A5067539705- Gut microbiota and health
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Evolution and Genetic Dynamics
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Human-Animal Interaction Studies
- Cystic Fibrosis Research Advances
- Microbial Community Ecology and Physiology
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- Probiotics and Fermented Foods
- Cell Image Analysis Techniques
- Microbial Natural Products and Biosynthesis
- Evolutionary Game Theory and Cooperation
- Gene Regulatory Network Analysis
- Genetics, Bioinformatics, and Biomedical Research
- Language and cultural evolution
- Gastrointestinal motility and disorders
- Nutritional Studies and Diet
- Child Nutrition and Feeding Issues
- Autism Spectrum Disorder Research
- Molecular Biology Techniques and Applications
Santa Fe Institute
2016-2025
Tel Aviv University
2005-2025
University of Washington
2013-2022
The University of Texas Southwestern Medical Center
2021
Royal Manchester Children's Hospital
2019
Seattle University
2014-2018
Human Genome Sciences (United States)
2013-2016
Columbia University
2012
Agricultural Research Organization
2012
Stanford University
2008-2010
Autism Genes, Again and Despite recent advances in sequencing technologies their lowered costs—effective, highly sensitive, specific of multiple genes interest from large cohorts remains expensive. O'Roak et al. (p. 1619 ; published online 15 November) modified molecular inversion probe methods for target-specific capture to resequence candidate thousands patients. The technique was applied 44 identify de novo mutations a cohort individuals with without autism spectrum disorder. analysis...
The human microbiome plays a key role in wide range of host-related processes and has profound effect on health. Comparative analyses the have revealed substantial variation species gene composition associated with variety disease states but may fall short providing comprehensive understanding impact this community host. Here, we introduce metagenomic systems biology computational framework, integrating data an silico systems-level analysis metabolic networks. Focusing gut microbiome,...
The human microbiome plays a key role in health and is associated with numerous diseases. Metagenomic-based studies are now generating valuable information about the composition of disease, demonstrating nonneutral assembly processes complex co-occurrence patterns. However, underlying ecological forces that structure still unclear. Specifically, compositional alone no mechanisms interaction, potential competition, or syntrophy, cannot clearly distinguish habitat-filtering species assortment...
Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed computational method, termed MAGI ( m erging ffected g enes into i ntegrated networks), simultaneously integrates protein–protein interactions and RNA-seq expression profiles during brain development discover “modules” enriched for de novo mutations in probands. applied this method...
The gut microbiota has been linked to various neurological disorders via the gut-brain axis. Diet influences composition of microbiota. ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate established for treatment therapy-resistant epilepsy in children. Its efficacy reducing seizures confirmed, but mechanisms remain elusive. also shown positive effects wide range other diseases, including Alzheimer's, depression, autism, cancer, and type 2 diabetes. We collected fecal...
The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject evolutionary constraint. To quantify cis- versus trans-acting contributions regulatory we performed genomic DNase I footprinting mouse across 25 cell tissue types, collectively defining ∼8.6 million transcription factor (TF) occupancy sites at nucleotide resolution. Here show that TF footprints conjointly encode...
Studies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods needed to integrate interpret these data in terms known biological mechanisms. Here, we introduce an analytical framework link species metabolite measurements, using a simple model predict effects community ecology on concentrations evaluating whether predictions agree with measured metabolomic profiles. We find that...
Objective Gestational diabetes mellitus (GDM) is a condition in which women without are diagnosed with glucose intolerance during pregnancy, typically the second or third trimester. Early diagnosis, along better understanding of its pathophysiology first trimester may be effective reducing incidence and associated short-term long-term morbidities. Design We comprehensively profiled gut microbiome, metabolome, inflammatory cytokines, nutrition clinical records 394 before GDM diagnosis. then...
Abstract Multi-omic studies of the human gut microbiome are crucial for understanding its role in disease across multiple functional layers. Nevertheless, integrating and analyzing such complex datasets poses significant challenges. Most notably, current analysis methods often yield extensive lists disease-associated features (e.g., species, pathways, or metabolites), without capturing multi-layered structure data. Here, we address this challenge by introducing “MintTea”, an intermediate...
The topology of metabolic networks may provide important insights not only into the capacity species, but also habitats in which they evolved. Here we introduce concept a network's “seed set”—the set compounds that, based on network topology, are exogenously acquired—and methodological framework to computationally infer seed given network. Such sets form ecological “interfaces” between and their surroundings, approximating effective biochemical environment each species. Analyzing 478 species...
Deciphering the modular organization of metabolic networks and understanding how modularity evolves have attracted tremendous interest in recent years. Here, we present a comprehensive large scale characterization across bacterial tree life, systematically quantifying >300 species. Three main determinants network are identified. First, size is an important topological determinant modularity. Second, several environmental factors influence modularity, with endosymbionts mammal-specific...
The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics microbial communities that populate diverse habitats. Over past decade, these advances have yielded an avalanche metagenomic data. current stage "van Leeuwenhoek"-like cataloguing, as well functional analyses, will likely accelerate DNA RNA sequencing, plus protein metabolic profiling capacities computational tools, continue improve. However, it is time...
The Firmicutes are a phylum of bacteria that dominate numerous polymicrobial habitats importance to human health and industry. Although these communities often densely colonized, broadly distributed contact-dependent mechanism interbacterial antagonism utilized by has not been elucidated. Here we show proteins belonging the LXG polymorphic toxin family present in Streptococcus intermedius mediate cell contact- Esx secretion pathway-dependent growth inhibition diverse Firmicute species....
Metagenomic sequencing is a promising approach for identifying and characterizing organisms their functional characteristics in complex, polymicrobial infections, such as airway infections people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only small proportion microbial reads analysis. In addition, many abundant microbes respiratory samples can produce large extracellular bacterial DNA originating either from biofilms...
Cystic fibrosis (CF) results in inflammation, malabsorption of fats and other nutrients, obstruction the gastrointestinal (GI) tract, yet mechanisms linking these disease manifestations to microbiome composition remain largely unexplored. Here we used metagenomic analysis systematically characterize fecal microbiomes children with without CF, demonstrating marked CF-associated taxonomic dysbiosis functional imbalance. We further showed that shifts were especially pronounced young CF...
Microbes have an astonishing capacity to transform their environments. Yet, the metabolic of a single species is limited and vast majority microorganisms form complex communities join forces exhibit capabilities far exceeding those achieved by any species. Such enhanced capacities represent promising route many medical, environmental, industrial applications call for development predictive, systems-level understanding synergistic microbial capacity. Here we present comprehensive...