Publications

See my google scholar profile for an up-to-date list.
* denotes equal contribution
underlined denotes Davenport lab member

Litichevskiy L, Considine M, Gill J, Shandar V, Cox TO, Descamps HC, Wright KM, Amses KR, Dohnalova L, Liou MJ, Tetlak M, Galindo-Fiallos MR, Wong AC, Lundgren P, Kim J, Uhr GT, Rahman RJ, Mason S, Merenstein C, Bushman FD, Raj A, Harding F, Chen Z, Prateek GV, Mullis M, Deighan AG, Robinson L, Tanes C, Bittinger K, Chakraborty M, Bhatt AS, Li H, Barnett I, Davenport ER, Broman KW, Cohen RL, Botstein D, Freund A, Di Francesco A, Churchill GA, Li M, and Thaiss CA. Interactions between the gut microbiome, dietary restriction, and aging in genetically diverse mice. bioRxiv: 10.1101 / 2023.11.28.568137v1
Cappas VM, Davenport ER, and Sykes DG. The microbiome and volatile organic compounds reflect the state of decomposition in an indoor environment. BioRxiv

Liu S, Rodriguez J, Munteanu V, Ronkowski C, Kumar Sharma N, Alser M, Andreace F, Blekhman R, Błaszczyk D, Chikhi R, Crandall KA, Libera KD, Francis D, Frolova A, Gancz AS, Huntley NE, Jaiswal P, Kosciolek T, Łabaj P, Łabaj W, Luan T, Mason C, Moustafa AM, Muralidharan HS, Mutlu O, Ghiasi NM, Rahnavard A, Sun F, Tian S, Tierney BT, Van Syoc E, Vicedomini R, Zackular JP, Zelikovsky A, Zielińska, Ganda E, Davenport ER, Pop M, Koslicki D, Mangul S. Analysis of metagenomic data. Nature Reviews Methods Primers. 2025;5(5)

Chen YY, Evavold CL, Mann M, Davenport ER, McFall-Ngai M, Bienko M, Ueda HR, Tian L, Tjahjono N, Anikeeva P, Gogo Liu J, Deans TL, and Shen X. What tool or method do you wish existed? Cell. 2024;187(17)
Nichols RG and Davenport ER. Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene. mSystems. 2024;10:e01480-24
Ryu EP, Gautam Y, Proctor DM, Bhandari D, Tandukar S, Gupta M, Prasad Gautam G, Relman DA, Shibl AA, Bahadur Sherchand J, Jha AR, and Davenport ER. Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized. Microbiome. 2024;12,228
Nichols RG, Rimal B, Hao F, Peters JM, Davenport ER, and Patterson AD. Chlorpyrifos modulates the mouse gut microbiota and metabolic activity. Environment International. 2024;192:109022
Taye B, Mekonnen Z, Belanger KD, and Davenport ER. Gut-microbiome profiles among Soil-Transmitted Helminths (STHs) infected Ethiopian children enrolled in the school-based mass deworming program. PLoS Neglected Tropical Diseases 18(10), e0012485

Gancz AS, Farrer AG, Nixon M, Arriola L, Adler C, Davenport ER, Gully N, Cooper A, Britton K, Dobney K, Silverman J, Weyrich L. Ancient dental calculus reveals novel oral microbiome diversity in pre-Industrialized British people. Nature Microbiology. 2023;8,2315-2325
Kelliher JM, Rudolph M, Vangay P, Abbas A, Borton MA, Santistevan C, Davenport ER, Davenport DW, Erazo NG, Herman C, Karstens L, Kocurek B, Lutz HL, Myers KS, Ockert I, Rodriguez FE, Saunders JK, Smith ML, Vogtmann E, Windsor A, Wood-Charlson EM, Woodley L, Eloe-Fadrosh EA. Promoting cohort-based learning for community standards in microbiome research. Nature Microbiology. 2023;8, 751-753

Jeganathan NA, Davenport ER, Yochum GS, and Koltun WA. The microbiome in diverticulitis. Current Opinion in Physiology. 2021;22
Amato KR, Arrieta M, Azad MB, Bailey MT, Broussard JL, Bruggeling CE, Claud EC, Costello EK, Davenport ER, Dutilh BE, Swain Ewald HA, Ewald P, Hanlon EC, Julion W, Keshavarzian A, Maurice CF, Miller GE, Preidis GA, Segurel L, Singer B, Subramanian S, Zhao L, and Kuzawa CW. The human gut microbiome and health inequities. PNAS. 2021;118(25)
Marderstein AR, Davenport ER, Kulm S, Van Hout CV, Elemento O, Clark AG. Leveraging phenotyping variability to identify genetic interactions in human phenotypes. American Journal of Human Genetics. 2021;108(1)

Gong X, Davenport ER, Wang D, Clark AG. Lack of spatial and temporal genetic structure of Anguilla japonica populations. Conservation Genetics. 2019
Kachoo P*, Eraso JM*, Beres SB, Olsen RJ, Zhu L, Nasser W, Bernard PE, Cantu CC., Ojeda Saavedtra M, José Arredondo M, Strope B, Do H, Kumaraswami M, Vuopio J, Gröndahl-Yli-Hannuksela K, Kristinsson KG, Gottfredsson M, Pesonen M, Pensar J, Davenport ER, Clark AG, Corander J, Caugant DA, Gaini S, Magnusses MD, Porter AR, DeLeoFR, and Musser JM. Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis. Nature Genetics. 2019;51(3)

Jha AR, Davenport ER, Gautam Y, Bhandari D, Tandukar S, Ng K, Holmes S, Prasad Gautam G, Bahadur Sherchand J, Bustamante CD, and Sonnenburg JL. Gut microbiome transition across a life gradient in Himalaya. PLoS Biology. 2018;16(11):e2005396 (epub 2018 Nov 15)

Davenport ER. Tooth be told, genetics influence oral microbiome. Cell Host & Microbe. 2017;22(3)
Davenport ER*, Sanders JG*, Song SJ, Amato KR, Clark AG, and Knight R. The human microbiome in evolution. BMC Biology. 2017;15:127
Goodrich JK, Davenport ER, Clark AG, and Ley RE. The relationship between the human genome and microbiome comes into view. Annual Reviews Genetics. 2017;51 (epub head of print)
Davenport ER. Tooth be told, genetics influences oral microbiome. Cell Host & Microbe. 2017;22(3) [Commentary - not peer reviewed]
Igartua C, Davenport ER, Gilad Y, Nicolae DL, Pinto J, and Ober C. Host genetic variation in mucosal immunity pathways influences the upper airway microbiome. Microbiome. 2017;5:16

Davenport ER, Goodrich JK, Bell JT, Spector TD, Ley RE, and Clark AG. ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins. BMC Genomics. 2016;17:941
Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD, and Bell JT. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biology. 2016;17(1):189
Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, Ober C, Spector TD, Bell JT, Clark AG, and Ley RE. Genetic determinants of the gut microbiome in UK twins. Cell Host & Microbe. 2016;19(5), 731-743
Goodrich JK*, Davenport ER*, Waters JL*, Clark AG, and Ley RE. Cross-species comparisons of host genetic associations with the microbiome. Science. 2016;352(6285), 532-535
Davenport ER .Elucidating the role of the host genome in shaping microbiome composition Gut Microbes. 2016;7(2), 178-184
Blischak JD, Davenport ER, Wilson G. A quick introduction to version control with Git and GitHub. PLoS Computational Biology. 2016;12(1):e1004668

Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C, and Gilad Y. Genome-wide association studies of the human gut microbiota. PLoS One. 2015;10(11):e0140301

Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, and Gilad Y. Epigenetic modifications are associated with inter-species gene expression in primates. Genome Biology. 2014; 15(12):547.
Davenport ER, Mizrahi-Man O, Michelini K, Barreiro LB, Ober C, and Gilad Y. Seasonal variation in human gut microbiome composition. PloS One. 2014;9(3):e90731