Publications

Names of LMAMR members are shown in bold.

JOURNAL ARTICLES (2018-PRESENT)

      

 

 

 

Lawson PA, Saavedra Perez L, and Sankaranarayanan K (2023). Reclassification of Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia as Thomasclavelia cocleata gen. nov., comb. nov., Thomasclavelia ramosa comb. nov., gen. nov., Thomasclavelia spiroformis comb. nov. and Thomasclavelia saccharogumiacomb. nov. International Journal of Systematic and Evolutionary Microbiology 73(1). Link

Lewis CM Jr, Akinyi MY, DeWitte SN, and Stone AC (2023). Ancient pathogens provide a window into health and well-being. PNAS 120(4): e2209476119. Link

Haffner JJ, Katemauswa M, Kagone TS, Hossain E, Jacobson D, Flores K, Parab AR, Obregon-Tito AJ, Tito RY, Reyes LM, Troncoso-Corzo L, Guija-Poma E, Meda N, Carabin H, Honap TP, Sankaranarayanan K, Lewis CM Jr, and McCall L-I (2022). Untargeted Fecal metabolomic analyses across an industrialization gradient reveal shared metabolites and impact of industrialization on fecal microbiome-metabolome interactions. mSystems 7(6):e0071022. Link

Beans JA, Trinidad SB, Blacksher E, Hiratsuka VY, Spicer P, Woodahl EL, Boyer BB, Lewis CM Jr, Gaffney PM, Garrison NA, and Burke W (2022). Communicating precision medicine research: multidisciplinary teams and diverse communities. Public Health Genomics. 25: 155–163. Link

Sugiyama N, Sugiyama S, Cagnato C, France CAM, Iriki A, Hughes K, Singleton RR, Thornton E, and Hofman CA (2022). Earliest evidence of primate captivity and translocation supports gift diplomacy between Teotihuacan and the Maya. PNAS 119 (47): e2212431119. Link

Austin RM, Zuckerman M, Honap TP, Lee H, Ward GK, Warinner C, Sankaranarayanan K, and Hofman CA (2022). Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection. Communications Biology 5: 1050. Link

Mychajliw AM, Ellwood ER, Alagona PS, Anderson RS, Balisi M, Biber E, Brown JL, George J, Hendy A, Higgins LM, Hofman CA, Leger A, Ordeñana M, Pauly GB, Putnam BJ, Randall JM, Riley SPD, Shultz AJ, Stegner MA, Wake TA, and Lindsey EL (2022). Lessons for conservation from beneath the pavement. Conservation Biology 36(6): e13983. Link

Elliot Smith E, Rick TC, and Hofman CA (2022). Investigating fishing strategies and habitat differences in late Holocene sturgeon (Acipenser spp.) from the Oregon coast through coupled genetic and isotope analyses. Quaternary Science Advances 7: 100062. Link

Reeder-Myers LA, Braje TJ, Hofman CA, Elliott Smith EA, Garland C, Grone M, Hadden CS, Hatch M, Hunt T, Kelley A, LeFebvre MJ, Lockman M, McKechnie I, McNiven IJ, Newsom B, Pluckhahn T, Sanchez G, Schwadron M, Smith K, Smith T, Spiess A, Tayac G, Thompson VD, Vollman T, Weitzel EM, and Rick TC (2022). Indigenous oyster fisheries persisted for millennia and should inform future management. Nature Communications 13: 2383. Link

Vågene ÅJ, Honap TP, Harkins KM, Rosenberg MS, Giffin K, Cárdenas-Arroyo F, Leguizamón LP, Arnett J, Buikstra JE, Herbig A, Krause J, Stone AC, and Bos KI (2022). Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. Nature Communications 13(1): 1195. Link

Rick TC, Braje TJ, Graham L, Easterday K, Hofman CA, Holguin BE, Mychajliw AM, Reeder-Myers LA, and Reynolds MD (2022). Cultural keystone places and the Chumash landscapes of Kumqaq’, Point Conception, California. American Antiquity 1-18. Link

Rick TC, Alsharekh AM, Braje TJ, Crowther A, Erlandson JM, Fuller DQ, Gill KM, Groucutt HS, Guagnin M, Helm R, Hofman CA, Horton M, Kay A, Korisettar R, Radimilahy C, Reeder-Myers LA, Shipton C, Wright HT, Petraglia M, and Boivin N (2022). Coring, profiling, and trenching: archaeological field strategies for investigating the Pleistocene-Holocene-Anthropocene Continuum. Quaternary International 628: 1-17. Link

Eller AR, Canington SL, Saiyed ST, Austin RM, Hofman CA, and Sholts SB (2021). What does it mean to be wild? Assessing human influence on the environments of nonhuman primate specimens in museum collections. Ecology and Evolution 00: 1-13. Link

Rampelli S, Turroni S, Debandi F, Alberdi A, Schnorr SL, Hofman CA, Taddia A, Helg R, Biagi E, Brigidi P, D’Amico F, Cattani M, and Candela M (2021). The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs. iScience 24(8): 102816. Link

Fotedar R, Sankaranarayanan K, Caldwell ME, Zeyara A, Al Malki A, Kaul R, Al Shamari H, Ali M, Al Marri M, and Lawson PA (2021). Reclassification of Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis as Falseniella ignava gen. nov., comb. nov., Hutsoniella sourekii gen. nov., comb. nov., and Ruoffia tabacinasalis gen. nov., comb. nov., and description of Ruoffia halotolerans sp. nov., isolated from hypersaline Inland Sea of Qatar. Antonie Van Leeuwenhoek 114(8): 1181-1193. Link

Jacobson D, Moore K, Gunderson C, Rowland M, Austin R, Honap TP, Xu J, Warinner C, Sankaranarayanan K, and Lewis CM Jr (2021). Shifts in gut and vaginal microbiomes are associated with cancer recurrence time in women with ovarian cancer. PeerJ 9: e11574. Link

Zuckerman M, Austin RM, and Hofman CA (2021). Historical anatomical collections of human remains: Exploring their reinterpretation as representations of racial violence. Annals of the American Academy of Political and Social Science 694(1): 39-47. Link

Reding DM, Castañeda-Rico S, Shirazi S, Hofman CA, Cancellare IA, Lance SL, Beringer J, Clark WR, and Maldonado JE (2021). Mitochondrial genomes of the USA distribution of gray fox (Urocyon cinereoargenteus) reveals a major phylogeographic break at the Great Plains Suture Zone. Frontiers in Ecology and Evolution 9: 666800. Link

Hoffman K, Liu Z, Hossain E, Bottazzi ME, Hotez PJ, Jones KM, and McCall L-I (2021). Alterations to the cardiac metabolome induced by chronic T. cruzi infection relate to the degree of cardiac pathology. ACS Infectious Diseases 7(6): 1638-1649. Link

Parab AR, Thomas D, Lostracco-Johnson S, Siqueira-Neto JL, McKerrow JH, Dorrestein PC, and McCall L-I (2021). Dysregulation of glycerophosphocholines in the cutaneous lesion caused by Leishmania major in experimental murine models. Pathogens 10(5): 593. Link

Fellows Yates JA, Velsko IM, Aron F, Posth C, Hofman CA, Austin RM, Parker CE, Mann AE, Nägele K, Arthur KW, Arthur JW, Bauer CC, Crevecoeur I, Cupillard C, Curtis MC, Dalén L, Díaz-Zorita Bonilla M, Díez Fernández-Lomana JC, Drucker DG, Escribano Escrivá E, Francken M, Gibbon VE, González Morales MR, Grande Mateu A, Harvati K, Henry AG, Humphrey L, Menéndez M, Mihailović D, Peresani M, Rodríguez Moroder S, Roksandic M, Rougier H, Sázelová S, Stock JT, Straus LG, Svoboda J, Teßmann B, Walker MJ, Power RC, Lewis CM Jr, Sankaranarayanan K, Guschanski K, Wrangham RW, Dewhirst FE, Salazar-García DC, Krause J, Herbig A, and Warinner C (2021). The evolution and changing ecology of the African hominid oral microbiome. PNAS 118(20): e2021655118. Link

Grindle ED, Rick TC, Dagtas ND, Austin RM, Wellman H, Gobalet K, and Hofman CA (2021). Green or white? Morphology, ancient DNA, and the identification of archaeological North American Pacific Coast sturgeon. Journal of Archaeological Science: Reports 36: 102887. Link

McCall L-I (2021). Quo vadis? Central rules of pathogen and disease tropism. Frontiers in Cellular and Infection Microbiology 11: 640987. Link

Parab AR and McCall L-I (2021). Tryp-ing Up metabolism: Role of metabolic adaptations in kinetoplastid disease pathogenesis. Infection and Immunity 89(4): e00644-20. Link

Lanman RB, Hylkema L, Boone CM, Allée B, Castillo RO, Moreno SA, Flores MF, DeSilva U, Bingham B, and Kemp BM (2021). Ancient DNA analysis of archaeological specimens extends Chinook salmon’s known historic range to San Francisco Bay’s tributaries and southernmost watershed. PLoS One 16(4): e0244470. Link

Rampelli S, Turroni S, Mallol C, Hernandez C, Galván B, Sistiaga A, Biagi E, Astolfi A, Brigidi P, Benazzi S, Lewis CM Jr, Warinner C, Hofman CA, Schnorr SL, and Candela M (2021). Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. Communications Biology 4(1): 169. Link

McCall L-I (2021). mSphere of influence: forgotten questions. mSphere 6(3): e0052021. Link

Jacobson DK, Honap TP, Ozga AT, Meda N, Kagoné TS, Carabin H, Spicer P, Tito RY, Obregon-Tito AJ, Reyes LM, Troncoso-Corzo L, Guija-Poma E, Sankaranarayanan K, and Lewis CM Jr (2021). Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle. Scientific Reports 11(1): 1724. Link

Wellman HP, Austin RM, Dagtas ND, Moss ML, Rick TC, and Hofman CA (2020). Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction. Proceedings of the Royal Society B Biological Sciences 287(1940): 20202343. Link

Mann AE, Fellows Yates FE, Fagernäs Z, Austin RM, Nelson E, and Hofman CA (2020). Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus. Quaternary International (In Press). Link

Jacobson DK, Honap TP, Monroe C, Lund J, Houk BA, Novotny AC, Robin C, Marini E, and Lewis CM Jr (2020). Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. Philosophical Transactions of the Royal Society B Biological Sciences 375(1812): 20190586. Link

Stone AC, Lewis CM Jr, and Schuenemann VJ (2020). Insights into health and disease from ancient biomolecules. Philosophical Transactions of the Royal Society B Biological Sciences 375(1812): 20190568. Link

Halffman CM, Potter BA, McKinney HJ, Tsutaya T, Finney BP, Kemp BM, Bartelink EJ, Wooller MJ, Buckley M, Clark CT, Johnson JJ, Bingham BL, Lanoë FB, Sattler RA, and Reuther JD (2020) Ancient Beringian paleodiets revealed through multiproxy stable isotope analyses. Science Advances 6(36): eabc1968. Link

Kemp BM, Bingham B, Frome R, Labonte M, Palmer E, Parsons ES, Gobalet KW, and Rosenthal J (2020). Subduing the influence of PCR inhibitors on amplifying aged, degraded, and low copy number DNA: PCR enhancer cocktail-p and rescue PCR. PLOS One 15(6): e0234745. Link

Mychajliw AM, Rick TC, Dagtas ND, Erlandson JM, Culleton BJ, Kennett DJ, Buckley M, and Hofman CA (2020). Biogeographic problem-solving reveals the Late Pleistocene translocation of a short-faced bear to the California Channel Islands. Scientific Reports 10(1): 15172. Link

Fotedar R, Caldwell ME, Sankaranarayanan K, Al-Zeyara A, Al-Malki A, Kaul R, Al Marri M, Al-Shamari HS, and Lawson PA (2020). Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf. International Journal of Systematic and Evolutionary Microbiology 70(7): 4130-4138. Link

Erlandson JM, Braje TJ, Ainis AF, Culleton BJ, Gill KM, Hofman CA, Kennett DJ, Reeder-Myers LA, and Rick TC (2020). Maritime Paleoindian technology, subsistence, and ecology at an ~11,700 year old Paleocoastal site on California’s Northern Channel Islands, USA. PLoS One 15(9): e0238866. Link

Villanea FA, Kitchen A, and Kemp BM (2020). Applications of Bayesian skyline plots and approximate Bayesian computation for human demography. Human Biology 91(4): 279-296. Link

Pott LN, Austin RM, Eller AR, Hofman CA, and Sholts SB (2020). Population-level assessment of atlas occipitalization in artificially modified crania from pre-Hispanic Peru. PLoS One 15(9): e0239600. Link

Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, Cachet X, Caraballo-Rodriguez AM, Da Silva RR, Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Le Gouellec A, Ludwig M, Martin H C, McCall L-I, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyne O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, and Dorrestein PC (2020). Feature-based molecular networking in the GNPS analysis environment. Nature Methods 17(9): 905-908. Link

Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL 2nd, Kamenik Z, Le Gouellec A, Lu A, McCall L-I, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, and Dorrestein PC (2020). ReDU: a framework to find and reanalyze public mass spectrometry data. Nature Methods 17(9): 901-904. Link

Bernatchez JA and McCall L-I (2020). Insights gained into respiratory infection pathogenesis using lung tissue metabolomics. PLoS Pathogens 16(7): e1008662. Link

Hossain E, Khanam S, Dean DA, Wu C, Lostracco-Johnson S, Thomas D, Kane SS, Parab AR, Flores K, Katemauswa M, Gosmanov C, Hayes SE, Zhang Y, Li D, Woelfel-Monsivais C, Sankaranarayanan K, and McCall L-I (2020). Mapping of host-parasite-microbiome interactions reveals metabolic determinants of tropism and tolerance in Chagas disease. Science Advances 6(30): eaaz2015. Link

Fagernäs Z, Garcia Collado MI, Hendy J, Hofman CA, Speller C, Velsko I, and Warinner C (2020). A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus. Journal of Archaeological Science 118: 105135. Link

Dávalos LM, Austin RM, Balisi MA, Begay RL, Hofman CA, Kemp ME, Lund JR, Monroe C, Mychajliw AM, Nelson EA, Nieves-Colón MA, Redondo SA, Sabin S, Tsosie KS, and Yracheta JM (2020). Pandemics’ historical role in creating inequality. Science 368(6497): 1322-1323. Link

Eller AR, Pobiner B, Friend S, Austin RM, Hofman CA, and Sholts SB (2020). A chomped chimp: New evidence of tooth marks on an adult chimpanzee (Pan troglodytes verus). American Journal of Physical Anthropology 172(1): 140-147. Link

Nguyen TD, Lesani M, Forrest I, Lan Y, Dean DA, Gibaut QMR, Guo Y, Hossain E, Olvera M, Panlilio H, Parab AR, Wu C, Bernatchez JA, Cichewicz RH, and McCall L-I (2020). Local phenomena shape backyard soil metabolite composition. Metabolites 10(3): 86. Link

Borry M, Cordova B, Perri A, Wibowo M, Honap TP, Ko J, Yu J, Britton K, Girdland-Flink L, Power RC, Stuijts I, Salazar-García DC, Hofman CA, Hagan R, Samdapawindé Kagoné T, Meda N, Carabin H, Jacobson DK, Reinhard K, Lewis CM Jr, Kostic A, Jeong C, Herbig A, Hübner A, and Warinner C (2020) CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ 8: e9001. Link

Lewis CM Jr, McCall L-I, Sharp RR, and Spicer PG (2020). Ethical priority of the most actionable system of biomolecules: the metabolome. American Journal of Physical Anthropology 171(2): 177-181. Link

Der Sarkissian C, Möller P, Hofman CA, Ilsøe P, Rick TC, Schiøtte T, Sørensen MV, Dalén L, and Orlando L (2020). Unveiling the ecological applications of ancient DNA from mollusk shells. Frontiers in Ecology and Evolution 8: 37. Link

McCall L-I, Callewaert C, Zhu Q, Song SJ, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, and Dominguez-Bello MG (2020). Home chemical and microbial transitions across urbanization. Nature Microbiology 5(1):108-115. Link

Barton L, Bingham B, Sankaranarayanan K, Monroe C, Thomas A, and Kemp BM (2020). The earliest farmers of northwest China exploited grain-fed pheasants not chickens. Scientific Reports 10: 2556. Link

Honap TP, Sankaranarayanan K, Schnorr SL, Ozga AT, Warinner C, Lewis CM Jr (2020). Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. PLoS One 15(1): e0226930. Link

Singh B, Bernatchez JA, McCall L-I, Calvet CM, Ackermann J, Souza JM, Thomas D, Silva EM, Bachovchin KA, Klug DM, Jalani HB, Bag S, Buskes MJ, Leed SE, Roncal NE, Penn EC, Erath J, Rodriguez A, Sciotti RJ, Campbell RF, McKerrow J, Siqueira-Neto JL, Ferrins L, and Pollastri MP (2020). Scaffold and parasite hopping: Discovery of new protozoal proliferation inhibitors. ACS Medicinal Chemistry Letters 11(3): 249-257. Link

Schnorr SL, Hofman CA, Netshifhefhe SR, Duncan FD, Honap TP, Lesnik J, and Lewis CM Jr (2019). Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa. BMC Microbiology 19: 164. Link

Aronsen GP, Fehren-Schmitz L, Krigbaum J, Kamenov GD, Conlogue GJ, Warinner C, Ozga AT, Sankaranarayanan K, Griego A, DeLuca DW, Eckels HT, Byczkiewicz RK, Grgurich T, Pelletier NA, Brownlee SA, Marichal A, Williamson K, Tonoike Y, and Bellantoni NF (2019). “The dead shall be raised”: Multidisciplinary analysis of human skeletons reveals complexity in 19th century immigrant socioeconomic history and identity in New Haven, Connecticut. PLoS One 14(9): e0219279. Link

Boudreau PD, Miller BW, McCall L-I, Almaliti J, Reher R, Hirata K, Le T, Siqueira-Neto JL, Hook V, and Gerwick WH (2019). Design of gallinamide A analogs as potent inhibitors of the cysteine proteases human cathepsin L and Trypanosoma cruzi cruzain. Journal of Medicinal Chemistry 62(20): 9026-9044. Link

Hagan RW, Hofman CA, Hübner A, Reinhard K, Schnorr S, Lewis CM Jr, Sankaranarayanan K, and Warinner CG (2019). Comparison of extraction methods for recovering ancient microbial DNA from paleofeces. American Journal of Physical Anthropology 171(2): 275-284. Link

Winters M, Monroe C, Barta JL, and Kemp BM (2019). Evaluating the efficiency of primer extension capture as a method to enrich DNA extractions. Journal of Forensic Sciences 64(4): 1145-1151. Link

Patel NB, Obregón-Tito AJ, Tito RY, Trujillo-Villaroel O, Marin-Reyes L, Troncoso-Corzo L, Guija-Poma E, Lewis CM Jr, Lawson PA. Citroniella saccharovorans gen. nov. sp. nov., a member of the family Peptoniphilaceae isolated from a human fecal sample from a coastal traditional community member. International Journal of Systematic and Evolutionary Microbiology 69(4): 1142-1148. Link

De Los Santos R, Monroe C, Worl R, Worl R, Schroeder KB, and Kemp BM (2019). Genetic diversity and relationships of Tlingit moieties. Human Biology 91(2): 95-116. Link

Ziesemer KA, Ramos-Madrigal J, Mann AE, Brandt BW, Sankaranarayanan K, Ozga AT, Hoogland M, Hofman CA, Salazar-García DC, Frohlich B, Milner GR, Stone AC, Aldenderfer M, Lewis CM Jr, Hofman CL, Warinner C, and Schroeder H (2019). The efficacy of whole human genome capture on ancient dental calculus and dentin. American Journal of Physical Anthropology 168(3): 496-509. Link

Hofman CA and Warinner C (2019). Ancient DNA 101: An introductory guide in the era of high-throughput sequencing. The SAA Archaeological Record Volume 19(1): 18-25. Link

Austin RM, Sholts SB, Williams L, Kistler L, and Hofman CA (2019). Opinion: To curate the molecular past, museums need a carefully considered set of best practices. PNAS 116(5): 1471-1474.  Link

Lindo J, Haas R, Hofman CA, Apata M, Moraga M, Verdugo R, Watson JT, Llave CV, Witonsky D, Pacheco EV, Beall C, Warinner C, Novembre J, Aldenderfer M, and Di Rienzo A (2018). The genetic prehistory of the Andean highlands 7,000 Years BP though European contact. Science Advances (4)11: eaau4921. Link

Jeong C, Wilkin S, Amgalantugs T, Bouwman AS, Taylor WTT, Hagan RW, Bromage S, Tsolmon S, Trachsel C, Grossmann J, Littleton J, Makarewicz CA, Krigbaum J, Burri M, Scott A, Davaasambuu G, Wright J, Irmer F, Myagmar E, Boivin N, Robbeets M, Rühli FJ, Krause J, Frohlich B, Hendy J, and Warinner C (2018). Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe. PNAS 115(48): E11248-E11255. Link

Palmer E, Tushingham S, and Kemp BM (2018). Human use of small forage fish: Improved ancient DNA species identification techniques reveal long term record of sustainable mass harvesting of smelt fishery in the northeast Pacific Rim. Journal of Archaeological Science 99: 143-152. Link

Hofman CA, Rick TC, Erlandson JM, Reeder-Myers L, Welch AJ, and Buckley M (2018). Collagen fingerprinting and the earliest marine mammal hunting in North America. Scientific Reports 8: 10014. Link

Siqueira-Neto JL, Debnath A, McCall L-I, Bernatchez JA, Ndao M, Reed SL, and Rosenthal PJ (2018). Cysteine proteases in protozoan parasites. PLoS Neglected Tropical Diseases 12(8): e0006512. Link

Hendy J, Warinner C, Bouwman A, Collins MJ, Fiddyment S, Fischer R, Hagan R, Hofman CA, Holst M, Chaves E, Klaus L, Larson G, Mackie M, McGrath K, Mundorff AZ, Radini A, Rao H, Trachsel C, Velsko IM, and Speller CF (2018). Proteomic evidence of dietary sources in ancient dental calculus. Proceedings of the Royal Society B 285: 20180977. Link

Newsom SN and McCall L-I (2018). Metabolomics: Eavesdropping on silent conversations between hosts and their unwelcome guests. PLoS Pathogens 14(4): e1006926. Link

Mann AE, Sabin S, Ziesemer K, Vågene ÅJ, Schroeder H, Ozga AT, Sankaranarayanan K, Hofman CA, Yates JAF, Salazar-García DC, Frohlich B, Aldenderfer M, Hoogland M, Read C, Milner GR, Stone AC, Lewis Jr CM, Krause J, Hofman C, Bos KI, and Warinner C (2018). Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports 8: 9822. Link

Johnson BM, Kemp BM, and Thorgaard GH (2018). Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha.  PLOS One 13(1): e0190059. Link

Conrad C, Barceló LP, Seminoff JA, Tomaszewicz CT, Labonte M, Kemp BM, Jones EL, Stoyka M, Bruner K, and Pastron A (2018). Ancient DNA analysis and stable isotope ecology of sea turtles (Cheloniidae) from the Gold Rush-era (1850s) Eastern Pacific Ocean. Open Quaternary 4: 1-13. Link

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall L-I, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, and Dorrestein PC (2018). Best practices for analysing microbiomes. Nature Reviews Microbiology 16: 410-422. Link

McCall L-I, Tripathi A, Vargas F, Knight R, Dorrestein PC, Siqueira-Neto JL (2018). Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome. PLoS Neglected Tropical Diseases 12(3): e0006344. Link

Honap TP, Pfister L-A, Housman G, Mills S, Tarara RP, Suzuki K, Cuozzo FP, Sauther ML, Rosenberg MS, and Stone AC (2018). Mycobacterium leprae genomes from naturally infected nonhuman primates. PLoS Neglected Tropical Diseases 12(1): e0006190. Link