• 4457 Citations
  • 28 h-Index
1993 …2020

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

  • 4457 Citations
  • 28 h-Index
  • 72 Article
  • 3 Chapter
  • 2 Comment/debate
  • 2 Review article
2020

Advancing the understanding of treponemal disease in the past and present

Baker, B. J., Crane-Kramer, G., Dee, M. W., Gregoricka, L. A., Henneberg, M., Lee, C., Lukehart, S. A., Mabey, D. C., Roberts, C. A., Stodder, A. L. W., Stone, A. C. & Winingear, S., 2020, (Accepted/In press) In : American journal of physical anthropology.

Research output: Contribution to journalArticle

3 Scopus citations

Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities

Nieves-Colón, M. A., Pestle, W. J., Reynolds, A. W., Llamas, B., De La Fuente, C., Fowler, K., Skerry, K. M., Crespo-Torres, E., Bustamante, C. D., Stone, A. C. & Mulligan, C., Mar 1 2020, In : Molecular biology and evolution. 37, 3, p. 611-626 16 p.

Research output: Contribution to journalArticle

3 Scopus citations

Differential DNA methylation of vocal and facial anatomy genes in modern humans

Gokhman, D., Nissim-Rafinia, M., Agranat-Tamir, L., Housman, G., García-Pérez, R., Lizano, E., Cheronet, O., Mallick, S., Nieves-Colón, M. A., Li, H., Alpaslan-Roodenberg, S., Novak, M., Gu, H., Osinski, J. M., Ferrando-Bernal, M., Gelabert, P., Lipende, I., Mjungu, D., Kondova, I., Bontrop, R. & 21 others, Kullmer, O., Weber, G., Shahar, T., Dvir-Ginzberg, M., Faerman, M., Quillen, E. E., Meissner, A., Lahav, Y., Kandel, L., Liebergall, M., Prada, M. E., Vidal, J. M., Gronostajski, R. M., Stone, A. C., Yakir, B., Lalueza-Fox, C., Pinhasi, R., Reich, D., Marques-Bonet, T., Meshorer, E. & Carmel, L., Dec 1 2020, In : Nature communications. 11, 1, 1189.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution

Morales-Arce, A. Y., Harris, R. B., Stone, A. C. & Jensen, J. D., May 1 2020, In : Evolution. 74, 5, p. 992-1001 10 p.

Research output: Contribution to journalArticle

Genomic insights into the early peopling of the Caribbean

Nägele, K., Posth, C., Orbegozo, M. I., De Armas, Y. C., Godoy, S. T. H., Herrera, U. M. G., Nieves-Colón, M. A., Sandoval-Velasco, M., Mylopotamitaki, D., Radzeviciute, R., Laffoon, J., Pestle, W. J., Ramos-Madrigal, J., Lamnidis, T. C., Schaffer, W. C., Carr, R. S., Day, J. S., Antúnez, C. A., Rivero, A. R., Martínez-Fuentes, A. J. & 9 others, Crespo-Torres, E., Roksandic, I., Stone, A. C., Lalueza-Fox, C., Hoogland, M., Roksandic, M., Hofman, C. L., Krause, J. & Schroeder, H., Jul 24 2020, In : Science. 369, 6502, p. 456-460 5 p.

Research output: Contribution to journalArticle

Getting sick in the Neolithic

Stone, A. C., Mar 1 2020, In : Nature Ecology and Evolution. 4, 3, p. 286-287 2 p.

Research output: Contribution to journalComment/debate

Identification of the geographic origins of people buried in the cemetery of the Salesian Mission of Tierra del Fuego through the analyses of mtDNA and stable isotopes

Motti, J. M. B., Winingear, S., Valenzuela, L. O., Nieves-Colón, M. A., Harkins, K. M., García Laborde, P., Bravi, C. M., Guichón, R. A. & Stone, A. C., Oct 2020, In : Journal of Archaeological Science: Reports. 33, 102559.

Research output: Contribution to journalArticle

Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates

Housman, G., Quillen, E. E. & Stone, A. C., Jan 1 2020, (Accepted/In press) In : American journal of physical anthropology.

Research output: Contribution to journalArticle

2 Scopus citations

Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques

Emery, M. V., Bolhofner, K., Winingear, S., Oldt, R., Montes, M., Kanthaswamy, S., Buikstra, J. E., Fulginiti, L. C. & Stone, A. C., May 2020, In : Forensic Science International: Genetics. 46, 102272.

Research output: Contribution to journalArticle

2019

Ancient DNA in the study of ancient disease

Stone, A. C. & Ozga, A. T., Jan 1 2019, Ortner's Identification of Pathological Conditions in Human Skeletal Remains. Elsevier, p. 183-210 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Scopus citations

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

Housman, G., Havill, L. M., Quillen, E. E., Comuzzie, A. G. & Stone, A. C., Jul 1 2019, In : Cartilage. 10, 3, p. 335-345 11 p.

Research output: Contribution to journalArticle

6 Scopus citations

Metagenomic analysis of dental calculus in ancient Egyptian baboons

Ottoni, C., Guellil, M., Ozga, A. T., Stone, A. C., Kersten, O., Bramanti, B., Porcier, S. & Van Neer, W., Dec 1 2019, In : Scientific reports. 9, 1, 19637.

Research output: Contribution to journalArticle

Open Access

Oral microbiome diversity in chimpanzees from Gombe National Park

Ozga, A. T., Gilby, I., Nockerts, R. S., Wilson, M. L., Pusey, A. & Stone, A. C., Dec 1 2019, In : Scientific reports. 9, 1, 17354.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

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

Ziesemer, K. A., Ramos-Madrigal, J., Mann, A. E., Brandt, B. W., Sankaranarayanan, K., Ozga, A. T., Hoogland, M., Hofman, C. A., Salazar-García, D. C., Frohlich, B., Milner, G. R., Stone, A. C., Aldenderfer, M., Lewis, C. M., Hofman, C. L., Warinner, C. & Schroeder, H., Mar 2019, In : American journal of physical anthropology. 168, 3, p. 496-509 14 p.

Research output: Contribution to journalArticle

1 Scopus citations
2018

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

Nieves-Colón, M. A., Ozga, A. T., Pestle, W. J., Cucina, A., Tiesler, V., Stanton, T. W. & Stone, A. C., Aug 2018, In : American journal of physical anthropology. 166, 4, p. 824-836 13 p.

Research output: Contribution to journalArticle

3 Scopus citations

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

Mann, A. E., Sabin, S., Ziesemer, K., Vågene, Å. J., Schroeder, H., Ozga, A. T., Sankaranarayanan, K., Hofman, C. A., Fellows Yates, J. A., Salazar-García, D. C., Frohlich, B., Aldenderfer, M., Hoogland, M., Read, C., Milner, G. R., Stone, A. C., Lewis, C. M., Krause, J., Hofman, C., Bos, K. I. & 1 others, Warinner, C., Dec 1 2018, In : Scientific reports. 8, 1, 9822.

Research output: Contribution to journalArticle

15 Scopus citations

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

Cruz-Dávalos, D. I., Nieves-Colón, M. A., Sockell, A., Poznik, G. D., Schroeder, H., Stone, A. C., Bustamante, C. D., Malaspinas, A. S. & Ávila-Arcos, M. C., Aug 14 2018, In : BMC Genomics. 19, 1, 608.

Research output: Contribution to journalArticle

5 Scopus citations

Mycobacterium leprae genomes from naturally infected nonhuman primates

Honap, T. P., Pfister, L. A., Housman, G., Mills, S., Tarara, R. P., Suzuki, K., Cuozzo, F. P., Sauther, M. L., Rosenberg, M. S. & Stone, A., Jan 2018, In : PLoS Neglected Tropical Diseases. 12, 1, e0006190.

Research output: Contribution to journalArticle

21 Scopus citations

Novel anelloviruses identified in buccal swabs of Antarctic fur seals

Crane, A., Goebel, M. E., Kraberger, S., Stone, A. & Varsani, A., Jul 3 2018, (Accepted/In press) In : Virus Genes. p. 1-5 5 p.

Research output: Contribution to journalArticle

1 Scopus citations
2017

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, A. D., Oliveira, M. A. B., Ruiz-Miranda, C. R. & Stone, A., Feb 1 2017, In : American Journal of Primatology. 79, 2, p. 1-12 12 p.

Research output: Contribution to journalArticle

3 Scopus citations

Determining the population affinity of an unprovenienced human skull for repatriation

Watkins, J. K., Blatt, S. H., Bradbury, C. A., Alanko, G. A., Kohn, M. J., Lytle, M. L., Taylor, J., Lacroix, D., Nieves-Colón, M. A., Stone, A. & Butt, D. P., Apr 1 2017, In : Journal of Archaeological Science: Reports. 12, p. 384-394 11 p.

Research output: Contribution to journalArticle

5 Scopus citations

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

Ritzman, T. B., Banovich, N., Buss, K. P., Guida, J., Rubel, M. A., Pinney, J., Khang, B., Ravosa, M. J. & Stone, A., Oct 1 2017, In : Journal of Human Evolution. 111, p. 139-151 13 p.

Research output: Contribution to journalArticle

7 Scopus citations

Insights from the genome sequence of Mycobacterium lepraemurium: Massive gene decay and reductive evolution

Benjak, A., Honap, T. P., Avanzi, C., Becerril-Villanueva, E., Estrada-García, I., Rojas-Espinosa, O., Stone, A. C. & Cole, S. T., Sep 1 2017, In : mBio. 8, 5, e01283-17.

Research output: Contribution to journalArticle

7 Scopus citations

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

Malukiewicz, J., Hepp, C. M., Guschanski, K. & Stone, A., Jan 1 2017, In : American Journal of Physical Anthropology. 162, 1, p. 157-169 13 p.

Research output: Contribution to journalArticle

6 Scopus citations
2016

Phylogenomic reconstruction supports supercontinent origins for Leishmania

Harkins, K. M., Schwartz, R. S., Cartwright, R. A. & Stone, A. C., Mar 1 2016, In : Infection, Genetics and Evolution. 38, p. 101-109 9 p.

Research output: Contribution to journalArticle

34 Scopus citations

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

Ozga, A. T., Nieves-Colón, M. A., Honap, T. P., Sankaranarayanan, K., Hofman, C. A., Milner, G. R., Lewis, C. M., Stone, A. & Warinner, C., Jun 1 2016, In : American journal of physical anthropology. 160, 2, p. 220-228 9 p.

Research output: Contribution to journalArticle

25 Scopus citations
2015

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

Schwartz, R. S., Harkins, K. M., Stone, A. C. & Cartwright, R. A., Jun 11 2015, In : BMC bioinformatics. 16, 1, 193.

Research output: Contribution to journalArticle

8 Scopus citations

Ancient pathogen genomics: Insights into timing and adaptation

Harkins, K. M. & Stone, A., Feb 1 2015, In : Journal of human evolution. 79, p. 137-149 13 p.

Research output: Contribution to journalArticle

26 Scopus citations

Natural and anthropogenic hybridization in two species of eastern Brazilian marmosets (Callithrix jacchus and C. penicillata)

Malukiewicz, J., Boere, V., Fuzessy, L. F., Grativol, A. D., De Oliveira E Silva, I., Pereira, L. C. M., Ruiz-Miranda, C. R., Valença, Y. M. & Stone, A., Jun 10 2015, In : PloS one. 10, 6, e0127268.

Research output: Contribution to journalArticle

25 Scopus citations

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

Guichón, R. A., Buikstra, J., Stone, A., Harkins, K. M., Suby, J. A., Massone, M., Prieto lglesias, A., Wilbur, A., Constantinescu, F. & Rodríguez Martín, C., 2015, In : International Journal of Paleopathology. 11, p. 92-101 10 p.

Research output: Contribution to journalArticle

4 Scopus citations

Screening ancient tuberculosis with qPCR: challenges and opportunities

Harkins, K. M., Buikstra, J. E., Campbell, T., Bos, K. I., Johnson, E. D., Krause, J. & Stone, A. C., Jan 19 2015, In : Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 370, 1660, p. 20130622 1 p.

Research output: Contribution to journalArticle

Screening ancient tuberculosis with qPCR: Challenges and opportunities

Harkins, K. M., Buikstra, J., Campbell, T., Bos, K. I., Johnson, E. D., Krause, J. & Stone, A., Jan 19 2015, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 370, 1660

Research output: Contribution to journalArticle

10 Scopus citations

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

Housman, G., Malukiewicz, J., Boere, V., Grativol, A. D., Pereira, L. C. M., Silva, I. D. O. E., Ruiz-Miranda, C. R., Truman, R. & Stone, A., Nov 16 2015, In : PLoS Neglected Tropical Diseases. 9, 11, e0004198.

Research output: Contribution to journalArticle

7 Scopus citations
2014

Erratum: Sequence diversity of pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity (Genome Biology and Evolution 5:12 (2512-2523) DOI: 10.1093/gbe/evt198)

Ferreira, Z., Hurle, B., Andrés, A. M., Kretzschmar, W. W., Mullikin, J. C., Cherukuri, P. F., Cruz, P., Hyma, K. E., Gonder, M. K., Stone, A., Tishkoff, S., Swanson, W. J., Green, E. D., Clark, A. G. & Seixas, S., 2014, In : Genome biology and evolution. 6, 2, p. 406 1 p.

Research output: Contribution to journalComment/debate

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, L. F., Grativol, A. D., French, J. A., De Oliveira E Silva, I., Pereira, L. C. M., Ruiz-Miranda, C. R., Valença, Y. M. & Stone, A., Dec 1 2014, In : American journal of physical anthropology. 155, 4, p. 522-536 15 p.

Research output: Contribution to journalArticle

18 Scopus citations

Population genetic structure of traditional populations in the peruvian central andes and implications for South American population history

Cabana, G. S., Lewis, C. M., Tito, R. Y., Alan Covey, R., Cáceres, A. M., De La Cruz, A. F., Durand, D., Housman, G., Hulsey, B. I., Iannacone, G. C., López, P. W., Martínez, R., Medina, Á., Dávila, O. O., Pinto, K. P. O., Santillán, S. I. P., Domínguez, P. R., Rubel, M., Smith, H. F., Smith, S. E. & 3 others, De Celis Massa, V. R., Lizárraga, B. & Stone, A., Jan 1 2014, In : Human biology. 86, 3, p. 147-165 19 p.

Research output: Contribution to journalArticle

15 Scopus citations

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

Bos, K. I., Harkins, K. M., Herbig, A., Coscolla, M., Weber, N., Comas, I., Forrest, S. A., Bryant, J. M., Harris, S. R., Schuenemann, V. J., Campbell, T. J., Majander, K., Wilbur, A. K., Guichon, R. A., Wolfe Steadman, D. L., Cook, D. C. O., Niemann, S., Behr, M. A., Zumarraga, M., Bastida, R. & 8 others, Huson, D., Nieselt, K., Young, D., Parkhill, J., Buikstra, J., Gagneux, S., Stone, A. & Krause, J., Oct 23 2014, In : Nature. 514, 7253, p. 494-497 4 p.

Research output: Contribution to journalArticle

236 Scopus citations

Rapid evolution of BRCA1 and BRCA2 in humans and other primates

Lou, D. I., McBee, R. M., Le, U. Q., Stone, A., Wilkerson, G. K., Demogines, A. M. & Sawyer, S. L., Jul 11 2014, In : BMC Evolutionary Biology. 14, 1, 155.

Research output: Contribution to journalArticle

18 Scopus citations
2013

An anthropological genetic perspective on creolization in the anglophone caribbean

Torres, J. B., Stone, A. & Kittles, R., May 1 2013, In : American journal of physical anthropology. 151, 1, p. 135-143 9 p.

Research output: Contribution to journalReview article

15 Scopus citations

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

Ferreira, Z., Hurle, B., Andrés, A. M., Kretzschmar, W. W., Mullikin, J. C., Cherukuri, P. F., Cruz, P., Gonder, M. K., Stone, A., Tishkoff, S., Swanson, W. J., Green, E. D., Clark, A. G. & Seixas, S., 2013, In : Genome biology and evolution. 5, 12, p. 2512-2523 12 p.

Research output: Contribution to journalArticle

1 Scopus citations
2012

Long-term balancing selection at the antiviral gene oas1 in central African chimpanzees

Ferguson, W., Dvora, S., Fikes, R. W., Stone, A. & Boissinot, S., Apr 2012, In : Molecular biology and evolution. 29, 4, p. 1093-1103 11 p.

Research output: Contribution to journalArticle

13 Scopus citations

Regulatory element copy number differences shape primate expression profiles

Iskow, R. C., Gokcumen, O., Abyzov, A., Malukiewicz, J., Zhu, Q., Sukumar, A. T., Pai, A. A., Mills, R. E., Habegger, L., Cusanovich, D. A., Rubel, M. A., Perry, G. H., Gerstein, M., Stone, A., Gilad, Y. & Lee, C., Jul 31 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 31, p. 12656-12661 6 p.

Research output: Contribution to journalArticle

18 Scopus citations
2010

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

Claw, K. G., Tito, R. Y., Stone, A. & Verrelli, B. C., 2010, In : Molecular biology and evolution. 27, 7, p. 1518-1529 12 p.

Research output: Contribution to journalArticle

17 Scopus citations

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

Stone, A., Battistuzzi, F. U., Kubatko, L. S., Perry, G. H., Trudeau, E., Lin, H. & Kumar, S., Oct 27 2010, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 365, 1556, p. 3277-3288 12 p.

Research output: Contribution to journalArticle

50 Scopus citations

Tuberculosis on the north coast of Peru: skeletal and molecular paleopathology of late pre-Hispanic and postcontact mycobacterial disease

Klaus, H. D., Wilbur, A. K., Temple, D. H., Buikstra, J., Stone, A., Fernandez, M., Wester, C. & Tam, M. E., Oct 2010, In : Journal of Archaeological Science. 37, 10, p. 2587-2597 11 p.

Research output: Contribution to journalArticle

45 Scopus citations
2009

Deficiencies and challenges in the study of ancient tuberculosis DNA

Wilbur, A. K., Bouwman, A. S., Stone, A., Roberts, C. A., Pfister, L. A., Buikstra, J. & Brown, T. A., Sep 2009, In : Journal of Archaeological Science. 36, 9, p. 1990-1997 8 p.

Research output: Contribution to journalArticle

52 Scopus citations

Tuberculosis and leprosy in perspective

Stone, A., Wilbur, A. K., Buikstra, J. & Roberts, C. A., 2009, In : American journal of physical anthropology. 140, SUPPL. 49, p. 66-94 29 p.

Research output: Contribution to journalArticle

66 Scopus citations
2008

Copy number variation and evolution in humans and chimpanzees

Perry, G. H., Yang, F., Marques-Bonet, T., Murphy, C., Fitzgerald, T., Lee, A. S., Hyland, C., Stone, A., Hurles, M. E., Tyler-Smith, C., Eichler, E. E., Carter, N. P., Lee, C. & Redon, R., Nov 2008, In : Genome research. 18, 11, p. 1698-1710 13 p.

Research output: Contribution to journalArticle

168 Scopus citations

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

Verrelli, B. C., Lewis, C. M., Stone, A. & Perry, G. H., Dec 2008, In : Molecular biology and evolution. 25, 12, p. 2735-2743 9 p.

Research output: Contribution to journalArticle

22 Scopus citations
2007

Ancient DNA and genetic continuity in the south central Andes

Lewis, C. M., Buikstra, J. & Stone, A., Jun 2007, In : Latin American Antiquity. 18, 2, p. 145-160 16 p.

Research output: Contribution to journalArticle

29 Scopus citations