Publications

A. Childebayeva*, T.S. Harman, J. Weinstein*, T.A. Day, T.D. Brutsaert, A.W. Bigham.  (2021) “Genome-Wide DNA Methylation Changes Associated with High-Altitude Acclimatization During an Everest Base Camp Trek.” Frontiers Physiology. In press.

A. Childebayeva*, J.M. Goodrich, N. Chesterman, F. Leon-Velarde, M. Rivera-Ch, M. Kiyamu, T.D. Brutsaert, A.W. Bigham, D.C. Dolinoy. (2021) “Blood Lead Levels in Peruvian Adults Are Associated with Proximity to Mining and DNA Methylation.” Environment International. 155.

D. Song, A.W. Bigham, F.S. Lee. (2021) “High-altitude deer mouse Hypoxia inducible factor-2α shows defective interaction with CREB-binding protein.” Journal of Biological Chemistry. Feb. 24. Online ahead of print.

A. Childebayeva*, J. M. Goodrich, F. M. Leon-Velarde, M. Rivera-Chira, M. Kiyamu, T.D. Brutsaert, D.C. Dolinoy, A.W. Bigham.  (2021) “Genome-Wide Epigenetic Signatures of Adaptive Developmental Plasticity in the Andes.” Genome Biology and Evolution. 13:evaa 239.

E.A. Werren*, O. Garcia*, A.W. Bigham. (2021) “Identifying adaptive alleles in the human genome: from selection mapping to functional validation.” Human Genetics. 140:241-276.

D. Song, B.E. Navalsky, W. Guan, C. Ingersoll, T. Wang, E. Loro, L. Eeles, K.B. Matchett, M.J. Percy, J. Walsby-Tickle, J. S.O. McCullagh, R.J. Medina, T.S. Khurana, A.W. Bigham, T.R. Lappin, F.S. Lee. (2020) “Tibetan PHD2, an allele  with loss of function properties.” Proceedings of the National Academy of  Sciences. 117:12230-12238.

T.D. Brutsaert, M. Kiyamu, G. Elias Revollendo, J.L. Isherwood*, F.S. Lee, M. Rivera-Ch, F. Leon-Velarde, S. Ghosh, A.W. Bigham. (2019) “Association of EGLN1 gene with high aerobic capacity of Peruvian Quechua at high altitude.” Proceedings of the National Academy of Sciences. 116:24006-24011.

A. Childebayeva*, T. Harman, J. Weinstein*, J. M. Goodrich, D.C. Dolinoy, T.A. Day, A.W. Bigham, T.D. Brutsaert. (2019) “DNA methylation changes are associated with an incremental ascent to high altitude.” Frontiers in Genetics. 10:1062.

S. Ghosh, M. Kiyamu, P. Contreras*, F. León‐Velarde, A. Bigham, T.D. Brutsaert. (2019) “Exhaled nitric oxide in ethnically diverse high‐altitude native populations: A comparative study.” American Journal of Physical Anthropology. 170:451-458.

H.L. Norton, E.E. Quillen, A.W. Bigham, L.N. Pearson, H. Dunsworth. (2019) “Human races are not like dog breeds: refuting a racist analogy” Evolution: Education and Outreach. 12:17.

C. Davi, A. Pastor, T. Oliveira, F.B. de Lima Neto, U. Braga-Neto, A.W. Bigham, M. Bamshad, E.T.A. Marques, B. Acioli-Santos. (2019) “Severe Dengue Prognosis Using Human Genome Data and Machine Learning.” IEEE Transactions on Biomedical Engineering. 66:2861-2868.

A. Childebayeva*, T.R. Jones, J. M. Goodrich, F. M. Leon-Velarde, M. Rivera-Chira, M. Kiyamu, T.D. Brutsaert, D.C. Dolinoy, A.W. Bigham. (2019) “LINE-1 and EPAS1 DNA methylation associations with high-altitude exposure.” Epigenetics. 14:1-15.

A.W. Bigham, K. Magnaye, D.M. Dunn, R.B. Weiss, M. Bamshad. (2018) “Complex Signatures of natural selection at GYPA.” Human Genetics. 137:151-160.

A.W. Bigham, A. Non. (2016) “The genetics anthropologist’s contribution to understanding race and racial health disparities.” Human Biology. 87:291-293

A.W. Bigham. (2016) “Genetics of human origin and evolution: high-altitude adaptations.” Current Opinion in Genetics and Development. 41:8-13.

R.D. Mackelprang, C.W. Scoville, C.R. Cohen, RO Ondondo, A.W. Bigham, C. Celum, M.S. Campbell, M. Essex, A. Wald, J. Kiarie, A. Ronald, G. Gray, J.R. Lingappa; Partners in Prevention HSV/HIV Transmission Study Team. (2015) “Toll-like receptor gene variants and bacterial vaginosis among HIV-1 infected and uninfected African women.” Genes and Immunology. 16:362-5

L.S. Emery, K.M. Magnaye, A.W. Bigham, J.M. Akey, M.J. Bamshad. (2015). Estimates of continental ancestry vary widely among individuals with the same mtDNA haplogroup. American Journal of Human Genetics. Advanced online publication. PDF

A.W. Bigham and F.S. Lee. (2014). Human high altitude adaptation: forward genetics meets the HIF pathway”. Genes and Development. 28:2189-2204. PDF.

A.W. Bigham, C.G. Julian, M.J. Wilson, E. Vargas, V.A. Browne,M.D. Shriver, L.G. Moore. (2014) ^“Maternal PRKAA1 and EDNRA genotypes are associated with birth weight, and PRKAA1 with uterine artery diameter and metabolic homeostasis at high altitude.” Physiological Genomics. 46:687-697. PDF

D. Song, L.S. Li, P.R. Arsenault, Q. Tan, A.W. Bigham, K.J. Heaton-Johnson, S.R. Master, F.S. Lee. (2014) “Defective Tibetan PHD2 Binding to p23 Links High Altitude Adaptation to Altered Oxygen Sensing.” Journal of Biological Chemistry. 289, 14656-14665. PDF

A.W. Bigham*, R.D. Mackelprang*, C. Celum, G. de Bruyn, K. Beima-Sofie K, G. John-Stewart, A. Ronald, N.R. Mugo , K.J. Buckingham, M.J. Bamshad, J.I. Mullins, M.J. McElrath, J.R. Lingappa. (2014) “Variants in host viral replication cycle genes are associated with heterosexual HIV-1 acquisition in Africans.” Journal of Acquired Immune Deficiency Syndromes. 66, 126-134. (*co-first authors) PDF

R.D. Mackelprang*, A.W. Bigham*, C. Celum, G. de Bruyn, K. Beima-Sofie K, G. John-Stewart, A. Ronald, N.R. Mugo , K.J. Buckingham, M.J. Bamshad, J.I. Mullins, M.J. McElrath, J.R. Lingappa. (2014) “Toll-like receptor polymorphism associations with HIV-1 outcomes among sub-Saharan Africans.” Journal of Infectious Disease. 209, 1623-1627. (*co-first authors) PDF

K.M. Beima-Sofie, A.W. Bigham, J.R. Lingappa, D. Wamalwa, R.D. Mackelprang, E. Maleche-Obimbo, B.A. Richardson, M.J. Bamshad, G.C. John-Stewart. (2013) “Toll-like Receptor (TLR) variants are associated with infant HIV-1 acquisition and peak plasma HIV-1 RNA level.” AIDS. 27, 2431-9. PDF

A.W. Bigham, M.J. Wilson, C.G. Julian, M. Kiyamu, E. Vargas, F. Leon-Velarde, M. Rivera-Chira, C. Rodriquez, V.A. Browne, E. Parra, T.D. Brutsaert, L.G. Moore, M.D. Shriver. (2013) “Andean and Tibetan patterns of adaptation to high altitude.” American Journal of Human Biology. 25, 190-7. PDF

J.A. Tennessen*, A.W. Bigham*, T.D. O’Connor*, W. Fu, E E. Kenny, S. Gravel, S. McGee, R. Do, X. Liu, G. Jun, H.M. Kang, D. Jordan, S.M. Leal, G. Abecasis, E. Boerwinkle, S. Sunyaev, M.J. Rieder, S. Gabriel, D. Altshuler, D.A. Nickerson, C.D. Bustamante, M.J. Bamshad, J.M. Akey, Broad GO, Seattle GO, on behalf of the NHLBI Exome Sequencing Project. (2012) “Evolution and functional impact of rare coding variation from deep sequencing of 2,440 human exomes.” Science. 337, 64-9. (*co-first authors) PDF

M. Kiyamu, A. Bigham, E. Parra, F. León-Velarde, M. Rivera, TD Brutsaert. (2012) “Developmental and genetic components explain enhanced pulmonary volumes of female Peruvian Quechua.” American Journal of Physical Anthropology. 148, 534-42. PDF

J.M. Galanter, J.C. Fernandez-Lopez, C.R. Gignoux, J. Barnholtz-Sloan, C. Fernandez-Rozadilla, M. Via, A. Hidalgo-Miranda, A.V. Contreras, L.U. Figueroa, P. Raska, G. Jimenez-Sanchez, I. Silva Zolezzi, M. Torres, C.R. Ponte, Y. Ruiz, A. Salas, E. Nguyen, C. Eng, L. Borjas, W. Zabala, G. Barreto, F. Rondón González, A. Ibarra, P. Taboada, L. Porras, F. Moreno, A. Bigham, A. Gutierrez G, T. Brutsaert, F. León-Velarde, L.G. Moore, E. Vargas, M. Cruz, J. Escobedo, J. Rodriguez-Santana, W. Rodriguez-Cintrón, R. Chapela, J.G. Ford, C. Bustamante, D. Seminara, M. Shriver, E. Ziv, E. Gonzalez Burchard, R. Haile, E. Parra, A. Carracedo; for the LACE Consortium. (2012) “Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas.” PLoS Genetics. 8:e1002554. PDF

E.E. Quillen, M. Bauchet, A.W. Bigham, M.E. Delgado-Burbano, F.X. Faust, Y.C. Klimentidis, X. Mao, M. Stoneking, M.D. Shriver. (2011) “OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and Europeans.” Human Genetics. 131, 1073-1080. PDF

C.G. Julian, E. Vargas, V.A. Browne, M.J. Wilson, A.W. Bigham, C. Rodriguez, J.M. McCord, L.G. Moore. (2011) “Potential role for elevated maternal enzymatic antioxidant status in Andean protection against altitude-associated SGA.” Journal of Maternal, Fetal, and Neonatal Medicine. 25, 1233-1240.

M.J. Bamshad, S.B. Ng, A.W. Bigham, H.K. Tabor, M.J. Emond, D.A. Nickerson, J. Shendure. (2011) “Exome sequencing as a tool for Mendelian disease gene discovery”. Nature Reviews Genetics. 12, 745-755. PDF

A.W. Bigham, K.J. Buckingham S. Husain, M.J. Emond, K.M. Bofferding, H. Gildersleeve, A. Rutherford, N.M. Astakhova, A.A. Perelygin, M.P. Busch, K.O. Murray, J.J. Sejvar, S. Green, J. Kriesel, M.A. Brinton, M. Bamshad. (2011) “Host Genetic Risk Factors for West Nile Virus Infection and Disease Progression”. PLoS One. 6, e24745. PDF

M.C. Hannibal, K.J. Buckingham, S.B. Ng, J.E. Ming, A.E. Beck, M.J. McMillin, H.I. Gildersleeve, A.W. Bigham, H.K. Tabor, H.C. Mefford, J. Cook, K. Yoshiura, T. Matsumoto, N. Matsumoto, N. Miyake, H. Tonoki, K. Naritomi, T. Kaname, T. Nagai, H. Ohashi, K. Kurosawa, J.W. Hou, T. Ohta, D. Liang, A. Sudo, C.A. Morris, S. Banka, G.C. Black, J. Clayton-Smith, D.A. Nickerson, E.H. Zackai, T.H. Shaikh, D. Donnai, N. Niikawa, J. Shendure, M.J. Bamshad. (2011) “Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome”. American Journal of Medical Genetics A. 155, 1511-6. PDF

V.A. Browne, L. Toledo-Jaldin, R.D. Davila, L.P. Lopez, H. Yamashiro, D. Cioffi-Ragan, C.G. Julian, M.J. Wilson, A.W. Bigham, M.D. Shriver, B. Honigman, E. Vargas, R.C. Roach, L.G. Moore. (2011) “High end-arteriolar resistance limits uterine artery blood flow and restricts fetal growth in preeclampsia and gestational hypertension at high altitude”. American Journal of Physiology Regulatory Integrative, and Comparative Physiology. 300, R1221-9. PDF

C. Rödelsperger, P. Krawitz, X. Bauer, J. Hecht, A.W. Bigham, M. Bamshad, B.J. de Condor, M.R. Schweiger, P.N. Robinson. (2011) “Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders.” Bioinformatics. 27, 829-36. PDF

R.D. Dávila, C.G. Julian, M.J. Wilson, V.A. Browne, C. Rodriguez, A.W. Bigham, M.D. Shriver, E. Vargas, L.G. Moore. (2011) “Do cytokines contribute to the Andean-associated protection from reduced fetal growth at high altitude?” Reproductive Science. 18, 79-87. PDF

S.B. Ng*, A.W. Bigham*, K.J. Buckingham, M.C. Hannibal, M.J. McMillin MJ, H.I. Gildersleeve, A.E. Beck, H.K. Tabor, G.M. Cooper, H.C. Mefford, C. Lee, E.H. Turner, J.D. Smith, M.J. Rieder, K. Yoshiura, N. Matsumoto, T. Ohta, N. Niikawa, D.A. Nickerson, M.J. Bamshad, J. Shendure. “Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome.” (2010) Nature Genetics. 42, 790-3. (*co-first authors) PDF

A.W. Bigham, M. Bauchet, D. Pinto, X. Mao, J.M. Akey, R. Mei, S. Scherer, C.G. Julian, M. Wilson, D. Lopez-Herraez, T. Brutsaert, E.J. Parra, L.G. Moore, and M.D. Shriver. (2010) “Identifying signatures of natural selection in Tibetan and Andean population using dense genome scan data”. PLOS Genetics. 6: e1001116. Selected for Faculty of 1000. PDF

R.D. Davila, C.G. Julian, M.J. Wilson, V.A. Browne, C. Rodriguez, A.W. Bigham, M.D. Shriver, E. Vargas, L.G. Moore. (2010) “Do anti-angiogenic or angiogenic factors contribute to the protection of birth weight at high altitude afforded by Andean ancestry?” Reproductive Science. 17, 861-70. PDF

K.A Ross, A.W. Bigham, M. Edwards, A. Gozdzik, G. Suarez-Kurtz, E.J. Parra. (2010) “Worldwide allele frequency distribution of four polymorphisms associated with warfarin dose requirements.” Journal of Human Genetics. 55, 582-9. PDF

M. Edwards, A.W. Bigham, J. Tan, S. Li, A. Gozdzik, K. Ross, L. Jin, E.J. Parra. (2010) “Association of the OCA2 Polymorphism His615Arg with Melanin Content in East Asian Populations: Further Evidence of Convergent Evolution of Skin Pigmentation. PLoS Genetics 6, e1000867. PDF

S.B. Ng, K.J. Buckingham, C. Lee, A.W. Bigham, H.K. Tabor, K.M. Dent, C.D. Huff, P.T. Shannon, E.W. Jabs, D.A. Nickerson, J. Shendure, M.J. Bamshad. (2010) “Exome sequencing identifies the cause of a Mendelian disorder.” Nature Genetics. 42, 30-5. PDF

A.W. Bigham, X. Mao, R. Mei, T. Brutseart, M. Wilson, C. Julian, E. Parra, J.M. Akey. L.G. Moore, M.D. Shriver. (2009) “Identifying Positive Selection Candidate Loci for High-Altitude Adaptation in Andean Populations.” Human Genomics. 4, 79-90. PDF

S.B. Ng, E.H. Turner, P.D. Robertson, S.D. Flygare, A.W. Bigham, C. Lee, T. Shaffer, M. Wong, A. Bhattacharjee, E.E. Eichler, M. Bamshad, D.A. Nickerson, J. Shendure. (2009) “Targeted capture and massively parallel sequencing of 12 human exomes.” Nature. 461, 272-6. PDF

A.L. Willig, K.R. Casazza, J. Divers, A.W. Bigham, B.A. Gower, G.R. Hunter, J.R. Fernandez. Metabolism. (2009) “Uncoupling protein 2 Ala55Val polymorphism is associated with a higher acute insulin response to glucose.” Metabolism. 58, 877-81. PDF

C.G. Julian, M.J. Wilson, M. Lopez, H. Yamashiro, W. Tellez, A. Rodriguez, A.W. Bigham, M.D. Shriver, C. Rodriguez, E. Vargas, L.G. Moore. (2009) “Augmented uterine artery blood flow and oxygen delivery protect Andeans from altitude-associated reductions in fetal growth.” American Journal of Physiology Regulatory Integrative, and Comparative Physiology. 296, R1564-75. PDF

A.W. Bigham, M. Kiyamu, F. León-Velarde, E.J. Parra, M. Rivera-Ch_,M.D. Shriver, and T.D. Brutsaert. (2008) “Angiotensin-Converting Enzyme Genotype and Arterial Oxygen Saturation at High Altitude in Peruvian Quechua.” High Altitude Medicine and Biology. 9, 167-178. PDF

M. J. Wilson, M. Lopez, M. Vargas, C. Julian, W. Tellez, A. Rodriguez, A. Bigham, J. F. Armaza, S. Niermeyer, M. Shriver, E. Vargas, L. G. Moore. (2007) “Greater uterine artery blood flow during pregnancy in multigenerational (Andean) than shorter-term (European) high-altitude residents.” American Journal of Physiology: Regulatory, Integrative, and Comparative Physiology. 293, R1313-1324. PDF

X. Mao, A. W. Bigham, R. Mei, G. Gutierrez, K.M. Weiss, T.D. Brutseart, F. Leon-Velarde, L. G. Moore, E. Vargas, P.M. McKeigue, M.D. Shriver, E.J. Parra. (2007) “A genomewide admixture mapping panel for Hispanic/Latino populations.” American Journal of Human Genetics. 80, 1171-1178. PDF

M.D. Shriver, R. Mei, A. Bigham, X. Mao, T.D. Brutseart, E.J. Parra, L. G. Moore. (2006) “Finding the genes underlying adaptation to hypoxia using genomic scans for genetic adaptation and admixture mapping.” Advances in Experimental Medicine and Biology. 588, 89-100.

M.F. Hammer, D. Garrigan, E. Wood, J.A. Wilder, Z. Mobasher, A.W. Bigham, J.G. Krenz and M.W. Nachman. (2004) “Heterogeneous patterns of variation among multiple human X-linked loci: The possible role of diversity reducing selection in non-Africans.” Genetics. 167, 1841-53. PDF