Universidad Andrés Bello | Faculty of Life Sciences
cbib@unab.cl | English ES
Integrative Science to Discover, Design & Transform

Center for Bioinformatics & Integrative Biology

A Latin American leader in AI protein design, structural biophysics, and lab-in-the-loop drug discovery at Universidad Andrés Bello. Funded by US Army, US Air Force, Wellcome LEAP, Purdue University, ANID, and major industrial partners.

1,237 TFLOPS
HPC Supercomputing
US Army & USAF
International Defense Grants
15+ Mining Co.
Industry Partnerships
Purdue & LEAP
Global Bio-Innovation

CBIB Iterative Loop

From In Silico AI to Automated Wet-Lab

Lab-in-the-Loop
  • 1. Biological & Genomic Exploration: High-throughput genomics, environmental sampling, & extremophile bio-prospecting.
  • 2. Molecule Synthesis & Drug Discovery: Automated bio-active synthesis, Octet BLI kinetics, & ion channel biophysics.
  • 3. Protein Engineering & AI Design: Generative AI protein modeling (ESM-2, AlphaFold3, DeepNano-AWS).
Core Methodology

Integrative Science Cycle

Connecting data, AI computational modeling, and automated wet-lab validation to accelerate discovery and industrial innovation.

1

Biological & Genomic Exploration

Metagenomics, environmental sample sequencing, and metabolite identification. Raw data feeds predictive models for proteins and ligands.

Principal Investigators:
Dr. José Manuel Pérez: Nanobiotechnology & Extremophile Microbiology
Dr. Jorge Valdés: High-Throughput Genomics
Dr. Juan Ugalde: Health Genomic Surveillance
2

Molecule Synthesis & Drug Discovery (Lab-in-the-Loop)

Bio-active molecule synthesis, high-throughput biological validation, Octet BLI kinetics, and automated microfluidic screening.

Principal Investigators:
Dra. Yorley Duarte: Bioactive Molecule Synthesis (iDDS Lab)
Dr. Ignacio Díaz: Ion Channel Biophysics
3

Protein Engineering & AI Protein Design

AI-assisted protein/nanobody design, structural optimization, molecular dynamics, and structural stability profiling.

Principal Investigators:
Dra. Valeria Márquez: AI Protein Design & Structural Modeling
Dra. Romina Sepúlveda: AI Protein Design & Sequence Optimization
Dr. Danilo González Nilo: Protein Production & Purification
Funding & Grants

Active Projects & International Defense Grants

CBIB maintains an exceptional portfolio of competitive grants funded by Chilean ANID and top international agencies (US Army, US Air Force, Wellcome LEAP).

International Defense & US Grants

US Department of Defense & Purdue Collaboration

  • US Army Active Project (Nanobodies) US Army

    Development of engineered nanobodies for biological defense and targeted diagnostic applications (PI: Dr. Danilo González Nilo).

  • US Air Force Active Project (Nanobubbles) USAF

    Nanobubble technology for advanced gas-liquid interfaces and material functionalization. (Full CBIB application evaluated for broader USAF center grant).

  • Wellcome LEAP & Purdue University Pre-selected

    International partnership with Purdue University (USA) for controlled antibiotic release utilizing nanobubble carriers.

ANID & Associative Chilean Grants

FONDEF, FONDEQUIP, Anillo & Núcleo Milenio

Dra. Yorley Duarte CINV (PI), 3 FONDEF Grants, Fondecyt Regular, ANID Exploración (Director).
Dra. Valeria Márquez FONDEQUIP Octet R4 (Director), FONDEF, Fondecyt Iniciación, ANID Exploración (PI).
Dr. José Manuel Pérez FONDEF Tecnologías Avanzadas (Director), Anillo Salares (Director), Fondecyt Regular.
Dr. Ignacio Díaz Franulic FONDEF, ANID Exploración (Alternate Director), Núcleo Milenio proposal.
Dra. Romina Sepúlveda FONDEF, Fondecyt Iniciación, Núcleo Milenio.
Dr. Juan Ugalde & Dr. Danilo González Centros Tecnológicos (PI), Fondecyt Regular, 3 FONDEF Grants.
Technology Transfer

Industrial Partnerships & Spin-Offs

Delivering high-tech solutions to global industries across mining, aquaculture, agriculture, and biotechnology.

Mining Dust Suppression

Nanobubble technology for industrial dust control in open-pit mining operations.

15+ Interested Mining Companies:
Codelco, BHP, SQM, ENAEX, Glencore, Lundin, Polpaico, AMSA.

Salmon Aquaculture Health

Novel antiparasitic formulations against Caligus sea lice in salmon farming.

Industry Partners:
Salmones Antártica & Tecnovax S.A.

Nanoprobiotics & Quantum Dots

Eco-friendly biosynthesized quantum dots & nanoprobiotics for health and agriculture.

CBIB Spin-Off:
Pewman Innovation

Microbiological Terroir

Metagenomic profiling of vineyard microbiomes for premium wine fermentation.

Industry Partner:
Viña Concha y Toro
AI Platform Architecture

DeepNano-AWS: Generative AI for Nanobody Design

A cloud-native architecture connecting generative protein language models (pLMs) with high-throughput molecular dynamics and automated wet-lab active learning loops.

1 In Silico Generative Design

Camelid & VNAR sequence databases fine-tuned on Amazon SageMaker using Protein Language Models (ESM-2, ProtGPT2).

2 Biophysical Filtering

3D structure prediction via AlphaFold3/RoseTTAFold2 on AWS HealthOmics, followed by MD simulations (GROMACS/NAMD) on AWS ParallelCluster.

3 Experimental Validation

Synthesis, expression, purification, and binding kinetics measurement ($K_d$) using Octet BLI & Nano-ITC calorimeters.

4 Active Learning Loop

Experimental affinity data is continuously fed back via AWS Step Functions & Lambda to retrain generative models.

Research Directors

Principal Investigators & Laboratories

Detailed research lines, specific laboratory initiatives, scientific profiles, teaching activities, and achievements of CBIB's leadership.

Director of CBIB

Dr. Fernando Danilo González Nilo

Professor & Director of CBIB

FG

Research Lines & Focus Areas

  • Structural Bioinformatics & MD: Microsecond simulations of macromolecular complexes.
  • Nanobiotechnology & Biomaterials: Rational design of nanocarriers for targeted therapeutic delivery.
  • Ion Channels & Biophysics: Structure-function relationships and gating mechanisms of membrane proteins.
Director of DBBS

Dra. Yorley Duarte Ayala

Director of iDDS Lab & Director of DBBS PhD Program

YD
Lab Name: Intelligent Drug Discovery & Delivery Systems Lab (iDDS lab)

Research Lines & Focus Areas

  • AI & CADD in Drug Discovery: Artificial Intelligence and Machine Learning in drug design and virtual screening.
  • Ion Channel Modulation: Molecular modeling of ion channel modulators and pain/neurological therapeutics.
  • Smart Drug Delivery Systems: Design of intelligent delivery systems for controlled drug release.
Lab Director & Founder

Dr. José Manuel Pérez Donoso

Associate Professor & Biotech Entrepreneur

JP
Laboratorio de Bionanotecnología y Microbiología bionanotechnologylab.com
Startup Founder: Pewman Innovation (Eco-friendly Quantum Dots & Biomining)

Research Lines & Focus Areas

  • Green Nanotechnology & Quantum Dots: Microbial biosynthesis of fluorescent quantum dots using extremophiles.
  • Bacterial Stress & Metal Tolerance: Heavy metal resistance mechanisms in Antarctic & Atacama microorganisms.
  • Biomining & Industrial Transfer: Bio-based materials for solar energy, optics, and sustainable mining.
Principal Investigator

Dra. Romina Sepúlveda

Researcher & Academic

RS

Research Lines & Focus Areas

  • Lipid Membrane Remodeling under Thermal Stress: Structural and biophysical characterization of lipid membrane remodeling under thermal stress in tomato (Solanum lycopersicum).
  • Agricultural Computer Vision: Computer vision applied to agricultural industry and plant biotechnology.
  • Membrane Biophysics & Electrophysiology: Structure-function relationships, gating mechanisms, and patch-clamp recordings.
Academic Courses Taught This Year:
  • Bioinformatics & Data Analysis: Biology & Biotechnology Engineering
  • Advanced Biostatistics & Programming: Biochemistry
Director of Bioinformatics Eng.

Dra. Hegaly Mendoza Vilches

Director of Bioinformatic Engineering School & PI

HM
Degrees: Biochemist (USACH), Ph.D. in Applied Sciences (Universidad de Talca)
Role: Director of Bioinformatic Engineering School, Faculty of Life Sciences

Research Lines & Focus Areas

  • Applied Bioinformatics & Data Science: Scientific programming, computational modeling of biological systems, and big data management.
  • Nanoparticle Systems & Vaccine Delivery: Chitosan and titanium dioxide nanoparticle formulations for biomedical & aquaculture applications.
  • Bioinformatic Education & Curriculum: Integration of computer science, mathematics, and life sciences in higher education.
Academic Secretary DBBS

Dra. Valeria Márquez Miranda

Assistant Professor & Academic Secretary

VM
Degrees: Bioinformatics Engineer (UTALCA), Ph.D. in Biotechnology (UNAB)
Lab: Peptide Discovery and Machine Learning Laboratory

Research Lines & Focus Areas

  • Peptide Design: Artificial Intelligence and machine learning for the design and discovery of novel peptides as therapeutics and biosensors.
  • Data Science: Machine learning models for the discovery of novel therapeutic molecules.
  • Computational Biophysics: Free energy calculations and large-scale molecular dynamics simulations of ion channels.
  • Computational Nanobiotechnology: In silico modeling and rational design of dendrimers and nanocarriers for nucleic acid delivery.
Principal Investigator

Dr. Ignacio Díaz Franulic

Assistant Professor & Researcher

ID

Research Lines & Focus Areas

  • Thermal Biophysics & TRP Channels: Thermodynamic and structural basis of temperature gating in Thermo-TRP channels.
  • Voltage-Sensor Remodeling: Gating mechanics, ion permeation, and proton-activated chloride channels (PAC/TMEM206).
  • Analgesic Discovery: Novel TRPV1 channel agonists with potent analgesic properties.
Principal Investigator

Dr. Jorge Valdés Avalos

Associate Professor & Systems Biologist

JV

Research Lines & Focus Areas

  • Extremophile Genomics: Genome reconstruction and metabolic modeling of bioleaching organisms (e.g. Acidithiobacillus).
  • Biomining Systems Biology: Multi-omics analysis of acidophilic bioleaching consortia for industrial metal recovery.
  • Human Microbiome Dynamics: Longitudinal oral and nasopharyngeal microbiome shifts in school populations.
Principal Investigator

Dr. Juan Ugalde

Principal Investigator & Bioinformatician

JU

Research Lines & Focus Areas

  • Metagenomic Workflows & Pipelines: Developer of automated bioinformatics tools (e.g. BugBuster).
  • Wastewater & Environmental Surveillance: Genomic tracking of drug-resistant pathogens (Salmonella, Moraxella).
  • Antarctic & Airborne Microbiomes: Atmospheric deposition dynamics and polar snow microbial ecology.
State-of-the-Art Facilities

Technology & Infrastructure

CBIB houses an integrated ecosystem of supercomputing hardware, biophysical calorimetry, bioreactors, electron microscopy, and analytical chemistry platforms.

High-Performance Computational Biology Laboratory

Dedicated Precision-Cooled Server Room & Supercomputing Cluster

~1,237 TFLOPS Peak Performance
CBIB High-Performance Computing Server Room
CBIB Dedicated Server Room High-capacity Uninterruptible Power Supplies (UPS) & Precision-Controlled Climate Cooling.

Our facility comprises more than eight high-performance servers configured with multiple CPUs and GPUs for intensive computational biology workloads:

GPU Acceleration Node
  • CPUs: 2x Intel Xeon Ice Lake Platinum 8380 (XCC) (80 Cores / 160 Threads)
  • GPUs: 10x NVIDIA RTX 6000 Ada Generation
  • RAM: 4 TB High-Speed System Memory
Massively Parallel Compute Node
  • CPUs: 2x AMD EPYC Milan 7763 (128 Cores / 256 Threads)
  • RAM: 4 TB High-Speed System Memory
  • Workloads: Genomics & Systems Biology
Software Suite: Schrödinger Suite, TeraChem, AMBER, AlphaFold, & In-House Custom Bioinformatic Tools. SysAdmin: Maximiliano Rojas

Bioreactor Systems & Fermentation Facility

Microbial Fermentation, Recombinant Protein Expression & Metabolic Engineering

Minifors 2 Benchtop Bioreactor Glass Vessel
0.5 – 6 L Fermentation Vessel

Minifors 2 Bioreactor Modular Benchtop

Compact, modular benchtop bioreactor designed for microbial fermentation, enzyme production, and protein expression. Features integrated software control for pH, dissolved oxygen ($dO_2$), temperature, and agitation rate.

Labfors 5 Fermentation System
1 – 10 L Scale-Up Fermentation

Labfors 5 Advanced Bioprocess System Industrial PAT

Advanced benchtop fermenter optimized for therapeutic protein production, metabolic engineering, and preclinical biomanufacturing. Equipped with Process Analytical Technology (PAT) and automated data logging.

Biophysical Calorimetry & Protein Purification Platform

Octet R4 BLI, ÄKTA Go FPLC, Nano-ITC & Nano-DSC

Octet R4 BLI System (Sartorius / FONDEQUIP)

4-channel Biolayer Interferometry (BLI) system for real-time label-free molecular interaction kinetics, antibody titering, and affinity ($K_d$) characterization. (Awarded by Dra. Valeria Márquez).

ÄKTA Go FPLC & TFF Filtration

Compact protein purification chromatography system (Cytiva) complemented by Tangential Flow Filtration (TFF) and refrigerated high-volume centrifuges (up to 4,000 mL per cycle) for large-scale nanobody & protein production.

Nano-ITC & Nano-DSC Calorimetry

Low-volume Isothermal Titration Calorimeter (190 µL) & Nano-DSC for label-free binding thermodynamics ($\Delta H, \Delta S$), stoichiometry, and thermal transition stability ($T_m$).

Calorimetry & Biophysical Characterization
Biophysical & Protein Engineering Core Senior Researcher: Dr. Alejandro Yévenes (20+ yrs enzymology experience)

Analytical Chemistry, Microscopy & Nanomaterial Suite

Chromatography, Particle Sizing, Mass Spectrometry & BSL-2 Cell Culture

BSL-2 Cell Culture Facility

CO₂ Incubator for mammalian & bacterial cell lines, sterile laminar flow hoods, and transfection stations.

Synergy H1 Multimode Reader

High-sensitivity fluorescence and luminescence detection in 96-well plate formats for enzyme and cell assays.

Chromatography (HPLC, GC/MS & FAAS)

Agilent 1260 HPLC, GC/MS, Microwave Chemical Reactor, and Flame Atomic Absorption Spectrometer (FAAS) for metal quantification.

Malvern Zetasizer & Drop Analyzer

Dynamic Light Scattering (DLS) & Zeta potential analysis for nanoparticle size, surface tension, and contact angle.

Electron Microscopy & UC7

Low-voltage TEM/SEM electron microscopy, Leica UC7 Ultramicrotome for ultrathin biological sample sectioning.

Nanobubble & General Prep

Nanobubble generator, sonicator, UV transilluminator, muffle furnace, drying ovens, and Heidolph™ magnetic stirrers.

Core Operations & Specialized Staff

CBIB facility operations are maintained by a dedicated team of specialists: System Administrator (Maximiliano Rojas), Bioinformatics Engineers, two Laboratory Managers, and Senior Researcher Dr. Alejandro Yévenes (20+ years of expertise in enzymology and protein characterization).

Meet Our Staff
Core Team

Support & Scientific Staff

Dedicated technical, administrative, and bioinformatic specialists ensuring seamless scientific operations at CBIB.

PJ

Pamela Jara

CBIB Executive Secretary

cbib@unab.cl

MR

Maximiliano Rojas

System Admin & Bioinformatician

HPC & Cluster Operations

AY

Dr. Alejandro Yévenes

Senior Researcher (20+ yrs Exp)

Enzymology & Protein Characterization

VF

Victoria Flores del Pino

Biochemist & Research Specialist

Molecular Biology

Get in Touch

Contact Information

Interested in research collaborations, joining the DBBS doctoral program, or exploring our facilities? Reach out to our administrative team.

Address Faculty of Life Sciences, Universidad Andrés Bello
Republica 330 / Santiago, Chile
Email Enquiries Director: fernando.gonzalez@unab.cl
General Secretariat: cbib@unab.cl
Phone +56 2 2770 3612

Send Us a Message