Umer Zeeshan Ijaz

Publications

1359 - CViewer: A Java-based integrated analysis toolkit for whole genome shotgun metagenomics and other meta’omics technologies

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1420 - NanoAmpli-Seq: A de novo protocol for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform

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Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment or Helicobacter pylori infection

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De Novo Growth of Methanogenic Granules Indicates a Biofilm Life-Cycle with Complex Ecology

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A sedimentary ancient DNA approach to elucidate the Labrador Sea paleoceanography over the last ~130,000 years

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SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities

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Unpicking the mysterious symbiosis of Mycoplasma in salmonids

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Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants.

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Methanogenic Granules Are Replicated, Whole Microbial Communities With Reproducible Responses To Environmental Cues

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Additional file 8 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 9 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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Additional file 9 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 9 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 1 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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data-set

Additional file 3 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 3 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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Additional file 2 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 4 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 3 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 10 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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data-set

Additional file 10 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 4 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 5 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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Additional file 6 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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data-set

Additional file 1 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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figshare

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data-set

Additional file 6 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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Additional file 7 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics

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Zenodo

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Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.

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Zenodo

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Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.

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Zenodo

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Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.

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Zenodo

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Swatting Flies: Biting Insects as Non‐Invasive Samplers for Mammalian Population Genomics

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Molecular Ecology

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Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

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BMC Research Notes

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Leveraging Cell‐Free Supernatants of Phyllospheric Bacteria to Combat Wheat Pathogens and Boost Growth

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Plant-Environment Interactions

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Microbiomes of high-rate anaerobic digestors reveal ‘Study’-specific factors and limitations of synthetic wastewater

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Water Research

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Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems

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npj Biofilms and Microbiomes

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Microbiota transplantation for cotton leaf curl disease suppression—core microbiome and transcriptome dynamics

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Communications Biology

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Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics

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Zenodo

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Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics

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Zenodo

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Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics

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Zenodo

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Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics

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Zenodo

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other

Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics

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Zenodo

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other

Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics

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Zenodo

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other

Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.

Published by

Zenodo

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other

Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.

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Zenodo

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Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.

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Zenodo

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other

OC1 High faecal pH and low total microbial load associate with normalisation of faecal calprotectin in children with Crohn\textquoterights disease treated with exclusive enteral nutrition; results from iPENS, a multicentre, prospective study

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Frontline Gastroenterology

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Beneficial modulation of the gut microbiome by leachates of Penicillium purpurogenum in the presence of clays: A model for the preparation and efficacy of historical Lemnian Earth

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PLOS ONE

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Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan

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Data in Brief

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Disease Resistance Correlates with Core Microbiome Diversity in Cotton

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Current Microbiology

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Microbiome-driven IBS metabotypes influence response to the low FODMAP diet: insights from the faecal volatome

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eBioMedicine

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Sedimentary ancient DNA sequences reveal marine ecosystem shifts and indicator taxa for glacial-interglacial sea ice conditions

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Quaternary Science Reviews

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Impact of commercial gut health interventions on caecal metagenome and broiler performance

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preprint

CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

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Microbiome

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Swatting flies: Biting insects as non-invasive samplers for mammalian population genomics

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Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan

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Data in Brief

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Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan

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Data in Brief

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Shotgun metagenomics reveals environmental instability reduces resistance to shocks by enriching specialist taxa with distinct two component regulatory systems

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P056 Cereal intake and diet-related microbial metabolites in faeces associate with recurrence of gut inflammation during food reintroduction in children with Crohn’s disease treated with exclusive enteral nutrition; iPENS a multicentre, prospective study

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Journal of Crohn's and Colitis

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P080 High faecal pH and low total microbial load associate with normalisation of faecal calprotectin in children with Crohn’s disease treated with exclusive enteral nutrition; results from iPENS, a multicentre, prospective study

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Journal of Crohn's and Colitis

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journal-article

Additional file 1 of CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

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figshare

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Additional file 1 of CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

Published by

figshare

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CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

Published by

figshare

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CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

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figshare

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other

O64 Microbiome-driven metabotypes influence response to the low FODMAP diet in IBS and implicate short chain fatty acids

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Gut

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OC2 Cereal intake and diet-related microbial metabolites in faeces associate with recurrence of gut inflammation during food reintroduction in children with Crohn\textquoterights disease treated with exclusive enteral nutrition; iPENS a multicentre, prospective study

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Frontline Gastroenterology

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P136 Faecal volatile organic compounds (VOCs) are correlated with bacterial taxa and functional genes in paediatric Crohn\textquoterights disease

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Gut

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Process stability in expanded granular sludge bed bioreactors enhances resistance to organic load shocks

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Journal of Environmental Management

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Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum

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npj Biofilms and Microbiomes

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intI 1 gene abundance from septic tanks in Thailand using validated intI 1 primers

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Applied and Environmental Microbiology

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Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities

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AQUA — Water Infrastructure, Ecosystems and Society

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Microbial electrosynthesis of acetate from CO2 in three-chamber cells with gas diffusion biocathode under moderate saline conditions

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Environmental Science and Ecotechnology

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Disease Resistance correlates with Core Microbiome Diversity in Cotton

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Balancing the scales: Impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities

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Cotton Microbiome Profiling and Cotton Leaf Curl Disease (CLCuD) Suppression through Microbial Consortia associated withGossypium arboreum

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intI1 primer selection for class 1 integron integrase gene and transcript quantification – validation and application for monitoringintl1 gene abundance within septic tanks in Thailand

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CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

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preprint

The stool microbiome in patients with psoriatic arthritis is altered but, unlike the skin microbiome, does not change following treatment: evidence for an underlying inflammatory drive from the intestine

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Molecular insights informing factors affecting low temperature anaerobic applications: Diversity, collated core microbiomes and complexity stability relationships in LCFA-fed systems

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Science of The Total Environment

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A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome

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Scientific Reports

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A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome

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OpenAlex

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A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome

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OpenAlex

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A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome

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OpenAlex

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The Effects of Smoking on Human Pharynx Microbiota Composition and Stability

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Microbiology Spectrum

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DOP52 The faecal bacterial and fungal microbiome of newly-diagnosed, treatment naïve children with Crohn’s disease and the modifying effects of exclusive enteral nutrition and re-introduction of habitual diet

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Journal of Crohn's and Colitis

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P380 Changes in faecal microbiome and metabolome are more pronounced in Crohn’s disease patients who adhered to the CD-TREAT diet and responded by calprotectin

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Journal of Crohn's and Colitis

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A Cross-Sectional Study of Potential Antimicrobial Resistance and Ecology in Gastrointestinal and Oral Microbial Communities of Young Normoweight Pakistani Individuals

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Microorganisms

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DOP31 Gut metabolomic and compositional signatures predict response to treatment with exclusive enteral nutrition in children with active Crohn’s disease

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Journal of Crohn's and Colitis

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Deploying an <i>In Vitro</i> Gut Model to Assay the Impact of the Mannan-Oligosaccharide Prebiotic Bio-Mos on the Atlantic Salmon ( <i>Salmo salar</i> ) Gut Microbiome

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Microbiology Spectrum

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Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet

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npj Biofilms and Microbiomes

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Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method

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Intestinal fatty acid binding protein is a disease biomarker in paediatric coeliac disease and Crohn’s disease

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BMC Gastroenterology

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The faecal metabolome and mycobiome in Parkinson's disease

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Parkinsonism & Related Disorders

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The faecal metabolome and mycobiome in Parkinson's disease

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Parkinsonism & Related Disorders

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Machine Learning Approach to Predict Quality Parameters for Bacterial Consortium-Treated Hospital Wastewater and Phytotoxicity Assessment on Radish, Cauliflower, Hot Pepper, Rice and Wheat Crops

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Water

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Machine Learning Approach to Predict Quality Parameters for Bacterial Consortium-Treated Hospital Wastewater and Phytotoxicity Assessment on Radish, Cauliflower, Hot Pepper, Rice and Wheat Crops

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Water

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Machine Learning Approach to Predict Quality Parameters for Bacterial Consortium-Treated Hospital Wastewater and Phytotoxicity Assessment on Radish, Cauliflower, Hot Pepper, Rice and Wheat Crops

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Water

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DOP68 CD-TREAT diet induces remission and improves quality of life in an open label trial in children and adults with active Crohn’s Disease

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Journal of Crohn's and Colitis

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DOP68 CD-TREAT diet induces remission and improves quality of life in an open label trial in children and adults with active Crohn’s Disease

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Journal of Crohn's and Colitis

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Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap

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Water Research

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Stratification of alopecia areata reveals involvement of CD4 T cell populations and altered faecal microbiota

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Clinical and Experimental Immunology

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Potential nitrification activity reflects ammonia oxidizing bacteria but not archaea activity across a soil-sediment gradient

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Estuarine, Coastal and Shelf Science

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Beyond Basic Diversity Estimates—Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data

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Microorganisms

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Autotrophic Denitrification of Nitrate Rich Wastewater in Fluidized Bed Reactors Using Pyrite and Elemental Sulfur as Electron Donors

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SSRN Electronic Journal

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Molecular Insights Informing Factors Affecting Low Temperature Anaerobic Applications: Diversity, Collated Core Microbiomes and Complexity Stability Relationships

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SSRN Electronic Journal

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Beyond Basic Diversity Estimates—Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data

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Microorganisms

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A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis

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npj Biofilms and Microbiomes

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Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate

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Frontiers in Microbiology

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Cross-sectional study of antimicrobial resistance and ecology in gastrointestinal and oral microbial communities of urban Pakistani adults

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A droplet-based microfluidic approach to isolating functional bacteria from gut microbiota

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Frontiers in Cellular and Infection Microbiology

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journal-article

Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method

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mSphere

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Autotrophic denitrification of nitrate rich wastewater in fluidized bed reactors using pyrite and elemental sulfur as electron donors

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Environmental Technology & Innovation

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Alopecia areata pathotypes are associated with distinct immune and intestinal microbiome signatures

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British Journal of Dermatology

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Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon

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Scientific Reports

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DOP66 The effect of exclusive enteral nutrition on circulating inflammatory protein levels in paediatric patients with Crohn’s Disease

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Journal of Crohn's and Colitis

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journal-article

Methanogenic granule growth and development is a continual process characterized by distinct morphological features

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Journal of Environmental Management

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journal-article

Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome

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Nature Communications

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Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

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Animal Microbiome

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P275 Analysis of exclusive enteral nutrition formulas in Crohn's disease – new insights into dietary triggers

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Gut

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OWE-1 Investigation of the metabolome and mycobiome in Parkinson\textquoterights disease

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Gut

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Inter-kingdom relationships in Crohn’s disease explored using a multi-omics approach

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Gut Microbes

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A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

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Frontiers in Microbiology

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O12 Reversion to baseline microbiome following successful course of exclusive enteral nutrition in paediatric Crohn's disease

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Gut

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Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap

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preprint

Key Drivers of Ecological Assembly in the Hindgut of Atlantic Cod (Gadus morhua) when Fed with a Macroalgal Supplemented diet – How Robust Is the Gut to Taxonomic Perturbation?

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other

Dietary triggers of gut inflammation following exclusive enteral nutrition in children with Crohn’s disease: a pilot study

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BMC Gastroenterology

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journal-article

Dietary Triggers of Gut Inflammation Following Exclusive Enteral Nutrition in Children with Crohn’s Disease: A Pilot Study

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preprint

SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

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Microbiome

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journal-article

Socioeconomic position links circulatory microbiota differences with biological age

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Scientific Reports

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journal-article

The mannose receptor (CD206) identifies a population of colonic macrophages in health and inflammatory bowel disease

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Scientific Reports

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Putative Antimicrobial Peptides Within Bacterial Proteomes Affect Bacterial Predominance: A Network Analysis Perspective

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Frontiers in Microbiology

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A Distinct, Flocculent, Acidogenic Microbial Community Accompanies Methanogenic Granules in Anaerobic Digesters

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Microbiology Spectrum

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Enrichment of the hydrogenotrophic methanogens for, in-situ biogas up-gradation by recirculation of gases and supply of hydrogen in methanogenic reactor

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Bioresource Technology

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MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni

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Journal of Bacteriology

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Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and surfactant‐assisted oil biodegradation

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Ecology and Evolution

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O49 Dietary triggers of colonic inflammation following exclusive enteral nutrition treatment in children with Crohn's disease

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Gut

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Microbial Community Assembly And Dynamics In Granular, Fixed-Biofilm And Planktonic Microbiomes Valorizing Long-Chain Fatty Acids At 20°C

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Bioresource Technology

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journal-article

ASSEMBLY AND DYNAMICS OF MICROBIAL COMMUNITIES IN GRANULAR, FIXED-BIOFILM AND PLANKTONIC METHANOGENIC MICROBIOMES VALORIZING LONG CHAIN FATTY ACID (LCFA)-RICH WASTEWATER

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preprint

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants

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Microbiome

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journal-article

The Impact of Enriched Resistant Starch Type‐2 Cookies on the Gut Microbiome in Hemodialysis Patients: A Randomized Controlled Trial

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Molecular Nutrition & Food Research

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journal-article

Biofilm carrier type affects biogenic sulfur-driven denitrification performance and microbial community dynamics in moving-bed biofilm reactors

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Chemosphere

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First Proof of Concept for Full-Scale, Direct, Low-Temperature Anaerobic Treatment of Municipal Wastewater

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Bioresource Technology

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journal-article

Genome erosion and evidence for an intracellular niche – exploring the biology of mycoplasmas in Atlantic salmon

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Aquaculture

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journal-article

Oral Ferric Maltol Does Not Adversely Affect the Intestinal Microbiome of Patients or Mice, but Ferrous Sulphate Does

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Nutrients

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journal-article

Oral Ferric Maltol Does Not Adversely Affect the Intestinal Microbiome of Patients or Mice, but Ferrous Sulphate Does

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Nutrients

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Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation

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Frontiers in Microbiology

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journal-article

DOP27 The fibre fermentative capacity of the gut microbiota is diminished in children with Crohn’s Disease and it is independent of disease activity or treatment with exclusive enteral nutrition

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Journal of Crohn's and Colitis

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journal-article

P83 Understanding differences in serum and mucosal immunopathotypes in Crohn's disease

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Gut

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journal-article

P091 Dietary triggers of colonic inflammation following treatment with exclusive enteral nutrition in children with Crohn’s disease

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Journal of Crohn's and Colitis

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journal-article

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

Summary

other

Development of a three-compartmentin vitrosimulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim

Summary

preprint

Use of null models to compare the assembly of northeast Atlantic bacterial community in the presence of crude oil with either chemical dispersant or biosurfactant

Summary

preprint

Use of null models to compare the assembly of northeast Atlantic bacterial community in the presence of crude oil with either chemical dispersant or biosurfactant

Summary

other

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduceCampylobacter

Summary

preprint

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

Summary

preprint

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

Summary

other

Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data

Summary

preprint

Deploying andin vitrogut model to assay the impact of a mannan-oligosaccharide prebiotic, Bio-MOS® on the Atlantic salmon (Salmo salar) gut microbiome

Summary

preprint

Carboxylic acids production and electrosynthetic microbial community evolution under different CO2 feeding regimens

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Bioelectrochemistry

Summary

journal-article

Feral populations of Brassica oleracea along Atlantic coasts in western Europe

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Ecology and Evolution

Summary

journal-article

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

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Microbiome

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journal-article

Size Shapes the Active Microbiome of the Methanogenic Granules, Corroborating a Biofilm Life Cycle

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mSystems

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journal-article

Alterations in Intestinal Microbiota of Children With Celiac Disease at Time of Diagnosis and on a Gluten-Free Diet

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Gastroenterology

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journal-article

Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems

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Science of The Total Environment

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journal-article

Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet?

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Nutrients

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journal-article

Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet?

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Nutrients

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journal-article

Growth and Break-Up of Methanogenic Granules Suggests Mechanisms for Biofilm and Community Development

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Frontiers in Microbiology

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journal-article

Analysis of 61 exclusive enteral nutrition formulas used in the management of active Crohn’s disease—new insights into dietary disease triggers

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Alimentary Pharmacology & Therapeutics

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journal-article

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

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Environmental Microbiology

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journal-article

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

Summary

preprint

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

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Environmental Microbiology

Summary

journal-article

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

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Environmental Microbiology

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journal-article

Disinfection exhibits systematic impacts on the drinking water microbiome

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Microbiome

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journal-article

Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations

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Microbiome

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journal-article

Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar

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Applied and Environmental Microbiology

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journal-article

Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems

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Water Research

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journal-article

Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems

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Water Research

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journal-article

P014 Identification of Crohn’s disease immunopathotypes

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Journal of Crohn's and Colitis

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journal-article

P050 Analysis of 61 exclusive enteral nutrition formulas used for induction of remission in Crohn’s disease: new insights on dietary disease triggers

Published by

Journal of Crohn's and Colitis

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journal-article

Propionate Production by Bioelectrochemically-Assisted Lactate Fermentation and Simultaneous CO2 Recycling

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Frontiers in Microbiology

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journal-article

Bile salt metabolism is not the only factor contributing to Clostridioides (Clostridium) difficile disease severity in the murine model of disease.

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Gut microbes

Summary

journal-article

EFFICIENT ENERGY SOLUTION FOR WASA FAISALABAD TAKING INTO CONSIDERATION THE ENVIRONMENTAL IMPACT ASSESSMENT

Published by

OpenAlex

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other

EFFICIENT ENERGY SOLUTION FOR WASA FAISALABAD TAKING INTO CONSIDERATION THE ENVIRONMENTAL IMPACT ASSESSMENT

Published by

OpenAlex

Summary

other

Reply to GASTRO-D-18-02688

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Gastroenterology

Summary

journal-article

In vitro and in vivo characterisation of Listeria monocytogenes outbreak isolates

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Food Control

Summary

journal-article

Molecular diagnosis of vaginitis: comparing qPCR and microbiome profiling approaches to current microscopy scoring

Published by

Journal of Clinical Microbiology

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journal-article

Next‐Generation Sequencing to Identify Lacustrine Haptophytes in the Canadian Prairies: Significance for Temperature Proxy Applications

Published by

Journal of Geophysical Research: Biogeosciences

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journal-article

The reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food re-introduction

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Alimentary Pharmacology & Therapeutics

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journal-article

DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies

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Scientific Reports

Summary

journal-article

Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance

Summary

other

MULTI-OMICS APPROACHES TO UNDERSTAND GASTRIC MUCOSA-ASSOCIATED LYMPHOID TISSUE (MALT) LYMPHOMA

Published by

Hematological Oncology

Summary

journal-article

The potential of sedimentary ancient DNA for reconstructing past sea ice evolution

Published by

The ISME Journal

Summary

journal-article

The potential of sedimentary ancient DNA for reconstructing past sea ice evolution

Published by

The ISME Journal

Summary

journal-article

Alopecia areata is characterised by dysregulation in systemic type 17 and type 2 cytokines, which may contribute to disease-associated psychological morbidity.

Published by

The British journal of dermatology

Summary

journal-article

Alopecia areata is characterized by dysregulation in systemic type 17 and type 2 cytokines, which may contribute to disease‐associated psychological morbidity

Published by

British Journal of Dermatology

Summary

journal-article

Inflammation associated ethanolamine facilitates infection by Crohn's disease-linked adherent-invasive Escherichia coli

Published by

EBioMedicine

Summary

journal-article

Inflammation associated ethanolamine facilitates infection by Crohn’s disease-linked adherent-invasive Escherichia coli

Published by

Access Microbiology

Summary

journal-article

Integrated phenotypic and genomics analysis to elucidate differences in stress resistance and virulence of Listeria monocytogenes strains

Published by

Access Microbiology

Summary

journal-article

A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078

Published by

mBio

Summary

journal-article

Solar Septic Tank: Next Generation Sequencing Reveals Effluent Microbial Community Composition as a Useful Index of System Performance

Published by

Water

Summary

journal-article

P602 CD-TREAT a novel dietary therapy of active Crohn’s disease using the exclusive enteral nutrition paradigm

Published by

Journal of Crohn's and Colitis

Summary

journal-article

P842 Multi-omics analysis suggests an active role of fungi in Crohn’s disease

Published by

Journal of Crohn's and Colitis

Summary

journal-article

ATH-09 Metabolomics & multi-omics analysis of Crohn's disease

Published by

Gut

Summary

journal-article

Biomarkers of sediment cores from site GS15-198-38

Published by

PANGAEA

Summary

data-set

Solar Septic Tank: Next Generation Sequencing Reveals Effluent Microbial Community Composition as a Useful Index of System Performance

Published by

Water

Summary

journal-article

Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems

Summary

other

PTH-075 Identification of IBD immunopathotypes

Published by

Gut

Summary

journal-article

Palynology of sediment cores from site GS15-198-38

Published by

PANGAEA

Summary

data-set

Palynology, biomarkers and droplet digital PCR data from the Late Quaternary of Site GS15-198-38, Greenland Sea

Published by

PANGAEA

Summary

other

Polarella glacialis droplet digital PCR data from sediment cores from site GS15-198-38

Published by

PANGAEA

Summary

data-set

Disinfection exhibits systematic impacts on the drinking water microbiome

Summary

other

Systems biology approach to elucidation of contaminants biodegradation in complex samples- integration of high-resolution analytical and molecular tools

Published by

Faraday Discussions

Summary

journal-article

Disinfection exhibits systematic impacts on the drinking water microbiome

Summary

other

Systems biology approach to elucidation of contaminant biodegradation in complex samples – integration of high-resolution analytical and molecular tools

Published by

Faraday Discussions

Summary

journal-article

Solar Septic Tank: Next Generation Sequencing Reveals Effluent Microbial Community Composition as a Useful Index of System Performance

Published by

Water

Summary

journal-article

P858 Crohn’s disease is characterised by a fungal dysbiosis

Published by

Journal of Crohn's and Colitis

Summary

journal-article

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

Summary

other

Diversity Converges During Community Assembly In Methanogenic Granules, Suggesting A Biofilm Life-Cycle

Summary

other

Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion

Published by

Scientific Reports

Summary

journal-article

NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.

Published by

GigaScience

Summary

journal-article

NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform

Summary

other

NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform

Published by

GigaScience

Summary

journal-article

NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform

Published by

GigaScience

Summary

journal-article

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter

Published by

Frontiers in Microbiology

Summary

journal-article

Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter

Summary

other

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter

Published by

Frontiers in Microbiology

Summary

journal-article

NanoAmpli-Seq - Bioinformatics Workflow v1 (protocols.io.u25eyg6)

Published by

protocols.io

Summary

data-set

NanoAmpli-Seq - Bioinformatics Workflow v1

Summary

preprint

NanoAmpli-Seq - Sample processing and sequencing library preparation workflow v1 (protocols.io.u26eyhe)

Published by

protocols.io

Summary

data-set

NanoAmpli-Seq - Sample processing and sequencing library preparation workflow v1

Summary

preprint

Biokinetics Of Microbial Consortia Using Biogenic Sulfur As A Novel Electron Donor For Sustainable Denitrification

Published by

Bioresource Technology

Summary

journal-article

An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights

Published by

PeerJ

Summary

journal-article

An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights

Summary

other

An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights

Summary

other

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus

Published by

Scientific Reports

Summary

journal-article

Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage.

Published by

FEMS microbiology ecology

Summary

journal-article

Comparison of Clinical Methods with the Faecal Gluten Immunogenic Peptide to Assess Gluten Intake in Coeliac Disease.

Published by

Journal of pediatric gastroenterology and nutrition

Summary

journal-article

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool

Published by

Microbiome

Summary

journal-article

Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans.

Published by

Physiological reports

Summary

journal-article

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass

Published by

Frontiers in Microbiology

Summary

journal-article

Effect of laser irradiation on cell function and its implications in Raman spectroscopy

Published by

Applied and Environmental Microbiology

Summary

journal-article

P856 The gut microbiota composition and metabolic activity of HLA-B27 transgenic rats with gut inflammation resembles the dysbiotic characteristics of human inflammatory bowel disease

Published by

Journal of Crohn's and Colitis

Summary

journal-article

Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples

Published by

Environmental Microbiology

Summary

journal-article

Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples

Summary

other

Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples

Summary

other

Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition

Published by

Gastroenterology

Summary

journal-article

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

Summary

other

Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

Published by

PeerJ

Summary

journal-article

IL-17 signalling restructures the nasal microbiome and drives dynamic changes following Streptococcus pneumoniae colonization

Published by

BMC Genomics

Summary

journal-article

Bacterial community analysis in upflow multilayer anaerobic reactor treating high-solids organic wastes

Published by

Biotechnology Progress

Summary

journal-article

AODTH-007 Dietary manipulation of the healthy human and colitic rat gut microbiome by cd-treat diet and exclusive enteral nutrition; a proof of concept study

Published by

Inflammatory Bowel Disease

Summary

conference-paper

Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors

Published by

Frontiers in Microbiology

Summary

journal-article

Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition

Published by

GCB Bioenergy

Summary

journal-article

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred

Published by

PLOS ONE

Summary

journal-article

DOP008 Dietary manipulation of the healthy human and colitic murine gut microbiome by CD-TREAT diet and exclusive enteral nutrition; a proof of concept study

Published by

Journal of Crohn's and Colitis

Summary

journal-article

Letter: reproducible evidence shows that exclusive enteral nutrition significantly reduces faecal calprotectin concentrations in children with active Crohn's disease

Published by

Alimentary Pharmacology & Therapeutics

Summary

journal-article

Collection of datasets containing the extension to SeqENV pipeline, Illumina sequencing data from sugarcane including subhabitats from soil, rhizsophere, stem and root and two marine datasets and analysis results

Summary

other

Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use

Summary

other

Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use

Published by

PLOS Pathogens

Summary

journal-article

Comparison of the human gastric microbiota in hypochlorhydric states arising as a result ofHelicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use

Summary

preprint

Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use

Published by

PLOS Pathogens

Summary

journal-article

Seqenv: linking sequences to environments through text mining

Published by

PeerJ

Summary

journal-article

Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure

Published by

Water Research

Summary

journal-article

Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)

Published by

Biodiversity Data Journal

Summary

journal-article

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities

Published by

Molecular Ecology

Summary

journal-article

Response to Kaakoush et al.

Published by

The American Journal of Gastroenterology

Summary

journal-article

The effect of DNA extraction methodology on gut microbiota research applications

Published by

BMC Res Notes

Summary

journal-article

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

Published by

BMC Bioinformatics

Summary

journal-article

OP018. The impact of ‘Crohn’s Disease-TReatment-with-EATing’ diet (CD-TREAT diet) and exclusive enteral nutrition on healthy gut bacteria metabolism

Published by

Journal of Crohn's and Colitis

Summary

journal-article

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines

Published by

OpenAlex

Summary

other

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines

Published by

OpenAlex

Summary

other

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines

Published by

Microb. Biotechnol.

Summary

journal-article

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

Published by

BMC Genomics

Summary

journal-article

Emerging investigators series: microbial communities in full-scale drinking water distribution systems – a meta-analysis

Published by

Environ. Sci.: Water Res. Technol.

Summary

journal-article

Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in well-controlled Type 2 Diabetes

Published by

Proceedings of the Nutrition Society

Summary

journal-article

Host–microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intake

Published by

British Journal of Nutrition

Summary

journal-article

The skin microbiome in psoriatic arthritis: methodology development and pilot data

Published by

The Lancet

Summary

journal-article

A detailed analysis of the gut microbial diversity and metabolic activity in children with obesity of different aetiology and lean controls

Published by

Proc. Nutr. Soc.

Summary

journal-article

Bacterial diversity along a 2600km river continuum

Published by

Environmental Microbiology

Summary

journal-article

Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process

Published by

Proc. IEEE

Summary

journal-article

Metagenomic Evidence for the Presence of Comammox Nitrospira -Like Bacteria in a Drinking Water System

Published by

mSphere

Summary

journal-article

Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O<inf>2</inf>-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment

Published by

Current Microbiology

Summary

journal-article

Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition

Published by

Am J Gastroenterol

Summary

journal-article

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

Published by

Nucleic Acids Research

Summary

journal-article

Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process

Published by

Proceedings of the IEEE

Summary

journal-article

Bacterial diversity along a 2 600 km river continuum

Summary

report

Bacterial diversity along a 2 600 km river continuum

Summary

report

O-05: Metagenomic analysis of the gut microbiome during a course of Exclusive Enteral Nutrition (EEN) provides novel insights on mechanism of EEN action

Published by

Journal of Crohn's and Colitis

Summary

journal-article

Binning metagenomic contigs by coverage and composition

Published by

Nature Methods

Summary

journal-article

Multidirectional scattering models for 3-dimensional ultrasound imaging

Published by

Journal of Ultrasound in Medicine

Summary

journal-article

Multidirectional scattering models for 3-dimensional ultrasound imaging

Published by

Journal of Ultrasound in Medicine

Summary

journal-article

Multidirectional Scattering Models for 3-Dimensional Ultrasound Imaging

Published by

Journal of Ultrasound in Medicine

Summary

journal-article

A clinical system for three-dimensional extended-field-of-view ultrasound

Published by

BJR

Summary

journal-article

Optimization strategies for ultrasound volume registration

Published by

Measurement Science and Technology

Summary

journal-article

Three-dimensional ultrasound imaging

Published by

Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine

Summary

journal-article

Phase boundary estimation in electrical impedance tomography using the Hooke and Jeeves pattern search method

Published by

Measurement Science and Technology

Summary

journal-article

Unscented Kalman filter approach to tracking a moving interfacial boundary in sedimentation processes using three-dimensional electrical impedance tomography

Published by

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

Summary

journal-article

Directional Algebraic Reconstruction Technique for Electrical Impedance Tomography

Published by

Journal of the Korean Physical Society

Summary

journal-article

3D ultrasound

Summary

conference-paper

Application of direct search optimization in electrical impedance tomography

Summary

conference-paper

3D electrical impedance tomography and mammography phantom study

Summary

conference-paper

Nonstationary phase boundary estimation in electrical impedance tomography using unscented Kalman filter

Published by

Journal of Computational Physics

Summary

journal-article

Electrical resistance imaging of a time-varying interface in stratified flows using an unscented Kalman filter

Published by

Measurement Science and Technology

Summary

journal-article

Moving interfacial boundary estimation in stratified flow of two immiscible liquids using electrical resistance tomography

Published by

Measurement Science and Technology

Summary

journal-article

Particle swarm optimization technique for elliptic region boundary estimation in electrical impedance tomography

Published by

AIP Conference Proceedings

Summary

conference-paper

Sensitivity map generation in electrical capacitance tomography using mixed normalization models

Published by

Measurement Science and Technology

Summary

journal-article

Electrical resistance imaging of two-phase flow through rod bundles

Published by

AIP Conference Proceedings

Summary

conference-paper

Dynamic estimation of interfacial boundary in a stratified flow with electrical impedance tomography

Summary

conference-paper

Image reconstruction using unscented Kalman filter in electrical impedance tomography

Summary

conference-paper

Interface estimation in stratified two-phase flows with electrical resistance tomography and assessment of current injection patterns

Summary

conference-paper

Nonstationary phase boundary estimation in electrical impedance tomography based on the interacting multiple model scheme

Published by

Measurement Science and Technology

Summary

journal-article

Computational strategies for protein quantitation in 2D electrophoresis gel image processor for matlab

Published by

Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies, FBIT 2007

Summary

conference-paper

Computational Strategies for Protein Quantitation in 2D Electrophoresis Gel Image Processor for Matlab

Published by

2007 Frontiers in the Convergence of Bioscience and Information Technologies

Summary

conference-paper

Concentration distribution estimation of fluid through electrical impedance tomography based on interacting multiple model scheme

Published by

Flow Measurement and Instrumentation

Summary

journal-article

Estimation of time-dependent heat flux and measurement bias in two-dimensional inverse heat conduction problems

Published by

International Journal of Heat and Mass Transfer

Summary

journal-article

Mammography phantom studies using 3D electrical impedance tomography with numerical forward solver

Published by

Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies, FBIT 2007

Summary

conference-paper

Mammography Phantom Studies Using 3D Electrical Impedance Tomography with Numerical Forward Solver

Published by

2007 Frontiers in the Convergence of Bioscience and Information Technologies

Summary

conference-paper

Kinematic Models for non-stationary elliptic region boundary in electrical impedance tomography

Summary

conference-paper

Kinematic models for non-stationary elliptic region boundaries in electrical impedance tomography

Published by

Journal of Research Institute of Advanced Technology Cheju National University

Summary

journal-article

2D electrophoresis gel image processor for Matlab

Summary

conference-paper

Kinematic models for non-stationary elliptic region boundary in electrical impedance tomography

Summary

conference-paper

On handling unexpected uncertainties in GPS through a covariance compensation extended Kalman filter

Summary

conference-paper

Effect of current patterns for stratified flow estimation in electrical impedance tomography

Summary

conference-paper

Compensation of servo track writing error in high track density disk drives

Summary

conference-paper

Process tomography-EIT application with interacting multiple model scheme

Summary

conference-paper

Effect of current injection patterns on dynamic electrical resistance imaging for fast transient processes

Published by

Proceedings of IEEE Sensors

Summary

conference-paper

Nondestructive dynamic process monitoring using electrical capacitance tomography

Published by

Key Engineering Materials

Summary

book

Phase boundary estimation in electrical resistance tomography with weighted multi-layered neural networks and front point approach

Published by

Measurement Science and Technology

Summary

journal-article

Policy-based management in ad hoc networks using geographic routing

Published by

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Summary

book

Policy-Based Management in Ad hoc Networks Using Geographic Routing

Published by

Information Networking. Advances in Data Communications and Wireless Networks

Summary

other

Policy-Based Management in Ad hoc Networks Using Geographic Routing

Published by

Information Networking. Advances in Data Communications and Wireless Networks

Summary

other

A new correction algorithm of servo track writing error for high track density disk drives

Summary

conference-paper

A PBNM system for mobile ad hoc network with geographic routing and dynamic position estimation

Summary

conference-paper

Innovations in dynamic electrical impedance tomography inverse solver: Kalman filter and IMM algorithm

Summary

conference-paper

Application of dependency constrained genetic algorithm on traveling salesman problem

Summary

conference-paper

Dynamic estimation in GPS through a covariance compensation extended Kalman filter

Published by

Journal of Research Institute of Advanced Technology Cheju National University

Summary

journal-article

Nonlinearity-compensation extended Kalman filter for handling unexpected measurement uncertainty in process tomography

Summary

conference-paper

Nonstationary boundary estimation in electrical impedance tomography based on the IMM scheme

Summary

conference-paper

Improvement of electrical impedance tomography images for the binary mixture system through image transform filter

Summary

conference-paper

Dynamic estimation in GPS through covariance compensation extended Kalman filter

Summary

conference-paper

N-layered dependency problems through hybrid genetic algorithms

Summary

conference-paper