Emily Davenport
Assistant Professor of Biology
-
305 Wartik
University Park, PA - exd44@psu.edu
Research Summary
Understanding the complex relationship humans have with our microbiomes, using high-throughput sequencing technologies and novel computational and statistical techniques.
Huck Graduate Students
Huck Affiliations
- Bioinformatics and Genomics
- One Health Microbiome Center
- Molecular, Cellular, and Integrative Biosciences
Links
Most Recent Publications
Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene
R Nichols, Emily Davenport, mSystems
Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized
Erica Ryu, Yoshina Gautam, Diana Proctor, Dinesh Bhandari, Sarmila Tandukar, Meera Gupta, Guru Gautam, David Relman, Ahmed Shibl, Jeevan Sherchand, Aashish Jha, Emily Davenport, 2024, Microbiome
Gut-microbiome profiles among Soil-transmitted helminths (STHs) infected Ethiopian children enrolled in the school-based mass deworming program
Bineyam Taye, Zeleke Mekonnen, Kenneth Belanger, Emily Davenport, 2024, PLOS Neglected Tropical Diseases on p. e0012485
Chlorpyrifos modulates the mouse gut microbiota and metabolic activity
R Nichols, Bipin Rimal, F Hao, J Peters, Emily Davenport, A Patterson, 2024, Environment International on p. 109022
What tool or method do you wish existed?
Yvonne Chen, Charles Evavold, Matthias Mann, Emily Davenport, Margaret McFall-Ngai, Magda Bienko, Hiroki Ueda, Lin Tian, Nikki Tjahjono, Polina Anikeeva, Jun-Jie Liu, Tara Deans, Xiaohua Shen, 2024, Cell on p. 4433-4438
Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain
Abigail S. Gancz, Andrew G. Farrer, Michelle P. Nixon, Sterling Wright, Luis Arriola, Christina Adler, Emily R. Davenport, Neville Gully, Alan Cooper, Kate Britton, Keith Dobney, Justin D. Silverman, Laura S. Weyrich, 2023, Nature Microbiology on p. 2315-2325
Cohort-based learning for microbiome research community standards
Julia M. Kelliher, Marisa Rudolph, Pajau Vangay, Arwa Abbas, Mikayla A. Borton, Emily R. Davenport, Karen W. Davenport, Natalia G. Erazo, Chloe Herman, Lisa Karstens, Brandon Kocurek, Holly L. Lutz, Kevin S. Myers, Ingrid Ockert, Francisca E. Rodriguez, Camille Santistevan, Jaclyn K. Saunders, Montana L. Smith, Emily Vogtmann, Amanda Windsor, Elisha M. Wood-Charlson, Lou Woodley, Emiley A. Eloe-Fadrosh, 2023, Nature Microbiology on p. 751-753
Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle
Erica P. Ryu, Emily R. Davenport, 2022, Annual Review of Animal Biosciences on p. 203-226
The human gut microbiome and health inequities
Katherine R. Amato, Marie Claire Arrieta, Meghan B. Azad, Michael T. Bailey, Josiane L. Broussard, Carlijn E. Bruggeling, Erika C. Claud, Elizabeth K. Costello, Emily R. Davenport, Bas E. Dutilh, Holly A. Swain Ewald, Paul Ewald, Erin C. Hanlon, Wrenetha Julion, Ali Keshavarzian, Corinne F. Maurice, Gregory E. Miller, Geoffrey A. Preidis, Laure Segurel, Burton Singer, Sathish Subramanian, Liping Zhao, Christopher W. Kuzawa, 2021, Proceedings of the National Academy of Sciences of the United States of America
Leveraging phenotypic variability to identify genetic interactions in human phenotypes
Andrew R. Marderstein, Emily R. Davenport, Scott Kulm, Cristopher V. Van Hout, Olivier Elemento, Andrew G. Clark, 2021, American Journal of Human Genetics on p. 49-67
Most-Cited Papers
Genetic Determinants of the Gut Microbiome in UK Twins
Julia K. Goodrich, Emily R. Davenport, Michelle Beaumont, Matthew A. Jackson, Rob Knight, Carole Ober, Tim D. Spector, Jordana T. Bell, Andrew G. Clark, Ruth E. Ley, 2016, Cell Host and Microbe on p. 731-743
The human microbiome in evolution
Emily R. Davenport, Jon G. Sanders, Se Jin Song, Katherine R. Amato, Andrew G. Clark, Rob Knight, 2017, BMC Biology
Seasonal variation in human gut microbiome composition
Emily R. Davenport, Orna Mizrahi-Man, Katelyn Michelini, Luis B. Barreiro, Carole Ober, Yoav Gilad, 2014, PLoS One on p. e90731
The Relationship between the Human Genome and Microbiome Comes into View
Julia K. Goodrich, Emily R. Davenport, Andrew G. Clark, Ruth E. Ley, 2017, Annual Review of Genetics on p. 413-433
Cross-species comparisons of host genetic associations with the microbiome
Julia K. Goodrich, Emily R. Davenport, Jillian L. Waters, Andrew G. Clark, Ruth E. Ley, 2016, Science on p. 532-535
Genome-wide association studies of the human gut microbiota
Emily R. Davenport, Darren A. Cusanovich, Katelyn Michelini, Luis B. Barreiro, Carole Ober, Yoav Gilad, 2015, PLoS One on p. e0140301
Heritable components of the human fecal microbiome are associated with visceral fat
Michelle Beaumont, Julia K. Goodrich, Matthew A. Jackson, Idil Yet, Emily R. Davenport, Sara Vieira-Silva, Justine Debelius, Tess Pallister, Massimo Mangino, Jeroen Raes, Rob Knight, Andrew G. Clark, Ruth E. Ley, Tim D. Spector, Jordana T. Bell, 2016, Genome Biology on p. 189
Gut microbiome transition across a lifestyle gradient in Himalaya
Aashish R. Jha, Emily R. Davenport, Yoshina Gautam, Dinesh Bhandari, Sarmila Tandukar, Katharine M. Ng, Gabriela K. Fragiadakis, Susan Holmes, Guru Prasad Gautam, Jeff Leach, Jeevan Bahadur Sherchand, Carlos D. Bustamante, Justin L. Sonnenburg, 2018, PLoS Biology on p. e2005396
A Quick Introduction to Version Control with Git and GitHub
John D. Blischak, Emily R. Davenport, Greg Wilson, 2016, PLoS Computational Biology on p. e1004668
The human gut microbiome and health inequities
Katherine R. Amato, Marie Claire Arrieta, Meghan B. Azad, Michael T. Bailey, Josiane L. Broussard, Carlijn E. Bruggeling, Erika C. Claud, Elizabeth K. Costello, Emily R. Davenport, Bas E. Dutilh, Holly A. Swain Ewald, Paul Ewald, Erin C. Hanlon, Wrenetha Julion, Ali Keshavarzian, Corinne F. Maurice, Gregory E. Miller, Geoffrey A. Preidis, Laure Segurel, Burton Singer, Sathish Subramanian, Liping Zhao, Christopher W. Kuzawa, 2021, Proceedings of the National Academy of Sciences of the United States of America
News Articles Featuring Emily Davenport
Nov 05, 2024
Microbes in mouth reflect lifestyle choices
New study in Nepal reveals that oral microbiomes differ among traditional foragers, agriculturalists and industrialists, and with behaviors like smoking and diet
Full Article
Jul 18, 2024
Microbiome Kickstart Workshop will assist newcomers to the field
The One Health Microbiome Center at Penn State has opened registration for its fifth annual Microbiome Kickstart Workshop. This free, comprehensive, workshop is a cornerstone training event for emerging researchers to launch their microbiome studies and network at Penn State.
Full Article
Nov 29, 2023
Study of ancient British oral microbiomes reveals shift following Black Death
The Second Plague Pandemic may have led to oral microbiomes that contribute to modern-day chronic disease, according to new research
Full Article
Feb 15, 2023
Free film and panel discussion reveals 'invisible' crisis of the microbial world
At 6 p.m. Thursday, March 2, Penn State’s Microbiome Center will present "The Invisible Extinction" — a movie that spotlights the trailblazing work and charismatic personalities of renowned scientists who aim to save the vanishing microbes that are essential for our survival.
Full Article