Publications

Journal Papers

Relative dispersion ratios following fecal microbiota transplant elucidate principles governing microbial migration dynamics

Yadid M Algavi, Elhanan Borenstein

Nature Communications, 15:4447, 2024

Diet-omics in the study of urban and rural crohn disease evolution (SOURCE) cohort

Tzipi Braun, Rui Feng, Amnon Amir, Nina Levhar, Hila Shacham, Ren Mao, Rotem Hadar, Itamar Toren, Yadid Algavi, Kathleen Abu-Saad, Shuoyu Zhuo, Gilat Efroni, Alona Malik, Orit Picard, Miri Yavzori, Bella Agranovich, Ta-Chiang Liu, Thaddeus S Stappenbeck, Lee Denson, Ofra Kalter-Leibovici, Eyal Gottlieb, Elhanan Borenstein, Eran Elinav, Minhu Chen, Shomron Ben-Horin, Yael Haberman

Nature Communications, 15:3764, 2024

The Borenstein Lab

Publications

Journal Papers

Relative dispersion ratios following fecal microbiota transplant elucidate principles governing microbial migration dynamics

Diet-omics in the study of urban and rural crohn disease evolution (SOURCE) cohort

Multi-omic integration of microbiome data for identifying disease-associated modules

Positive effects of diet-induced microbiome modification on GDM in mice following human faecal transfer

A manifold-based framework for studying the dynamics of the vaginal microbiome

A data-driven approach for predicting the impact of drugs on the human microbiome

Development and validation of a novel instrument to capture companion dog mortality data: the Dog Aging Project End of Life Survey

Associations between physical activity and cognitive dysfunction in older companion dogs: Results from the Dog Aging Project

Banking on a new understanding: translational opportunities from veterinary biobanks

A chemically controlled Cas9 switch enables temporal modulation of diverse effectors

Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis

Lifetime prevalence of owner-reported medical conditions in the 25 most common dog breeds in the Dog Aging Project pack

The microbiome’s fiber degradation profile and its relationship with the host diet

The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis

Integrating phylogenetic and functional data in microbiome studies

Evaluation of cognitive function in the Dog Aging Project: associations with baseline canine characteristics

Temporal Alignment of Longitudinal Microbiome Data

Lifetime prevalence of malignant and benign tumors in companion dogs: cross‐sectional analysis of Dog Aging Project (DAP) baseline survey

Age and Physical Activity Levels in Companion Dogs: Results From the Dog Aging Project

Once-daily feeding is associated with better health in companion dogs: results from the Dog Aging Project

An open science study of ageing in companion dogs

Associations between Neighborhood Disadvantage and Dog Walking among Participants in the Dog Aging Project

Demographic factors associated with joint supplement use in dogs from the Dog Aging Project

MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data

A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations

Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences

Gastrointestinal Factors Associated With Hospitalization in Infants With Cystic Fibrosis: Results From the Baby Observational and Nutrition Study

Microbial signature in IgE-mediated food allergies

MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline

The intestinal microbiome, weight, and metabolic changes in women treated by adjuvant chemotherapy for breast and gynecological malignancies

Patterns of salivary microbiota injury and oral mucositis in recipients of allogeneic hematopoietic stem cell transplantation

Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome

Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure

Defining and evaluating microbial contributions to metabolite variation in microbiome-metabolome association studies

Human gut bacteria contain acquired interbacterial defence systems

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

Microbial community design: methods, applications, and opportunities

Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century”

The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy

Competitive lottery-based assembly of selected clades in the human gut microbiome

Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss

The skin microbiome of the Neotropical frog Craugastor fitzingeri: Inferring potential bacterial-host-pathogen interactions from metagenomic data

Taxa-function robustness in microbial communities

BURRITO: An interactive multi-omic tool for visualizing taxa-function relationships in microbiome data

Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis

The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition

A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria

Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome

Microbiome sharing between children, livestock and household surfaces in western Kenya

Systematic characterization and analysis of the taxonomic drivers of functional shifts in the human microbiome

Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome

High-Resolution Characterization of the Human Microbiome

An alignment-free ‘metapeptide’strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing

Evolutionary assembly patterns of prokaryotic genomes

An algorithm for designing minimal microbial communities with desired metabolic capacities

Getting Personal About Nutrition

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

Where next for microbiome research?

The discovery of integrated gene networks for autism and related disorders

Hsp90 promotes kinase evolution

Conservation of trans-acting circuitry during mammalian regulatory evolution

Mapping the Inner Workings of the Microbiome: Genomic-and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

Emergent biosynthetic capacity in simple microbial communities

Metagenomic systems biology and metabolic modeling of the human microbiome: From species composition to community assembly rules

Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

Genome-scale Co-evolutionary Inference Identifies Functions and Clients of Bacterial Hsp90

Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

Circuitry and dynamics of human transcription factor regulatory networks