1359 - CViewer: A Java-based integrated analysis toolkit for whole genome shotgun metagenomics and other meta’omics technologies
other
Umer Zeeshan Ijaz
Publications
1420 - NanoAmpli-Seq: A de novo protocol for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform
other
Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment or Helicobacter pylori infection
other
De Novo Growth of Methanogenic Granules Indicates a Biofilm Life-Cycle with Complex Ecology
other
A sedimentary ancient DNA approach to elucidate the Labrador Sea paleoceanography over the last ~130,000 years
other
SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities
other
Unpicking the mysterious symbiosis of Mycoplasma in salmonids
other
Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants.
other
Methanogenic Granules Are Replicated, Whole Microbial Communities With Reproducible Responses To Environmental Cues
other
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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data-set
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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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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Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics
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other
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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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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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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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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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 10 of Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics
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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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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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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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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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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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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-set
Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics
Zenodo
other
Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.
Zenodo
other
Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.
Zenodo
other
Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.
Zenodo
other
Swatting Flies: Biting Insects as Non‐Invasive Samplers for Mammalian Population Genomics
Molecular Ecology
journal-article
Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics
BMC Research Notes
journal-article
Leveraging Cell‐Free Supernatants of Phyllospheric Bacteria to Combat Wheat Pathogens and Boost Growth
Plant-Environment Interactions
journal-article
Microbiomes of high-rate anaerobic digestors reveal ‘Study’-specific factors and limitations of synthetic wastewater
Water Research
journal-article
Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems
npj Biofilms and Microbiomes
journal-article
Microbiota transplantation for cotton leaf curl disease suppression—core microbiome and transcriptome dynamics
Communications Biology
journal-article
Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics
Zenodo
other
Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics
Zenodo
other
Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics
Zenodo
other
Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics
Zenodo
other
Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics
Zenodo
other
Data Tables, Workflow, and R Scripts: Microbiota Transplantation for Cotton Leaf Curl Disease Suppression: Core Microbiome and Transcriptome Dynamics
Zenodo
other
Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.
Zenodo
other
Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.
Zenodo
other
Data Tables and R Scripts: Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.
Zenodo
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
Frontline Gastroenterology
journal-article
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
PLOS ONE
journal-article
Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan
Data in Brief
journal-article
Disease Resistance Correlates with Core Microbiome Diversity in Cotton
Current Microbiology
journal-article
Microbiome-driven IBS metabotypes influence response to the low FODMAP diet: insights from the faecal volatome
eBioMedicine
journal-article
Sedimentary ancient DNA sequences reveal marine ecosystem shifts and indicator taxa for glacial-interglacial sea ice conditions
Quaternary Science Reviews
journal-article
Impact of commercial gut health interventions on caecal metagenome and broiler performance
preprint
CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
Microbiome
journal-article
Swatting flies: Biting insects as non-invasive samplers for mammalian population genomics
preprint
Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan
Data in Brief
journal-article
Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan
Data in Brief
journal-article
Shotgun metagenomics reveals environmental instability reduces resistance to shocks by enriching specialist taxa with distinct two component regulatory systems
preprint
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
Journal of Crohn's and Colitis
journal-article
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
Journal of Crohn's and Colitis
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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other
Additional file 1 of CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
figshare
other
CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
figshare
other
CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
figshare
other
O64 Microbiome-driven metabotypes influence response to the low FODMAP diet in IBS and implicate short chain fatty acids
Gut
journal-article
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
Frontline Gastroenterology
journal-article
P136 Faecal volatile organic compounds (VOCs) are correlated with bacterial taxa and functional genes in paediatric Crohn\textquoterights disease
Gut
journal-article
Process stability in expanded granular sludge bed bioreactors enhances resistance to organic load shocks
Journal of Environmental Management
journal-article
Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum
npj Biofilms and Microbiomes
journal-article
intI 1 gene abundance from septic tanks in Thailand using validated intI 1 primers
Applied and Environmental Microbiology
journal-article
Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities
AQUA — Water Infrastructure, Ecosystems and Society
journal-article
Microbial electrosynthesis of acetate from CO2 in three-chamber cells with gas diffusion biocathode under moderate saline conditions
Environmental Science and Ecotechnology
journal-article
Disease Resistance correlates with Core Microbiome Diversity in Cotton
preprint
Balancing the scales: Impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities
preprint
Cotton Microbiome Profiling and Cotton Leaf Curl Disease (CLCuD) Suppression through Microbial Consortia associated withGossypium arboreum
preprint
intI1 primer selection for class 1 integron integrase gene and transcript quantification – validation and application for monitoringintl1 gene abundance within septic tanks in Thailand
preprint
CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
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
preprint
Molecular insights informing factors affecting low temperature anaerobic applications: Diversity, collated core microbiomes and complexity stability relationships in LCFA-fed systems
Science of The Total Environment
journal-article
A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome
Scientific Reports
journal-article
A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome
OpenAlex
other
A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome
OpenAlex
other
A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome
OpenAlex
other
The Effects of Smoking on Human Pharynx Microbiota Composition and Stability
Microbiology Spectrum
journal-article
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
Journal of Crohn's and Colitis
journal-article
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
Journal of Crohn's and Colitis
journal-article
A Cross-Sectional Study of Potential Antimicrobial Resistance and Ecology in Gastrointestinal and Oral Microbial Communities of Young Normoweight Pakistani Individuals
Microorganisms
journal-article
DOP31 Gut metabolomic and compositional signatures predict response to treatment with exclusive enteral nutrition in children with active Crohn’s disease
Journal of Crohn's and Colitis
journal-article
Deploying an In Vitro Gut Model to Assay the Impact of the Mannan-Oligosaccharide Prebiotic Bio-Mos on the Atlantic Salmon ( Salmo salar ) Gut Microbiome
Microbiology Spectrum
journal-article
Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet
npj Biofilms and Microbiomes
journal-article
Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method
preprint
Intestinal fatty acid binding protein is a disease biomarker in paediatric coeliac disease and Crohn’s disease
BMC Gastroenterology
journal-article
The faecal metabolome and mycobiome in Parkinson's disease
Parkinsonism & Related Disorders
journal-article
The faecal metabolome and mycobiome in Parkinson's disease
Parkinsonism & Related Disorders
journal-article
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
Water
journal-article
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
Water
journal-article
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
Water
journal-article
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
Journal of Crohn's and Colitis
journal-article
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
Journal of Crohn's and Colitis
journal-article
Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap
Water Research
journal-article
Stratification of alopecia areata reveals involvement of CD4 T cell populations and altered faecal microbiota
Clinical and Experimental Immunology
journal-article
Potential nitrification activity reflects ammonia oxidizing bacteria but not archaea activity across a soil-sediment gradient
Estuarine, Coastal and Shelf Science
journal-article
Beyond Basic Diversity Estimates—Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data
Microorganisms
journal-article
Autotrophic Denitrification of Nitrate Rich Wastewater in Fluidized Bed Reactors Using Pyrite and Elemental Sulfur as Electron Donors
SSRN Electronic Journal
journal-article
Molecular Insights Informing Factors Affecting Low Temperature Anaerobic Applications: Diversity, Collated Core Microbiomes and Complexity Stability Relationships
SSRN Electronic Journal
journal-article
Beyond Basic Diversity Estimates—Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data
Microorganisms
journal-article
A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis
npj Biofilms and Microbiomes
journal-article
Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate
Frontiers in Microbiology
journal-article
Cross-sectional study of antimicrobial resistance and ecology in gastrointestinal and oral microbial communities of urban Pakistani adults
preprint
A droplet-based microfluidic approach to isolating functional bacteria from gut microbiota
Frontiers in Cellular and Infection Microbiology
journal-article
Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method
mSphere
journal-article
Autotrophic denitrification of nitrate rich wastewater in fluidized bed reactors using pyrite and elemental sulfur as electron donors
Environmental Technology & Innovation
journal-article
Alopecia areata pathotypes are associated with distinct immune and intestinal microbiome signatures
British Journal of Dermatology
journal-article
Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon
Scientific Reports
journal-article
DOP66 The effect of exclusive enteral nutrition on circulating inflammatory protein levels in paediatric patients with Crohn’s Disease
Journal of Crohn's and Colitis
journal-article
Methanogenic granule growth and development is a continual process characterized by distinct morphological features
Journal of Environmental Management
journal-article
Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome
Nature Communications
journal-article
Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae
Animal Microbiome
journal-article
P275 Analysis of exclusive enteral nutrition formulas in Crohn's disease – new insights into dietary triggers
Gut
journal-article
OWE-1 Investigation of the metabolome and mycobiome in Parkinson\textquoterights disease
Gut
journal-article
Inter-kingdom relationships in Crohn’s disease explored using a multi-omics approach
Gut Microbes
journal-article
A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease
Frontiers in Microbiology
journal-article
O12 Reversion to baseline microbiome following successful course of exclusive enteral nutrition in paediatric Crohn's disease
Gut
journal-article
Microbiomes in drinking water treatment and distribution: a meta-analysis from source to tap
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?
other
Dietary triggers of gut inflammation following exclusive enteral nutrition in children with Crohn’s disease: a pilot study
BMC Gastroenterology
journal-article
Dietary Triggers of Gut Inflammation Following Exclusive Enteral Nutrition in Children with Crohn’s Disease: A Pilot Study
preprint
SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities
Microbiome
journal-article
Socioeconomic position links circulatory microbiota differences with biological age
Scientific Reports
journal-article
The mannose receptor (CD206) identifies a population of colonic macrophages in health and inflammatory bowel disease
Scientific Reports
journal-article
Putative Antimicrobial Peptides Within Bacterial Proteomes Affect Bacterial Predominance: A Network Analysis Perspective
Frontiers in Microbiology
journal-article
A Distinct, Flocculent, Acidogenic Microbial Community Accompanies Methanogenic Granules in Anaerobic Digesters
Microbiology Spectrum
journal-article
Enrichment of the hydrogenotrophic methanogens for, in-situ biogas up-gradation by recirculation of gases and supply of hydrogen in methanogenic reactor
Bioresource Technology
journal-article
MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni
Journal of Bacteriology
journal-article
Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and surfactant‐assisted oil biodegradation
Ecology and Evolution
journal-article
O49 Dietary triggers of colonic inflammation following exclusive enteral nutrition treatment in children with Crohn's disease
Gut
journal-article
Microbial Community Assembly And Dynamics In Granular, Fixed-Biofilm And Planktonic Microbiomes Valorizing Long-Chain Fatty Acids At 20°C
Bioresource Technology
journal-article
ASSEMBLY AND DYNAMICS OF MICROBIAL COMMUNITIES IN GRANULAR, FIXED-BIOFILM AND PLANKTONIC METHANOGENIC MICROBIOMES VALORIZING LONG CHAIN FATTY ACID (LCFA)-RICH WASTEWATER
preprint
Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants
Microbiome
journal-article
The Impact of Enriched Resistant Starch Type‐2 Cookies on the Gut Microbiome in Hemodialysis Patients: A Randomized Controlled Trial
Molecular Nutrition & Food Research
journal-article
Biofilm carrier type affects biogenic sulfur-driven denitrification performance and microbial community dynamics in moving-bed biofilm reactors
Chemosphere
journal-article
First Proof of Concept for Full-Scale, Direct, Low-Temperature Anaerobic Treatment of Municipal Wastewater
Bioresource Technology
journal-article
Genome erosion and evidence for an intracellular niche – exploring the biology of mycoplasmas in Atlantic salmon
Aquaculture
journal-article
Oral Ferric Maltol Does Not Adversely Affect the Intestinal Microbiome of Patients or Mice, but Ferrous Sulphate Does
Nutrients
journal-article
Oral Ferric Maltol Does Not Adversely Affect the Intestinal Microbiome of Patients or Mice, but Ferrous Sulphate Does
Nutrients
journal-article
Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation
Frontiers in Microbiology
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
Journal of Crohn's and Colitis
journal-article
P83 Understanding differences in serum and mucosal immunopathotypes in Crohn's disease
Gut
journal-article
P091 Dietary triggers of colonic inflammation following treatment with exclusive enteral nutrition in children with Crohn’s disease
Journal of Crohn's and Colitis
journal-article
Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter
other
Development of a three-compartmentin vitrosimulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim
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
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
other
Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduceCampylobacter
preprint
Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae
preprint
Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae
other
Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data
preprint
Deploying andin vitrogut model to assay the impact of a mannan-oligosaccharide prebiotic, Bio-MOS® on the Atlantic salmon (Salmo salar) gut microbiome
preprint
Carboxylic acids production and electrosynthetic microbial community evolution under different CO2 feeding regimens
Bioelectrochemistry
journal-article
Feral populations of Brassica oleracea along Atlantic coasts in western Europe
Ecology and Evolution
journal-article
Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter
Microbiome
journal-article
Size Shapes the Active Microbiome of the Methanogenic Granules, Corroborating a Biofilm Life Cycle
mSystems
journal-article
Alterations in Intestinal Microbiota of Children With Celiac Disease at Time of Diagnosis and on a Gluten-Free Diet
Gastroenterology
journal-article
Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems
Science of The Total Environment
journal-article
Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet?
Nutrients
journal-article
Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet?
Nutrients
journal-article
Growth and Break-Up of Methanogenic Granules Suggests Mechanisms for Biofilm and Community Development
Frontiers in Microbiology
journal-article
Analysis of 61 exclusive enteral nutrition formulas used in the management of active Crohn’s disease—new insights into dietary disease triggers
Alimentary Pharmacology & Therapeutics
journal-article
Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts
Environmental Microbiology
journal-article
Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts
preprint
Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts
Environmental Microbiology
journal-article
Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts
Environmental Microbiology
journal-article
Disinfection exhibits systematic impacts on the drinking water microbiome
Microbiome
journal-article
Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations
Microbiome
journal-article
Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar
Applied and Environmental Microbiology
journal-article
Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems
Water Research
journal-article
Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems
Water Research
journal-article
P014 Identification of Crohn’s disease immunopathotypes
Journal of Crohn's and Colitis
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
Journal of Crohn's and Colitis
journal-article
Propionate Production by Bioelectrochemically-Assisted Lactate Fermentation and Simultaneous CO2 Recycling
Frontiers in Microbiology
journal-article
Bile salt metabolism is not the only factor contributing to Clostridioides (Clostridium) difficile disease severity in the murine model of disease.
Gut microbes
journal-article
EFFICIENT ENERGY SOLUTION FOR WASA FAISALABAD TAKING INTO CONSIDERATION THE ENVIRONMENTAL IMPACT ASSESSMENT
OpenAlex
other
EFFICIENT ENERGY SOLUTION FOR WASA FAISALABAD TAKING INTO CONSIDERATION THE ENVIRONMENTAL IMPACT ASSESSMENT
OpenAlex
other
Reply to GASTRO-D-18-02688
Gastroenterology
journal-article
In vitro and in vivo characterisation of Listeria monocytogenes outbreak isolates
Food Control
journal-article
Molecular diagnosis of vaginitis: comparing qPCR and microbiome profiling approaches to current microscopy scoring
Journal of Clinical Microbiology
journal-article
Next‐Generation Sequencing to Identify Lacustrine Haptophytes in the Canadian Prairies: Significance for Temperature Proxy Applications
Journal of Geophysical Research: Biogeosciences
journal-article
The reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food re-introduction
Alimentary Pharmacology & Therapeutics
journal-article
DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies
Scientific Reports
journal-article
Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance
other
MULTI-OMICS APPROACHES TO UNDERSTAND GASTRIC MUCOSA-ASSOCIATED LYMPHOID TISSUE (MALT) LYMPHOMA
Hematological Oncology
journal-article
The potential of sedimentary ancient DNA for reconstructing past sea ice evolution
The ISME Journal
journal-article
The potential of sedimentary ancient DNA for reconstructing past sea ice evolution
The ISME Journal
journal-article
Alopecia areata is characterised by dysregulation in systemic type 17 and type 2 cytokines, which may contribute to disease-associated psychological morbidity.
The British journal of dermatology
journal-article
Alopecia areata is characterized by dysregulation in systemic type 17 and type 2 cytokines, which may contribute to disease‐associated psychological morbidity
British Journal of Dermatology
journal-article
Inflammation associated ethanolamine facilitates infection by Crohn's disease-linked adherent-invasive Escherichia coli
EBioMedicine
journal-article
Inflammation associated ethanolamine facilitates infection by Crohn’s disease-linked adherent-invasive Escherichia coli
Access Microbiology
journal-article
Integrated phenotypic and genomics analysis to elucidate differences in stress resistance and virulence of Listeria monocytogenes strains
Access Microbiology
journal-article
A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078
mBio
journal-article
Solar Septic Tank: Next Generation Sequencing Reveals Effluent Microbial Community Composition as a Useful Index of System Performance
Water
journal-article
P602 CD-TREAT a novel dietary therapy of active Crohn’s disease using the exclusive enteral nutrition paradigm
Journal of Crohn's and Colitis
journal-article
P842 Multi-omics analysis suggests an active role of fungi in Crohn’s disease
Journal of Crohn's and Colitis
journal-article
ATH-09 Metabolomics & multi-omics analysis of Crohn's disease
Gut
journal-article
Biomarkers of sediment cores from site GS15-198-38
PANGAEA
data-set
Solar Septic Tank: Next Generation Sequencing Reveals Effluent Microbial Community Composition as a Useful Index of System Performance
Water
journal-article
Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems
other
PTH-075 Identification of IBD immunopathotypes
Gut
journal-article
Palynology of sediment cores from site GS15-198-38
PANGAEA
data-set
Palynology, biomarkers and droplet digital PCR data from the Late Quaternary of Site GS15-198-38, Greenland Sea
PANGAEA
other
Polarella glacialis droplet digital PCR data from sediment cores from site GS15-198-38
PANGAEA
data-set
Disinfection exhibits systematic impacts on the drinking water microbiome
other
Systems biology approach to elucidation of contaminants biodegradation in complex samples- integration of high-resolution analytical and molecular tools
Faraday Discussions
journal-article
Disinfection exhibits systematic impacts on the drinking water microbiome
other
Systems biology approach to elucidation of contaminant biodegradation in complex samples – integration of high-resolution analytical and molecular tools
Faraday Discussions
journal-article
Solar Septic Tank: Next Generation Sequencing Reveals Effluent Microbial Community Composition as a Useful Index of System Performance
Water
journal-article
P858 Crohn’s disease is characterised by a fungal dysbiosis
Journal of Crohn's and Colitis
journal-article
A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078
other
Diversity Converges During Community Assembly In Methanogenic Granules, Suggesting A Biofilm Life-Cycle
other
Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion
Scientific Reports
journal-article
NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.
GigaScience
journal-article
NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
other
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
GigaScience
journal-article
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
GigaScience
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
Frontiers in Microbiology
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
other
Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter
Frontiers in Microbiology
journal-article
NanoAmpli-Seq - Bioinformatics Workflow v1 (protocols.io.u25eyg6)
protocols.io
data-set
NanoAmpli-Seq - Bioinformatics Workflow v1
preprint
NanoAmpli-Seq - Sample processing and sequencing library preparation workflow v1 (protocols.io.u26eyhe)
protocols.io
data-set
NanoAmpli-Seq - Sample processing and sequencing library preparation workflow v1
preprint
Biokinetics Of Microbial Consortia Using Biogenic Sulfur As A Novel Electron Donor For Sustainable Denitrification
Bioresource Technology
journal-article
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights
PeerJ
journal-article
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights
other
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights
other
16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus
Scientific Reports
journal-article
Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage.
FEMS microbiology ecology
journal-article
Comparison of Clinical Methods with the Faecal Gluten Immunogenic Peptide to Assess Gluten Intake in Coeliac Disease.
Journal of pediatric gastroenterology and nutrition
journal-article
The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool
Microbiome
journal-article
Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans.
Physiological reports
journal-article
Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass
Frontiers in Microbiology
journal-article
Effect of laser irradiation on cell function and its implications in Raman spectroscopy
Applied and Environmental Microbiology
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
Journal of Crohn's and Colitis
journal-article
Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples
Environmental Microbiology
journal-article
Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples
other
Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples
other
Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition
Gastroenterology
journal-article
A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078
other
Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences
PeerJ
journal-article
IL-17 signalling restructures the nasal microbiome and drives dynamic changes following Streptococcus pneumoniae colonization
BMC Genomics
journal-article
Bacterial community analysis in upflow multilayer anaerobic reactor treating high-solids organic wastes
Biotechnology Progress
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
Inflammatory Bowel Disease
conference-paper
Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors
Frontiers in Microbiology
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
GCB Bioenergy
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
PLOS ONE
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
Journal of Crohn's and Colitis
journal-article
Letter: reproducible evidence shows that exclusive enteral nutrition significantly reduces faecal calprotectin concentrations in children with active Crohn's disease
Alimentary Pharmacology & Therapeutics
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
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
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
PLOS Pathogens
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
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
PLOS Pathogens
journal-article
Seqenv: linking sequences to environments through text mining
PeerJ
journal-article
Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure
Water Research
journal-article
Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)
Biodiversity Data Journal
journal-article
Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities
Molecular Ecology
journal-article
Response to Kaakoush et al.
The American Journal of Gastroenterology
journal-article
The effect of DNA extraction methodology on gut microbiota research applications
BMC Res Notes
journal-article
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
BMC Bioinformatics
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
Journal of Crohn's and Colitis
journal-article
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines
OpenAlex
other
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines
OpenAlex
other
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines
Microb. Biotechnol.
journal-article
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
BMC Genomics
journal-article
Emerging investigators series: microbial communities in full-scale drinking water distribution systems – a meta-analysis
Environ. Sci.: Water Res. Technol.
journal-article
Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in well-controlled Type 2 Diabetes
Proceedings of the Nutrition Society
journal-article
Host–microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intake
British Journal of Nutrition
journal-article
The skin microbiome in psoriatic arthritis: methodology development and pilot data
The Lancet
journal-article
A detailed analysis of the gut microbial diversity and metabolic activity in children with obesity of different aetiology and lean controls
Proc. Nutr. Soc.
journal-article
Bacterial diversity along a 2600km river continuum
Environmental Microbiology
journal-article
Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process
Proc. IEEE
journal-article
Metagenomic Evidence for the Presence of Comammox Nitrospira -Like Bacteria in a Drinking Water System
mSphere
journal-article
Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2 -Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment
Current Microbiology
journal-article
Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition
Am J Gastroenterol
journal-article
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
Nucleic Acids Research
journal-article
Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process
Proceedings of the IEEE
journal-article
Bacterial diversity along a 2 600 km river continuum
report
Bacterial diversity along a 2 600 km river continuum
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
Journal of Crohn's and Colitis
journal-article
Binning metagenomic contigs by coverage and composition
Nature Methods
journal-article
Multidirectional scattering models for 3-dimensional ultrasound imaging
Journal of Ultrasound in Medicine
journal-article
Multidirectional scattering models for 3-dimensional ultrasound imaging
Journal of Ultrasound in Medicine
journal-article
Multidirectional Scattering Models for 3-Dimensional Ultrasound Imaging
Journal of Ultrasound in Medicine
journal-article
A clinical system for three-dimensional extended-field-of-view ultrasound
BJR
journal-article
Optimization strategies for ultrasound volume registration
Measurement Science and Technology
journal-article
Three-dimensional ultrasound imaging
Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine
journal-article
Phase boundary estimation in electrical impedance tomography using the Hooke and Jeeves pattern search method
Measurement Science and Technology
journal-article
Unscented Kalman filter approach to tracking a moving interfacial boundary in sedimentation processes using three-dimensional electrical impedance tomography
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
journal-article
Directional Algebraic Reconstruction Technique for Electrical Impedance Tomography
Journal of the Korean Physical Society
journal-article
3D ultrasound
conference-paper
Application of direct search optimization in electrical impedance tomography
conference-paper
3D electrical impedance tomography and mammography phantom study
conference-paper
Nonstationary phase boundary estimation in electrical impedance tomography using unscented Kalman filter
Journal of Computational Physics
journal-article
Electrical resistance imaging of a time-varying interface in stratified flows using an unscented Kalman filter
Measurement Science and Technology
journal-article
Moving interfacial boundary estimation in stratified flow of two immiscible liquids using electrical resistance tomography
Measurement Science and Technology
journal-article
Particle swarm optimization technique for elliptic region boundary estimation in electrical impedance tomography
AIP Conference Proceedings
conference-paper
Sensitivity map generation in electrical capacitance tomography using mixed normalization models
Measurement Science and Technology
journal-article
Electrical resistance imaging of two-phase flow through rod bundles
AIP Conference Proceedings
conference-paper
Dynamic estimation of interfacial boundary in a stratified flow with electrical impedance tomography
conference-paper
Image reconstruction using unscented Kalman filter in electrical impedance tomography
conference-paper
Interface estimation in stratified two-phase flows with electrical resistance tomography and assessment of current injection patterns
conference-paper
Nonstationary phase boundary estimation in electrical impedance tomography based on the interacting multiple model scheme
Measurement Science and Technology
journal-article
Computational strategies for protein quantitation in 2D electrophoresis gel image processor for matlab
Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies, FBIT 2007
conference-paper
Computational Strategies for Protein Quantitation in 2D Electrophoresis Gel Image Processor for Matlab
2007 Frontiers in the Convergence of Bioscience and Information Technologies
conference-paper
Concentration distribution estimation of fluid through electrical impedance tomography based on interacting multiple model scheme
Flow Measurement and Instrumentation
journal-article
Estimation of time-dependent heat flux and measurement bias in two-dimensional inverse heat conduction problems
International Journal of Heat and Mass Transfer
journal-article
Mammography phantom studies using 3D electrical impedance tomography with numerical forward solver
Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies, FBIT 2007
conference-paper
Mammography Phantom Studies Using 3D Electrical Impedance Tomography with Numerical Forward Solver
2007 Frontiers in the Convergence of Bioscience and Information Technologies
conference-paper
Kinematic Models for non-stationary elliptic region boundary in electrical impedance tomography
conference-paper
Kinematic models for non-stationary elliptic region boundaries in electrical impedance tomography
Journal of Research Institute of Advanced Technology Cheju National University
journal-article
2D electrophoresis gel image processor for Matlab
conference-paper
Kinematic models for non-stationary elliptic region boundary in electrical impedance tomography
conference-paper
On handling unexpected uncertainties in GPS through a covariance compensation extended Kalman filter
conference-paper
Effect of current patterns for stratified flow estimation in electrical impedance tomography
conference-paper
Compensation of servo track writing error in high track density disk drives
conference-paper
Process tomography-EIT application with interacting multiple model scheme
conference-paper
Effect of current injection patterns on dynamic electrical resistance imaging for fast transient processes
Proceedings of IEEE Sensors
conference-paper
Nondestructive dynamic process monitoring using electrical capacitance tomography
Key Engineering Materials
book
Phase boundary estimation in electrical resistance tomography with weighted multi-layered neural networks and front point approach
Measurement Science and Technology
journal-article
Policy-based management in ad hoc networks using geographic routing
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
book
Policy-Based Management in Ad hoc Networks Using Geographic Routing
Information Networking. Advances in Data Communications and Wireless Networks
other
Policy-Based Management in Ad hoc Networks Using Geographic Routing
Information Networking. Advances in Data Communications and Wireless Networks
other
A new correction algorithm of servo track writing error for high track density disk drives
conference-paper
A PBNM system for mobile ad hoc network with geographic routing and dynamic position estimation
conference-paper
Innovations in dynamic electrical impedance tomography inverse solver: Kalman filter and IMM algorithm
conference-paper
Application of dependency constrained genetic algorithm on traveling salesman problem
conference-paper
Dynamic estimation in GPS through a covariance compensation extended Kalman filter
Journal of Research Institute of Advanced Technology Cheju National University
journal-article
Nonlinearity-compensation extended Kalman filter for handling unexpected measurement uncertainty in process tomography
conference-paper
Nonstationary boundary estimation in electrical impedance tomography based on the IMM scheme
conference-paper
Improvement of electrical impedance tomography images for the binary mixture system through image transform filter
conference-paper
Dynamic estimation in GPS through covariance compensation extended Kalman filter
conference-paper
N-layered dependency problems through hybrid genetic algorithms
conference-paper