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Works (50 of 117)

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Page 1 of 3

Metagenomic Profiling of Airborne Microbial Communities from Aircraft Filters and Face Masks

2025-02-27 | Preprint
DOI: 10.1101/2025.02.26.25322977
Contributors: Oliyad Jeilu; Jack T. Sumner; Anahid A. Moghadam; Kelsey N. Thompson; Curtis Huttenhower; Charlie Catlett; Erica M. Hartmann
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Crossref

Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth

2025-02-17 | Preprint
DOI: 10.1101/2025.02.13.638109
Contributors: Samuel D. Gamboa-Tuz; Marcel Ramos; Eric Franzosa; Curtis Huttenhower; Nicola Segata; Sehyun Oh; Levi Waldron
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Crossref

Virulence factor discovery identifies associations between the Fic gene family and Fap2 + fusobacteria in colorectal cancer microbiomes

mBio
2025-02-05 | Journal article
DOI: 10.1128/mbio.03732-24
Contributors: Geicho Nakatsu; Duhyun Ko; Monia Michaud; Eric A. Franzosa; Xochitl C. Morgan; Curtis Huttenhower; Wendy S. Garrett; Martin J. Blaser
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Crossref

Response of the gut microbiome and metabolome to dietary fiber in healthy dogs

mSystems
2025-01-21 | Journal article
DOI: 10.1128/msystems.00452-24
Contributors: Amrisha Bhosle; Matthew I. Jackson; Aaron M. Walsh; Eric A. Franzosa; Dayakar V. Badri; Curtis Huttenhower; Katrine Whiteson
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Crossref

Quantifying Metagenomic Strain Associations from Microbiomes with Anpan

2025-01-07 | Preprint
DOI: 10.1101/2025.01.06.631550
Contributors: Andrew R. Ghazi; Kelsey N. Thompson; Amrisha Bhosle; Zhendong Mei; Yan Yan; Fenglei Wang; Kai Wang; Eric A. Franzosa; Curtis Huttenhower
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Crossref

Profiling lateral gene transfer events in the human microbiome using WAAFLE

Nature Microbiology
2025-01-02 | Journal article
DOI: 10.1038/s41564-024-01881-w
Contributors: Tiffany Y. Hsu; Etienne Nzabarushimana; Dennis Wong; Chengwei Luo; Robert G. Beiko; Morgan Langille; Curtis Huttenhower; Long H. Nguyen; Eric A. Franzosa
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Crossref

MaAsLin 3: Refining and extending generalized multivariable linear models for meta-omic association discovery

2024-12-14 | Preprint
DOI: 10.1101/2024.12.13.628459
Contributors: William A. Nickols; Thomas Kuntz; Jiaxian Shen; Sagun Maharjan; Himel Mallick; Eric A. Franzosa; Kelsey N. Thompson; Jacob T. Nearing; Curtis Huttenhower
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Crossref

Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?

2024-11-09 | Preprint
DOI: 10.1101/2024.11.08.622677
Contributors: William Austin Nickols; Lauren J McIver; Aaron Walsh; Yancong Zhang; Jacob Nearing; Francesco Asnicar; Long Nguyen; Erica M Hartmann; Eric A. Franzosa; Curtis Huttenhower et al.
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Crossref

Compositional Differential Abundance Testing: Defining and Finding a New Type of Health-Microbiome Associations

2024-06-06 | Preprint
DOI: 10.1101/2024.06.04.596112
Contributors: Siyuan Ma; Curtis Huttenhower; Lucas Janson
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Crossref

Author Correction: Optimized model architectures for deep learning on genomic data

Communications Biology
2024-05-23 | Journal article
DOI: 10.1038/s42003-024-06318-y
Contributors: Hüseyin Anil Gündüz; René Mreches; Julia Moosbauer; Gary Robertson; Xiao-Yin To; Eric A. Franzosa; Curtis Huttenhower; Mina Rezaei; Alice C. McHardy; Bernd Bischl et al.
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Crossref

Optimized model architectures for deep learning on genomic data

Communications Biology
2024-04-30 | Journal article
DOI: 10.1038/s42003-024-06161-1
Contributors: Hüseyin Anil Gündüz; René Mreches; Julia Moosbauer; Gary Robertson; Xiao-Yin To; Eric A. Franzosa; Curtis Huttenhower; Mina Rezaei; Alice C. McHardy; Bernd Bischl et al.
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Crossref

Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children

Science Advances
2023-12-22 | Journal article
DOI: 10.1126/sciadv.adi0497
Contributors: Kevin S. Bonham; Guilherme Fahur Bottino; Shelley Hoeft McCann; Jennifer Beauchemin; Elizabeth Weisse; Fatoumata Barry; Rosa Cano Lorente; Curtis Huttenhower; Muriel Bruchhage; Viren D’Sa et al.
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Crossref

Profiling novel lateral gene transfer events in the human microbiome

2023-08-12 | Preprint
DOI: 10.1101/2023.08.08.552500
Contributors: Tiffany Y. Hsu; Etienne Nzabarushimana; Dennis Wong; Chengwei Luo; Robert G. Beiko; Morgan Langille; Curtis Huttenhower; Long H. Nguyen; Eric A. Franzosa
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Crossref

Optimized model architectures for deep learning on genomic data

2023-03-24 | Preprint
DOI: 10.21203/rs.3.rs-2527257/v1
Contributors: Philipp Münch; Hüseyin Anil Gündüz; René Mreches; Julia Moosbauer; Gary Robertson; Xiao-Yin To; Eric Franzosa; Curtis Huttenhower; Mina Rezaei; Alice McHardy et al.
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Crossref

Integrated molecular approaches for fermented food microbiome research

FEMS Microbiology Reviews
2023-03-10 | Journal article
DOI: 10.1093/femsre/fuad001
Contributors: Aaron M Walsh; John Leech; Curtis Huttenhower; Hue Delhomme-Nguyen; Fiona Crispie; Christian Chervaux; Paul D Cotter
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Crossref

Microbiome epidemiology and association studies in human health

Nature Reviews Genetics
2023-02 | Journal article
DOI: 10.1038/s41576-022-00529-x
Contributors: Hannah VanEvery; Eric A. Franzosa; Long H. Nguyen; Curtis Huttenhower
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Crossref

Human threat learning is associated with gut microbiota composition

PNAS Nexus
2022-11-01 | Journal article
DOI: 10.1093/pnasnexus/pgac271
Contributors: Javiera P Oyarzun; Thomas M Kuntz; Yoann Stussi; Olivia T Karaman; Sophia Vranos; Bridget L Callaghan; Curtis Huttenhower; Joseph E LeDoux; Elizabeth A Phelps; Paulo Boggio
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Crossref

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Genome Biology
2022-10-03 | Journal article
DOI: 10.1186/s13059-022-02753-4
Contributors: Siyuan Ma; Dmitry Shungin; Himel Mallick; Melanie Schirmer; Long H. Nguyen; Raivo Kolde; Eric Franzosa; Hera Vlamakis; Ramnik Xavier; Curtis Huttenhower
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Crossref

Human threat learning is associated with gut microbiota composition

2022-06-16 | Preprint
DOI: 10.1101/2022.06.13.495985
Contributors: Javiera P. Oyarzun; Thomas M. Kuntz; Yoann Stussi; Olivia T. Karaman; Sophia Vranos; Bridget L. Callaghan; Curtis Huttenhower; Joseph E. LeDoux; Elizabeth A. Phelps
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Crossref

Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn’s disease

JCI Insight
2022-05-23 | Journal article
DOI: 10.1172/jci.insight.157013
Contributors: Shiying Zhang; Xochitl Morgan; Belgin Dogan; Francois-Pierre Martin; Suzy Strickler; Akihiko Oka; Jeremy Herzog; Bo Liu; Scot E. Dowd; Curtis Huttenhower et al.
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Crossref

Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite

Cell
2022-02 | Journal article
DOI: 10.1016/j.cell.2022.01.002
Contributors: Sun-Yang Park; Chitong Rao; Katharine Z. Coyte; Gavin A. Kuziel; Yancong Zhang; Wentao Huang; Eric A. Franzosa; Jing-Ke Weng; Curtis Huttenhower; Seth Rakoff-Nahoum
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Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper

Bioinformatics
2022-01-12 | Journal article
DOI: 10.1093/bioinformatics/btab752
Contributors: Alexander G McFarland; Nolan W Kennedy; Carolyn E Mills; Danielle Tullman-Ercek; Curtis Huttenhower; Erica M Hartmann; Peter Robinson
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Crossref

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

Microbiome
2021-12 | Journal article
DOI: 10.1186/s40168-020-00961-3
Contributors: Ya Wang; Yan Yan; Kelsey N. Thompson; Sena Bae; Emma K. Accorsi; Yancong Zhang; Jiaxian Shen; Hera Vlamakis; Erica M. Hartmann; Curtis Huttenhower
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Crossref

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper

2021-05-28 | Other
DOI: 10.1101/2021.05.27.446007
Contributors: Alexander G. McFarland; Nolan W. Kennedy; Carolyn E. Mills; Danielle Tullman-Ercek; Curtis Huttenhower; Erica M. Hartmann
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A Phase 1b Safety Study of SER-287, a Spore-Based Microbiome Therapeutic, for Active Mild to Moderate Ulcerative Colitis

Gastroenterology
2021-01 | Journal article
DOI: 10.1053/j.gastro.2020.07.048
Contributors: Matthew R. Henn; Edward J. O’Brien; Liyang Diao; Brian G. Feagan; William J. Sandborn; Curtis Huttenhower; Jennifer R. Wortman; Barbara H. McGovern; Sherry Wang-Weigand; David I. Lichter et al.
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Crossref

Strain-level epidemiology of microbial communities and the human microbiome

Genome Medicine
2020-12 | Journal article
DOI: 10.1186/s13073-020-00765-y
Contributors: Yan Yan; Long H. Nguyen; Eric A. Franzosa; Curtis Huttenhower
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Crossref

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

2020-11-17 | Preprint
DOI: 10.21203/rs.3.rs-59563/v2
Contributors: Ya Wang; Yan Yan; Kelsey N. Thompson; Sena Bae; Emma K. Accorsi; Yancong Zhang; Jiaxian Shen; Hera Vlamakis; Erica M. Hartmann; Curtis Huttenhower
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Crossref

Population Structure Discovery in Meta-Analyzed Microbial Communities and Inflammatory Bowel Disease

2020-08-31 | Preprint
DOI: 10.1101/2020.08.31.261214
Contributors: Siyuan Ma; Dmitry Shungin; Himel Mallick; Melanie Schirmer; Long H. Nguyen; Raivo Kolde; Eric Franzosa; Hera Vlamakis; Ramnik Xavier; Curtis Huttenhower
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Crossref

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

2020-08-18 | Preprint
DOI: 10.21203/rs.3.rs-59563/v1
Contributors: Ya Wang; Yan Yan; Kelsey N. Thompson; Sena Bae; Emma K. Accorsi; Yancong Zhang; Jiaxian Shen; Hera Vlamakis; Erica M. Hartman; Curtis Huttenhower
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Crossref

PICRUSt2 for prediction of metagenome functions

Nature Biotechnology
2020-06-01 | Journal article
DOI: 10.1038/s41587-020-0548-6
Contributors: Gavin M. Douglas; Vincent J. Maffei; Jesse R. Zaneveld; Svetlana N. Yurgel; James R. Brown; Christopher M. Taylor; Curtis Huttenhower; Morgan G. I. Langille
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Crossref

Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children

2020-02-14 | Preprint
DOI: 10.1101/2020.02.13.944181
Contributors: Kevin S Bonham; Guilherme Fahur Bottino; Shelley Hoeft McCann; Jennifer Beauchemin; Elizabeth Weisse; Fatoumata Barry; Rosa Cano-Lorente; Curtis Huttenhower; Muriel M.K. Bruchhage; Viren D'Sa et al.
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Crossref

Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions

The Journal of Nutrition
2019-11 | Journal article
DOI: 10.1093/jn/nxz154
Contributors: Michael I McBurney; Cindy Davis; Claire M Fraser; Barbara O Schneeman; Curtis Huttenhower; Kristin Verbeke; Jens Walter; Marie E Latulippe
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Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

Nature Communications
2019-07-17 | Journal article
DOI: 10.1038/s41467-019-10927-1
Contributors: Himel Mallick; Eric A. Franzosa; Lauren J. Mclver; Soumya Banerjee; Alexandra Sirota-Madi; Aleksandar D. Kostic; Clary B. Clish; Hera Vlamakis; Ramnik J. Xavier; Curtis Huttenhower
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Crossref

HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor

2018-04-17 | Other
DOI: 10.1101/299115
Contributors: Lucas Schiffer; Rimsha Azhar; Lori Shepherd; Marcel Ramos; Ludwig Geistlinger; Curtis Huttenhower; Jennifer B Dowd; Nicola Segata; Levi Waldron
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Crossref

Experimental design and quantitative analysis of microbial community multiomics

Genome Biology
2017-12 | Journal article
DOI: 10.1186/s13059-017-1359-z
Contributors: Himel Mallick; Siyuan Ma; Eric A. Franzosa; Tommi Vatanen; Xochitl C. Morgan; Curtis Huttenhower
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Accessible, curated metagenomic data through ExperimentHub

Nature Methods
2017-10-31 | Journal article
DOI: 10.1038/nmeth.4468
Contributors: Edoardo Pasolli; Lucas Schiffer; Paolo Manghi; Audrey Renson; Valerie Obenchain; Duy Tin Truong; Francesco Beghini; Faizan Malik; Marcel Ramos; Jennifer B Dowd et al.
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Crossref

Microbial strain-level population structure and genetic diversity from metagenomes

Genome Research
2017-04-06 | Journal article
DOI: 10.1101/gr.216242.116
Contributors: Duy Tin Truong; Adrian Tett; Edoardo Pasolli; Curtis Huttenhower; Nicola Segata
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Crossref

A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans -4-hydroxy- l -proline

Science
2017-02-10 | Journal article
DOI: 10.1126/science.aai8386
Contributors: B. J. Levin; Y. Y. Huang; S. C. Peck; Y. Wei; A. Martínez-del Campo; J. A. Marks; E. A. Franzosa; C. Huttenhower; E. P. Balskus
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A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

2013 | Journal article
DOI:

10.1371/journal.pcbi.1002863

Part of ISSN:

1553-7358
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

A tiered hidden Markov model characterizes multi-scale chromatin states

2013 | Journal article
DOI:

10.1016/j.ygeno.2013.03.009

Part of ISSN:

0888-7543
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

Biodiversity and functional genomics in the human microbiome

2013 | Journal article
DOI:

10.1016/j.tig.2012.09.005

Part of ISSN:

0168-9525
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

Computational meta’omics for microbial community studies

2013 | Journal article
DOI:

10.1038/msb.2013.22

Part of ISSN:

1744-4292
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

2013 | Journal article
DOI:

10.1093/nar/gkt661

Part of ISSN:

0305-1048
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

Correction: Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

2013 | Journal article
DOI:

10.1371/annotation/4669e9e7-fd12-4a01-be2a-617b956ec0bb

Part of ISSN:

1553-7374
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

2013 | Journal article
DOI:

10.1093/database/bat013

Part of ISSN:

1758-0463
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

2013 | Journal article
DOI:

10.1186/2049-2618-1-13

Part of ISSN:

2049-2618
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

Functional profiling of the gut microbiome in disease-associated inflammation

2013 | Journal article
DOI:

10.1186/gm469

Part of ISSN:

1756-994X
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

2013 | Journal article
DOI:

10.1038/ismej.2013.167

Part of ISSN:

1751-7362
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

2013 | Journal article
DOI:

10.1186/2049-2618-1-17

Part of ISSN:

2049-2618
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search

P698 Characterization of the tissue-associated microbiome in active and inactive IBD

2013 | Journal article
DOI:

10.1016/s1873-9946(13)60719-9

Part of ISSN:

1873-9946
Source: Self-asserted source
Curtis Huttenhower via Crossref Metadata Search
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Peer review (16 reviews for 11 publications/grants)

Review activity for Genome medicine. (1)
Review activity for Microbiome (1)
Review activity for Nature (3)
Review activity for Nature aging. (1)
Review activity for Nature biotechnology. (1)
Review activity for Nature communications (2)
Review activity for Nature methods. (1)
Review activity for Nature microbiology. (3)
Review activity for Nature reviews methods primers. (1)
Review activity for Nature reviews. (1)
Review activity for PLoS computational biology. (1)
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