The knight lab subscribes to an openaccess scientific model, providing free, opensource software tools and making all protocols and data publicly available in order to increase general interest. The microbiome immunity project is a research collaboration between dr. Rob knight, daniel mcdonald, uc san diego researchers at the university of california san diego have been applying their highperformance computing expertise by porting the popular unifrac. See who you know at knight lab, leverage your professional network, and get. Rob knight is a professor at the university of california, san diego, with appointments in bioengineering, pediatrics, and computer science and engineering. Unifrac microbiome tool optimized for computer gpus. All knight lab software is based on an open access model and is available for download at consortia advances connections between human health and microbes.
Notable projects include the american gut project, earth microbiome project. The gut microbiome the combined genetic material of the microorganisms in the gut is influenced and shaped by a number of factors including host genetics, diet, age and environmental. The knight lab will also coordinate efforts to predict proteinprotein interactions and design small molecules. Analyzing microbiomestheir impact on our health and our. The center for microbiome innovation seeks applications for a postdoctoral position in microbiomefocused bioinformatics. Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. Evident is a webbased software tool with an interactive user interface, implemented in html. Bill is a software developer at berkeley lab, with a ms in computer science from clemson university and a phd in philosophy, with a focus in formal ontology, from the university at buffalo.
Listen to advancing technology and microbiome research amid covid19 pandemicrob knightcenter for microbiome innovation, uc san diego and 2,031 more episodes by finding genius. New insights range from an enhanced understanding of how. As we work on these problems, we produce cuttingedge digital work, research, and thought innovating across every part of the mediamaking process. The knight lab uses and develops stateoftheart computational and. Knight lab march 3, 2014 42 share platypus conquistador is a bioinformatics command line tool for the confirmation of the presenceabsence of a specific taxon or set of taxa in environmental shotgun sequence reads. The hospital microbiome project explores how reservoirs for fungal, bacterial, and viral pathogens are established and maintained in the hospital environment, which is largely unknown. Restorflora is the first probiotic bacteriotherapy product that has combined three of the worlds most well studied and widely used probiotic strains saccharomyces boulardii, bacillus subtilis hu58 and. Microbiome research is uncovering the enormous potential for developing drugs, such a live biotherapeutic products, from the microbiome. Our current collaborators include work carried out with the rob knight lab and we hope to grow our work partnering with other fundamental microbiome labs. Rob knight, director of the center for microbiome innovation at the university of california, san diego. Qiime is an open source software package for comparison and analysis of microbial.
They will also build a resource to collect all of the microbiome immunity project predictions. Microbiome immunity project research world community grid. The knight lab uses and develops stateoftheart computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and. We apply those methods to find patterns in microbial communities that predict and diagnose human diseases. Rob knights lab at the university of california, san diego, processes over 100,000 samples per year as a part of several microbiome projects. Rob knight born 1976 in dunedin, new zealand is a professor at the university of california, san diego and the cofounder of the american gut project. Rob knight, phd exponential medicine november 2019. Metagenomic wgs sequencing and analysis metagenomic whole genome shotgun mwgs sequencing provides insights. A healthy gut microbiome is multifaceted and relies heavily upon all 3 of. Down syndrome microbiome research enable special needs. Qiimes framework was originally built at the knight lab, then at the university of colorado at boulder and led by postdoctoral scholar greg caporaso.
Knight and the knight lab at uc san diego use state of the art computation and bioinformatics to understand the microbiome and what affects it. Rob knight his lab has produced many of the software tools and laboratory techniques that enabled highthroughput microbiome science, including the qiime pipeline and unifrac. The three fundamental aspects of gut health include. Apply and develop new methods and tools for microbiome. Hamidreza was one of the key members of my lab and had significant contribution to the development and optimization of protocols and pipelines in my sequencing platform. Knight, smarr raise profile of microbiome research. Purchase microbiome labs products buy megasporebiotic. Knight is on the forefront of this exciting research. The thackray lab is interested in understanding the role of the microbiome in womens health and reproductive disorders. Advancing technology and microbiome research amid covid19. Knights lab is also sequencing microbiomes submitted to a university of arizona study focused specifically on dogs and human health.
A public resource for microbiome bioinformatics benchmarking using artifically constructed i. American gut is a crowdfunded research project cofounded by dr. Uc san diego researchers optimize microbiome tool for. The knight lab uses and develops stateoftheart computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and communities in different ecosystems, including the complex microbial ecosystems of the human body. Hospitalacquired or nosocomial infections affect over 1 million people in the united states alone each year. In the knights lab she is conducting computational analysis, processing, and sorting with the microbiome, antibiotics, and growth infant cohort magic project with dr. Samples were shipped on dry ice to the knight lab at the university of. By leveraging the thermo fisher platform for science software software. Knight lab march 3, 2014 0 share exploration of environmental and hostassociated microbiota relies on robust, highthroughput molecular and microbiological techniques to produce highquality reproducible data. Researchers at ucsd will use gpus to seek clues in the human microbiome to the mysteries covid19.
Qiime2 is an opensource bioinformatics pipeline for performing microbiome analysis from raw dna sequencing data. The dan knights lab links microbial community patterns to human health, modeling microbial. Microbiome research continues to develop and advance, requiring organizations to be flexible in their approach to discovery and development. Knight lab march 3, 2014 42 share platypus conquistador is a bioinformatics command line tool for the confirmation of the presenceabsence of a specific taxon or set of taxa in environmental shotgun. Ramnik xavier of the broad institute of mit and harvard and the massachusetts general hospital, dr. Establishing causality in microbiome studies youtube. Dan knights is an assistant professor in the department of computer science and engineering and the biotechnology institute at the university of minnesota. Patterns of oral microbiota diversity in adults and.
Analysis protocols, with software versions, are available at tools and technology. We highlight recent advances in microbiome research methods and take you on a tour of the knight lab. Im an associate professor of microbiome science at the university of manitoba, canada. Opensource microbiome pipeline for highthroughput research. Software used for analysis in various knight lab projects knight lab analyses. Knights lab was studying an appendage called the type iii secretion system. Complex microbial communities shape the dynamics of various environments. Microbiome research amid covid19 pandemicrob knight. Nih videocast establishing causality in microbiome studies.
Using cuttingedge sequencing technologies, coupled with bioinformatics and advanced. The knight lab has produced many of the software tools and laboratory techniques that enabled highthroughput microbiome science, including the qiime pipeline and unifrac. We recently demonstrated that metabolism and the gut microbiome is altered. Rob knight is the founding director of the center for microbiome innovation, an agile center in the jacobs school of engineering with the school of medicine and the division of biological sciences as. His lab has produced many of the software tools and laboratory techniques that enabled highthroughput microbiome science, including the qiime pipeline cited.
Rob knight is a professor in the department of pediatrics at the university of california at san diego, among many other things he is a member of the steering. For example, knights lab has developed software for microbiome analysis, lab protocols for looking at thousands of microbiomes simultaneously. He is also a cofounder of the earth microbiome project, and his labs research involves the development of laboratory and computational techniques to. Our computational microbiology lab develops methods that bring precision medicine to the microbiome. She hopes the experience and knowledge gained from the lab will help her reach her goal of being a physician. With catherine lozupone, developed unifrac, a software tool that. Please keep in mind, that modules 2 and 3 are meant to provide a glimpse into our world of data. Qiime2 is designed to take users from raw sequencing data generated on the illumina or other platforms through publication quality graphics and statistics.