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Se-Jin Song · SciRah

Researcher profile · Semantic Scholar

Se-Jin Song

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Se-Jin Song — researcher profile on SciRah

h-index: 37
Works: 90
Citations: 38K

Most-cited papers

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
E. Bolyen, J. Rideout, M. Dillon, N. Bokulich +108 more
2019Nature Biotechnology20K citations Open access
Semantic Scholar
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
L. Thompson, Jon G. Sanders, D. McDonald, Amnon Amir +299 more
2017Nature5,510 citations Open access
Semantic Scholar
The treatment-naïve microbiome in new-onset Crohn’s disease
D. Gevers, S. Kugathasan, L. Denson, Y. Vázquez-Baeza +28 more
2014Cell Host and Microbe3,008 citations Open access
Semantic Scholar
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
E. Bolyen, J. Rideout, M. Dillon, N. Bokulich +106 more
20181,200 citations Open access
Semantic Scholar
Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Greg D. Poore, E. Kopylova, Qi-Yun Zhu, Carolina S. Carpenter +13 more
2020Nature875 citations Open access
Semantic Scholar
American Gut: an Open Platform for Citizen Science Microbiome Research
D. McDonald, E. Hyde, J. Debelius, James T. Morton +54 more
2018mSystems799 citations Open access
Semantic Scholar
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
E. Bolyen, J. Rideout, M. Dillon, N. Bokulich +108 more
2019Nature Biotechnology724 citations Open access
Semantic Scholar
Greengenes2 unifies microbial data in a single reference tree
D. McDonald, Yueyu Jiang, M. Balaban, Kalen Cantrell +21 more
2023Nature Biotechnology666 citations Open access
Semantic Scholar
Advancing our understanding of the human microbiome using QIIME
J. Navas-Molina, J. Peralta-Sánchez, A. González, P. McMurdie +12 more
2013Methods in Enzymology546 citations Open access
Semantic Scholar
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies
Se-Jin Song, Amnon Amir, J. Metcalf, K. Amato +3 more
2016mSystems422 citations Open access
Semantic Scholar
The Effects of Captivity on the Mammalian Gut Microbiome
V. McKenzie, Se-Jin Song, F. Delsuc, T. Prest +15 more
2017Integrative and Comparative Biology410 citations Open access
Semantic Scholar
The human microbiome in evolution
Emily R. Davenport, Jon G. Sanders, Se-Jin Song, K. Amato +2 more
2017BMC Biology311 citations Open access
Semantic Scholar
Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes
K. Amato, Jon G. Sanders, Se-Jin Song, Michael G. Nute +25 more
2018The ISME Journal301 citations Open access
Semantic Scholar
The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions
P. Engel, W. Kwong, Q. McFrederick, K. E. Anderson +29 more
2016mBio301 citations Open access
Semantic Scholar
Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats
Se-Jin Song, Jon G. Sanders, F. Delsuc, J. Metcalf +22 more
2020mBio299 citations Open access
Semantic Scholar
Balance Trees Reveal Microbial Niche Differentiation
James T. Morton, Jon G. Sanders, R. Quinn, D. McDonald +9 more
2017mSystems246 citations Open access
Semantic Scholar
Learning accurate representations of microbe-metabolite interactions
James T. Morton, A. Aksenov, L. Nothias, J. Foulds +13 more
2019Nature Methods220 citations Open access
Semantic Scholar
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
J. Shaffer, L. Nothias, L. Thompson, Jon G. Sanders +47 more
2022Nature Microbiology172 citations Open access
Semantic Scholar
Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome
Bryn C. Taylor, F. Lejzerowicz, Marion Poirel, J. Shaffer +12 more
2020mSystems172 citations Open access
Semantic Scholar
Tiny microbes, enormous impacts: what matters in gut microbiome studies?
J. Debelius, Se-Jin Song, Y. Vázquez-Baeza, Z. Xu +2 more
2016Genome Biology145 citations Open access
Semantic Scholar
Evaluating the impact of domestication and captivity on the horse gut microbiome
J. Metcalf, Se-Jin Song, James T. Morton, Sophie J. Weiss +10 more
2017Scientific Reports132 citations Open access
Semantic Scholar
Home chemical and microbial transitions across urbanization
Laura-Isobel McCall, C. Callewaert, Qi-Yun Zhu, Se-Jin Song +15 more
2019Nature Microbiology119 citations Open access
Semantic Scholar
Engineering the microbiome for animal health and conservation
Se-Jin Song, Douglas C. Woodhams, C. Martino, Celeste Allaband +4 more
2019Experimental biology and medicine94 citations Open access
Semantic Scholar
Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding
Se-Jin Song, Jincheng Wang, C. Martino, Lingjing Jiang +23 more
2021i Medicina85 citations Open access
Semantic Scholar
Walls talk: Microbial biogeography of homes spanning urbanization
Jean F. Ruiz-Calderón, H. Cavallin, Se-Jin Song, A. Novoselac +9 more
2016Science Advances84 citations Open access
Semantic Scholar
Major shifts in gut microbiota during development and its relationship to growth in ostriches
Elin Videvall, Se-Jin Song, H. Bensch, M. Strandh +7 more
2019Molecular Ecology81 citations Open access
Semantic Scholar
Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations: Statistical Power for Microbiome Studies.
C. Casals-Pascual, A. González, Y. Vázquez-Baeza, Se-Jin Song +2 more
2020Gastroenterology79 citations
Semantic Scholar
The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat
E. Hyde, J. Navas-Molina, Se-Jin Song, Jordan G. Kueneman +9 more
2016mSystems76 citations Open access
Semantic Scholar
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
C. Marotz, Kellen J. Cavagnero, Se-Jin Song, D. McDonald +6 more
2021mSystems74 citations Open access
Semantic Scholar
A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project
Aurélie Cotillard, Agnès Cartier-Meheust, N. Litwin, Soline Chaumont +10 more
2021American Journal of Clinical Nutrition70 citations Open access
Semantic Scholar
Robustness of cancer microbiome signals over a broad range of methodological variation
G. Sepich-Poore, D. McDonald, E. Kopylova, Caitlin Guccione +17 more
2024Oncogene68 citations Open access
Semantic Scholar
How delivery mode and feeding can shape the bacterial community in the infant gut
Se-Jin Song, M. Dominguez-Bello, R. Knight
2013Canadian Medical Association Journal64 citations Open access
Semantic Scholar
Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue
Whitney A. Kodama, Z. Xu, J. Metcalf, Se-Jin Song +4 more
2018Journal of Forensic Sciences53 citations Open access
Semantic Scholar
Early-life gut dysbiosis linked to juvenile mortality in ostriches
Elin Videvall, Se-Jin Song, H. Bensch, M. Strandh +7 more
2020Microbiome51 citations Open access
Semantic Scholar
From Sample to Multi-Omics Conclusions in under 48 Hours
R. Quinn, J. Navas-Molina, E. Hyde, Se-Jin Song +14 more
2016mSystems51 citations Open access
Semantic Scholar
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
Kalen Cantrell, Marcus W. Fedarko, G. Rahman, D. McDonald +26 more
2021mSystems50 citations Open access
Semantic Scholar
Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors
J. Tap, F. Lejzerowicz, Aurélie Cotillard, M. Pichaud +5 more
2023Nature Communications39 citations Open access
Semantic Scholar
Greengenes2 enables a shared data universe for microbiome studies
D. McDonald, Yueyu Jiang, M. Balaban, Kalen Cantrell +21 more
2023bioRxiv37 citations Open access
Semantic Scholar
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity
C. Martino, Benjamin P. Kellman, Daniel R. Sandoval, T. M. Clausen +32 more
2020bioRxiv32 citations Open access
Semantic Scholar
A multi-study analysis enables identification of potential microbial features associated with skin aging signs
Tyler Myers, Amina Bouslimani, Shi Huang, Shalisa Hansen +10 more
2024Frontiers in Aging30 citations Open access
Semantic Scholar
Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations
Doratha A. Byrd, Jun Chen, E. Vogtmann, Autumn G Hullings +10 more
2019PLoS ONE29 citations Open access
Semantic Scholar
Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype
C. Martino, D. McDonald, Kalen Cantrell, A. Dilmore +8 more
2022mSystems27 citations Open access
Semantic Scholar
Is there convergence of gut microbes in blood-feeding vertebrates?
Se-Jin Song, Jon G. Sanders, Daniel T. Baldassarre, J. Chaves +9 more
2019Philosophical Transactions of the Royal Society of London. Biological Sciences27 citations Open access
Semantic Scholar
Are microbiome studies ready for hypothesis-driven research?
A. Tripathi, C. Marotz, A. González, Y. Vázquez-Baeza +8 more
2018Current Opinion in Microbiology24 citations Open access
Semantic Scholar
Temporal nutrition analysis associates dietary regularity and quality with gut microbiome diversity: insights from the Food & You digital cohort
Rohan Singh, D. McDonald, Alejandra Ríos Hernández, Se-Jin Song +3 more
2025Nature Communications23 citations Open access
Semantic Scholar
Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota
Kate A. Sabey, Se-Jin Song, A. Jolles, R. Knight +1 more
2020The ISME Journal23 citations Open access
Semantic Scholar
Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies
C. Brennan, P. Belda-Ferre, Simone Zuffa, Vincent Charron-Lamoureux +14 more
2024mSystems19 citations Open access
Semantic Scholar
Author Correction: Greengenes2 unifies microbial data in a single reference tree
D. McDonald, Yueyu Jiang, M. Balaban, Kalen Cantrell +21 more
2023Nature Biotechnology19 citations Open access
Semantic Scholar
Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References
Daniel Hakim, S. Wandro, K. Zengler, L. Zaramela +7 more
2022mSystems17 citations Open access
Semantic Scholar
Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis
Tyler Myers, Se-Jin Song, Yang Chen, B. De Pessemier +13 more
2025Communications Biology13 citations Open access
Semantic Scholar

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