Chin K, Kaarim TS, Simpson C, Stevens NJ, Dunnum JL, Cook JA, and Taylor WTT. (2025) Global natural history infrastructure requires international solidarity, support, and investment in local capacity: lessons from Mongolia. Proceedings of the National Academy of Sciences 122 (6) e2411232122, https://www.pnas.org/doi/epub/10.1073/pnas.2411232122
Velsko IM, Warinner C. (2025) Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences. NPJ Biofilms and Microbiomes 11(19), https://doi.org/10.1038/s41522-024-00642-1
Kelmelis S, Walden JP, Green Mink K, Hoggarth JA, Ebert C, Freiwald C, Watkins TB, Izzo VSR, Biggie M, Thompson RA, Warinner C, Awe JJ. (2025) Biocultural Taphonomies and Analysis of an Emerging Terminal Classic (AD 750-900) Maya Deathway. In press at Journal of Archaeological Method and Theory 32 (22), https://doi.org/10.1007/s10816-024-09689-y
Bergstrom A, Fellows Yates J, Warinner C. (2024) Comment: Ancient DNA holds insights into past organisms and ecosystems – handle them with more care. Nature, 10 December 2024, https://www.nature.com/articles/d41586-024-03993-z
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. (2024) Exploring the potential of dental calculus to shed light on past human migrations in Oceania. Nature Communications, https://www.nature.com/articles/s41467-024-53920-z
Ghalichi A, Reinhold S, Rohrlach AB, Kalmykov AA, Childebayeva A, Yu H, Aron F, Semerau L, Bastert-Lamprichs K, Belinskiy AB, Berezina NY, Berezin YB, Broomandkhoshbacht N, Buzhilova AP, Erlikh VR, EVteev AA, Fehren-Schmitz L, Gambashidze I, Kantorovich AR, Kolesnichenko KB, Lordkipanidze D, Magomedov RG, Malek-Custodis K, Mariaschk D, Maslov VE, Mkrtchyan L, Nagler A, Fazeli Nashli H, Ochir M, Piotrovskiy YY, Saribekyan M, Sheremetev AG, Stöllner T, Thomalsky J, Vardanyan B, Posth C, Krause J, Warinner C, Hansen S, Haak W. (2024) The rise and transformation of Bronze Age pastoralists in the Caucasus. Nature,https://doi.org/10.1038/s41586-024-08113-5
Pan J, Liu X, Schiavinato S, Tressières G, Aury JM, Oliveira P, Wincker P, Arsuaga J, Bayarsaikhan J, Carbonell E, Lira Garrido J, Gilbert A, Hermes T, Warinner C, Kalmykov A, Lordkipanidze D, Mackiewicz P, Mohaseb A, Richter K, Shapiro B, Shnaider S, Southon J, Stefaniak K, Summers G, Asperen E, Vanishvili N, Hill E, Kuznetsov P, Reinhold S, Berthon R, Taylor W, Hekkala E, Orlando, L. (2024) Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses. Molecular Ecology, 33(19):e17527, https://doi.org/10.1111/mec.17527.
Barquera R, del Castillo-Chávez O, Nägele K, Hernández-Zaragoza DI, Szolek A, Rohrlach AB, Childebayeva A, Penman B, Acuña-Alonzo V, Bianco RA, Ramallo P, Lara-Riegos JC, Moo-Mezeta ME, Torres-Romero JC, Tzec-Puch CI, Kohlbacher O, Warinner C, Krause J*. (2024) Archaeogenetic analysis of a ritual mass burial at Chichén Itzá. Nature. https://www.nature.com/articles/s41586-024-07509-7
Michel M, Skourtanioti E, Pierini F, Barquera R, Bianco R, Carlhoff S, Coppola Bove L, Freilich S, Giffin K, Guevara EK, Hermes T, Hiss A, Knolle F, Mötsch A, Nelson EA, Neumann G, Papac L, Penske S, Rohrlach AB, Salem N, Semerau L, Villalba-Mouco, Abadie I, Aldenderfer M, Baquedano Perez E, Brown M, Carrion Santafe EC, Chenghwa T, Conteras Martinez M, Cruz Berrocal M, Czubak JM, Damsek L, Duffett Carlson KS, Durand R, Ernée M, Fantaneanu C, Frenzel H, García Atiénzar, Guillén S, Hsieh E, Karwowski M, Kinaston R, Küssner M, Lai L, Look C, Majander K, Mandl K, Mazzarello V, McCormick M, Murphy R, Nemeth R, Nordqvist K, Onkamo P, Olmo Enciso L, Orschiedt J, Paz de Miguel Ibáñez M, Peltola S, Romero A, Rubino S, Sajantila A, Salazar García D, Serrano E, Shaydullaev S, Slaus M, Stanco L, Swanston T, Teschler-Nicola M, Valentin F, Van der Vijver K, Varney T, Vigil-Escalera Guirado A, Waters C, Weiss-Krejci E, Winter E, Lamnidis TC, Prüfer K, Nägele K, Spyrou M, Schiffels S, Stockhammer PW, Haak W, Posth C, Warinner C, Bos K, Herbig A, Krause K. (2024) Ancient Plasmodium genomes shed light on the history of human malaria. Nature. https://www.nature.com/articles/s41586-024-07546-2
Warinner C. (2024) Fifteen years of research and outreach in the High Himalayas of Nepal. In Situ Magazine, Spring 2024.
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*. (2024) Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000, https://f1000research.com/articles/12-926/v2.
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
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
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
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.
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.
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. (2021) Ten millennia of hepatitis B virus evolution. Science 374 (6565): 182-188.
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 (2021). The evolution and changing ecology of the African hominid oral microbiome. PNAS 118 (20) e2021655118. https://doi.org/10.1073/pnas.2021655118
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.
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.
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.
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.
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.
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.
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
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.
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).
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.
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*, 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.
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.
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
Barquera R, Bernal Felipe N, Warinner C. “Acerca de las pandemias y epidemias en el México de ayer y hoy: de la época prehispánica al siglo xxi”. (2026) In: Cuerpos Multiples: Miradas Interdisciplinarias en Antropología, Eds: Maria del Carmen Lerma Gómez, Anabella Barragán Solís. Secretaría de Cultura Instituto Nacional de Antropología e Historia, Ciudad de México.
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
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. 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.
