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
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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
PDF
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
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| 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
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| 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
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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
PDF
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
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
PDF
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
PDF
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
PDF
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
PDF
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
PDF
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
Researcher
Center for Research and Formation in Artificial Intelligence, Universidad de los Andes
Graduate Research Visting Student
Advanced Robotics and Computationally AugmenteD Environments Lab, Johns Hopkins University
Graduate Research Assistant
Center for Research and Formation in Artificial Intelligence, Universidad de los Andes
Undergraduate and Graduate Research Assistant
Research Group in Nanobiomaterials, Cellular Engineering, and Bioprinting, Biomedical Engineering Department, Universidad de los Andes
Education
M.Sc. in Biomedical Engineering
Universidad de los Andes
Bogotá, Colombia
Main focus in Machine Learning.
B.Sc. in Biomedical Engineering
Universidad de los Andes
Bogotá, Colombia
Engineering Leadership Program – Based on Gordon-MIT Engineering Leadership Program
Senior Leader
Universidad de los Andes
Bogotá, Colombia
Contact
Cra. 1 E No. 19A - 40
Universidad de Los Andes
Bogotá, Colombia Email
paola.ruizp96@gmail.com