A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America

Impact of antiretroviral drugs on the microbiome

(2018) Sandra Pinto-Cardoso et al.   Current Opinion in HIV and AIDS

Producing HIV estimates: from global advocacy to country planning and impact measurement

(2017) Mary Mahy et al.   Global Health Action

Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients

(2017) María J. Villanueva-Millán et al.   Journal of the International AIDS Society

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

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

(2017) Sandra Pinto-Cardoso et al.   Scientific Reports

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome

(2016) Cynthia L. Monaco et al.   Cell Host & Microbe

Microbiota-Produced Succinate Improves Glucose Homeostasis via Intestinal Gluconeogenesis

(2016) Filipe De Vadder et al.   Cell Metabolism

Intestinal Interleukin-17 Receptor Signaling Mediates Reciprocal Control of the Gut Microbiota and Autoimmune Inflammation

(2016) Pawan Kumar et al.   IMMUNITY

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

(2016) Sophie Weiss et al.   ISME Journal

Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria

(2016) Shih Keng Loong et al.   JOURNAL OF CLINICAL LABORATORY ANALYSIS

Gut Mucosal Barrier Dysfunction, Microbial Dysbiosis, and Their Role in HIV-1 Disease Progression

(2016) Joseph C. Mudd et al.   JOURNAL OF INFECTIOUS DISEASES

Compositional data in neuroscience: If you’ve got it, log it!

(2016) Paul F. Smith et al.   JOURNAL OF NEUROSCIENCE METHODS

Human Th17 Cells Lack HIV-Inhibitory RNases and Are Highly Permissive to Productive HIV Infection

(2016) Aaron Christensen-Quick et al.   JOURNAL OF VIROLOGY

Altered intestinal permeability in patients with relapsing–remitting multiple sclerosis: A pilot study

(2016) Maria Chiara Buscarinu et al.   Multiple Sclerosis Journal

Universality of human microbial dynamics

(2016) Amir Bashan et al.   NATURE

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline

(2016) Mark Davids et al.   PLoS One

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data

(2016) Patricio Jeraldo et al.   Frontiers in Microbiology

The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation

(2016) Christina Engels et al.   Frontiers in Microbiology

Altered intestinal permeability in patients with relapsing–remitting multiple sclerosis: A pilot study

(2016) Maria Chiara Buscarinu et al.   Multiple Sclerosis Journal

Mucosal Interactions between Genetics, Diet, and Microbiome in Inflammatory Bowel Disease

(2016) Abigail Basson et al.   Frontiers in Immunology

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

(2016) Jonathan Thorsen et al.   Microbiome

Gut Microbiota Linked to Sexual Preference and HIV Infection

(2016) Marc Noguera-Julian et al.   EBioMedicine

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities

(2016) Kim-Anh Lê Cao et al.   PLoS One

Gut microbiota diversity predicts immune status in HIV-1 infection

(2015) Piotr Nowak et al.   AIDS

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

(2015) Brendan J. Kelly et al.   BIOINFORMATICS

Intestinal Blautia Is Associated with Reduced Death from Graft-versus-Host Disease

(2015) Robert R. Jenq et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella

(2015) Petia Kovatcheva-Datchary et al.   Cell Metabolism

Genetic and environmental control of host-gut microbiota interactions

(2015) Elin Org et al.   GENOME RESEARCH

Analyses of Intestinal Microbiota: Culture versus Sequencing: Figure 1

(2015) Andreas Hiergeist et al.   ILAR JOURNAL

Th1/17 Polarization of CD4 T Cells Supports HIV-1 Persistence during Antiretroviral Therapy

(2015) Hong Sun et al.   JOURNAL OF VIROLOGY

Short chain fatty acids potently induce latent HIV-1 in T-cells by activating P-TEFb and multiple histone modifications

(2015) Biswajit Das et al.   VIROLOGY

Statistical Analysis and Interpolation of Compositional Data in Materials Science

(2015) Misha Z. Pesenson et al.   ACS Combinatorial Science

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Intestinal Microbiota, Microbial Translocation, and Systemic Inflammation in Chronic HIV Infection

(2014) Duy M. Dinh et al.   JOURNAL OF INFECTIOUS DISEASES

The Histone Deacetylase Inhibitor Vorinostat (SAHA) Increases the Susceptibility of Uninfected CD4+ T Cells to HIV by Increasing the Kinetics and Efficiency of Postentry Viral Events

(2014) M. B. Lucera et al.   JOURNAL OF VIROLOGY

Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals

(2014) J F Vázquez-Castellanos et al.   Mucosal Immunology

Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity

(2014) Sophie Leclercq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bayesian-multiplicative treatment of count zeros in compositional data sets

(2014) Josep-Antoni Martín-Fernández et al.   STATISTICAL MODELLING

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota

(2014) Soo Ching Lee et al.   PLoS Neglected Tropical Diseases

A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects

(2014) Ece A. Mutlu et al.   PLoS Pathogens

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

Alterations in the Gut Microbiota Associated with HIV-1 Infection

(2013) Catherine A. Lozupone et al.   Cell Host & Microbe

Gut TFH and IgA: key players for regulation of bacterial communities and immune homeostasis

(2013) Lucia M Kato et al.   IMMUNOLOGY AND CELL BIOLOGY

Intestinal Dysbiosis and Depletion of Butyrogenic Bacteria in Clostridium difficile Infection and Nosocomial Diarrhea

(2013) V. C. Antharam et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Impaired CD4+ T-Cell Restoration in the Small Versus Large Intestine of HIV-1–Positive South Africans Receiving Combination Antiretroviral Therapy

(2013) Edana Cassol et al.   JOURNAL OF INFECTIOUS DISEASES

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species

(2013) Inés Martínez et al.   PLoS One

Incomplete Normalization of Regulatory T-Cell Frequency in the Gut Mucosa of Colombian HIV-Infected Patients Receiving Long-Term Antiretroviral Treatment

(2013) Cesar M. Rueda et al.   PLoS One

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism

(2013) Ivan Vujkovic-Cvijin et al.   Science Translational Medicine

Characterization of HIV Type 1 Envelope Sequence Among Viral Isolates Circulating in the Northern Region of Colombia, South America

(2012) José-Luis Villarreal et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

The split personality of regulatory T cells in HIV infection

(2012) M. F. Chevalier et al.   BLOOD

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

(2012) Benoit Liquet et al.   BMC BIOINFORMATICS

Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome

(2012) Scott A. Handley et al.   CELL

Long-term monitoring of the human intestinal microbiota composition

(2012) Mirjana Rajilić-Stojanović et al.   ENVIRONMENTAL MICROBIOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Follicular helper T cells serve as the major CD4 T cell compartment for HIV-1 infection, replication, and production

(2012) Matthieu Perreau et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

(2012) Patricio S. La Rosa et al.   PLoS One

Global trends in molecular epidemiology of HIV-1 during 2000–2007

(2011) Joris Hemelaar et al.   AIDS

Protective HIV-specific CD8+ T cells evade Treg cell suppression

(2011) Shokrollah Elahi et al.   NATURE MEDICINE

Acute HIV-1 Infection

(2011) Myron S. Cohen et al.   NEW ENGLAND JOURNAL OF MEDICINE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data

(2009) Bjoern H Menze et al.   BMC BIOINFORMATICS

Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection

(2009) B. Kantor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA