About Me

I am a computer scientist with leading research interests in Deep Learning applied to Computational Biology and Bioinformatics.

I am an Assistant Professor at the Department of Informatics Engineering, University of Coimbra and a researcher at CISUC. I hold a PhD in Computer Science from University of Aveiro (2010).

Highlights
In the news!

Our work was promoted by the main Portuguese media, such as Jornal Público, Jornal Observador and Jornal Expresso.

Double conference award!

The Pharmacogenetic Anticancer Drug Response model, received a Best Paper award at CBMS2022 and Best Poster award at ESCI 2022

Organization of LPB2022

LPB2022 is the 1st edition of the Portuguese Competition of Bioinformatics.

22 teams on the race!

Research interests
Drug–target prediction

Deep Learning models for predition of Drug-Protein interations.

Drug Generative models

Language models for de novo generation of SMILES of molecules with desired properties.

Genetic variants analysis

Analysis of genetic variants to find those associated with a specific trait or disease.

Pharmacogenomics

Computational models of how genetic profiles influences the effect of drugs.

Featured Publications

Deep Generative Model for Therapeutic Targets using Transcriptomic Disease- Associated Data - USP7 case study

Briefings in Bioinformatics (IF:13.99)

DTITR: End-to-end drug–target binding affinity prediction with transformers

Computers in Biology and Medicine (IF:6.69)

Designing Optimized Drug Candidates With Generative Adversarial Network

Journal of Cheminformatics (IF:8.48)

Optimizing blood–brain barrier permeation through deep reinforcement learning for de novo drug design

Oxford Bioinformatics (IF:6.93)
Complete and updated list of Publications

Google Scholar

Team

Invited Adjunt Professor
ISEC, Polytechnic Institute of Coimbra (IPC)        

Maryam Abbasi

PhD student
Semi-Supervised and Interpretable Deep Learning Architectures to Predict Drug- Target Binding Affinity.

Nelson Monteiro

PhD student
Reinforcement Learning for biased de novo Drug Discovery

Tiago Pereira

PhD student
Deep Learning Architectures for Optimal Analysis of Type 2 Diabetes Heritability

Daniel Martins

PhD student
Few-Shot Deep Learning Architectures for Drug Discovery

Luis Torres

PhD student
Application of a Computational Biomarker-based Model to Predict Conversion to Alzheimer’s Disease

Anuschka da Silva Spínola

PhD student
A Clinical Decision Support System for Amyotrophic Lateral Sclerosis Prognosis

Fabiano Papaiz
Students:

- Gonçalo Coelho, Master's in Data Science and Engineering, UC
- Elmer Carlos, Master in Computational Biology, UC
- Pedro Quesado, Master in Data Science and Engineering, UC
- Raul Sofia, Informatics Engineering, UC
- Paulo Correia, Biochemistry Degree, UC
                                                                

Former PhD Students:

- Edgar Coelho, former PhD student, Lead Data Scientist at MarketerHire
- Fernanda Correia, former PhD student, Adjunt Professor at ISEP, IPC
- António Cruz, former PhD student, Researcher at CISUC, UC
                                                                

Interested in joining?