Publications

Academic publications

Chengzhen Dai, Claire Duvallet, An Ni Zhang, Mariana Matus, Newsha Ghaeli, Shinkyu Park, Noriko Endo, Siavash Isazadeh, Kazi Jamil, Carlo Ratti, and Eric Alm.
“Multi-site sampling and risk prioritization reveals the public health relevance of antibiotic resistance genes found in sewage environments.”
in preparation.

Claire Duvallet, Caroline Zellmer, Pratik Panchal, Shrish Budree, Madji Osman, and Eric Alm.
“Framework for rational donor selection in fecal microbiota transplant clinical trials.”
in preparation.
Associated github: cduvallet/donor-selection

Mariana Matus, Claire Duvallet, Newsha Ghaeli, Melissa Kido Soule, Krista Longnecker, Ilana Brito, Carlo Ratti, Elizabeth B. Kujawinski, Eric Alm.
“Untargeted detection of human health and activity markers in residential wastewater through microbiome sequencing and metabolomics.”
in preparation.

Claire Duvallet, Kara Larson, Scott Snapper, Sonia Iosim, Ann Lee, Katherine Freer, Kara May, Eric Alm, and Rachel Rosen.
“Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function.”
bioRxiv (2018). doi: 10.1101/476580.
Associated github: cduvallet/aspiration-analysis-public

Keegan Korthauer*, Patrick K Kimes*, Claire Duvallet^, Alejandro Reyes^, Ayshwarya Subramanian^, Mingxiang Teng, Chinmay Shukla, Eric J Alm, and Stephanie C Hicks.
“A practical guide to methods controlling false discoveries in computational biology.”
Genome Biology (2019). doi: 10.1186/s13059-019-1716-1.
Associated github: pkimes/benchmark-fdr

Thomas Gurry, HST Microbiome Consortium, Sean M Gibbons, Sean M Kearney, Ashwin Ananthakrishnan, Xiaofang Jiang, Claire Duvallet, Zain Kassam, and Eric J Alm.
“Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort.”
Scientific Reports (2018) 8(1): 12699. doi: 10.1038/s41598-018-30783-1

Sean M. Gibbons, Claire Duvallet, and Eric J. Alm.
“Correcting for batch effects in case-control microbiome studies.” 
PLoS Computational Biology (2018) 14(4): e1006102. doi: 10.1371/journal.pone.0176335

Claire Duvallet.
“Meta-analysis generates and prioritizes hypotheses for translational microbiome research.”
Microbial Biotechnology (2018). doi: 10.1111/1751-7915.13047

Claire Duvallet, Sean M. Gibbons, Thomas Gurry, Rafael A. Irizarry, and Eric J. Alm.
“Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.” 
Nature Communications (2017). doi: 10.1038/s41467-017-01973-8
Associated github: cduvallet/microbiomeHD
Associated data: zenodo record 840333.

Scott W. Olesen, Claire Duvallet, and Eric J. Alm.
“dbOTU3: A new implementation of distribution-based OTU calling.” 
PloS ONE 12, no. 5 (2017): e0176335. doi: 10.1371/journal.pone.0176335

Non-peer reviewed academic content

[Tutorial] Claire Duvallet and Mehrbod Estaki. “QIIME 2 for Experienced Microbiome Researchers.” QIIME 2 docs. (2018).

[Tutorial] Claire Duvallet. “Developing a plug-in for dummies.” QIIME 2 developer docs. (2018).

[Tutorial] Claire Duvallet. “Publishing your plugin on conda.” QIIME 2 developer docs. (2018).

[Blog post] Claire Duvallet. “Beyond dysbiosis: disease-specific and shared microbiome responses to disease.Nature Microbiology Community Forum. December 2017.

[Dataset] Claire Duvallet, Sean M. Gibbons, Thomas Gurry, Rafael A. Irizarry, and Eric J. Alm. (2017). MicrobiomeHD: the human gut microbiome in health and disease. Zenodo. doi: 10.5281/zenodo.797943

Software

Percentile normalization
Correcting batch effects in case-control microbiome studies. (Gibbons et al., 2018)

Distribution-based OTU calling
New implementation of Preheim et al.’s distribution-based OTU clustering algorithm. (Preheim et al., 2013; Olesen et al., 2017).

Amplicon sequencing pipeline
End-to-end pipeline to process 16S data.

Other

[Blog post] Claire Duvallet. “Learning to Engage in Deep Conversations.” MIT Graduate Admissions blog (2018).

[Resource] Claire Duvallet and Monika Avello. “Graduate student support resources flowchart.” I and another student on iREFS created this flowchart to help graduate students find support at MIT.