List of works - Catherine A. Lozupone

A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome

scientific article published on 19 February 2020

Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon

scientific article published on 07 April 2021

Alterations in the gut microbiota associated with HIV-1 infection

scientific article

An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men

article

Artificial Selection: Finding Function amongst Randomized Sequences

article

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

scientific article published on 01 September 2019

Biogeography and habitat modelling of high-alpine bacteria

scientific article

Blood type and the microbiome- untangling a complex relationship with lessons from pathogens

scientific article published on 11 July 2020

Can gut microbiota of men who have sex with men influence HIV transmission?

scientific article published on 10 February 2020

Cohabiting family members share microbiota with one another and with their dogs

scientific article

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation

scientific article (publication date: October 2011)

Correction to: An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men

scientific article published on 06 April 2020

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

scientific article

Dietary fat promotes antibiotic-induced Clostridioides difficile mortality in mice

scientific article published on 01 April 2022

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

scientific article published on 21 December 2017

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties

scientific article published on 27 September 2016

Diversity, stability and resilience of the human gut microbiota

scientific article

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

scientific article

Evolution of mammals and their gut microbes

scientific article (publication date: 20 June 2008)

Evolution of symbiotic bacteria in the distal human intestine

scientific article

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

scientific article

Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens

scientific article published on 06 March 2017

Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals.

scientific article published on 26 March 2018

Functional Microbiomics in Liver Transplantation: Identifying Novel Targets for Improving Allograft Outcomes

scientific article published on 01 April 2019

Getting to know the microbiome

scientific article published on 14 March 2016

Global patterns in bacterial diversity

scientific article

Global patterns in the biogeography of bacterial taxa

scientific article published in January 2011

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

scientific article published on 3 June 2010

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort

scientific article published on 23 October 2018

Gut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease

scientific article published on 12 March 2015

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus

scientific article published on 25 October 2017

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection

article

Gut microbiota in adolescents and the association with fatty liver: the EPOCH study

scientific article published on 18 April 2018

Gut microbiota phenotypes of obesity

scientific article published on 01 July 2019

HIV-induced alteration in gut microbiota: driving factors, consequences, and effects of antiretroviral therapy

scientific article

Host-bacterial coevolution and the search for new drug targets

scientific article published on February 2008

Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension

scientific article

Human gut microbiome viewed across age and geography

scientific article

Human-associated microbial signatures: examining their predictive value

scientific article

Identifying genetic determinants needed to establish a human gut symbiont in its habitat

scientific article

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

scientific article

Intestinal Parasites Infections among HIV Infected Children Under Antiretrovirals Treatment in Yaounde, Cameroon

scientific article published on 01 April 2020

Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery

scientific article published on 20 July 2018

Meta-analyses of studies of the human microbiota

scientific article

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil

scientific article published on 7 September 2007

Microbial Biodiversity: Straight from the Dolphin's Mouth

scientific article published in December 2017

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

scientific article published on 5 September 2010

Microbiome and metabolome data integration provides insight into health and disease

scientific article

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Muc5b is required for airway defence

scientific journal article

Multiple-Ascending-Dose Phase 1 Clinical Study of the Safety, Tolerability, and Pharmacokinetics of CRS3123, a Narrow-Spectrum Agent with Minimal Disruption of Normal Gut Microbiota

scientific article published on 20 December 2019

Normalization and microbial differential abundance strategies depend upon data characteristics

scientific article

Obesity alters gut microbial ecology

scientific article

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

scientific article

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites

scientific article published on September 2017

Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea).

scientific article

Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants

scientific article published on 4 September 2017

Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands

scientific article published on 16 January 2018

Programmed death 1 expression on HIV-specific CD4+ T cells is driven by viral replication and associated with T cell dysfunction

scientific article published on 01 August 2007

PyCogent: a toolkit for making sense from sequence

scientific article published in January 2007

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

QIIME allows analysis of high-throughput community sequencing data

scientific article

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

scientific article

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

scientific article

Reply to Moossavi and Azad, "Quantifying and Interpreting the Association between Early-Life Gut Microbiota Composition and Childhood Obesity"

article

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

scientific article published on 01 August 2019

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

scientific article

SCNIC: Sparse correlation network investigation for compositional data

scientific article published in 2022

Selection of the simplest RNA that binds isoleucine

scientific article

Short pyrosequencing reads suffice for accurate microbial community analysis

scientific article published on 18 September 2007

Size, constant sequences, and optimal selection

scientific article

Soil bacterial and fungal communities across a pH gradient in an arable soil

scientific article published on 6 May 2010

Species divergence and the measurement of microbial diversity

scientific article

Stable tRNA-based phylogenies using only 76 nucleotides

scientific article published on 17 June 2010

Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells

article

Systems Analysis of Gut Microbiome Influence on Metabolic Disease in HIV-Positive and High-Risk Populations

scientific article published on 18 May 2021

The HIV-Associated Enteric Microbiome Has Gone Viral

scientific article

The UniFrac significance test is sensitive to tree topology

scientific article published on 7 July 2015

The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework

scientific article

The convergence of carbohydrate active gene repertoires in human gut microbes

scholarly article

The environment, epigenome, and asthma

scientific article

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins

scientific article published in October 2011

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis

scientific article

The mind-body-microbial continuum

scientific article

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients

scientific article

UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context

scientific article (publication date: 7 August 2006)

UniFrac: a new phylogenetic method for comparing microbial communities

scientific article

UniFrac: an effective distance metric for microbial community comparison

scientific article

Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease

scientific article published on 6 March 2018

VOLARE: visual analysis of disease-associated microbiome-immune system interplay

scientific article published on 20 August 2019

Visualizing microbiome-immune system interplay

scientific article published on 01 February 2019

Widespread colonization of the lung by Tropheryma whipplei in HIV infection

scientific article published on May 2013

Worlds within worlds: evolution of the vertebrate gut microbiota

scientific article (publication date: October 2008)

specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data

scientific article published in 2022

List of works by Catherine A. Lozupone

A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome

Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon

Alterations in the gut microbiota associated with HIV-1 infection

An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men

Artificial Selection: Finding Function amongst Randomized Sequences

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

Biogeography and habitat modelling of high-alpine bacteria

Blood type and the microbiome- untangling a complex relationship with lessons from pathogens

Can gut microbiota of men who have sex with men influence HIV transmission?

Cohabiting family members share microbiota with one another and with their dogs

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation

Correction to: An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

Dietary fat promotes antibiotic-induced Clostridioides difficile mortality in mice

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties

Diversity, stability and resilience of the human gut microbiota

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

Evolution of mammals and their gut microbes

Evolution of symbiotic bacteria in the distal human intestine

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens

Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals.

Functional Microbiomics in Liver Transplantation: Identifying Novel Targets for Improving Allograft Outcomes

Getting to know the microbiome

Global patterns in bacterial diversity

Global patterns in the biogeography of bacterial taxa

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort

Gut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection

Gut microbiota in adolescents and the association with fatty liver: the EPOCH study

Gut microbiota phenotypes of obesity

HIV-induced alteration in gut microbiota: driving factors, consequences, and effects of antiretroviral therapy

Host-bacterial coevolution and the search for new drug targets

Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension

Human gut microbiome viewed across age and geography

Human-associated microbial signatures: examining their predictive value

Identifying genetic determinants needed to establish a human gut symbiont in its habitat

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

Intestinal Parasites Infections among HIV Infected Children Under Antiretrovirals Treatment in Yaounde, Cameroon

Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery

Meta-analyses of studies of the human microbiota

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil

Microbial Biodiversity: Straight from the Dolphin's Mouth

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

Microbiome and metabolome data integration provides insight into health and disease

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Muc5b is required for airway defence

Multiple-Ascending-Dose Phase 1 Clinical Study of the Safety, Tolerability, and Pharmacokinetics of CRS3123, a Narrow-Spectrum Agent with Minimal Disruption of Normal Gut Microbiota

Normalization and microbial differential abundance strategies depend upon data characteristics

Obesity alters gut microbial ecology

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites

Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea).

Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants

Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands

Programmed death 1 expression on HIV-specific CD4+ T cells is driven by viral replication and associated with T cell dysfunction

PyCogent: a toolkit for making sense from sequence

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

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

QIIME allows analysis of high-throughput community sequencing data

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

Reply to Moossavi and Azad, "Quantifying and Interpreting the Association between Early-Life Gut Microbiota Composition and Childhood Obesity"

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

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

SCNIC: Sparse correlation network investigation for compositional data

Selection of the simplest RNA that binds isoleucine

Short pyrosequencing reads suffice for accurate microbial community analysis

Size, constant sequences, and optimal selection

Soil bacterial and fungal communities across a pH gradient in an arable soil

Species divergence and the measurement of microbial diversity

Stable tRNA-based phylogenies using only 76 nucleotides

Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells

Systems Analysis of Gut Microbiome Influence on Metabolic Disease in HIV-Positive and High-Risk Populations

The HIV-Associated Enteric Microbiome Has Gone Viral

The UniFrac significance test is sensitive to tree topology