Bioinformatician | Computational Biologist | Systems Biology Researcher
I am a bioinformatician and computational biologist working in systems biology, genome-scale metabolic modeling, microbiome analysis, and scientific software development. My work focuses on integrating mechanistic models and multi-omics data to understand metabolism and gene regulation across biological systems.
- Systems Biology
- Genome-Scale Metabolic Models (GEMs)
- Metabolism & Expression (ME) Models
- Microbiome Modeling
- Bioinformatics & Multi-omics
- Metagenomics
- Rule-Based Modeling
- Computational Biology Software Development
| Tool | Role | Link |
|---|---|---|
| coralME | Co-developer | https://github.com/jdtibochab/coralme |
| Atlas | Principal developer | https://github.com/glucksfall/atlas |
| Pleione | Principal developer | https://github.com/glucksfall/pleione |
| Pleiades | Principal developer | https://github.com/glucksfall/pleiades |
| Sterope | Principal developer | https://github.com/glucksfall/sterope |
| Alcyone | Principal developer | https://github.com/glucksfall/alcyone |
| PythonCyc | Maintainer / improved fork | https://pypi.org/project/PythonCyc/ |
- 🧠 Systems modeling: ME-models + rule-based modeling
- 🧫 Microbiomes: human, animal, marine, and environmental systems
- 🧬 Multi-omics: metagenomics, exomes, regulatory networks
- 🧰 Software: full modeling ecosystem (reconstruction → calibration → analysis)
📚 Full list: https://scholar.google.com/citations?user=z2gowFcAAAAJ
Full publication list (26 publications)
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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.
Proceedings of the National Academy of Sciences (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)
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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 (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 (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-Yáñez 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, Santibáñez R, Aguirre C, Galgani JE, Garrido D.
British Journal of Nutrition (2019)
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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)
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Leveraging AI to generate fast and accurate surrogate models of bacteria to predict processes in terrestrial systems
Tibocha-Bonilla JD, Santibáñez-Palominos R, Neal M, Zengler K.
ORAU Envisioning Scientific Partnerships Symposium (2025) -
FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models
Raman K, Kratochvíl M, Olivier BG, König M, Sengupta P, Kuppa Baskaran DK, Nguyen TVN, Lobo D, Wilken SE, Tiwari KK, Raghu AK, Palanikumar I, Raajaraam L, Ibrahim M, Balakrishnan S, Umale S, Bergmann F, Malpani T, Satagopam VP, Schneider R, Beber ME, Keating S, Anton M, Renz A, Lakshmanan M, Lee DY, Koduru L, Mostolizadeh R, Dias O, Cunha E, Oliveira A, Lee YQ, Zengler K, Santibáñez-Palominos R, Kumar M, Barberis M, Puniya BL, Helikar T, Dinh HV, Suthers PF, Maranas CD, Casini I, Loghmani SB, Veith N, Leonidou N, Li F, Chen Y, Nielsen J, Lee G, Lee SM, Kim GB, Monteiro PT, Teixeira MC, Kim HU, Lee SY, Liebal UW, Blank LM, Lieven C, Tarzi C, Angione C, Blaise ME, Aytar ÇP, Kulyashov M, Akberdin I, Kim D, Yoon SH, Xu Z, Gautam J, Scott WT Jr., Schaap PJ, Koehorst JJ, Zuñiga C, Canto-Encalada G, Benito-Vaquerizo S, Parera Olm I, Suarez-Diez M, Yuan Q, Ma H, Islam MM, Papin JA, Zorrilla F, Patil KR, Basile A, Nogales J, Granado San León, Castillo-Alfonso F, Olivares-Hernández R, Canto-Encalada G, Vigueras-Ramírez G, Hermjakob H, Dräger A, Malik-Sheriff RS.
bioRxiv (2024) -
Proteome allocation of the microbiome reveals how diet and metabolic dysbiosis impact disease
Tibocha-Bonilla JD, Santibáñez-Palominos R, Weng Y, Kumar M, Zengler K.
bioRxiv (2024) -
Automated generation of context-specific Gene Regulatory Networks with a weighted approach in D. melanogaster
Murgas L, Contreras-Riquelme S, Martínez JE, Villaman C, Santibáñez R, Martin AJM.
bioRxiv (2020) -
Rule-Based Models and Applications in Biology
Bustos Á, Fuenzalida I, Santibáñez R, Pérez-Acle T, Martin AJM.
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
Suárez R, Santibáñez R, Parra D, Coppi AA, Abrahão LM, Sasahara TH, Mpodozis J.
Journal of Anatomy (2011)
Conference presentations (7)
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Development and interrogation of a metabolic and gene expression model at genome scale for Synechocystis PCC 6803
Santibáñez-Palominos R, Tibocha-Bonilla JD, Zengler K.
15th Workshop on Cyanobacteria (2025)
📍 Vanderbilt University, Nashville, Tennessee, USA
📄 Proceedings: PDF
📊 Slides: PDF
📝 Abstract: PDF -
iSynME: Development and interrogation of a computational model of the Synechocystis PCC 6803 metabolism and gene expression at genome scale
Santibáñez-Palominos R, Tibocha-Bonilla JD, Zengler K.
CyanoWorld Online Seminar (2022)
📍 Online seminar
📄 Proceedings: PDF
📊 Slides: PDF
📝 Abstract: PDF -
An automatically reconstructed model of bacterial gene regulation enables simulation, prediction, and perturbation of gene responses
Santibáñez R, Garrido D, Martin AJM.
System Microbiology Workshop, FEMS2019 (July 7–11, 2019)
📍 SEC Centre, Glasgow, UK
📄 Proceedings: PDF
📊 Slides: PDF
📝 Abstract: PDF -
Pleiades Toolkit: Automatic rule-based modeling of bacterial gene regulation enables simulation, prediction, and perturbation of gene responses
Santibáñez R, Garrido D, Martin AJM.
15th International Society for Computational Biology Student Council Symposium (ISCB SCS) and Computational Modeling of Biological Systems (SysMod) Community of Special Interest (COSI), 27th Intelligent Systems for Molecular Biology & the 18th European Conference on Computational Biology (Joint Conference) (July 21–25, 2019)
📍 Congress Center Basel, Basel, Switzerland
📄 Proceedings: PDF
📊 Slides: PDF
📝 Abstract: PDF -
Stochastic Modeling of Gene Regulatory Networks in Escherichia coli
Santibáñez R, Garrido D, Perez-Acle T, Martin AJM.
4th International Synthetic & Systems Biology Summer School (SSBSS) (July 17–21, 2017)
📍 Robinson College, University of Cambridge, Cambridge, UK
📄 Proceedings: PDF
📊 Slides: PDF
📝 Abstract: PDF -
Stochastic Modeling of Gene Regulatory Networks in Escherichia coli
Santibáñez R, Garrido D, Perez-Acle T, Martin AJM.
13th International Society for Computational Biology Student Council Symposium (ISCB SCS) (July 21, 2017)
📍 Prague Congress Centre, Prague, Czech Republic
📄 Proceedings: PDF
📊 Slides: PDF
📝 Abstract: PDF -
Modeling and Stochastic Simulation of Gene Regulatory Networks in Escherichia coli
Santibáñez R, Garrido D, Perez-Acle T, Martin AJM.
3rd ISCB UK Regional Student Group’s Bioinformatics Student Symposium (SymBioSys17) (August 2017)
📍 Aberystwyth University, Aberystwyth, UK
📄 Proceedings: PDF
📊 Slides: PDF
📝 Abstract: PDF
Poster presentations (16)
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Advanced Integrative Computational Tools for Predictive Design and Simulation of Secure Biosystems
Santibáñez-Palominos R, Tibocha-Bonilla JD, Neal M, Yang B, Wu C, Sebesta J, Yu J, Xiong W, Zengler K, Guarnieri M.
DOE Genomic Sciences Program Annual Meeting (2026)
📍 Hyatt Regency Crystal City at Reagan National Airport, Arlington, Virginia, USA
🌐 https://genomicscience.energy.gov/nrel-imagine/
📊 Poster: PDF
📝 Abstract: PDF -
Advanced Integrative Computational Tools for Predictive Design and Simulation of Secure Biosystems
Santibáñez-Palominos R, Tibocha-Bonilla JD, Neal M, Yang B, Wu C, Sebesta J, Yu J, Xiong W, Zengler K, Guarnieri M.
DOE Genomic Sciences Program Annual Meeting (2025)
📍 Hyatt Regency Crystal City at Reagan National Airport, Arlington, Virginia, USA
📊 Poster: PDF
📝 Abstract: PDF -
coralME - An automated pipeline to accelerate the reconstruction of metabolism and gene expression models for microbiome research
Santibáñez-Palominos R, Tibocha-Bonilla JD, Zengler K.
Center for Microbiome Innovation International Microbiome Meeting (CIMM) (2025)
📍 Robert Paine Scripps Forum for Science, Society and the Environment Auditorium, Scripps Institution of Oceanography, La Jolla, California, USA
📊 Poster: PDF
📝 Abstract: PDF -
Computational Modeling to Enable Predictive Secure Biosystems Designs
Santibáñez-Palominos R, Tibocha-Bonilla JD, Yang B, Wu C, Yu J, Xiong W, Zengler K, Guarnieri M.
DOE Genomic Sciences Program Annual Meeting (2024)
📍 Bethesda North Marriott Hotel & Conference Center, Bethesda, Maryland, USA
📊 Poster: PDF
📝 Abstract: PDF -
Automated Pipeline to Accelerate the Reconstruction of Metabolism and Gene Expression Models
Santibáñez-Palominos R, Tibocha-Bonilla JD, Zengler K.
9th Conference on Constraint-Based Reconstruction and Analysis (COBRA) (2024)
📍 Omni San Diego Hotel, San Diego, California, USA
📊 Poster: PDF
📝 Abstract: PDF -
Modeling Bacterial Metabolism and Expression to Develop Biocontainment Strategies
Santibáñez-Palominos R, Tibocha-Bonilla JD, Estefan B, Arianpour B, Patel K, Zuñiga C, Zengler K, Guarnieri M.
DOE Genomic Sciences Program Annual Meeting
📍 Virtual Meeting
📊 Poster: PDF
📝 Abstract: PDF -
Pleiades Toolkit: Automatic rule-based modeling of bacterial gene regulation enables simulation, prediction, and perturbation of gene responses
Santibáñez R, Garrido D, Martin AJM.
15th ISCB SCS and SysMod COSI, ISMB/ECCB Joint Conference (2019)
📍 Congress Center Basel, Basel, Switzerland
📊 Poster: PDF
📝 Abstract: PDF -
Reconstrucción de Modelos de Regulación Génica y Calibración usando Computación de Alto Rendimiento
Santibáñez R, Garrido D, Martin AJM.
XIV Seminario Internacional Inteligencia Artificial Fundación COPEC-UC (International Seminar COPEC-UC: Artificial Intelligence) (2018)
📍 Centro de Extensión UC, Pontificia Universidad Católica de Chile, Santiago, Chile
📊 Poster: PDF
📝 Abstract: PDF -
Stochastic Modeling of Gene Regulation of Escherichia coli K-12
Santibáñez R, Garrido D, Martin AJM.
XXIV Congreso Latinoamericano de Microbiología (ALAM2018) (2018)
📍 CentroParque, Parque Araucano, Santiago, Chile
📊 Poster: PDF
📝 Abstract: PDF -
Automatic Reconstruction of Rule-Based Gene Regulatory Network Models and its Calibration
Santibáñez R, Garrido D, Martin AJM.
5th ISCB-LA SOIBIO EMBnet Joint Bioinformatics Conference and 3rd Latin America Student Council Symposium (2018)
📍 Universidad Andrés Bello, Viña del Mar, Chile
📊 Poster: PDF
📝 Abstract: PDF -
Automatic Rule-Based Model Reconstruction and Model Calibration of a Gene Regulatory Network
Santibáñez R, Garrido D, Martin AJM.
5th European Student Council Symposium and 17th European Conference on Computational Biology (ECCB 2018) (2018)
📍 Stavros Niarchos Foundation Cultural Center, Athens, Greece
📊 Poster: PDF
📝 Abstract: PDF -
Stochastic Modeling of Gene Regulatory Networks in Escherichia coli
Santibáñez R, Garrido D, Perez-Acle T, Martin AJM.
2nd International Conference in Bioinformatics, Simulations and Modeling (iCBSM) (2017)
📍 Universidad de Talca, Talca, Chile
📊 Poster: PDF
📝 Abstract: PDF -
Modeling and Stochastic Simulation of Gene Regulatory Networks in Escherichia coli
Santibáñez R, Garrido D, Perez-Acle T, Martin AJM.
3rd ISCB UK Regional Student Group's Bioinformatics Student Symposium (SymBioSys17) (August 2017)
📍 Aberystwyth University, Aberystwyth, UK
📊 Poster: PDF
📝 Abstract: PDF -
Stochastic Modeling of Gene Regulatory Networks in Escherichia coli
Santibáñez R, Garrido D, Perez-Acle T, Martin AJM.
13th International Society for Computational Biology Student Council Symposium (ISCB SCS) and the 25th Intelligent Systems for Molecular Biology & the 16th European Conference on Computational Biology (Joint Conference) (July 21, 2017)
📍 Prague Congress Centre, Prague, Czech Republic
📊 Poster: PDF
📝 Abstract: PDF -
Stochastic Modeling of Gene Regulatory Networks in Escherichia coli
Santibáñez R, Garrido D, Perez-Acle T, Martin AJM.
4th International Synthetic & Systems Biology Summer School (SSBSS) (July 17–21, 2017)
📍 Robinson College, University of Cambridge, Cambridge, UK
📊 Poster: PDF
📝 Abstract: PDF -
Reconstruction of Gene Regulatory Models from data and their calibration with High-Performance Computing
Santibáñez R, Garrido D, Perez-Acle T, Martin AJM.
XII Seminario Internacional de Bioingeniería Fundación COPEC-UC (COPEC-UC International Seminar: Bioengineering) (2017)
📍 Centro de Extensión UC, Pontificia Universidad Católica de Chile, Santiago, Chile
📊 Poster: PDF
📝 Abstract: PDF