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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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Quantitative proteomic analysis of extracellular vesicle subgroups isolated by an optimized method combining polymer‐based precipitation and size exclusion chromatography

Journal of extracellular vesicles, 2021-04, Vol.10 (6), p.e12087-n/a

2021

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Regulation by transcription factors in bacteria: beyond description

FEMS microbiology reviews, 2009-01, Vol.33 (1), p.133-151

2009

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Modeling core metabolism in cancer cells: surveying the topology underlying the Warburg effect

PloS one, 2010-08, Vol.5 (8), p.e12383-e12383

2010

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Transcriptional and Microenvironmental Landscape of Macrophage Transition in Cancer: A Boolean Analysis

Frontiers in immunology, 2021-06, Vol.12, p.642842-642842

2021

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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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Type 2 diabetes, gut microbiome, and systems biology: A novel perspective for a new era

Gut microbes, 2022-12, Vol.14 (1), p.2111952-2111952

2022

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Unveiling functional heterogeneity in breast cancer multicellular tumor spheroids through single-cell RNA-seq

Scientific reports, 2020-07, Vol.10 (1), p.12728, Article 12728

2020

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Macrophage Boolean networks in the time of SARS-CoV-2

Frontiers in immunology, 2022-10, Vol.13, p.997434-997434

2022

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Uncoding the interdependency of tumor microenvironment and macrophage polarization: insights from a continuous network approach

Frontiers in immunology, 2023-05, Vol.14, p.1150890-1150890

2023

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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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Author Correction: Effect of metformin and metformin/linagliptin on gut microbiota in patients with prediabetes

Scientific reports, 2024-09, Vol.14 (1), p.21124-1, Article 21124

2024

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Evolution of Centrality Measurements for the Detection of Essential Proteins in Biological Networks

Frontiers in physiology, 2016-08, Vol.7, p.375-375

2016

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Analysis of Epithelial-Mesenchymal Transition Metabolism Identifies Possible Cancer Biomarkers Useful in Diverse Genetic Backgrounds

Frontiers in oncology, 2020-07, Vol.10, p.1309-1309

2020

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Boolean modeling reveals that cyclic attractors in macrophage polarization serve as reservoirs of states to balance external perturbations from the tumor microenvironment

Frontiers in immunology, 2022-12, Vol.13, p.1012730-1012730

2022

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Dysbiosis signatures of gut microbiota and the progression of type 2 diabetes: a machine learning approach in a Mexican cohort

Frontiers in endocrinology (Lausanne), 2023-06, Vol.14, p.1170459-1170459

2023

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Stochastic Analysis of the RT-PCR Process in Single-Cell RNA-Seq

Mathematics (Basel), 2021-10, Vol.9 (19), p.2515

2021

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Filling kinetic gaps: dynamic modeling of metabolism where detailed kinetic information is lacking

PloS one, 2009-03, Vol.4 (3), p.e4967-e4967

2009

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A network perspective on the ecology of gut microbiota and progression of type 2 diabetes: Linkages to keystone taxa in a Mexican cohort

Frontiers in endocrinology (Lausanne), 2023-04, Vol.14, p.1128767

2023

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On Deep Landscape Exploration of COVID-19 Patients Cells and Severity Markers

Frontiers in immunology, 2021-09, Vol.12, p.705646-705646

2021

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Exploring metabolic anomalies in COVID-19 and post-COVID-19: a machine learning approach with explainable artificial intelligence

Frontiers in molecular biosciences, 2024-09, Vol.11, p.1429281

2024

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Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine

Frontiers in physiology, 2016-12, Vol.7, p.606-606

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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Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues

1st ed. 2018., 2018

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Diffusion on PCA-UMAP Manifold: The Impact of Data Structure Preservation to Denoise High-Dimensional Single-Cell RNA Sequencing Data

Biology (Basel, Switzerland), 2024-07, Vol.13 (7), p.512

2024

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

Quantitative proteomic analysis of extracellular vesicle subgroups isolated by an optimized method combining polymer‐based precipitation and size exclusion chromatography

Regulation by transcription factors in bacteria: beyond description

Modeling core metabolism in cancer cells: surveying the topology underlying the Warburg effect

Transcriptional and Microenvironmental Landscape of Macrophage Transition in Cancer: A Boolean Analysis

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

Type 2 diabetes, gut microbiome, and systems biology: A novel perspective for a new era

Unveiling functional heterogeneity in breast cancer multicellular tumor spheroids through single-cell RNA-seq

Macrophage Boolean networks in the time of SARS-CoV-2

Uncoding the interdependency of tumor microenvironment and macrophage polarization: insights from a continuous network approach

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

Author Correction: Effect of metformin and metformin/linagliptin on gut microbiota in patients with prediabetes

Evolution of Centrality Measurements for the Detection of Essential Proteins in Biological Networks

Analysis of Epithelial-Mesenchymal Transition Metabolism Identifies Possible Cancer Biomarkers Useful in Diverse Genetic Backgrounds

Boolean modeling reveals that cyclic attractors in macrophage polarization serve as reservoirs of states to balance external perturbations from the tumor microenvironment

Dysbiosis signatures of gut microbiota and the progression of type 2 diabetes: a machine learning approach in a Mexican cohort

Stochastic Analysis of the RT-PCR Process in Single-Cell RNA-Seq

Filling kinetic gaps: dynamic modeling of metabolism where detailed kinetic information is lacking

A network perspective on the ecology of gut microbiota and progression of type 2 diabetes: Linkages to keystone taxa in a Mexican cohort

On Deep Landscape Exploration of COVID-19 Patients Cells and Severity Markers

Exploring metabolic anomalies in COVID-19 and post-COVID-19: a machine learning approach with explainable artificial intelligence

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine

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

Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues

Diffusion on PCA-UMAP Manifold: The Impact of Data Structure Preservation to Denoise High-Dimensional Single-Cell RNA Sequencing Data

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