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Metagenomic analysis of dental calculus in ancient Egyptian baboons.

Ottoni C, Guellil M, Ozga AT, Stone AC, Kersten O, Bramanti B, Porcier S, Van Neer W.

Sci Rep. 2019 Dec 23;9(1):19637. doi: 10.1038/s41598-019-56074-x.


Oral microbiome diversity in chimpanzees from Gombe National Park.

Ozga AT, Gilby I, Nockerts RS, Wilson ML, Pusey A, Stone AC.

Sci Rep. 2019 Nov 22;9(1):17354. doi: 10.1038/s41598-019-53802-1.


Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities.

Nieves-Colón MA, Pestle WJ, Reynolds AW, Llamas B, de la Fuente C, Fowler K, Skerry KM, Crespo-Torres E, Bustamante CD, Stone AC.

Mol Biol Evol. 2019 Nov 9. pii: msz267. doi: 10.1093/molbev/msz267. [Epub ahead of print]


Volatilised pyrene: A phase 1 study demonstrating a new method of visualising fingermarks with comparisons to iodine fuming.

Chang I, Stone ACA, Hanney OC, Gee WJ.

Forensic Sci Int. 2019 Dec;305:109996. doi: 10.1016/j.forsciint.2019.109996. Epub 2019 Oct 21.


The lineages of the first humans to reach northeastern Siberia and the Americas.

Stone AC.

Nature. 2019 Jun;570(7760):170-172. doi: 10.1038/d41586-019-01374-5. No abstract available.


The RNA binding protein HuR influences skeletal muscle metabolic flexibility in rodents and humans.

Mynatt RL, Noland RC, Elks CM, Vandanmagsar B, Bayless DS, Stone AC, Ghosh S, Ravussin E, Warfel JD.

Metabolism. 2019 Aug;97:40-49. doi: 10.1016/j.metabol.2019.05.010. Epub 2019 May 23.


Fetal Hemoglobin Modulators May Be Associated With Symptomology of Football Players with Sickle Cell Trait.

Flansburg C, Balentine CM, Grieger RW, Lund J, Ciambella M, White D, Coris E, Gonzalez E, Stone AC, Madrigal L.

South Med J. 2019 May;112(5):289-294. doi: 10.14423/SMJ.0000000000000976.


Genetic-Based Susceptibility of a Foundation Tree to Herbivory Interacts With Climate to Influence Arthropod Community Composition, Diversity, and Resilience.

Stone AC, Gehring CA, Cobb NS, Whitham TG.

Front Plant Sci. 2018 Dec 11;9:1831. doi: 10.3389/fpls.2018.01831. eCollection 2018.


The efficacy of whole human genome capture on ancient dental calculus and dentin.

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, Schroeder H.

Am J Phys Anthropol. 2019 Mar;168(3):496-509. doi: 10.1002/ajpa.23763. Epub 2018 Dec 26.


Methadone maintenance treatment among patients exposed to illicit fentanyl in Rhode Island: Safety, dose, retention, and relapse at 6 months.

Stone AC, Carroll JJ, Rich JD, Green TC.

Drug Alcohol Depend. 2018 Nov 1;192:94-97. doi: 10.1016/j.drugalcdep.2018.07.019. Epub 2018 Aug 25.


In-solution Y-chromosome capture-enrichment on ancient DNA libraries.

Cruz-Dávalos DI, Nieves-Colón MA, Sockell A, Poznik GD, Schroeder H, Stone AC, Bustamante CD, Malaspinas AS, Ávila-Arcos MC.

BMC Genomics. 2018 Aug 14;19(1):608. doi: 10.1186/s12864-018-4945-x.


Novel anelloviruses identified in buccal swabs of Antarctic fur seals.

Crane A, Goebel ME, Kraberger S, Stone AC, Varsani A.

Virus Genes. 2018 Oct;54(5):719-723. doi: 10.1007/s11262-018-1585-9. Epub 2018 Jul 3.


Differential preservation of endogenous human and microbial DNA in dental calculus and dentin.

Mann AE, Sabin S, Ziesemer K, Vågene ÅJ, Schroeder H, Ozga AT, Sankaranarayanan K, Hofman CA, Fellows Yates JA, Salazar-García DC, Frohlich B, Aldenderfer M, Hoogland M, Read C, Milner GR, Stone AC, Lewis CM Jr, Krause J, Hofman C, Bos KI, Warinner C.

Sci Rep. 2018 Jun 29;8(1):9822. doi: 10.1038/s41598-018-28091-9.


Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments.

Nieves-Colón MA, Ozga AT, Pestle WJ, Cucina A, Tiesler V, Stanton TW, Stone AC.

Am J Phys Anthropol. 2018 Aug;166(4):824-836. doi: 10.1002/ajpa.23472. Epub 2018 Mar 30.


A Biomechanical Comparison of Fifth Metatarsal Jones Fracture Fixation Methods.

Duplantier NL, Mitchell RJ, Zambrano S, Stone AC, Delgado DA, Lambert BS, Moreno MR, Harris JD, McCulloch PC, Lintner DM, Varner KE.

Am J Sports Med. 2018 Apr;46(5):1220-1227. doi: 10.1177/0363546517753376. Epub 2018 Feb 21.


Assessment of DNA Methylation Patterns in the Bone and Cartilage of a Nonhuman Primate Model of Osteoarthritis.

Housman G, Havill LM, Quillen EE, Comuzzie AG, Stone AC.

Cartilage. 2019 Jul;10(3):335-345. doi: 10.1177/1947603518759173. Epub 2018 Feb 19.


Mycobacterium leprae genomes from naturally infected nonhuman primates.

Honap TP, Pfister LA, Housman G, Mills S, Tarara RP, Suzuki K, Cuozzo FP, Sauther ML, Rosenberg MS, Stone AC.

PLoS Negl Trop Dis. 2018 Jan 30;12(1):e0006190. doi: 10.1371/journal.pntd.0006190. eCollection 2018 Jan.


Insights from the Genome Sequence of Mycobacterium lepraemurium: Massive Gene Decay and Reductive Evolution.

Benjak A, Honap TP, Avanzi C, Becerril-Villanueva E, Estrada-García I, Rojas-Espinosa O, Stone AC, Cole ST.

mBio. 2017 Oct 17;8(5). pii: e01283-17. doi: 10.1128/mBio.01283-17.


Facing the facts: The Runx2 gene is associated with variation in facial morphology in primates.

Ritzman TB, Banovich N, Buss KP, Guida J, Rubel MA, Pinney J, Khang B, Ravosa MJ, Stone AC.

J Hum Evol. 2017 Oct;111:139-151. doi: 10.1016/j.jhevol.2017.06.014. Epub 2017 Aug 9.


Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes.

Malukiewicz J, Hepp CM, Guschanski K, Stone AC.

Am J Phys Anthropol. 2017 Jan;162(1):157-169. doi: 10.1002/ajpa.23105. Epub 2016 Oct 20.


Application of PE-RADSeq to the study of genomic diversity and divergence of two Brazilian marmoset species (Callithrix jacchus and C. penicillata).

Malukiewicz J, Guschanski K, Grativol AD, Oliveira MA, Ruiz-Miranda CR, Stone AC.

Am J Primatol. 2017 Feb;79(2):1-12. doi: 10.1002/ajp.22587. Epub 2016 Aug 12.


Correction: Validation of qPCR Methods for the Detection of Mycobacterium in New World Animal Reservoirs.

Housman G, Malukiewicz J, Boere V, Grativol AD, Pereira LC, Silva IO, Ruiz-Miranda CR, Truman R, Stone AC.

PLoS Negl Trop Dis. 2016 May 24;10(5):e0004756. doi: 10.1371/journal.pntd.0004756. eCollection 2016 May.


Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus.

Ozga AT, Nieves-Colón MA, Honap TP, Sankaranarayanan K, Hofman CA, Milner GR, Lewis CM Jr, Stone AC, Warinner C.

Am J Phys Anthropol. 2016 Jun;160(2):220-8. doi: 10.1002/ajpa.22960. Epub 2016 Mar 16.


Phylogenomic reconstruction supports supercontinent origins for Leishmania.

Harkins KM, Schwartz RS, Cartwright RA, Stone AC.

Infect Genet Evol. 2016 Mar;38:101-109. doi: 10.1016/j.meegid.2015.11.030. Epub 2015 Dec 18.


Pre-Columbian tuberculosis in Tierra del Fuego? Discussion of the paleopathological and molecular evidence.

Guichón RA, Buikstra JE, Stone AC, Harkins KM, Suby JA, Massone M, Prieto Lglesias A, Wilbur A, Constantinescu F, Rodríguez Martín C.

Int J Paleopathol. 2015 Dec;11:92-101. doi: 10.1016/j.ijpp.2015.09.003. Epub 2015 Nov 17.


Validation of qPCR Methods for the Detection of Mycobacterium in New World Animal Reservoirs.

Housman G, Malukiewicz J, Boere V, Grativol AD, Pereira LC, Silva Ide O, Ruiz-Miranda CR, Truman R, Stone AC.

PLoS Negl Trop Dis. 2015 Nov 16;9(11):e0004198. doi: 10.1371/journal.pntd.0004198. eCollection 2015 Nov. Erratum in: PLoS Negl Trop Dis. 2016 May;10(5):e0004756.


A composite genome approach to identify phylogenetically informative data from next-generation sequencing.

Schwartz RS, Harkins KM, Stone AC, Cartwright RA.

BMC Bioinformatics. 2015 Jun 11;16:193. doi: 10.1186/s12859-015-0632-y.


Natural and Anthropogenic Hybridization in Two Species of Eastern Brazilian Marmosets (Callithrix jacchus and C. penicillata).

Malukiewicz J, Boere V, Fuzessy LF, Grativol AD, de Oliveira E Silva I, Pereira LC, Ruiz-Miranda CR, Valença YM, Stone AC.

PLoS One. 2015 Jun 10;10(6):e0127268. doi: 10.1371/journal.pone.0127268. eCollection 2015.


Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

Cabana GS, Lewis CM Jr, Tito RY, Covey RA, Cáceres AM, Cruz AF, Durand D, Housman G, Hulsey BI, Iannacone GC, López PW, Martínez R, Medina Á, Dávila OO, Pinto KP, Santillán SI, Domínguez PR, Rubel M, Smith HF, Smith SE, Massa VR, Lizárraga B, Stone AC.

Hum Biol. 2014 Summer;86(3):147-65. Erratum in: Hum Biol. 2015 Oct;87(4):376-377.


Ancient pathogen genomics: insights into timing and adaptation.

Harkins KM, Stone AC.

J Hum Evol. 2015 Feb;79:137-49. doi: 10.1016/j.jhevol.2014.11.002. Epub 2014 Dec 18.


Screening ancient tuberculosis with qPCR: challenges and opportunities.

Harkins KM, Buikstra JE, Campbell T, Bos KI, Johnson ED, Krause J, Stone AC.

Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130622. doi: 10.1098/rstb.2013.0622.


Hybridization effects and genetic diversity of the common and black-tufted marmoset (Callithrix jacchus and Callithrix penicillata) mitochondrial control region.

Malukiewicz J, Boere V, Fuzessy LF, Grativol AD, French JA, de Oliveira e Silva I, Pereira LC, Ruiz-Miranda CR, Valença YM, Stone AC.

Am J Phys Anthropol. 2014 Dec;155(4):522-36. doi: 10.1002/ajpa.22605. Epub 2014 Sep 3. Erratum in: Am J Phys Anthropol. 2015 Sep;158(1):173.


Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.

Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK, Guichon RA, Wolfe Steadman DL, Cook DC, Niemann S, Behr MA, Zumarraga M, Bastida R, Huson D, Nieselt K, Young D, Parkhill J, Buikstra JE, Gagneux S, Stone AC, Krause J.

Nature. 2014 Oct 23;514(7523):494-7. doi: 10.1038/nature13591. Epub 2014 Aug 20.


Rapid evolution of BRCA1 and BRCA2 in humans and other primates.

Lou DI, McBee RM, Le UQ, Stone AC, Wilkerson GK, Demogines AM, Sawyer SL.

BMC Evol Biol. 2014 Jul 11;14:155. doi: 10.1186/1471-2148-14-155.


Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity.

Ferreira Z, Hurle B, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Gonder MK, Stone AC, Tishkoff S, Swanson WJ; NISC Comparative Sequencing Program, Green ED, Clark AG, Seixas S.

Genome Biol Evol. 2013;5(12):2512-23. doi: 10.1093/gbe/evt198. Erratum in: Genome Biol Evol. 2014;6(2):406.


An anthropological genetic perspective on Creolization in the Anglophone Caribbean.

Torres JB, Stone AC, Kittles R.

Am J Phys Anthropol. 2013 May;151(1):135-43. doi: 10.1002/ajpa.22261. Epub 2013 Mar 29.


Regulatory element copy number differences shape primate expression profiles.

Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12656-61. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13.


Long-term balancing selection at the antiviral gene OAS1 in Central African chimpanzees.

Ferguson W, Dvora S, Fikes RW, Stone AC, Boissinot S.

Mol Biol Evol. 2012 Apr;29(4):1093-103. doi: 10.1093/molbev/msr247. Epub 2011 Nov 21.


Echocardiographic evidence of pulmonary hypertension is associated with increased 1-year mortality in patients admitted with chronic obstructive pulmonary disease.

Stone AC, Machan JT, Mazer J, Casserly B, Klinger JR.

Lung. 2011 Jun;189(3):207-12. doi: 10.1007/s00408-011-9293-4. Epub 2011 May 10.


More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure.

Stone AC, Battistuzzi FU, Kubatko LS, Perry GH Jr, Trudeau E, Lin H, Kumar S.

Philos Trans R Soc Lond B Biol Sci. 2010 Oct 27;365(1556):3277-88. doi: 10.1098/rstb.2010.0096.


Drought negatively affects communities on a foundation tree: growth rings predict diversity.

Stone AC, Gehring CA, Whitham TG.

Oecologia. 2010 Nov;164(3):751-61. doi: 10.1007/s00442-010-1684-3. Epub 2010 Jun 26.


Haplotype structure and divergence at human and chimpanzee serotonin transporter and receptor genes: implications for behavioral disorder association analyses.

Claw KG, Tito RY, Stone AC, Verrelli BC.

Mol Biol Evol. 2010 Jul;27(7):1518-29. doi: 10.1093/molbev/msq030. Epub 2010 Jan 29.


Tuberculosis and leprosy in perspective.

Stone AC, Wilbur AK, Buikstra JE, Roberts CA.

Am J Phys Anthropol. 2009;140 Suppl 49:66-94. doi: 10.1002/ajpa.21185.


Different selective pressures shape the molecular evolution of color vision in chimpanzee and human populations.

Verrelli BC, Lewis CM Jr, Stone AC, Perry GH.

Mol Biol Evol. 2008 Dec;25(12):2735-43. doi: 10.1093/molbev/msn220. Epub 2008 Oct 1.


Copy number variation and evolution in humans and chimpanzees.

Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R.

Genome Res. 2008 Nov;18(11):1698-710. doi: 10.1101/gr.082016.108. Epub 2008 Sep 4.


Mitochondrial DNA and the peopling of South America.

Lewis CM Jr, Lizárraga B, Tito RY, López PW, Iannacone GC, Medina A, Martínez R, Polo SI, De La Cruz AF, Cáceres AM, Stone AC.

Hum Biol. 2007 Apr;79(2):159-78.


Diet and the evolution of human amylase gene copy number variation.

Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC.

Nat Genet. 2007 Oct;39(10):1256-60. Epub 2007 Sep 9.


Other systemic manifestations of chronic obstructive pulmonary disease.

Stone AC, Nici L.

Clin Chest Med. 2007 Sep;28(3):553-7, vi. Review.


Mitochondrial and Y chromosome diversity in the English-speaking Caribbean.

Benn Torres J, Kittles RA, Stone AC.

Ann Hum Genet. 2007 Nov;71(Pt 6):782-90. Epub 2007 Jun 27.


Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

Parker-Katiraee L, Carson AR, Yamada T, Arnaud P, Feil R, Abu-Amero SN, Moore GE, Kaneda M, Perry GH, Stone AC, Lee C, Meguro-Horike M, Sasaki H, Kobayashi K, Nakabayashi K, Scherer SW.

PLoS Genet. 2007 May 4;3(5):e65. Epub 2007 Mar 12.

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