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
Correction to: Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized (Microbiome, (2024), 12, 1, (228), 10.1186/s40168-024-01941-7)
Erica P. Ryu, Yoshina Gautam, Diana M. Proctor, Dinesh Bhandari, Sarmila Tandukar, Meera Gupta, Guru Prasad Gautam, David A. Relman, Ahmed A. Shibl, Jeevan Bahadur Sherchand, Aashish R. Jha, Emily R. Davenport, 2024, Microbiome
Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized
Erica P. Ryu, Yoshina Gautam, Diana M. Proctor, Dinesh Bhandari, Sarmila Tandukar, Meera Gupta, Guru Prasad Gautam, David A. Relman, Ahmed A. Shibl, Jeevan Bahadur Sherchand, Aashish R. Jha, Emily R. Davenport, 2024, Microbiome
Chlorpyrifos modulates the mouse gut microbiota and metabolic activity
Robert G. Nichols, Bipin Rimal, Fuhua Hao, Jeffrey Maurice Peters, Emily R. Davenport, Andrew D. Patterson, 2024, Environmental International
Gut-microbiome profiles among Soil-transmitted helminths (STHs) infected Ethiopian children enrolled in the school-based mass deworming program
Bineyam Taye, Zeleke Mekonnen, Kenneth D. Belanger, Emily R. Davenport, 2024, PLoS Neglected Tropical Diseases
What tool or method do you wish existed?
Yvonne Y. Chen, Charles L. Evavold, Matthias Mann, Emily R. Davenport, Margaret McFall-Ngai, Magda Bienko, Hiroki R. Ueda, Lin Tian, Nikki Tjahjono, Polina Anikeeva, Jun Jie Gogo Liu, Tara L. 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 Gancz, Andrew Farrer, M Nixon, Sterling Wright, Luis Arriola, Luis Arriola, Christina Alder, Emily Davenport, Christina Adler, Emily R. Davenport, Neville Gully, Neville Gully, Alan Cooper, Alan Cooper, Kate Britton, Kate Britton, Keith Dobney, Keith Dobney, Justin Silverman, Laura Weyrich, 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
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
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
The relationship between the gut microbiome and host gene expression: a review
Robert G. Nichols, Emily R. Davenport, 2020, Human Genetics
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