Curtis Huttenhower

发表

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor

Levi Waldron, Curtis Huttenhower, Nicola Segata, 2018, bioRxiv.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Francesco Asnicar, Mingxun Wang, Pieter C. Dorrestein, 2018 .

A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)

Shibu Yooseph, Curtis Huttenhower, Barbara A. Methé, 2012, PloS one.

HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor

Levi Waldron, Curtis Huttenhower, Lori Shepherd, 2018 .

A reproducible approach to high-throughput biological data acquisition and integration

Levi Waldron, Daniela Börnigen, Curtis Huttenhower, 2015, PeerJ.

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

Curtis Huttenhower, Danielle Tullman-Ercek, Erica M. Hartmann, 2022, Bioinform..

Complex host genetics influence the microbiome in inflammatory bowel disease

Dan Knights, Hailiang Huang, Jenny Sauk, 2014, Genome Medicine.

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

Curtis Huttenhower, Nicola Segata, Timothy L. Tickle, 2014, The ISME Journal.

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

Yves Moreau, Søren Brunak, Lieven Thorrez, 2013, Nucleic acids research.

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Tommi Vatanen, Harri Lähdesmäki, Jorma Ilonen, 2015, Cell host & microbe.

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Francesco Asnicar, Rob Knight, Dan Knights, 2019, Nature Communications.

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types

Martha L. Bulyk, Levi Waldron, Curtis Huttenhower, 2016, Genome Biology.

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Paolo Manghi, Edoardo Pasolli, Francesco Asnicar, 2020, Nature Communications.

PICRUSt2 for prediction of metagenome functions

Gavin M Douglas, Curtis Huttenhower, Morgan G I Langille, 2020, Nature Biotechnology.

The 15th Genomic Standards Consortium meeting

Adam M. Phillippy, Folker Meyer, Frank Oliver Glöckner, 2013 .

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Eric S. Lander, Tommi Vatanen, Curtis Huttenhower, 2015, Science Translational Medicine.

American Gut: an Open Platform for Citizen-Science Microbiome Research

Rob Knight, Pieter C. Dorrestein, Hosein Mohimani, 2018 .

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy

Aleksandar Milosavljevic, Cristian Coarfa, Curtis Huttenhower, 2012, PloS one.

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Paolo Manghi, Edoardo Pasolli, Francesco Asnicar, 2019, Cell host & microbe.

Metagenomic biomarker discovery and explanation

Levi Waldron, Curtis Huttenhower, Nicola Segata, 2011 .

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

Noam Shental, Carrie M. Mosher, Iris Barshack, 2017, Science.

STAT3 Expression, Molecular Features, Inflammation Patterns, and Prognosis in a Database of 724 Colorectal Cancers

Shuji Ogino, Curtis Huttenhower, Mai Yamauchi, 2011, Clinical Cancer Research.

Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis

Mingyang Song, Yin Cao, Reiko Nishihara, 2015, Gut.

Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum

Levi Waldron, Reiko Nishihara, Shuji Ogino, 2012, Gut.

Chapter 12: Human Microbiome Analysis

Curtis Huttenhower, Xochitl C. Morgan, C. Huttenhower, 2012, PLoS Comput. Biol..

Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

Olga G. Troyanskaya, A. P. Hayes, Michael Costanzo, 2009, PLoS genetics.

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

Bo Wang, Michael A Kennedy, Curtis Huttenhower, 2013, Microbiome.

Identifying personal microbiomes using metagenomic codes

Katherine H. Huang, Curtis Huttenhower, Eric A Franzosa, 2015, Proceedings of the National Academy of Sciences.

A tiered hidden Markov model characterizes multi-scale chromatin states.

John Quackenbush, Guo-Cheng Yuan, Curtis Huttenhower, 2013, Genomics.

Biodiversity and functional genomics in the human microbiome.

Curtis Huttenhower, Nicola Segata, Xochitl C Morgan, 2013, Trends in genetics : TIG.

Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.

Curtis Huttenhower, Olga G Troyanskaya, Matthew A. Hibbs, 2009, Methods in molecular biology.

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

Levi Waldron, Curtis Huttenhower, Nicola Segata, 2012, Genome Biology.

Functional and phylogenetic assembly of microbial communities in the human microbiome.

Curtis Huttenhower, Afrah Shafquat, Regina Joice, 2014, Trends in microbiology.

Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism

James Borneman, Curtis Huttenhower, Justin L Sonnenburg, 2014, The ISME Journal.

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

Tommi Vatanen, Raivo Kolde, Harri Lähdesmäki, 2016, Cell.

Corrections: Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity (vol 167, pg 1125, 2016)

Jingyuan Fu, Martin Jaeger, Curtis Huttenhower, 2016 .

Strains, functions and dynamics in the expanded Human Microbiome Project

Arthur Brady, Michelle G. Giglio, Jonathan Crabtree, 2017, Nature.

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Kevin S. Bonham, Rob Knight, Antonio Gonzalez, 2019, Nature.

Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry

Lewis Y. Geer, Curtis Huttenhower, Olga G Troyanskaya, 2007, Proceedings of the National Academy of Sciences.

American Gut: an Open Platform for Citizen Science Microbiome Research

Rob Knight, Pieter C. Dorrestein, Hosein Mohimani, 2018, mSystems.

Text Extraction Using Shape Context Matching

Siddhartha Brahma, Curtis Huttenhower, C. Huttenhower, 2006 .

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

Morris A. Swertz, Jingyuan Fu, Yurii S. Aulchenko, 2016, Science.

Colorectal cancer: a tale of two sides or a continuum?

Shuji Ogino, Curtis Huttenhower, Edward Giovannucci, 2012, Gut.

Translating microbiome futures

Richard Bonneau, Jun Wang, Curtis Huttenhower, 2018, Nature Biotechnology.

Enterotypes in the landscape of gut microbial community composition

Falk Hildebrand, Peer Bork, Rob Knight, 2017, Nature Microbiology.

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

Emmanuel Dias-Neto, Joel Dudley, Mark Hernandez, 2016, Microbiome.

Global chemical effects of the microbiome include new bile-acid conjugations

Julie C. Lumeng, Rob Knight, Mingxun Wang, 2020, Nature.

Tryptophan Biosynthesis Protects Mycobacteria from CD4 T-Cell-Mediated Killing

Thomas R. Ioerger, Curtis Huttenhower, James C. Sacchettini, 2013, Cell.

Accessible, curated metagenomic data through ExperimentHub

Paolo Manghi, Edoardo Pasolli, Levi Waldron, 2017, Nature Methods.

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

John D. Spengler, Curtis Huttenhower, Afrah Shafquat, 2016, mSystems.

Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

Thomas R. Ioerger, Curtis Huttenhower, James C. Sacchettini, 2012, PLoS pathogens.

Translating the human microbiome

Rob Knight, Jeroen Raes, Curtis Huttenhower, 2013, Nature Biotechnology.

Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P‐POD)

Kara Dolinski, Dannie Durand, Rose Oughtred, 2011, Current protocols in bioinformatics.

Advancing the Microbiome Research Community

Rob Knight, Dan Knights, J. Gregory Caporaso, 2014, Cell.

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

Curtis Huttenhower, Nicola Segata, C. Huttenhower, 2011, PloS one.

Hypomethylation of the IGF2 DMR in colorectal tumors, detected by bisulfite pyrosequencing, is associated with poor prognosis.

Shuji Ogino, Curtis Huttenhower, Aditi Hazra, 2010, Gastroenterology.