Paola Ruiz Puentes

Biomedical Engineer

About Me

Currently I am the AI Manager at IGCPharma. In november, 2022 I graduated Cum Laude from my M.Sc. In Biomedical Engineering with an emphasis in Artificial Intelligence from Universidad de Los Andes. I'm also a Biomedical Engineer graduated Magna Cum Laude from the same university. I was a researcher at the Biomedical Computer Vision (BCV) research group and at the Center for Research and Formation in Artificial Intelligence (CINFONIA), under supervision of Prof. Pablo Arbeláez Ph.D., until July 2023.

I am a highly motivated and results-driven researcher with a passion for drug development and discovery, molecular biology, and genetics, both in-vitro research and how to address these problems with the aid of Machine Learning techniques. I have participated since 2018 on multidisciplinary projects with the Research Group in Nanobiomaterials, Cellular Engineering, and Bioprinting from the Biomedical Engineering Department of Los Andes University.

My primary research focuses on using graph neural networks to predict specific bioactivities of peptides or ligand-protein interactions. Furthermore, I also work with a holistic understanding of surgeries, specifically on Endoscopic Surgeries and responsible and sustainable petroleum extraction employing automated Petrography. I've also participated in two datasets creation process', one for Endoscopic Surgeries and the Ego4D dataset lead by META Research!

Aditionally, I was a Visiting Graduate Scholar at the Advanced Robotics and Computationally Augmented Environments (ARCADE) research group, led by Prof. Mathias Unberath Ph.D. at Johns Hopkins University from January 2022 to October 2022.

Under the supervision of Prof. Pablo Arbeláez and Prof. Juan Carlos Cruz, my master’s thesis focused on finding antimicrobial and translocator peptides to overcome microbial resistance. This research aimed to merge deep learning with molecular dynamics simulations and in-vitro validation of in-silico results.

Besides research, I love reading science fiction books and manual activities such as painting and bullet journaling.

Machine Learning Publications

Pupillometry in telerobotic surgery: A comparative evaluation of algorithms for cognitive effort estimation

Paola Ruiz Puentes, Roger D Soberanis-Mukul, Ayberk Acar, Iris Gupta, Joyraj Bhowmick1, Yizhou Li, Ahmed Ghazi, Peter Kazanzides, Jie Ying Wu, Mathias Unberath.
Medical Robotics, 2023
PDF

Estimation and prediction of the air–water interfacial tension in conventional and peptide surface-active agents by random Forest regression

Fabián Ricardo, Paola Ruiz Puentes, Luis H Reyes, Juan C Cruz, Oscar Alvarez, Diego Pradilla.
Chemical Engineering Science, 2023
PDF

Towards holistic surgical scene understanding

Natalia Valderrama, Paola Ruiz Puentes, Isabela Hernández, Nicolás Ayobi, Mathilde Verlyck, Jessica Santander, Juan Caicedo, Nicolás Fernández, Pablo Arbeláez.
MICCAI, 2022
PDF

Rational Discovery of Antimicrobial Peptides by Means of Artificial Intelligence

Paola Ruiz Puentes, Maria C Henao, Javier Cifuentes, Carolina Muñoz-Camargo, Luis H Reyes, Juan C Cruz, Pablo Arbeláez.
Membranes MDPI, 2022
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Predicting target–ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery

Paola Ruiz Puentes*, Laura Rueda-Gensini*, Natalia Valderrama*, Isabela Hernández, Cristina González, Laura Daza, Carolina Muñoz-Camargo, Juan C Cruz, Pablo Arbeláez.
Scientific Reports, 2022
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Ego4d: Around the world in 3,000 hours of egocentric video

Kristen Grauman, ...., Paola Ruiz Puentes, ...., Jitendra Malik. 84 Authors
Conference on Computer Vision and Pattern Recognition (CVPR), 2022
PDF | Project Page

PharmaNet: Pharmaceutical discovery with deep recurrent neural networks

Paola Ruiz Puentes*, Natalia Valderrama*, Cristina González, Laura Daza, Carolina Muñoz-Camargo, Juan C Cruz, Pablo Arbeláez.
PLOS ONE, 2021
PDF | Project Page | Code

Design, screening, and testing of non-rational peptide libraries with antimicrobial activity: In silico and experimental approaches

Paola Ruiz Puentes*, María C Henao, Carlos E Torres, Saúl C Gómez, Laura A Gómez, Juan C Burgos, Pablo Arbeláez, Johann F Osma, Carolina Muñoz-Camargo, Luis H Reyes, Juan C Cruz.
Antibiotics MDPI, 2020
PDF

Pharmaceutical Delivery Publications

Multifunctional magnetoliposomes as drug delivery vehicles for the potential treatment of Parkinson’s disease

Javier Cifuentes, Santiago Cifuentes-Almanza, Paola Ruiz Puentes, Valentina Quezada, Andrés Fernando González Barrios, María-Angélica Calderón-Peláez, Myriam Lucia Velandia-Romero, Marjan Rafat, Carolina Muñoz-Camargo, Sonia L Albarracín, Juan C Cruz.
Frontiers in Bioengineering and Biotechnology, 2023
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Tailoring Magnetite-Nanoparticle-Based Nanocarriers for Gene Delivery: Exploiting CRISPRa Potential in Reducing Conditions

David Arango, Javier Cifuentes, Paola Ruiz Puentes, Tatiana Beltran, Amaury Bittar, Camila Ocasión, Carolina Muñoz-Camargo, Natasha I Bloch, Luis H Reyes, Juan C Cruz.
Nanomaterials MDPI, 2023
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Unlocking cellular barriers: silica nanoparticles and fullerenol conjugated cell-penetrating agents for enhanced intracellular drug delivery

Eduardo Ravelo-Nieto, Javier Cifuentes, Paola Ruiz Puentes, Laura Rueda-Gensini, Valentina Quezada, Carlos Ostos, Carolina Muñoz-Camargo, Luis H Reyes, Alvaro Duarte-Ruiz, Juan C Cruz.
Frontiers in Bioengineering and Biotechnology, 2023
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Microfluidic synthesis and purification of magnetoliposomes for potential applications in the gastrointestinal delivery of difficult-to-transport drugs

Carlos E Torres, Javier Cifuentes, Saúl C Gómez, Valentina Quezada, Kevin A Giraldo, Paola Ruiz Puentes, Laura Rueda-Gensini, Julian A Serna, Carolina Muñoz-Camargo, Luis H Reyes, Johann F Osma, Juan C Cruz.
Pharmaceutics MDPI, 2022
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Translocating peptides of biomedical interest obtained from the spike (S) glycoprotein of the SARS-CoV-2

Maria C Henao, Camila Ocasion, Paola Ruiz Puentes, Cristina González-Melo, Valentina Quezada, Javier Cifuentes, Arnovis Yepes, Juan C Burgos, Juan C Cruz, Luis H Reyes.
Membranes MDPI, 2022
PDF

Microfluidic synthesis and purification of magnetoliposomes for potential applications in the gastrointestinal delivery of difficult-to-transport drugs

Carlos E Torres, Javier Cifuentes, Saúl C Gómez, Valentina Quezada, Kevin A Giraldo, Paola Ruiz Puentes, Laura Rueda-Gensini, Julian A Serna, Carolina Muñoz-Camargo, Luis H Reyes, Johann F Osma, Juan C Cruz.
Pharmaceutics MDPI, 2022
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Assessing cellular internalization and endosomal escape abilities of novel BUFII-Graphene oxide nanobioconjugates

Julian Daniel Torres-Vanegas, Javier Cifuentes, Paola Ruiz Puentes, Valentina Quezada, Andres J Garcia-Brand, Juan C Cruz, Luis H Reyes.
Frontiers in Chemistry, 2022
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Buforin II-Escherichia coli's DNA interactome: Detailed biophysical characterization revealed nanoscale complexes likely formed by DNA supercoiling

Daniela Rubio-Olaya, Javier Cifuentes, Paola Ruiz Puentes, Octavio A Castañeda, Luis H Reyes, Jorge Duitama, Carolina Muñoz, Juan C Cruz.
bioRxiv, 2022
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Tailoring Iron Oxide Nanoparticles for Efficient Cellular Internalization and Endosomal Escape

Laura Rueda-Gensini, Javier Cifuentes, Maria Claudia Castellanos, Paola Ruiz Puentes, Julian A Serna, Carolina Muñoz-Camargo, Juan C Cruz.
Nanomaterials, 2020
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Enzyme-based electrochemical biosensors for microfluidic platforms to detect pharmaceutical residues in wastewater

Ana Lucia Campaña, Sergio Leonardo Florez, Mabel Juliana Noguera, Olga P Fuentes, Paola Ruiz Puentes, Juan C Cruz, Johann F Osma.
Biosensors, 2019
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Awards

Cum Laude

Universidad de los Andes, 2022

It is granted to those students whose accumulated GPA is in the top 5% of the GPAs of the graduates of their faculty for the past five years. Universidad de los Andes.

Activity Recognition Winners at the MISAW Challenge 2020

MISAW Challenge, MICCAI 2020

Integrant of Team Uniandes. We won first place in the activity recognition task at the MIcro-Surgical Anastomose Workflow recognition on training sessions Challenge part of MICCAI 2020

Magna Cum Laude

Universidad de los Andes, 2019

It is granted to those students whose accumulated GPA is in the top 1% of the GPAs of the graduates of their faculty for the past five years. Universidad de los Andes.

La noche de los mejores

Ministerio de Educación, Colombia, 2019

It is granted to those students with the best scores in the graduate national exam.

Best semester GPA

Universidad de los Andes, 2019

Best semester GPA of the Biomedical Engineering Department.

Best semester GPA

Universidad de los Andes, 2018

Best semester GPA of the Biomedical Engineering Department.

Work Experience

2023

Researcher

Center for Research and Formation in Artificial Intelligence, Universidad de los Andes

2022

Graduate Research Visting Student

Advanced Robotics and Computationally AugmenteD Environments Lab, Johns Hopkins University

2020 - 2022

Graduate Research Assistant

Center for Research and Formation in Artificial Intelligence, Universidad de los Andes

2018 - 2021

Undergraduate and Graduate Research Assistant

Research Group in Nanobiomaterials, Cellular Engineering, and Bioprinting, Biomedical Engineering Department, Universidad de los Andes

Education

2020 - 2022

M.Sc. in Biomedical Engineering

Universidad de los Andes

Bogotá, Colombia

Main focus in Machine Learning.

2015 - 2019

B.Sc. in Biomedical Engineering

Universidad de los Andes

Bogotá, Colombia

2018 - 2019

Engineering Leadership Program – Based on Gordon-MIT Engineering Leadership Program

Senior Leader

Universidad de los Andes

Bogotá, Colombia

Contact

Address
Cra. 1 E No. 19A - 40
Universidad de Los Andes
Bogotá, Colombia
Email
paola.ruizp96@gmail.com