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MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

mSystems, 2020-01, Vol.5 (1)

2020

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Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

Nature communications, 2023-09, Vol.14 (1), p.5682-13, Article 5682

2023

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More is Different: Metabolic Modeling of Diverse Microbial Communities

mSystems, 2023-04, Vol.8 (2), p.e0127022

2023

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Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes

Nature communications, 2024-08, Vol.15 (1), p.7416-20, Article 7416

2024

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Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease

BMC biology, 2024-04, Vol.22 (1), p.93-93, Article 93

2024

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Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers

Genome medicine, 2018-10, Vol.10 (1), p.78-13, Article 78

2018

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Editorial: Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer

Frontiers in physiology, 2017-07, Vol.8, p.537-537

2017

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From taxonomy to metabolic output: what factors define gut microbiome health?

Gut microbes, 2021-01, Vol.13 (1), p.1

2021

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Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer

Frontiers in oncology, 2022-07, Vol.12, p.914594

2022

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Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics

PloS one, 2021-02, Vol.16 (2), p.e0247534-e0247534

2021

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Probability estimation with machine learning methods for dichotomous and multicategory outcome: Applications

Biometrical journal, 2014-07, Vol.56 (4), p.564-583

2014

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Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

mSystems, 2023-06, Vol.8 (3), p.e0002823-e0002823

2023

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Effective Design of Multifunctional Peptides by Combining Compatible Functions

PLoS computational biology, 2016-04, Vol.12 (4), p.e1004786-e1004786

2016

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Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort

Frontiers in endocrinology (Lausanne), 2021-01, Vol.11, p.602326-602326

2021

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Yeast mating and image-based quantification of spatial pattern formation

PLoS computational biology, 2014-06, Vol.10 (6), p.e1003690-e1003690

2014

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MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

mSystems, 2020-02, Vol.5 (1)

2020

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Bifidobacterium infantis supplementation versus placebo in early life to improve immunity in infants exposed to HIV: a protocol for a randomized trial

BMC complementary medicine and therapies, 2023-10, Vol.23 (1), p.367-367, Article 367

2023

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Damage Repair versus Aging in an Individual-Based Model of Biofilms

mSystems, 2020-10, Vol.5 (5)

2020

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Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires

PloS one, 2012-11, Vol.7 (11), p.e49774-e49774

2012

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Use and abuse of correlation analyses in microbial ecology

The ISME Journal, 2019-11, Vol.13 (11), p.2647-2655

2019

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Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut

Communications biology, 2021-03, Vol.4 (1), p.316-316, Article 316

2021

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Coarse graining the human gut microbiome

Cell host & microbe, 2023-07, Vol.31 (7), p.1076-1078

2023

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Nature biotechnology, 2019-08, Vol.37 (8), p.852-857

2019

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Early and comprehensive management of atrial fibrillation: executive summary of the proceedings from the 2nd AFNET-EHRA consensus conference ‘research perspectives in AF’

European heart journal, 2009-12, Vol.30 (24), p.2969-2980

2009

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MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

More is Different: Metabolic Modeling of Diverse Microbial Communities

Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers

Editorial: Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer

From taxonomy to metabolic output: what factors define gut microbiome health?

Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer

Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics

Probability estimation with machine learning methods for dichotomous and multicategory outcome: Applications

Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

Effective Design of Multifunctional Peptides by Combining Compatible Functions

Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort

Yeast mating and image-based quantification of spatial pattern formation

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

Bifidobacterium infantis supplementation versus placebo in early life to improve immunity in infants exposed to HIV: a protocol for a randomized trial

Damage Repair versus Aging in an Individual-Based Model of Biofilms

Antimicrobial Peptide against Mycobacterium Tuberculosis That Activates Autophagy Is an Effective Treatment for Tuberculosis

Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires

Use and abuse of correlation analyses in microbial ecology

Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut

Coarse graining the human gut microbiome

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Early and comprehensive management of atrial fibrillation: executive summary of the proceedings from the 2nd AFNET-EHRA consensus conference ‘research perspectives in AF’

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