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Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“Vitamin B and vitamin D as modulators of gut microbiota in overweight individuals” | Jiang, Shangfei | International Journal of Food Sciences and Nutrition | Vitamin B, Vitamin D, Obesity, Gut microbiome, Diet |
“Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome” | Taylor, Bryn | mSystems | Gut microbiome, Gut metabolome, Diet, Fermented foods, CLA, Conjugated linoeic acid |
“Multiple-Disease Detection and Classification across Cohorts via Microbiome Search” | Su, Xiaoquan | mSystems | Disease detection, Classification, Search-based strategy, Big data, Microbiome Search Engine, MSE |
“Finding Archetypal Spaces Using Neural Networks” | van Dijk, David | IEEE Xplore | Archetypal analysis, Archetypes, AAnet, Archetypal Analysis network |
“Human Skin, Oral, and Gut Microbiomes Predict Chronological Age” | Huang, Shi | mSystems | Age Prediction, Skin, Oral, Gut |
“Effects of the microalgae Chlamydomonas on gastrointestinal health” | Fields, Francis | Journal of Functional Foods | Chlamydomonas reinhardtii, Green algae, Microalgae, Gastrointenstinal health, Bowel discomfort |
“In Vitro Evaluation of Different Prebiotics on the Modulation of Gut Microbiota Composition and Function in Morbid Obese and Normal-Weight Subjects” | Nogacka, Alicja | International Journal of Molecular Sciences | Gut microbiome, Adulthood, Dysbiosis, In vitro model, Obesity, Prebiotics, Inulin-type fructans, 1-Kestose |
“Red Wine Consumption Associated With Increased Gut Microbiota α-Diversity in 3 Independent Cohorts” | Le Roy, Caroline | Gatroenterology | Red Wine, Alcohol, Polyphenols, TwinsUK |
Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies” | Liao, Tianhua | Genome Biology | tmap, Topological data analysis, Population-scale microbiome, MWAS, Nonlinear patterns, Stratification |
“The microbiome and its potential for pharmacology” | Chavira, Aries | Handbook of Experimental Pharmacology | Immunotherapy, FMT, Fecal microbiome transplant, Precision medicine, Diseases, Drugs, Metabolism |
“Synthetic ecology of the human gut microbiota” | Vrancken, Gino | Nature Reviews | Gut microbiome, Ecosystem, Microbes, Health, Diet, In vitro systems |
“The urinary tract microbiome in older women exhibits host genetics and environmental influences” | Adebayo, Adewale | bioRxiv | Urogenital tract, Aging, UTI, Genetics, Urobiome, Bladder microbiome |
“Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity” | Kaplan, Robert | Genome Biology | Epidemiology, HCHS/SOL, Hispanics, Latinos, Latinas, Latinx, Immigrants |
“Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads” | Sanders, Jon | Genome Biology | Metagenomics, DNA sequencing, Protocol optimization, Library preparation methods |
“Neighborhoods to Nucleotides—Advances and Gaps for an Obesity Disparities Systems Epidemiology Model” | Jankowska, Marta | Genetic Epidemiology | Epidemiology, Obesity, Hispanics, Latinos, Latinas, Latinx, Health disparities, N2N |
“Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations” | Byrd, Doratha | PLoS One | 16S rRNA gene amplicon, Sequencing, FOBT, FTA, FIT, Ethanol, RNAlater, ICCs, SCCs |
“Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny” | Amato, Katherine | Genome Biology | Primates, Cercopithecines, Inter-individual variation, Old World monkey |
“Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data” | Tackmmann, Janko | Cell Systems | FlashWeave, Metadata, Microbial interactions, Abundance, Co-occurrence, Co-abundance |
“Robust Regression with Compositional Covariates” | Mishra, Aditya | AarXiv preprint | Microbiome profiling data, Statistical regression framework, Human body mass, Amplicon data, Robust estimators |
“Defining Dysbiosis for a Cluster of Chronic Diseases” | Wilkins, Lamont | Scientific Reports | Dysbiosis, Chronic disease, Antibiotics, Bacteroides, Prevotella, Ruminococcus, Microbial diversity |
“A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota” | Cao, Liu | mSystems | Microbiome, Mass specrometry, Metagenomics, Isolates, Cystic fibrosis, Association networks |
“Beyond the gut: Skin microbiome compositional changes are associated with BMI” | Brandwein, Michael | Human Microbiome Journal | Skin microbiome, BMI, Obesity, Corynebacterium, Biomarker |
“Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2” | Bolyen, Evan | Nature Biotechnology | Interactive, Visualization tools, Bioinformatics, Data, Open-source software |
“Dimensionality reduction of the Human Microbiome data” | Samardžić, Mirjana | University of Novi Sad | Dimensionality reduction, Human microbiome, OTUs, Random Forest Classifier |
“Gut microbiota phenotypes of obesity” | Stanislawski, Maggie | npj Biofilms and Microbiomes | Obesity, Western populations, Prevotella, BMI, Socioeconomic status, Diet |
“Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome” | Kosnicki, Kassi | Addiction Biology | Alcohol, 20% Ethanol, Dysbiosis, Lactobaclli |
“Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota” | Tito, Raul Y | Gut | Blastocystis, Flemish Gut Flora Project, IBD, Inflammatory bowel disease |
“Age-and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults” | de la Cuesta-Zuluaga, Jacobo | mSystems | Human life span, Sex-dependent differences, Health, Gut diversity |
“Quantifying and Understanding Well-to-Well Contamination in Microbiome Research” | Minich, Jeremiah | mSystems | Contamination, DNA extraction, 96-well plates |
“Establishing microbial composition measurement standards with reference frames” | Morton, James | Nature Communications | Differential abundance, Reference frames, Relative abundance |
“Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome” | Rodionov, Dmitry | Frontiers in Microbiology | Micronutrients, B-group vitamins, Metabolic pathways, Metabolic pehnotypes, Metabolism |
“Microbial networks in SPRING-Semi-parametric rank-based correlation and partial correlation for quantiative microbiome data” | Yoon, Grace | Frontiers in Genetics | Microbial association networks, Semi-parametric estimators, Correlation, Statistical analysis |
“Composition of gut microbiota and its association with body mass index and lifestyle factors in a cohort of 7-18 years old children from the American Gut Project” | Bai, Jinbing | Pediatric Obesity | BMI, Body mass index, Obesity, Exercise, Diet, Actinobacteria, Proteobacteria, Firmicutes |
“GABA-modulating bacteria of the human gut microbiota” | Strandwitz, Philip | Nature Microbiology | GABA, Production pathways, Host functions, Bacteroides fragilis |
“Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data” | Washburne, Alex | Ecological Monographs | Community ecology, Phylogeny, Phylofactorization, Relative abundance, Algorithm |
“Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn’s Disease” | Mills, Robert | mSystems | CD, Crohn’s disease, Faecalibacerium, Escherichia, Metaproteomics, Metagenomics, IBD, Inflammatory bowel disease |
“Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects” | Nguyen, Tanya | Schizophrenia Research | Gut-brain axis, Psychiatric research, Schizophrenia |
“Calour: an Interactive, Microbe-Centric Analysis Tool” | Xu, Zhenjiang | mSystems | Microbiome analysis, Data exploration, Interactive heatmap, Visualization |
“Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians” | Allaband, Celeste | Clinical Gastroenterology and Hepatology | Study design, Inter-/intra-subject variability, Clinician |
Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“Gut microbiota diversity across ethnicities in the United States” | Brooks, Andrew | PLoS Biology | Ethnicity, Christensenellaceae, Health disparity, Therapeutics |
“Identifying and Predicting Novelty in Microbiome Studies” | Su, Xiaoquan | mBio | Microbiome Search Engine, MSE, Novelty, Taxonomic similarity, 16S rRNA, Microbiome focus index, MFI, Microboime attention score, MAS, Big data |
“Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn’s Disease Patient” | Fang, Xin | Frontiers in Microbiology | Dysbiosis, Escherichia coli, IBD, Crohn’s disease, CD |
“Striped UniFrac: enabling microbiome analysis at unprecedented scale” | McDonald, Daniel | Nature Methods | UniFrac, Microbiome comparison, Phylogeny |
“Competitive lottery-based assembly of selected clades in the human gut microbiome” | Verster, Adrian | Microbiome | Competitive lottery model, Niche, Akkermansia, Dialister, Phascolarctobacterium, Microbiome composition |
“Daylight exposure modulates bacterial communities associated with household dust” | Fahimipour, Ashkaan | Microbiome | Sunlight, Light exposure, Built environment, Dust communities, Source tracking |
“Qiita: rapid, web-enabled microbiome meta-analysis” | Gonzalez, Antonio | Nature Methods | QIITA, Multiomics, Open-source platforms, Meta-analysis |
“Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity” | Bankevich, Anton | Cell Systems | Microbial diversity, Metagenomics, Algorithm, Metagenome |
“Are microbiome studies ready for hypothesis-driven research?” | Tripathi, Anupriya | Current Opinion in Microbiology | Hypothesis-driven research programs, Spatial maps, Standardization |
“Best practices for analysing microbiomes” | Knight, Rob | Nature Reviews Microbiology | Microbiome study, Molecular analysis technology, Multiomics, Experimental design |
“American Gut: an Open Platform for Citizen Science Microbiome Research” | McDonald, Daniel | mSystems | American Gut manuscript, Cross-cohort comparison, Beta diversity, Human microbiome |
Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes” | Jiang, Lingjing | mSystems | Differential abundance testing, Discrete false-discovery rate, dS-FDR, Bioinformatics, Statistics |
“Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project” | Liu, Menghan | Microbiome | Oxalobacter formigenes, O. formigenes, Colonizing patterns, Host-microbe relationships |
“Motivations of participants in the citizen science of microbiomics: data from the British Gut Project” | Del Savio, Lorenzo | Genetics in Medicine | Databases, Survey, Participation, Research efforts, Citizen science, British Gut Project |
“Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project” | Bettengill, James | PeerJ | Listeria, Salmonella, Segel’s Law, V4 region, Public health |
“Gut Instinct: Creating Scientific Theories with Online Learners” | Pandey, Vineet | Proceedings of the 2017 CHI Conference on Human Factors in Computing Systems | HCI, Citizen science, Gut Instinct, Online learning, Crowdsourcing |
“The Microbiome and Human Biology” | Knight, Rob | Annual Review of Genomics and Human Genetics | Sequencing technology, Metagenomics, Metabolomics, Development |
“Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping” | Amir, Amnon | mSystems | Bloom filtering, Deblur, Room-temperature shipping, Gammaproteobacteria |
“Normalization and microbial differential abundance strategies depend upon data characteristics” | Weiss, Sophie | Microbiome | Normalization, Differential abundance, 16S rRNA, Taxon |
“Comparison of Collection Methods for Fecal Samples in Microbiome Studies” | Vogtmann, Emily | American Journal of Epidemiology | Method testing, Fecal microbiome, Ethanol, RNAlater, FOBT cards, Fecal immunochemical |
Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies” | Loftfield, Erikka | Cancer Epidemiology, Biomarkers & Prevention | Metabolome, Method testing, Epidemiologic studies, 95% ethanol, FOBT, FIT |
“Tiny microbes, enormous impacts: what matters in gut microbiome studies?” | Debelius, Justine | Genome Biology | Biological factors, Technological factors, Integrated studies, Meta-analysis |
“Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort” | Gonzalez, Antonio | mSystems | Nitrates, Migraines, Headaches, Oral microbiome, American Gut Project |
“Heritable components of the human fecal microbiome are associated with visceral fat” | Beaumont, Michelle | Genome Biology | Fecal microbiome, BMI, Obesity, Abdominal adiposity, Twin study, TwinsUK, Visceral fat |
“Integrating citizen science with online learning to ask better questions” | Pandey, Vineet | arXiv preprint | HCI, Citizen science, Gut Instinct, Online learning |
“Extreme Dysbiosis of the Microbiome in Critical Illness” | McDonald, Daniel | mSphere | Critical illnesses, Dysbiosis, ICU, SourceTracker |
“Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness” | Wischmeyer, Paul | Current Opinion in Critical Care | Dysbiosis, Infections, Sepsis, Organ failure, ICU, Probiotics |
“Microbiome-wide association studies link dynamic microbial consortia to disease” | Gilbert, Jack A | Nature | Health care, Diseases, Biomarkers, Time-series, Association studies |
“Genetic Determinants of the Gut Microbiome in UK Twins” | Goodrich, Julia | Cell Host & Microbe | Twin study, Candidate genes, Bifidobacterium, Lactase gene locus, TwinsUK |
“Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies” | Song, Se Jin | mSystems | Fecal microbiome, Preservation methods, Stability, Method testing, Ethanol, FTA cards, OMNIgene |
“From Sample to Multi-Omics Conclusions in under 48 Hours” | Quinn, Robert | mSystems | Multi-Omics, Skin, Feces, Oral cavity, Fermented foods, Houeshold surfaces, Home food fermentation, Polymicrobial infections |
“Geography and Location Are the Primary Drivers of Office Microbiome Composition” | Chase, John | mSystems | Office microbiome, Built environment, Skin contact, Indoors |
“Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project” | Debelius, Justine | Journal of Microbiology & Biology Education | Crowdsourcing, American Gut Project, Participatory science, Public participation |
Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“Can Your Microbiome Tell You What to Eat?” | Vanamala, Jairam | Cell Metabolism | Diet, Gut microbiome, Blood glucose, Food |
“Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project” | Hua, Xing | EBioMedicine | Adult microbiome, Dysbiosis, Allergy, Allergies, Type I hypersensitivity disorders, Clostridiales, Bacteroidales |
“Context and the human microbiome” | McDonald, Daniel | Microbiome | American Gut Project, Reference database, Meta-analysis |
“The microbiome of uncontacted Amerindians” | Clemente, Jose | ScienceAdvances | Yanomami, Amerindians, AR genes, Antibiotic resistance |
“Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients” | McDonald, Daniel | Microbial Ecology in Health and Disease | ASD, Autism spectrum disorder |
Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“Dietary effects on human gut microbiome diversity” | Xu, Zhenjiang | British Journal of Nutrition | Diet, Gut microbiome |
“Diversity and composition of the adult fecal microbiome associated with history of cesarean birth or appendectomy: Analysis of the American Gut Project” | Goedert, James | EBioMedicine | Cesarean birth, C. section, Obesity, Diseases |
“Gut Microbes and the Brain: Paradigm Shift in Neuroscience” | Mayer, Emeran A | The Journal of Neuroscience | Neurocine and endocrine signaling mechanisms, Pathophysiological, Brain diseases, CNS, Neuroscience |
“Human genetics shape the gut microbiome” | Goodrich, Julia K | Cell Press | Genetics, Phenotypes, Twin studies, TwinsUK Christensenellaceae, Christensenella minuta, BMI, Metabolism |
Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“EMPeror: a tool for visualizing high-throughput microbial community data” | Vazquez-Baeza, Yoshiki | Gigascience | Microbial ecology, QIIME, EMPeror, Data visualization |
“Meta-analyses of studies of the human microbiota” | Lozupone, Catherine A | Genome Research | QIIME, Cross-study comparisons, 16S rRNA gene |
“From molecules to dynamic biological communities” | McDonald, Daniel | Biology & Philosophy | Timeseries, Microbial community analysis, Operational taxonomic units, OUT |
“A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets” | Koren, Omry | PLoS Computational Biology | Enterotypes, Human Microbiome Project, HMP, Meta-analysis |
“Advancing our understanding of the human microbiome using QIIME” | Navas-Molina, José A. | Methods in Enzymology | Highthroughput sequencing, Microbial community analyses, QIIME |
Title |
First Author |
Journal |
Pubmed Keywords |
---|---|---|---|
“Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing” | Bokulich, Nicholas | Nature Methods | Read length, Read abundance, Filtering strategies, Amplicon sequencing |
“The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome” | Gevers, Dirk | PLoS Biology | Human Microbiome Project, HMP, Metagenomics |
“The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome” | McDonald, Daniel | Gigascience | Biological Observation Matrix, BIOM, Bioinformatics, QIIME, Metagenomics, Microbial ecology |
“A framework for human microbiome research” | The Human Microbiome Project Consortium | Nature | Human Microbiome Project, HMP, Population-scale, Metagenomics, Bioinformatics |
“Structure, function and diversity of the healthy human microbiome” | The Human Microbiome Project Consortium | Nature | Ecology, Microbiology, Genomics, Diversity |
“Human gut microbiome viewed across age and geography” | Yatsunenko, Tanya | Nature | Geography differences, Age differences, Different populations, Kinship, Amazonas, Malawi, U.S., Twins |
“Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms” | Caporaso, Gregory J | The ISME Journal | Illumnia HiSeq2000, QIIME, Bioinformatics |
“An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea” | McDonald, Daniel | The ISME Journal | Phylogenetics, Taxonomy, Greengenes |
“Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences” | Soergel, David | The ISME Journal | 16s rRNA, Taxonomy, Paired-end sequencing, Primers |