Personal information

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https://davenport-lab.github.io

Countries

United States

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Employment (2)

Penn State University: University Park, PA, US

2019-08-15 to present | Assistant Professor (Biology)
Employment
Source: Self-asserted source
Emily R. Davenport

Cornell University: Ithaca, NY, US

2014-12 to 2019-08-14 | Postdoc (Molecular Biology and Genetics)
Employment
Source: Self-asserted source
Emily R. Davenport

Education and qualifications (2)

University of Chicago: Chicago, IL, US

2009-10 to 2014-12 | PhD (Human Genetics)
Education
Source: Self-asserted source
Emily R. Davenport

University of Wisconsin Madison: Madison, WI, US

2003-09 to 2007-05 | BS (Bacteriology)
Education
Source: Self-asserted source
Emily R. Davenport

Funding (2)

Characterizing human-microbiome interactions via molecular and functional genomic approaches

2022-09-07 to 2027-07-31 | Grant
National Institute of General Medical Sciences (Bethesda, US)
URL: https://app.dimensions.ai/details/grant/grant.12966180
GRANT_NUMBER: R35GM146980
Source: Self-asserted source
Emily R. Davenport via DimensionsWizard

Modeling Human Gut Microbiome Community Structure in Healthy and Diseased States

2016-02-23 to 2019-02-22 | Grant
National Institute of Diabetes and Digestive and Kidney Diseases (Bethesda, US)
URL: https://grants.uberresearch.com/100000062/F32DK109595/Modeling-Human-Gut-Microbiome-Community-Structure-in-Healthy-and-Diseased-States
GRANT_NUMBER: 1F32DK109595-01
Source: Self-asserted source
Emily R. Davenport via DimensionsWizard

Works (37)

Analysis of metagenomic data

Nature Reviews Methods Primers
2025-01-23 | Journal article | Author
DOI: 10.1038/s43586-024-00376-6
Part of ISSN: 2662-8449
Contributors: Shaopeng Liu; Judith S Rodriguez; Viorel Munteanu; Cynthia Ronkowski; Nitesh Kumar Sharma; Mohammed Alser; Francesco Andreace; Ran Blekhman; Dagmara Błaszczyk; Rayan Chikhi et al.
Source: Self-asserted source
Emily R. Davenport

Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene

mSystems
2025-01-21 | Journal article
DOI: 10.1128/msystems.01480-24
Contributors: Robert G. Nichols; Emily R. Davenport; Jack A. Gilbert
Source: check_circle
Crossref

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized

Microbiome
2024-11-04 | Journal article
DOI: 10.1186/s40168-024-01941-7
Part of ISSN: 2049-2618
Contributors: 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 et al.
Source: Self-asserted source
Emily R. Davenport

Chlorpyrifos modulates the mouse gut microbiota and metabolic activity

Environment International
2024-10 | Journal article
DOI: 10.1016/j.envint.2024.109022
Part of ISSN: 0160-4120
Contributors: Robert G. Nichols; Bipin Rimal; Fuhua Hao; Jeffrey M. Peters; Emily R. Davenport; Andrew D. Patterson
Source: Self-asserted source
Emily R. Davenport

Gut-microbiome profiles among Soil-transmitted helminths (STHs) infected Ethiopian children enrolled in the school-based mass deworming program

PLOS Neglected Tropical Diseases
2024-10-15 | Journal article
DOI: 10.1371/journal.pntd.0012485
Part of ISSN: 1935-2735
Contributors: Bineyam Taye; Zeleke Mekonnen; Kenneth D. Belanger; Emily R. Davenport
Source: Self-asserted source
Emily R. Davenport

What tool or method do you wish existed?

Cell
2024-08 | Journal article
DOI: 10.1016/j.cell.2024.07.043
Part of ISSN: 0092-8674
Contributors: 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 et al.
Source: Self-asserted source
Emily R. Davenport

Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene

2024-07-17 | Preprint
DOI: 10.1101/2024.07.15.603574
Contributors: Robert G Nichols; Emily R Davenport
Source: check_circle
Crossref

Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain

Nature Microbiology
2023-11-29 | Journal article
DOI: 10.1038/s41564-023-01527-3
Contributors: Abigail S. Gancz; Andrew G. Farrer; Michelle P. Nixon; Sterling Wright; Luis Arriola; Christina Adler; Emily R. Davenport; Neville Gully; Alan Cooper; Kate Britton et al.
Source: check_circle
Crossref

Interactions between the gut microbiome, dietary restriction, and aging in genetically diverse mice

2023-11-29 | Preprint | Author
DOI: 10.1101/2023.11.28.568137
Contributors: Lev Litichevskiy; Maya Considine; Jasleen Gill; Vasuprada Shandar; Timothy Cox; Hélène, C. Descamps; Kevin Wright; Kevin R. Amses; Lenka Dohnalová; Megan J. Liou et al.
Source: Self-asserted source
Emily R. Davenport

Cohort-based learning for microbiome research community standards

Nature Microbiology
2023-04-17 | Journal article
DOI: 10.1038/s41564-023-01361-7
Contributors: 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 et al.
Source: check_circle
Crossref

The Microbiome and Volatile Organic Compounds Reflect the State of Decomposition in an Indoor Environment

2022-05-19 | Preprint
DOI: 10.1101/2022.05.18.492585
Contributors: Veronica M. Cappas; Emily R. Davenport; Dan G. Sykes
Source: check_circle
Crossref

The microbiome of diverticulitis

Current Opinion in Physiology
2021-08 | Journal article
DOI: 10.1016/j.cophys.2021.06.006
Contributors: Nimalan Arjun Jeganathan; Emily R Davenport; Gregory S Yochum; Walter A Koltun
Source: check_circle
Crossref

The human gut microbiome and health inequities

Proceedings of the National Academy of Sciences
2021-06-22 | Journal article
DOI: 10.1073/pnas.2017947118
Contributors: 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 et al.
Source: check_circle
Crossref

The relationship between the gut microbiome and host gene expression: a review

Human Genetics
2021-05-22 | Journal article
DOI: 10.1007/s00439-020-02237-0
Contributors: Robert G. Nichols; Emily R. Davenport
Source: check_circle
Crossref

Taming the beasts inside

eLife
2021-03-23 | Journal article
DOI: 10.7554/eLife.67634
Contributors: Erica P Ryu; Emily R Davenport
Source: check_circle
Crossref

Leveraging phenotypic variability to identify genetic interactions in human phenotypes.

American journal of human genetics
2020-12 | Journal article
DOI: 10.1016/j.ajhg.2020.11.016
PMID: 33326753
Contributors: Marderstein AR; Davenport ER; Kulm S; Van Hout CV; Elemento O; Clark AG
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Genetic Variation Shapes Murine Gut Microbiota via Immunity.

Trends in immunology
2019-12 | Journal article
DOI: 10.1016/j.it.2019.11.009
PMID: 31806285
Contributors: Davenport ER
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations

Conservation genetics.
2019-06 | Journal article
DOI: 10.1007/s10592-019-01146-8
OTHER-ID:

IND606437495
Contributors: Gong X; Davenport ER; Wang D; Clark AG
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis.

Nature genetics
2019-02 | Journal article
DOI: 10.1038/s41588-018-0343-1
PMID: 30778225
Contributors: Kachroo P; Eraso JM; Beres SB; Olsen RJ; Zhu L; Nasser W; Bernard PE; Cantu CC; Saavedra MO; Arredondo MJ et al.
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Gut microbiome transition across a lifestyle gradient in Himalaya.

PLoS biology
2018-11 | Journal article
DOI: 10.1371/journal.pbio.2005396
PMID: 30439937
PMC: PMC6237292
Contributors: Jha AR; Davenport ER; Gautam Y; Bhandari D; Tandukar S; Ng KM; Fragiadakis GK; Holmes S; Gautam GP; Leach J et al.
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Gut microbiome transition across a lifestyle gradient in Himalaya

2018-01-27 | Other
DOI: 10.1101/253450
Contributors: Aashish R Jha; Emily R Davenport; Yoshina Gautam; Dinesh Bhandari; Sarmila Tandukar; Katharine Ng; Susan Holmes; Guru Prasad Gautam; Jeevan Bahadur Sherchand; Carlos Bustamante et al.
Source: check_circle
Crossref

The human microbiome in evolution.

BMC biology
2017-12-27 | Journal article
DOI: 10.1186/s12915-017-0454-7
PMID: 29282061
PMC: PMC5744394
Source: Self-asserted source
Emily R. Davenport

The Relationship Between the Human Genome and Microbiome Comes into View.

Annual review of genetics
2017-11 | Journal article
DOI: 10.1146/annurev-genet-110711-155532
PMID: 28934590
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Tooth Be Told, Genetics Influences Oral Microbiome.

Cell host & microbe
2017-09 | Journal article
DOI: 10.1016/j.chom.2017.08.018
PMID: 28910628
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome.

2017-02 | Journal article
PMID: 28143570
PMC: PMC5286564
Contributors: Igartua C; Davenport ER; Gilad Y; Nicolae DL; Pinto J; Ober C
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins.

2016-11 | Journal article
PMID: 27871240
PMC: PMC5117602
Contributors: Davenport ER; Goodrich JK; Bell JT; Spector TD; Ley RE; Clark AG
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Heritable components of the human fecal microbiome are associated with visceral fat.

2016-09 | Journal article
PMID: 27666579
PMC: PMC5036307
Contributors: Beaumont M; Goodrich JK; Jackson MA; Yet I; Davenport ER; Vieira-Silva S; Debelius J; Pallister T; Mangino M; Raes J et al.
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome

2016-07-05 | Other
DOI: 10.1101/062232
Contributors: Catherine Igartua; Emily R Davenport; Yoav Gilad; Dan L Nicolae; Jayant Pinto; Carole Ober
Source: Self-asserted source
Emily R. Davenport via Crossref Metadata Search

Genetic Determinants of the Gut Microbiome in UK Twins.

2016-05 | Journal article
DOI: 10.1016/j.chom.2016.04.017
PMID: 27173935
Contributors: Goodrich JK; Davenport ER; Beaumont M; Jackson MA; Knight R; Ober C; Spector TD; Bell JT; Clark AG; Ley RE
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Cross-species comparisons of host genetic associations with the microbiome.

2016-04 | Journal article
DOI: 10.1126/science.aad9379
PMID: 27126034
Contributors: Goodrich JK; Davenport ER; Waters JL; Clark AG; Ley RE
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Elucidating the role of the host genome in shaping microbiome composition.

2016-03 | Journal article
DOI: 10.1080/19490976.2016.1155022
PMID: 26939746
PMC: PMC4856462
Contributors: Davenport ER
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Nasal Microbiome Composition Is Associated with Chitotriosidase (Chit1) Activity in Adult Hutterites.

2016-03 | Journal article
DOI: 10.1513/AnnalsATS.201508-521MG
PMID: 27027937
Contributors: Igartua C; Davenport ER; Chupp GL; Elias JA; Gilad Y; Ober C; Pinto JM
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

A Quick Introduction to Version Control with Git and GitHub.

2016-01 | Journal article
DOI: 10.1371/journal.pcbi.1004668
PMID: 26785377
Contributors: Blischak JD; Davenport ER; Wilson G
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Genome-Wide Association Studies of the Human Gut Microbiota.

2015 | Journal article
DOI: 10.1371/journal.pone.0140301
PMID: 26528553
PMC: PMC4631601
Contributors: Davenport ER; Cusanovich DA; Michelini K; Barreiro LB; Ober C; Gilad Y
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Epigenetic modifications are associated with inter-species gene expression variation in primates.

2014 | Journal article
DOI: 10.1186/PREACCEPT-2025469919139083
PMID: 25468404
PMC: PMC4290387
Contributors: Zhou X; Cain CE; Myrthil M; Lewellen N; Michelini K; Davenport ER; Stephens M; Pritchard JK; Gilad Y
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Seasonal variation in human gut microbiome composition.

2014 | Journal article
DOI: 10.1371/journal.pone.0090731
PMID: 24618913
PMC: PMC3949691
Contributors: Davenport ER; Mizrahi-Man O; Michelini K; Barreiro LB; Ober C; Gilad Y
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs.

2013 | Journal article
DOI: 10.1371/journal.pone.0053608
PMID: 23308262
PMC: PMC3538547
Contributors: Mizrahi-Man O; Davenport ER; Gilad Y
Source: Self-asserted source
Emily R. Davenport via Europe PubMed Central

Peer review (46 reviews for 20 publications/grants)

Review activity for Biology letters. (2)
Review activity for Cell host & microbe. (3)
Review activity for Cell host & microbe. (8)
Review activity for Cell. (1)
Review activity for Critical reviews in microbiology. (1)
Review activity for eLife (1)
Review activity for Genome biology. (4)
Review activity for Genome research. (3)
Review activity for Genomics, proteomics and bioinformatics. (2)
Review activity for Journal of evolutionary biology. (2)
Review activity for JoVE. (2)
Review activity for Microbial ecology. (1)
Review activity for Microbiome (1)
Review activity for Nature communications (1)
Review activity for Nature microbiology. (3)
Review activity for npj biofilms and microbiomes. (4)
Review activity for Scientific reports. (3)
Review activity for The annals of applied statistics. (1)
Review activity for The journal of allergy and clinical immunology (1)
Review activity for Trends in genetics. (2)
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