Gonzalez-Morelo K., Garrido D. (2024)

Cross-feeding interactions of gut microbes mediated by O-linked glycans from casein glycomacropeptide

Journal of Functional Foods 118

Roman L., Melis-Arcos F., Proschle T., Saa P., Garrido D. (2024)

Genome-scale metabolic modeling of the human milk oligosaccharide utilization by Bifidobacterium longum subsp. infantis

mSystems 9 3

Silva-Andrade C., Rodriguez M., Garrido D., Martin A. (2024)

Using metabolic networks to predict cross-feeding and competition interactions between microorganisms

Microbiology Spectrum

Nunez S., Barra M., Garrido D. (2023)

Developing a Fluorescent Inducible System for Free Fucose Quantification in Escherichia coli

Biosensors-Basel 13 3

Chen C., Tien C., Chen Y., Garrido D., Farzi A., Herzog H., Fan H., Chen Y. (2023)

Effect of Sucralose Intake on Human and Mouse/Rat Gut Microbiota Composition: A Systematic Review and Meta-Analysis

FOOD REVIEWS INTERNATIONAL

Serebrinsky-Duek K., Barra M., Danino T., Garrido D. (2023)

Engineered Bacteria for Short-Chain-Fatty-Acid-Repressed Expression of Biotherapeutic Molecules

Microbiology Spectrum 11 2

Vega-Sagardia M., Delgado J., Ruiz-Moyano S., Garrido D. (2023)

Proteomic analyses of Bacteroides ovatus and Bifidobacterium longum in xylan bidirectional culture shows sugar cross-feeding interactions

FOOD RESEARCH INTERNATIONAL 170

Vega-Sagardia M., Cabezon E., Delgado J., Ruiz-Moyano S., Garrido D. (2023)

Screening Microbial Interactions During Inulin Utilization Reveals Strong Competition and Proteomic Changes in Lacticaseibacillus paracasei M38

Probiotics and Antimicrobial Proteins

Gonzalez-Morelo K., Galan-Vasquez E., Melis F., Perez-Rueda E., Garrido D. (2023)

Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides

Frontiers in Molecular Biosciences 10

Torres-Miranda A., Melis-Arcos F., Garrido D. (2022)

Characterization and Identification of Probiotic Features in Lacticaseibacillus Paracasei Using a Comparative Genomic Analysis Approach

Probiotics and Antimicrobial Proteins 14 6 1211-1224

Silva-Andrade C., Martin A., Garrido D. (2022)

Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance

Microorganisms 10 2 213

Thomson P., Santibáñez R., Rodríguez-Salas C., Flores-Yañez C., Garrido D. (2022)

Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs

PeerJ 10 e12965

Hirmas B., Gasaly N., Orellana G., Vega-Sagardía M., Saa P., Gotteland M., Garrido D. (2022)

Metabolic Modeling and Bidirectional Culturing of Two Gut Microbes Reveal Cross-Feeding Interactions and Protective Effects on Intestinal Cells

mSystems 8

Garrido D., Martín A.J.M, Pérez-Rueda E. (2022)

Systems Modeling: Approaches and Applications - Volume II

Frontiers in Molecular Biosciences 9

Santibáñez R., Rodríguez-Salas C., Flores-Yáñez C., Garrido D., Thomson P. (2021)

Assessment of Changes in the Oral Microbiome That Occur in Dogs with Periodontal Disease

Veterinary Sciences 8 291

Díaz R., Torres-Miranda A., Orellana G., Garrido D. (2021)

Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota

Microorganisms 9 9 1906

Saa P., Urrutia A., Silva-Andrade C., Martín A.J., Garrido D. (2021)

Modeling Approaches for Probing Cross-Feeding Interactions in the Human Gut Microbiome

Computational and Structural Biotechnology Journal

Santibáñez R., Garrido D., Martin A.J.M. (2020)

Atlas: Automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages

Bioinformatics btaa1040

Barra m., Danino T., Garrido D. (2020)

Engineered Probiotics for Detection and Treatment of Inflammatory Intestinal Diseases

Frontiers in Bioengineering and Biotechnology 8 265

Altamirano A., Saa P., Garrido D. (2020)

Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools

Computational and Structural Biotechnology Journal In press

González-Morelo KJ, Vega-Sagardía M and Garrido D (2020) Molecular Insights Into O-Linked Glycan Utilization by Gut Microbes. Front. Microbiol. 11:591568. doi: 10.3389/fmicb.2020.591568 (2020)

Molecular Insights Into O-Linked Glycan Utilization by Gut Microbes

Frontiers in Microbiology 11 2834

Martin AJ., Pérez-Rueda E., Garrido D. (2020)

Systems Modeling: Approaches and Applications

Frontiers in Molecular Biosciences 7 620464

Santibañez R, Garrido D, Martin A.J. (2019)

Pleione: A tool for statistical and multi-objective calibration of Rule- based models

Scientific Reports 9 15104

Thomson P., Santibañez R., Aguirre C., Galgani J., Garrido D. (2019)

Short-Term Impact of Sucralose Consumption on the Metabolic Response and Gut Microbiome of Healthy Adults

British Journal of Nutrition 1 1-23

Gutierrez N., Garrido D. (2019)

Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes

mSystems 4 e00185-19

Thomson P., Medina D.A., Ortúzar M.V., Gotteland M. and Garrido D. (2018)

Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides

Food Research International

Fuentes-Valdés J.J., Soto-Liebe K., Pérez-Pantoja D., Tamames J., Belmar L., Pedrós-Alió C., Garrido D. and Vásquez M. (2018)

Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay

Standards in Genomic Sciences 13 9pp

Valenzuela M.J., Caruffo M., Herrera Y., Medina D.A., Coronado M., Feijoó C.G., Muñoz S., Garrido D., Troncoso M., Figueroa G., Toro M., Reyes-Jara A., Magne F. and Navarrete P. (2018)

Evaluating the capacity of human gut microorganisms to colonize the zebrafish larvae (Danio rerio)

Frontiers in Microbiology 9 14pp

Thomson P., Medina D.A. and Garrido D. (2018)

Human milk oligosaccharides and infant gut bifidobacteria: Molecular strategies for their utilization

Food Microbiology 75 37-46

Medina D.A., Pinto F., Ortúzar M.V. and Garrido D. (2018)

Simulation and modeling of dietary changes in the infant gut microbiome

FEMS Microbiology Ecology 94 9 11pp

Perez-Acle T., Fuenzalida I., Martin A.J.M., Santibáñez R., Avaria R., Bernardin A., Bustos A.M., Garrido D., Dushoff J. and Liu J.H. (2018)

Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach

Biochemical and Biophysical Research Communications 498 2 342-351

Medina D.A., Pedreros J.P., Turiel D., Quezada N., Pimentel F., Escalona A. and Garrido D. (2017)

Distinct patterns in the gut microbiota after surgical or medical therapy in obese patients

PeerJ 5 e3443 22pp

Pinto F., Medina D.A., Pérez-Correa J.R. and Garrido D. (2017)

Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome

Frontiers in Microbiology 8 12pp

Medina D.A., Pinto F., Ovalle A., Thomson P. and Garrido D. (2017)

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome

International Journal of Molecular Sciences 18 10 16pp

Garrido D., Ruiz-Moyano S., Kirmiz N., Davis J.C., Totten S.M., Lemay D.G., Ugalde J.A., German J.B., Lebrilla C.B. and Mills D.A. (2016)

A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596

Scientific Reports 6 18pp

Davis J.C., Totten S.M., Huang J.O., Nagshbandi S., Kirmiz N., Garrido D.A., Lewis Z.T., Wu L.D., Smilowitz J.T., German J.B., Mills D.A. and Lebrilla C.B. (2016)

Identification of Oligosaccharides in Feces of Breast-fed Infants and Their Correlation with the Gut Microbial Community

Molecular & Cellular Proteomics 15 9 2987-3002

Garrido D., Ruiz-Moyano S., Lemay D.G., Sela D.A., German J.B. and Mills D.A. (2015)

Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria

Scientific Reports 5 13517 17pp

Ozcan S, Kim BJ, Ro G, Kim JH, Bereuter TL, Reiter C, Dimapasoc L, Garrido D, Mills DA, Grimm R, Lebrilla CB, An HJ. 2014. Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior. Sci Rep 4:4963. (2014)

Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior.

Scientific Reports 4 4963-4968

Hyeyoung L., Garrido D., Mills D.A. and Barile D. (2014)

Hydrolysis of milk gangliosides by infant-gut associated bifidobacteria determined by microfluidic chips and high-resolution mass spectrometry

Electrophoresis

Ruiz-Moyano S, Totten SM, Garrido DA, Smilowitz JT, German JB, Lebrilla CB, Mills DA. 2013. Variation in consumption of human milk oligosaccharides by infant gut-associated strains of Bifidobacterium breve. Applied and Environmental Microbiology. 79: 6040-6049. (2013)

Variation in consumption of human milk oligosaccharides by infant gut-associated strains of Bifidobacterium breve.

Applied and Environmental Microbiology 79 19 6040-6049