Metabolism and gene expression models for the microbiome reveal how diet and metabolic dysbiosis impact disease
Santibáñez-Palominos R, Tibocha-Bonilla JD, Weng Y, Kumar M, Zengler K.
Cell Systems (2026)

Unveiling organ-specific metabolism of Citrus clementina
Passi A, Tec-Campos D, Kumar M, Tibocha-Bonilla JD, Zuñiga C, Peacock B, Hale A, Santibáñez-Palominos R, Borneman J, Zengler K.
PNAS (2025)

Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida
Tibocha-Bonilla JD, Gandhi V, Lieng C, Moyne O, Santibáñez-Palominos R, Zengler K.
npj Systems Biology and Applications (2025)

Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering
Malcı K, Santibáñez R, Jonguitud-Borrego N, Santoyo-Garcia JH, Kerkhoven EJ, Rios-Solis L.
Microbial Cell Factories (2023)

Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages
Santibáñez R, Garrido D, Martin AJM.
Bioinformatics (2021)

Accessing the Role of Trust Profiles for the Economic Growth of Societies: A Stochastic Rule-Based Simulation Using the Prisoner's Dilemma Game
Monares P, Liu JH, Santibañez R, Bernardin A, Fuenzalida I, Perez-Acle T, Zhang RJ.
IEEE Transactions on Computational Social Systems (2020)

Pleione: A tool for statistical and multi-objective calibration of Rule-based models
Santibáñez R, Garrido D, Martin AJM.
Scientific Reports (2019)

Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach
Perez-Acle T, Fuenzalida I, Martin AJM, Santibáñez R, Avaria R, Bernardin A, Bustos AM, Garrido D, Dushoff J, Liu JH.
Biochemical and Biophysical Research Communications (2018)

Influence of Florfenicol Treatments on Marine-Sediment Microbiomes: A Metagenomic Study of Bacterial Communities in Proximity to Salmon Aquaculture in Southern Chile
Lynch S, Thomson P, Santibáñez R, Avendaño-Herrera R.
Antibiotics (2025)

Impact of Periodontal Disease on the Oral Microbiome of Cats
Thomson P, Santibáñez R, Garrido D, Iturriaga MP, Flores C.
Current Microbiology (2025)

Preliminary Functional Analysis of the Gut Microbiome in Colic Horses
Thomson P, Garrido D, Santibáñez R, Lara F.
Animals (Basel) (2024)

Characterization of microbial communities and predicted metabolic pathways in the uterus of healthy mares
Thomson P, Pareja J, Núñez A, Santibáñez R, Castro R.
Open Veterinary Journal (2022)

Ocular Microbiome in a Group of Clinically Healthy Horses
Santibáñez R, Lara F, Barros TM, Mardones E, Cuadra F, Thomson P.
Animals (Basel) (2022)

Isolation and Identification of Staphylococcus Species Obtained from Healthy Companion Animals and Humans
Thomson P, García P, Miles J, Isla D, Yáñez C, Santibáñez R, Núñez A, Flores-Yáñez C, Del Río C, Cuadra F.
Veterinary Sciences (2022)

Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs
Thomson P, Santibáñez R, Rodríguez-Salas C, Flores-Yañez C, Garrido D.
PeerJ (2022)

Assessment of Changes in the Oral Microbiome That Occur in Dogs with Periodontal Disease
Santibáñez R, Rodríguez-Salas C, Flores-Yáñez C, Garrido D, Thomson P.
Veterinary Sciences (2021)

Short-term impact of sucralose consumption on the metabolic response and gut microbiome of healthy adults
Thomson P, Santibañez R, Aguirre C, Galgani JE, Garrido D.
British Journal of Nutrition (2019)

First metagenomic analysis of the Andean condor gut microbiome reveals microbial diversity and wide resistome
Martinez-Hernandez JE, Berrios P, Santibáñez R, Cuesta Astroz Y, Sanchez C, Martin AJM, Trombert AN.
PeerJ (2023)

Whole-exome sequencing of oral epithelial dysplasia samples reveals an association with new genes
Adorno-Farias D, Santos JND, González-Arriagada W, Tarquinio S, Santibáñez Palominos RA, Martín AJM, Fernandez-Ramires R.
Brazilian Oral Research (2023)

Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster
Murgas L, Contreras-Riquelme S, Martínez-Hernandez JE, Villaman C, Santibáñez R, Martin AJM.
Interface Focus (2021)

Leveraging AI to generate fast and accurate surrogate models of bacteria to predict processes in terrestrial systems
Juan D. Tibocha-Bonilla, Rodrigo Santibáñez-Palominos, Maxwell Neal, Karsten Zengler.
Available online (2025)

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models
Karthik Raman, Miroslav Kratochvíl, Brett G. Olivier, Matthias König, Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran, Tung V N Nguyen, Daniel Lobo, St Elmo Wilken, Krishna Kumar Tiwari, Aswathy K. Raghu, Indumathi Palanikumar, Lavanya Raajaraam, Maziya Ibrahim, Sanjaay Balakrishnan, Shreyansh Umale, Frank Bergmann, Tanisha Malpani, Venkata P Satagopam, Reinhard Schneider, Moritz E. Beber, Sarah Keating, Mihail Anton, Alina Renz, Meiyappan Lakshmanan, Dong-Yup Lee, Lokanand Koduru, Reihaneh Mostolizadeh, Oscar Dias, Emanuel Cunha, Alexandre Oliveira, Yi Qing Lee, Karsten Zengler, Rodrigo Santibáñez-Palominos, Manish Kumar, Matteo Barberis, Bhanwar Lal Puniya, Tomáš Helikar, Hoang V. Dinh, Patrick F. Suthers, Costas D. Maranas, Isabella Casini, Seyed Babak Loghmani, Nadine Veith, Nantia Leonidou, Feiran Li, Yu Chen, Jens Nielsen, GaRyoung Lee, Sang Mi Lee, Gi Bae Kim, Pedro T. Monteiro, Miguel C. Teixeira, Hyun Uk Kim, Sang Yup Lee, Ulf W. Liebal, Lars M. Blank, Christian Lieven, Chaimaa Tarzi, Claudio Angione, Manga Enuh Blaise, Çelik Pınar Aytar, Mikhail Kulyashov, llya Akberdin, Dohyeon Kim, Sung Ho Yoon, Zhaohui Xu, Jyotshana Gautam, William T. Scott Jr., Peter J. Schaap, Jasper J. Koehorst, Cristal Zuñiga, Gabriela Canto-Encalada, Sara Benito-Vaquerizo, Ivette Parera Olm, Maria Suarez-Diez, Qianqian Yuan, Hongwu Ma, Mohammad Mazharul Islam, Jason A. Papin, Francisco Zorrilla, Kiran Raosaheb Patil, Arianna Basile, Juan Nogales, Granado San León, Freddy Castillo-Alfonso, Roberto Olivares-Hernández, Gabriela Canto-Encalada, Gabriel Vigueras-Ramírez, Henning Hermjakob, Andreas Dräger, Rahuman S Malik-Sheriff.
bioRxiv (2024)

Proteome allocation of the microbiome reveals how diet and metabolic dysbiosis impact disease
Juan D. Tibocha-Bonilla, Rodrigo Santibáñez-Palominos, Yuhan Weng, Manish Kumar, Karsten Zengler.
bioRxiv (2024)

Automated generation of context-specific Gene Regulatory Networks with a weighted approach in D. melanogaster
Leandro Murgas, Sebastian Contreras-Riquelme, J. Eduardo Martínez, Camilo Villaman, Rodrigo Santibáñez, Alberto J.M. Martin.
bioRxiv (2020)

Rule-Based Models and Applications in Biology
Á. Bustos, I. Fuenzalida, Rodrigo Santibáñez, T. Pérez-Acle, Alberto J.M. Martin.
Methods in Molecular Biology, Vol. 1819 (2018)

Shared and differential traits in the accessory olfactory bulb of caviomorph rodents with particular reference to the semiaquatic capybara
R. Suárez, Rodrigo Santibáñez, D. Parra, A. A. Coppi, L. M. Abrahão, T. H. Sasahara, J. Mpodozis.
Journal of Anatomy (2011)