Leo Lahti

About

Computational scientist obsessed with quantitative analysis of complex natural and social systems, and advancing open scholarship. We do data analysis, modeling and simulations, with a particular focus on microbial and societal ecosystems.

Work

University of Turku

|

Associate Professor

Finland

→

Education

Aalto University

Finland
→
Doctor of Science in Technology

University of Helsinki

Finland
→
Bachelor of Science / Practical Philosophy

Helsinki University of Technology

Finland
→
Master of Science in Technology

Publications

Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles

other

microbiome R package (v.3.5)

other

The gut microbiome is a significant risk factor for future chronic lung disease

other

Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults

journal-article

Enhancing biomarkers with co-abundance

other

Distinct Diet-Microbiota-Metabolism Interactions in Overweight and Obese Pregnant Women: a Metagenomics Approach

journal-article

Role of Gut Microbiota in Statin-Associated New-Onset Diabetes—a Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort

other

What are patterns of rise and decline?

other

Interdisciplinary collaboration in studying newspaper materiality

CEUR Workshop Proceedings

conference-paper

Integrating open science in the humanities: the case of computational history

other

Prebiotic Xylo-Oligosaccharides Ameliorate High-Fat-Diet-Induced Hepatic Steatosis in Rats

Nutrients

journal-article

Integrating open science in the humanities: the case of computational history

other

Integrating open science in the humanities: the case of computational history

other

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

journal-article

Gut microbiota-derived extracellular vesicles form a distinct entity from gut microbiota

other

Gut microbiota composition is associated with temperament traits in infants

journal-article

Gut Microbiota and Host Gene Mutations in Colorectal Cancer Patients and Controls of Iranian and Finnish Origin

journal-article

Gut Microbiota Composition in Mid-Pregnancy Is Associated with Gestational Weight Gain but Not Prepregnancy Body Mass Index

journal-article

Prebiotic Xylo-Oligosaccharides Ameliorate High-Fat-Diet-Induced Hepatic Steatosis in Rats

Nutrients

journal-article

Gut Microbiome as a Risk Factor for Future CKD

other

Learning and teaching biological data science in the Bioconductor community

other

Fractional modelling of COVID-19 transmission incorporating asymptomatic and super-spreader individuals

other

A Quantitative Approach to Book-Printing in Sweden and Finland, 1640–1828

Historical Methods: A Journal of Quantitative and Interdisciplinary History

journal-article

A Quantitative Approach to Book-Printing in Sweden and Finland, 1640–1828

Historical Methods: A Journal of Quantitative and Interdisciplinary History

journal-article

Laki estää tehokkaiden tutkimusmenetelmien käytön

other

Bibliographic Data Science and the History of the Book (c. 1500–1800)

journal-article

Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population

other

Microbiome data science

other

FdeSolver: A Julia Package for Solving Fractional Differential Equations

other

International Campaign to Abolish Nuclear Weapons (ICAN). Public appeal to the Finnish parliament to join the United Nations international agreement to ban nuclear weapons. Signed together with 121 Finnish influencers in research, culture and politics. January 2021.

other

Examining the healthy human microbiome concept

other

Examining the Early Modern Canon: The English Short Title Catalogue and Large-Scale Patterns of Cultural Production

other

Opening academic publishing - Development and application of systematic evaluation criteria

report

Reply to the Letter to the Editor: Gut microbiota composition is associated with temperament traits in infants

other

Opening academic publishing - Development and application of systematic evaluation criteria

report

Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis

other

COMPREHENSIVE BIOMARKER PROFILING OF HYPERTENSION IN 36,985 FINNISH INDIVIDUALS

other

Breast Milk Proteome: Changes in the Different Stages of Lactation and Impacts of Gestational Diabetes Mellitus and Body Mass Index

other

A Hierarchical Ornstein-Uhlenbeck Model for Stochastic Time Series Analysis

Lecture Notes in Computer Science

conference-paper

A Hierarchical Ornstein-Uhlenbeck Model for Stochastic Time Series Analysis

Lecture Notes in Computer Science

conference-paper

Best practices in bibliographic data science

other

Microbial communities as dynamical systems

Current Opinion in Microbiology

other

Microbial communities as dynamical systems

Current Opinion in Microbiology

other

Microbial communities as dynamical systems

Current Opinion in Microbiology

other

Associations between gut microbiome and circulating cytokines: a cross-sectional analysis in the FINRISK 2002 population cohort

other

Prebiotic Xylo-oligosaccharides Targeting Faecalibacterium prausnitzii Prevent High Fat Diet-induced Hepatic Steatosis in Rats

working-paper

Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation : results from two observational, population-based microbiome studies

other

Interdisciplinary collaboration in studying newspaper materiality

CEUR Workshop Proceedings

conference-paper

Open Data Science

other

Assessing the safety of microbiome perturbations

other

Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies

other

Analytical determination of editions from bibliographic metadata

Studia Humaniora Ouluensia

conference-paper

Multi-stability and the origin of microbial community types

journal-article

Analytical determination of editions from bibliographic metadata

Studia Humaniora Ouluensia

conference-paper

Alchemy & algorithms: perspectives on the philosophy and history of open science

Research Ideas and Outcomes

other

Alchemy & algorithms: perspectives on the philosophy and history of open science

other

A National Public Sphere? Analyzing the Language, Location, and Form of Newspapers in Finland, 1771–1917

journal-article

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects

journal-article

Print culture and economic constraints : A quantitative analysis of book prices in eighteenth-century Britain

other

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

other

Diet, perceived intestinal well-being and compositions of fecal microbiota and short chain fatty acids in oat-using subjects with celiac disease or gluten sensitivity

journal-article

Association of Long-Term Habitual Dietary Fiber Intake since Infancy with Gut Microbiota Composition in Young Adulthood

other

Scaling up bibliographic data science

CEUR Workshop Proceedings

conference-paper

Scaling up bibliographic data science

CEUR Workshop Proceedings

conference-paper

Bone marrow metabolism is affected by body weight and response to exercise training varies according to anatomical location

other

Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms

journal-article

Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms

Digestive Diseases and Sciences

journal-article

The Emerging Paradigm of Bibliographic Data Science

other

Maternal prenatal psychological distress and hair cortisol levels associate with infant fecal microbiota composition at 2.5 months of age

journal-article

Fecal microbiota profiles of growing pigs and their relation to growth performance

other

The Emerging Paradigm of Bibliographic Data Science

other

Fewer culturable Lactobacillaceae species identified in faecal samples of pigs performing manipulative behaviour

other

Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering

working-paper

Greengenes2 unifies microbial data in a single reference tree

journal-article

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke

other

Associations between gut microbiota and incident fractures in the FINRISK cohort

other

Epidemic transmission modeling with fractional derivatives and environmental pathogens

other

Integration of polygenic and gut metagenomic risk prediction for common diseases

other

Algorithm 1047: FdeSolver, a Julia Package for Solving Fractional Differential Equations

other

Regular Exercise Training Induces More Changes on Intestinal Glucose Uptake from Blood and Microbiota Composition in Leaner Compared to Heavier Individuals in Monozygotic Twins Discordant for BMI

other

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

journal-article

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development

other

iSEEtree: interactive explorer for hierarchical data

other

Infant gut microbiota and negative and fear reactivity

other

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

other

A cohort study in family triads : impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life

other

Perinatal depressive and anxiety symptoms are associated with gut microbiota in pregnant women with overweight and obesity

other

Shotgun metagenomic analysis of the oral microbiome in gingivitis: a nested case-control study

other

Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours

other

Modelling spatial patterns in host-associated microbial communities

other

Gender differences in global antimicrobial resistance

other

A toolbox of machine learning software to support microbiome analysis

other

Maternal pre- and postnatal stress and maternal and infant gut microbiota features

other

Aberrations in the early pregnancy serum metabolic profile in women with prediabetes at two years postpartum

other

Skin microbiota variation in Indian families

other

Elementary methods provide more replicable results in microbial differential abundance analysis

other

Links between gut microbiota with specific serum metabolite groups in pregnant women with overweight or obesity

other

Exit time as a measure of ecological resilience

journal-article

Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort

other

Corpus Linguistics and Eighteenth Century Collections Online (ECCO)

journal-article

Ebola epidemic model with dynamic population and memory

other

Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action

other

Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort

other

Gut microbiome and atrial fibrillation: results from a large population-based study

other

Retrieval and Analysis of Eurostat Open Data with the eurostat Package

journal-article

Reconstructing intellectual networks: From the ESTC’s bibliographic metadata to historical material

other

Gut microbiota composition and function in pregnancy as determinants of prediabetes at two-year postpartum

other

Quantifying bias and uncertainty in historical data collections with probabilistic programming

other

Probabilistic analysis of early modern British book prices

other

The Anatomy of eighteenth Century Collections online (eCCO)1

journal-article

Probabilistic Multivariate Early Warning Signals

other

Potential pathobionts in vaginal microbiota are affected by fish oil and/or probiotics intervention in overweight and obese pregnant women

journal-article

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

other

Wrangling with non-standard data

other

Author Correction: Greengenes2 unifies microbial data in a single reference tree (Nature Biotechnology, (2023), 10.1038/s41587-023-01845-1)

other

Association of leisure time physical activity with gut microbiota composition in early adulthood

other

Digitaaliset ihmistieteet ja historiantutkimus

other

Effects of Obesity and Exercise on Hepatic and Pancreatic Lipid Content and Glucose Metabolism : PET Studies in Twins Discordant for BMI

other

Elementary methods provide more replicable results in microbial differential abundance analysis

other

Learning and teaching biological data science in the Bioconductor community

PLOS Computational Biology

journal-article

Gut microbiota-derived extracellular vesicles form a distinct entity from gut microbiota

mSystems

journal-article

Gut Microbiome as a Risk Factor for Future CKD

Kidney International Reports

journal-article

Fractional modelling of COVID-19 transmission incorporating asymptomatic and super-spreader individuals

Mathematical Biosciences

journal-article

Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population

Nature Communications

journal-article

Examining the healthy human microbiome concept

Nature Reviews Microbiology

journal-article

Assessing the safety of microbiome perturbations

Microbial Genomics

journal-article

Lifestyle associates with unique resistome and microbiome signatures in children

preprint

Biome-specific genome catalogues reveal functional potential of shallow sequencing

preprint

Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort

European Journal of Nutrition

journal-article

Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort

European Journal of Nutrition

journal-article

Elementary methods provide more replicable results in microbial differential abundance analysis

Briefings in Bioinformatics

journal-article

Skin microbiota variation in Indian families

PeerJ

journal-article

Skin microbiota variation in Indian families

PeerJ

journal-article

LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis

preprint

LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Analysis of Proteomics Data

BioRxiv

journal-article

Maternal pre- and postnatal stress and maternal and infant gut microbiota features

Psychoneuroendocrinology

journal-article

Maternal pre- and postnatal stress and maternal and infant gut microbiota features

Psychoneuroendocrinology

journal-article

Association of leisure time physical activity with gut microbiota composition in early adulthood

Scientific Reports

journal-article

Examining the healthy human microbiome concept (Oct, 10.1038/s41579-024-01107-0, 2024)

Nature Reviews Microbiology

journal-article

Fractional modelling of COVID-19 transmission incorporating asymptomatic and super-spreader individuals

ArXiv

journal-article

Gender differences in global antimicrobial resistance

Npj Biofilms and Microbiomes

journal-article

Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours

Journal of Advanced Research

journal-article

Perinatal depressive and anxiety symptoms are associated with gut microbiota in pregnant women with overweight and obesity

Brain, Behavior, & Immunity Health

journal-article

Reconstructing ecological community dynamics from limited observations

ArXiv

journal-article

Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort

Nature Communications

journal-article

iSEEtree: interactive explorer for hierarchical data

Bioinformatics Advances

journal-article

Epidemic transmission modeling with fractional derivatives and environmental pathogens

International Journal of Biomathematics

journal-article

A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life

Gut Microbes

journal-article

Role of Gut Microbiota in Statin-Associated New-Onset Diabetes-A Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort

Arteriosclerosis, Thrombosis, and Vascular Biology

journal-article

iSEEtree: interactive explorer for hierarchical data

Bioinformatics Advances

journal-article

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy (vol 7, pg e00167, 2023)

mSystems

journal-article

Effects of Obesity and Exercise on Hepatic and Pancreatic Lipid Content and Glucose Metabolism: PET Studies in Twins Discordant for BMI

Biomolecules

journal-article

Regular Exercise Training Induces More Changes on Intestinal Glucose Uptake from Blood and Microbiota Composition in Leaner Compared to Heavier Individuals in Monozygotic Twins Discordant for BMI

Nutrients

journal-article

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development

Nature Medicine

journal-article

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development

Nature Medicine

journal-article

Regular Exercise Training Induces More Changes on Intestinal Glucose Uptake from Blood and Microbiota Composition in Leaner Compared to Heavier Individuals in Monozygotic Twins Discordant for BMI

Nutrients

journal-article

Algorithm 1047: FdeSolver, a Julia Package for Solving Fractional Differential Equations

ACM Transactions on Mathematical Software

journal-article

Learning and teaching biological data science in the Bioconductor community

ArXiv

journal-article

Algorithm 1047: FdeSolver, a Julia Package for Solving Fractional Differential Equations

ACM Transactions on Mathematical Software

journal-article

Painting the Mona Lisa?

Septentrio Conference Series

journal-article

Epidemic transmission modeling with fractional derivatives and environmental pathogens

International Journal of Biomathematics

journal-article

Integration of polygenic and gut metagenomic risk prediction for common diseases

Nature Aging

journal-article

Shotgun metagenomic analysis of the oral microbiome in gingivitis: a nested case-control study

Journal of Oral Microbiology

journal-article

Associations between gut microbiota and incident fractures in the FINRISK cohort

npj Biofilms and Microbiomes

journal-article

Integrating host genetic and gut metagenomic risk prediction for common diseases

European Journal of Human Genetics

journal-article

Associations between gut microbiota and incident fractures in the FINRISK cohort

Npj Biofilms and Microbiomes

journal-article

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke

ISME Communications

journal-article

Greengenes2 unifies microbial data in a single reference tree (Jul, 10.1038/s41587-023-01845-1, 2023)

Nature Biotechnology

journal-article

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke

ISME Communications

journal-article

Greengenes2 unifies microbial data in a single reference tree

Nature Biotechnology

journal-article

Fewer culturable Lactobacillaceae species identified in faecal samples of pigs performing manipulative behaviour

Scientific Reports

journal-article

Fecal microbiota profiles of growing pigs and their relation to growth performance

Plos One

journal-article

Daily skin-to-skin contact alters microbiota development in healthy full-term infants

journal-article

Daily skin-to-skin contact alters microbiota development in healthy full-term infants

Gut Microbes

journal-article

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort (vol 54, pg 134, 2022)

Nature Genetics

journal-article

Bone marrow metabolism is affected by body weight and response to exercise training varies according to anatomical location

Diabetes, Obesity and Metabolism

journal-article

Associations between Stress Responses and Gut Microbiota Metabolites among Maternal Prenatal Psychological Distress Exposed Infants - FinnBrain Birth Cohort Study

Psychoneuroendocrinology

journal-article

Print culture and economic constraints: A quantitative analysis of book prices in eighteenth-century Britain

Explorations in Economic History

journal-article

Association of Long-Term Habitual Dietary Fiber Intake since Infancy with Gut Microbiota Composition in Young Adulthood

The Journal of Nutrition

journal-article

Validating and Extracting Information from National Identification Numbers in R: The Case of Finland and Sweden

The R Journal

journal-article

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

Microbial Biotechnology

journal-article

Shotgun metagenomic analysis of the oral microbiome in gingivitis: a nested case-control study

Journal of Oral Microbiology

journal-article

Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies

The Lancet Microbe

journal-article

Effects of Obesity and Exercise on Hepatic and Pancreatic Lipid Content and Glucose Metabolism: PET Studies in Twins Discordant for BMI

Biomolecules

journal-article

A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life

Gut Microbes

journal-article

Biochemical analyses can complement sequencing-based ARG load monitoring: a case study in Indian hospital sewage networks

preprint

Infant gut microbiota and negative and fear reactivity

Development and Psychopathology

journal-article

Skin microbiota variation in Indian families

preprint

Skin microbiota variation in Indian families

BioRxiv

journal-article

Microbiome-based risk prediction in incident heart failure: a community challenge

other

Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action

Frontiers in Microbiology

journal-article

Ebola epidemic model with dynamic population and memory

Chaos, Solitons & Fractals

journal-article

Dealing with dimensionality: the application of machine learning to multi-omics data

other

A toolbox of machine learning software to support microbiome analysis

Frontiers in Microbiology

journal-article

Dealing with dimensionality: the application of machine learning to multi-omics data

Bioinformatics

journal-article

Dealing with dimensionality: the application of machine learning to multi-omics data

Bioinformatics

journal-article

What are patterns of rise and decline?

Royal Society Open Science

journal-article

miaSim: an R/Bioconductor package to easily simulate microbial community dynamics

Methods in Ecology and Evolution

journal-article

miaSim: an R/Bioconductor package to easily simulate microbial community dynamics

Methods in Ecology and Evolution

journal-article

The preterm gut microbiota and administration routes of different probiotics: a randomized controlled trial

Pediatric Research

journal-article

Machine learning approaches in microbiome research: challenges and best practices

Frontiers in Microbiology

journal-article

The impact of fish oil and/or probiotics intervention on vaginal microbiota in overweight and obese pregnant women

Annals of Nutrition and Metabolism

journal-article

The gut microbiome is a significant risk factor for future chronic lung disease

Journal of Allergy and Clinical Immunology

journal-article

Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta

journal-article

Infant Left Amygdala Volume Is Negatively Associated with Fecal Microbiota Diversity

BioRxiv

journal-article

Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles

Microbiome

journal-article

Machine learning approaches in microbiome research: challenges and best practices

other

Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta

BMC Biology

journal-article

Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta

BMC Biology

journal-article

Gut microbiota composition and function in pregnancy as determinants of prediabetes at two-year postpartum

Acta Diabetologica

journal-article

What are patterns of rise and decline?

Royal Society Open Science

journal-article

Gut microbiota composition and function in pregnancy as determinants of prediabetes at two-year postpartum

Acta Diabetologica

journal-article

Gut microbiome and atrial fibrillation-results from a large population-based study

EBioMedicine

journal-article

The preterm gut microbiota and administration routes of different probiotics: a randomized controlled trial

journal-article

Fractional model of COVID–19 with pathogens as shedding effects

ArXiv

journal-article

miaSim: an R/Bioconductor package to easily simulate microbial community dynamics

journal-article

Ebola epidemic model with dynamic population and memory

Chaos, Solitons & Fractals

journal-article

Aberrations in the early pregnancy serum metabolic profile in women with prediabetes at two years postpartum

Metabolomics

journal-article

Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting

journal-article

Enhancing biomarkers with co-abundance

Nature Computational Science

journal-article

FdeSolver: A Julia Package for Solving Fractional Differential Equations

ArXiv

journal-article

Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults

Diabetes Care

journal-article

Infant Fecal Microbiota Composition and Attention to Emotional Faces

Emotion

journal-article

Infant fecal microbiota composition and attention to emotional faces.

Emotion

journal-article

Multi-Trait Genetic Analysis Reveals Clinically Interpretable Hypertension Subtypes

Circulation: Genomic and Precision Medicine

journal-article

Multi-Trait Genetic Analysis Reveals Clinically Interpretable Hypertension Subtypes

Circulation: Genomic and Precision Medicine

journal-article

Multi-Trait Genetic Analysis Reveals Clinically Interpretable Hypertension Subtypes

journal-article

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

mSystems

journal-article

Potential pathobionts in vaginal microbiota are affected by fish oil and/or probiotics intervention in overweight and obese pregnant women

Biomedicine & Pharmacotherapy

journal-article

Probabilistic Multivariate Early Warning Signals

Lecture Notes in Computer Science

journal-article

Probabilistic Multivariate Early Warning Signals

book-chapter

Quantifying the impact of ecological memory on the dynamics of interacting communities

PLOS Computational Biology

journal-article

Quantifying the impact of ecological memory on the dynamics of interacting communities

PLOS Computational Biology

journal-article

Quantifying the impact of ecological memory on the dynamics of interacting communities

journal-article

Skin microbiota diversity among genetically unrelated individuals of Indian origin

PeerJ

journal-article

Skin microbiota diversity among genetically unrelated individuals of Indian origin

journal-article

The Anatomy of Eighteenth Century Collections Online (ECCO)

Eighteenth Century Studies

journal-article

Towards standardized and reproducible research in skin microbiomes

Environmental Microbiology

journal-article

Towards standardized and reproducible research in skin microbiomes

Environmental Microbiology

journal-article

Towards standardized and reproducible research in skin microbiomes

other

Rekommendation och checklista för öppen vetenskap inom ömsesidig forsknings-, utvecklings- och innovationsverksamhet mellan forskningsorganisationer och företag

book

Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain and placenta

preprint

An Infancy-Onset 20-Year Dietary Counselling Intervention and Gut Microbiota Composition in Adulthood

Nutrients

journal-article

An Infancy-Onset 20-Year Dietary Counselling Intervention and Gut Microbiota Composition in Adulthood

Nutrients

journal-article

An Infancy-Onset 20-Year Dietary Counselling Intervention and Gut Microbiota Composition in Adulthood

Nutrients

journal-article

An Infancy-Onset 20-Year Dietary Counselling Intervention and Gut Microbiota Composition in Adulthood

journal-article

COMPREHENSIVE BIOMARKER PROFILING OF HYPERTENSION IN 36,985 FINNISH INDIVIDUALS

Journal of Hypertension

journal-article

Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood?

Developmental Psychobiology

journal-article

Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood?

journal-article

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Nature Genetics

journal-article

Comprehensive biomarker profiling of hypertension in 36 985 Finnish individuals

Journal of Hypertension

journal-article

Distinct Diet-Microbiota-Metabolism Interactions in Overweight and Obese Pregnant Women: a Metagenomics Approach

Microbiology Spectrum

journal-article

Distinct Diet-Microbiota-Metabolism Interactions in Overweight and Obese Pregnant Women: a Metagenomics Approach

Microbiology Spectrum

journal-article

Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting

Cell Metabolism

journal-article

Enhancing biomarkers with co-abundance

Nature Computational Science

journal-article

Open science recommendation and checklist for research, development and innovation activities in collaboration between research organisations and companies

book

Targeting Gut Microbiota to Treat Hypertension: A Systematic Review

International Journal of Environmental Research and Public Health

journal-article

Comprehensive biomarker profiling of hypertension in 36 985 Finnish individuals

journal-article

Quantifying the impact of ecological memory on the dynamics of interacting communities

preprint

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

Frontiers in Microbiology

journal-article

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

Frontiers in Microbiology

other

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

Frontiers in Microbiology

other

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

Frontiers in Microbiology

other

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

Frontiers in Microbiology

other

Corpus Linguistics and Eighteenth Century Collections Online (ECCO)

Research in Corpus Linguistics

journal-article

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

Genome Research

journal-article

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

journal-article

Exit time as a measure of ecological resilience

Science

journal-article

Exit time as a measure of ecological resilience

Science

journal-article

Gut microbiota diversity but not composition is related to saliva cortisol stress response at the age of 2.5 months

Stress: the International Journal on Biology of Stress

journal-article

Gut microbiota diversity but not composition is related to saliva cortisol stress response at the age of 2.5 months

Stress

journal-article

Gut microbiota diversity but not composition is related to saliva cortisol stress response at the age of 2.5 months

journal-article

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

Gut Pathogens

journal-article

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

Gut Pathogens

journal-article

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

Gut Pathogens

journal-article

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

Gut Pathogens

journal-article

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

Gut Pathogens

journal-article

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

Gut Pathogens

journal-article

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

Gut Pathogens

journal-article

Impact of combined consumption of fish oil and probiotics on the serum metabolome in pregnant women with overweight or obesity

EBioMedicine

journal-article

Impact of combined consumption of fish oil and probiotics on the serum metabolome in pregnant women with overweight or obesity

journal-article

Links between gut microbiome composition and fatty liver disease in a large population sample

Gut Microbes

journal-article

Links between gut microbiome composition and fatty liver disease in a large population sample

journal-article

METABOLIC PROFILING OF HYPERTENSION IN 36,985 FINNISH INDIVIDUALS

JACC: Journal of the American College of Cardiology

journal-article

MULTI-TRAIT GENETIC ANALYSIS OF HYPERTENSION REVEALS CLINICALLY INTERPRETABLE SUBTYPES

JACC: Journal of the American College of Cardiology

journal-article

Modelling spatial patterns in host-associated microbial communities

Environmental Microbiology

journal-article

Modelling spatial patterns in host‐associated microbial communities

Environmental Microbiology

journal-article

Probabilistic early warning signals

Ecology and Evolution

journal-article

Probabilistic early warning signals

Ecology and Evolution

journal-article

Probabilistic early warning signals

journal-article

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

Frontiers in Microbiology

journal-article

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

Frontiers in Microbiology

journal-article

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

Frontiers in Microbiology

journal-article

Systemic cross-talk between brain, gut, and peripheral tissues in glucose homeostasis: effects of exercise training (CROSSYS). Exercise training intervention in monozygotic twins discordant for body weight

BMC Sports Science, Medicine and Rehabilitation

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Systemic cross-talk between brain, gut, and peripheral tissues in glucose homeostasis: effects of exercise training (CROSSYS). Exercise training intervention in monozygotic twins discordant for body weight

journal-article

Targeting Gut Microbiota to Treat Hypertension: A Systematic Review

International Journal of Environmental Research and Public Health

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Targeting Gut Microbiota to Treat Hypertension: A Systematic Review

International Journal of Environmental Research and Public Health

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Targeting Gut Microbiota to Treat Hypertension: A Systematic Review

other

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

Nature Communications

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Three-Species Lotka-Volterra Model with Respect to Caputo and Caputo-Fabrizio Fractional Operators

Symmetry

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Three-Species Lotka-Volterra Model with Respect to Caputo and Caputo-Fabrizio Fractional Operators

Symmetry

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Three-Species Lotka-Volterra Model with Respect to Caputo and Caputo-Fabrizio Fractional Operators

Symmetry

journal-article

Three-Species Lotka-Volterra Model with Respect to Caputo and Caputo-Fabrizio Fractional Operators

Symmetry

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Three-Species Lotka-Volterra Model with Respect to Caputo and Caputo-Fabrizio Fractional Operators

Symmetry

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Three-Species Lotka-Volterra Model with Respect to Caputo and Caputo-Fabrizio Fractional Operators

Symmetry

journal-article

Three-Species Lotka-Volterra Model with Respect to Caputo and Caputo-Fabrizio Fractional Operators

Symmetry

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UNSUPERVISED CLUSTER ANALYSIS OF HYPERTENSIVE INDIVIDUALS IDENTIFIES A ROBUST HIGH-RISK SUBGROUP

Journal of Hypertension

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Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering

International Journal of Environmental Research and Public Health

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Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering

International Journal of Environmental Research and Public Health

journal-article

Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering

International Journal of Environmental Research and Public Health

journal-article

Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering

International Journal of Environmental Research and Public Health

journal-article

Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering

International Journal of Environmental Research and Public Health

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Xylo-oligosaccharides in prevention of hepatic steatosis and adipose tissue inflammation: associating taxonomic and metabolomic patterns in fecal microbiomes with biclustering

Preprints.org

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Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering

other

Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals

Journal of the American Heart Association

journal-article

Unsupervised hierarchical clustering identifies a metabolically challenged subgroup of hypertensive individuals

Journal of Clinical Hypertension

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Unsupervised hierarchical clustering identifies a metabolically challenged subgroup of hypertensive individuals

Journal of Clinical Hypertension

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Unsupervised hierarchical clustering identifies a metabolically challenged subgroup of hypertensive individuals

The Journal of Clinical Hypertension

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Three-species predator-prey model with respect to Caputo and Caputo-Fabrizio fractional operators

ArXiv

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Prebiotic Xylo-Oligosaccharides Ameliorate High-Fat-Diet-Induced Hepatic Steatosis in Rats

Nutrients

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Prebiotic Xylo-Oligosaccharides Ameliorate High-Fat-Diet-Induced Hepatic Steatosis in Rats

Nutrients

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Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery

journal-article

Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery

PeerJ

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Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process

ArXiv

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Intestinal microbiota analysis supports inclusion of gluten-free oats to diet of subjects with celiac disease or gluten sensitivity

Proceedings of the Nutrition Society

other

Intestinal microbiota analysis supports inclusion of gluten-free oats to diet of subjects with celiac disease or gluten sensitivity

Proceedings of the Nutrition Society

other

Intestinal microbiota analysis supports inclusion of gluten-free oats to diet of subjects with celiac disease or gluten sensitivity

Proceedings of the Nutrition Society

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Gut microbiota composition and saliva cortisol stress response at the age of 2.5 months

Psychoneuroendocrinology

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Eicosanoid Inflammatory Mediators Are Robustly Associated With Blood Pressure in the General Population

Journal of the American Heart Association

journal-article

Eicosanoid Inflammatory Mediators Are Robustly Associated With Blood Pressure in the General Population

Journal of the American Heart Association

journal-article

Eicosanoid Inflammatory Mediators Are Robustly Associated With Blood Pressure in the General Population

Journal of the American Heart Association

journal-article

Eicosanoid Inflammatory Mediators Are Robustly Associated With Blood Pressure in the General Population

Journal of the American Heart Association

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Diet, Perceived Intestinal Well-Being and Compositions of Fecal Microbiota and Short Chain Fatty Acids in Oat-Using Subjects with Celiac Disease or Gluten Sensitivity

Nutrients

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Diet, Perceived Intestinal Well-Being and Compositions of Fecal Microbiota and Short Chain Fatty Acids in Oat-Using Subjects with Celiac Disease or Gluten Sensitivity

Nutrients

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Diet, Perceived Intestinal Well-Being and Compositions of Fecal Microbiota and Short Chain Fatty Acids in Oat-Using Subjects with Celiac Disease or Gluten Sensitivity

Nutrients

journal-article

Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals

Journal of the American Heart Association

journal-article

Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals

Journal of the American Heart Association

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Infant fecal microbiota composition and attention to emotional faces

Emotion

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Infant fecal microbiota composition and attention to emotional faces

Emotion

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Maternal prenatal psychological distress and hair cortisol levels associate with infant fecal microbiota composition at 2.5 months of age

Psychoneuroendocrinology

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Scaling Up Bibliographic Data Science

Digital Humanities in the Nordic and Baltic Countries Publications

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Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota

FEMS Microbiology Ecology

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Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota

FEMS Microbiology Ecology

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Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota

FEMS Microbiology Ecology

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Interdisciplinary Collaboration in Studying Newspaper Materiality

Digital Humanities in the Nordic and Baltic Countries Publications

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Reconstructing Intellectual Networks

Digital Humanities in the Nordic and Baltic Countries Publications

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A Quantitative Approach to Book-Printing in Sweden and Finland, 1640–1828

Historical Methods: A Journal of Quantitative and Interdisciplinary History

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Bibliographic Data Science and the History of the Book (c. 1500–1800)

Cataloging & Classification Quarterly

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Microbiome data science

Journal of Biosciences

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Microbiome yarns: The Global Phenotype-Genotype Survey. Episode III: importance of microbiota diversification for microbiome function and biome health

Microbial Biotechnology

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Microbiome yarns: The Global Phenotype-Genotype Survey. Episode III: importance of microbiota diversification for microbiome function and biome health

Microbial Biotechnology

other

Microbiome yarns: The Global Phenotype-Genotype Survey. Episode III: importance of microbiota diversification for microbiome function and biome health

Microbial Biotechnology

other

Reply to the Letter to the Editor: Gut microbiota composition is associated with temperament traits in infants

Brain, Behavior, and Immunity

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Alchemy & algorithms: perspectives on the philosophy and history of open science

Research Ideas and Outcomes

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Microbiome Yarns: human biome reproduction, evolution and visual acuity

Microbial Biotechnology

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Open Data Science

book-chapter

Microbiome Yarns: human biome reproduction, evolution and visual acuity

other

Open Data Science

Lecture Notes in Computer Science

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A Hierarchical Ornstein-Uhlenbeck Model for Stochastic Time Series Analysis

book-chapter

Eicosanoid Variation is Strongly Related to Blood Pressure in the General Population

Circulation

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Microbial communities as dynamical systems

Current Opinion in Microbiology

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Signatures of ecological processes in microbial community time series

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Stability estimation of autoregulated genes under Michaelis-Menten-type kinetics

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A Hierarchical Ornstein-Uhlenbeck Model for Stochastic Time Series Analysis

Lecture Notes in Computer Science

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Alchemy & algorithms: perspectives on the philosophy and history of open science

Research Ideas and Outcomes

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Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies

FEMS Microbiology Reviews

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Multi-stability and the origin of microbial community types

The ISME Journal

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An Open Science Peer Review Oath

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Metagenomics meets time series analysis: unraveling microbial community dynamics

Current Opinion in Microbiology

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Fat, fibre and cancer risk in African Americans and rural Africans

Nature Communications

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Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

Scientific Reports

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Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

BMC Genomics

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A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging

Skeletal Muscle

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A Quantitative Study of History in the English Short-Title Catalogue (ESTC), 1470-1800

LIBER Quarterly

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Fat, fibre and cancer risk in African Americans and rural Africans

Nature Communications

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COLONIC MICROBIOME-METABONOME NETWORK INTERACTIONS IN AFRICAN AMERICANS AND NATIVE AFRICANS: A PROSPECTIVE 2-WEEK FOOD EXCHANGE STUDY

Gut

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Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

The ISME Journal

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Copy Number Alterations and Neoplasia-Specific Mutations in MELK, PDCD1LG2, TLN1, and PAX5 at 9p in Different Neoplasias

Genes, Chromosomes and Cancer

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Binning metagenomic contigs by coverage and composition

Nature Methods

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Binning metagenomic contigs by coverage and composition

Nature Methods

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An open science peer review oath

F1000Research

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Tipping elements in the human intestinal ecosystem.

Nature communications

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Tipping elements in the human intestinal ecosystem

Nature Communications

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The Open Science Peer Review Oath

F1000Research

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Copy Number Alterations and Neoplasia-Specific Mutations in MELK, PDCD1LG2, TLN1, and PAX5 at 9p in Different Neoplasias

Genes Chromosomes & Cancer

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A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases

Nucleic Acids Research

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A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases

Nucleic Acids Research

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Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data

PeerJ

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Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data.

PeerJ

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Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review

Briefings in Bioinformatics

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Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review

Briefings in Bioinformatics

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RPA: Probabilistic analysis of probe performance and robust summarization

ArXiv

journal-article

Targeted resequencing of 9p in acute lymphoblastic leukemia yields concordant results with array CGH and reveals novel genomic alterations

Genomics

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Targeted resequencing of 9p in acute lymphoblastic leukemia yields concordant results with array CGH and reveals novel genomic alterations

Genomics

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The adult intestinal core microbiota is determined by analysis depth and health status

Clinical Microbiology and Infection

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Fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases

ArXiv

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Global modeling of transcriptional responses in interaction networks

ArXiv

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Homozygous deletions of cadherin genes in chondrosarcoma—an array comparative genomic hybridization study

Cancer Genetics

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Homozygous deletions of cadherin genes in chondrosarcoma-an array comparative genomic hybridization study

Cancer Genetics

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MicroRNA profiling in pediatric acute lymphoblastic leukemia: novel prognostic tools

Leukemia & Lymphoma

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MicroRNA profiling in pediatric acute lymphoblastic leukemia: novel prognostic tools

Leukemia & Lymphoma

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MicroRNA profiling predicts survival in anti-EGFR treated chemorefractory metastatic colorectal cancer patients with wild-type KRAS and BRAF

Cancer Genetics

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MicroRNA profiling predicts survival in anti-EGFR treated chemorefractory metastatic colorectal cancer patients with wild-type KRAS and BRAF

Cancer Genetics

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The adult intestinal core microbiota is determined by analysis depth and health status

Clinical Microbiology and Infection

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MicroRNA microarrays on archive bone marrow core biopsies of leukemias-Method validation

Leukemia Research

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Probabilistic analysis of the human transcriptome with side information

ArXiv

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Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays

Ieee-Acm Transactions on Computational Biology and Bioinformatics

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Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays

IEEE Transactions on Computational Biology and Bioinformatics

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MicroRNA microarrays on archive bone marrow core biopsies of leukemias-Method validation

Leukemia Research

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Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms

Plos One

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Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms

Plos One

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Integrative Analysis of microRNA, mRNA and aCGH Data Reveals Asbestos- and Histology-Related Changes in Lung Cancer

Genes Chromosomes & Cancer

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Integrative Analysis of microRNA, mRNA and aCGH Data Reveals Asbestos- and Histology-Related Changes in Lung Cancer

Genes, Chromosomes and Cancer

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Dependency detection with similarity constraints

ArXiv

journal-article

Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review

ArXiv

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Array Comparative Genomic Hybridization Reveals Frequent Alterations of G1/S Checkpoint Genes in Undifferentiated Pleomorphic Sarcoma of Bone

Genes Chromosomes & Cancer

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Array Comparative Genomic Hybridization Reveals Frequent Alterations of G1/S Checkpoint Genes in Undifferentiated Pleomorphic Sarcoma of Bone

Genes, Chromosomes and Cancer

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A brief overview on the BioPAX and SBML standards for formal presentation of complex biological knowledge

ArXiv

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Global modeling of transcriptional responses in interaction networks

Bioinformatics

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Unique microRNA profile in Dupuytren's contracture supports deregulation of beta-catenin pathway

Modern Pathology

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Unique microRNA profile in Dupuytren's contracture supports deregulation of beta-catenin pathway

Modern Pathology

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Global modeling of transcriptional responses in interaction networks

Bioinformatics

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CDKN2A, NF2, and JUN Are Dysregulated Among Other Genes by miRNAs in Malignant Mesothelioma-A miRNA Microarray Analysis

Genes Chromosomes & Cancer

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DEPENDENCY DETECTION WITH SIMILARITY CONSTRAINTS

Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing

journal-article

DEPENDENCY DETECTION WITH SIMILARITY CONSTRAINTS

2009 Ieee International Workshop on Machine Learning For Signal Processing

book

CDKN2A , NF2 , and JUN are dysregulated among other genes by miRNAs in malignant mesothelioma-A miRNA microarray analysis

Genes, Chromosomes and Cancer

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Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines

Bmc Genomics

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Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines

BMC Genomics

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Integrating probe-level expression changes across generations of Affymetrix arrays

Nucleic Acids Research

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Associative clustering for exploring dependencies between functional genomics data sets

Ieee-Acm Transactions on Computational Biology and Bioinformatics

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Associative Clustering for Exploring Dependencies between Functional Genomics Data Sets

IEEE Transactions on Computational Biology and Bioinformatics

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Integrating probe-level expression changes across generations of Affymetrix arrays

Nucleic Acids Research

journal-article

Associative clustering

Machine Learning: Ecml 2004, Proceedings

book-chapter

Associative clustering

Lecture Notes in Computer Science

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