A Campaign-based Characterization of Spamming Strategies. - Pedro H. Calais; Douglas E. V. Pires; Dorgival Olavo Guedes Neto; Wagner Meira Jr.; Cristine Hoepers; Klaus Steding-Jessen (CEAS, 2008)

FPCluster: Uma estratégia eficiente de agrupamento out-of-core sem medida de similaridade. - Douglas E. V. Pires; Luam C. Totti; Rubens E. A. Moreira; Elverton C. Fazzion; Osvaldo L. H. M. Fonseca; Wagner Meira Jr.; Raquel Cardoso de Melo Minardi; Dorgival O. Guedes (SBBD (Short Papers), 2011)

HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids. - Valdete M. Gonçalves-Almeida; Douglas E. V. Pires; Raquel Cardoso de Melo Minardi; Carlos Henrique da Silveira; Wagner Meira Jr.; Marcelo M. Santoro (Bioinform., 2012)

FPCluster: An Efficient Out-of-core Clustering Strategy without a Similarity Metric. - Douglas E. V. Pires; Luam C. Totti; Rubens E. A. Moreira; Elverton C. Fazzion; Osvaldo L. H. M. Fonseca; Wagner Meira Jr.; Raquel Cardoso de Melo Minardi; Dorgival Olavo Guedes Neto (J. Inf. Data Manag., 2012)

aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction. - Douglas E. V. Pires; Raquel Cardoso de Melo Minardi; Carlos Henrique da Silveira; Frederico F. Campos; Wagner Meira Jr. (Bioinform., 2013)

mCSM: predicting the effects of mutations in proteins using graph-based signatures. - Douglas E. V. Pires; David B. Ascher; Tom L. Blundell (Bioinform., 2014)

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. - Douglas E. V. Pires; David B. Ascher; Tom L. Blundell (Nucleic Acids Res., 2014)

PDBest: a user-friendly platform for manipulating and enhancing protein structures. - Wellisson R. S. Gonçalves; Valdete M. Gonçalves-Almeida; Aleksander L. Arruda; Wagner Meira Jr.; Carlos Henrique da Silveira; Douglas E. V. Pires; Raquel Cardoso de Melo Minardi (Bioinform., 2015)

Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. - Douglas E. V. Pires; Tom L. Blundell; David B. Ascher (Nucleic Acids Res., 2015)

mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. - Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2016)

CSM-lig: a web server for assessing and comparing protein-small molecule affinities. - Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2016)

GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms. - João P. A. Moraes; Gisele L. Pappa; Douglas E. V. Pires; Sandro C. Izidoro (Nucleic Acids Res., 2017)

mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions. - Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2017)

Kinact: a computational approach for predicting activating missense mutations in protein kinases. - Carlos H. M. Rodrigues; David B. Ascher; Douglas E. V. Pires (Nucleic Acids Res., 2018)

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2018)

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions. - Carlos H. M. Rodrigues; Yoochan Myung; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2019)

mCSM-AB2: guiding rational antibody design using graph-based signatures. - Yoochan Myung; Carlos H. M. Rodrigues; David B. Ascher; Douglas E. V. Pires (Bioinform., 2020)

EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. - Douglas E. V. Pires; Wandré N. P. Veloso; Yoochan Myung; Carlos H. M. Rodrigues; Michael Silk; Pâmela M. Rezende; Francislon Silva; Joicymara S. Xavier; João P. L. Velloso; Carlos Henrique da Silveira; David B. Ascher (Bioinform., 2020)

mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. - Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2020)

mmCSM-AB: guiding rational antibody engineering through multiple point mutations. - Yoochan Myung; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2020)

mCSM-membrane: predicting the effects of mutations on transmembrane proteins. - Douglas E. V. Pires; Carlos H. M. Rodrigues; David B. Ascher (Nucleic Acids Res., 2020)

Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis. - Edward Airey; Stephanie Portelli; Joicymara S. Xavier; Yoochan Myung; Michael Silk; Malancha Karmakar; João P. L. Velloso; Carlos H. M. Rodrigues; Hardik H. Parate; Anjali Garg; Raghad Al-Jarf; Lucy Barr; et al. (Artificial Neural Networks, 3rd Edition, 2021)

A comparative analysis of sepsis digital phenotyping methods. - Anna Fedyukova; Douglas Pires; Daniel Capurro (ACSW, 2021)

Quantifying machine learning-induced overdiagnosis in sepsis. - Anna Fedyukova; Douglas Pires; Daniel Capurro (CoRR, 2021)

pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties. - Raghad Al-Jarf; Alex G. C. de Sá; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2021)

pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2021)

mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. - Carlos H. M. Rodrigues; Douglas E. V. Pires; David B. Ascher (Nucleic Acids Res., 2021)

MTR3D: identifying regions within protein tertiary structures under purifying selection. - Michael Silk; Douglas E. V. Pires; Carlos H. M. Rodrigues; Elston N. D'souza; Moshe Olshansky; Natalie Thorne; David B. Ascher (Nucleic Acids Res., 2021)

ThermoMutDB: a thermodynamic database for missense mutations. - Joicymara S. Xavier; Thanh-Binh Nguyen 007; Malancha Karmarkar; Stephanie Portelli; Pâmela M. Rezende; João P. L. Velloso; David B. Ascher; Douglas E. V. Pires (Nucleic Acids Res., 2021)

CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. - Thanh-Binh Nguyen 007; Douglas E. V. Pires; David B. Ascher (Briefings Bioinform., 2022)

GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms. - Vinícius de Almeida Paiva; Murillo Ventura Mendonça; Sabrina de Azevedo Silveira; David B. Ascher; Douglas E. V. Pires; Sandro C. Izidoro (Briefings Bioinform., 2022)

Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. - Qisheng Pan; Thanh-Binh Nguyen 007; David B. Ascher; Douglas E. V. Pires (Briefings Bioinform., 2022)

cropCSM: designing safe and potent herbicides with graph-based signatures. - Douglas E. V. Pires; Keith A. Stubbs; Joshua S. Mylne; David B. Ascher (Briefings Bioinform., 2022)

Evaluating hierarchical machine learning approaches to classify biological databases. - Pâmela M. Rezende; Joicymara S. Xavier; David B. Ascher; Gabriel R. Fernandes; Douglas E. V. Pires (Briefings Bioinform., 2022)

Structural landscapes of PPI interfaces. - Carlos H. M. Rodrigues; Douglas E. V. Pires; Tom L. Blundell; David B. Ascher (Briefings Bioinform., 2022)

toxCSM: comprehensive prediction of small molecule toxicity profiles. - Alex G. C. de Sá; Yangyang Long; Stephanie Portelli; Douglas E. V. Pires; David B. Ascher (Briefings Bioinform., 2022)

epitope3D: a machine learning method for conformational B-cell epitope prediction. - Bruna Moreira da Silva; Yoochan Myung; David B. Ascher; Douglas E. V. Pires (Briefings Bioinform., 2022)

CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function. - Yoochan Myung; Douglas E. V. Pires; David B. Ascher (Bioinform., 2022)

Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. - Aparna Elangovan; Yuan Li 012; Douglas E. V. Pires; Melissa J. Davis; Karin Verspoor (BMC Bioinform., 2022)

cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules. - Saba Iftkhar; Alex G. C. de Sá; João P. L. Velloso; Raghad Al-Jarf; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2022)

GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. - Charles Abreu Santana; Sandro C. Izidoro; Raquel Cardoso de Melo Minardi; Jonathan D. Tyzack; António J. M. Ribeiro; Douglas E. V. Pires; Janet M. Thornton; Sabrina de Azevedo Silveira (Nucleic Acids Res., 2022)

Designing an Interprofessional Online Course to Foster Learning Health Systems. - Sathana Dushyanthen; Dawn Choo; Meg Perrier; Kathleen Gray; Daniel Capurro; Douglas Pires; Brian E. Chapman; Graeme K. Hart; Kit Huckvale; Wendy W. Chapman; Kayley M. Lyons (MedInfo, 2023)

Adapting Pretrained Language Models for Solving Tabular Prediction Problems in the Electronic Health Record. - Christopher McMaster; David F. L. Liew; Douglas E. V. Pires (CoRR, 2023)

AI driven B-cell Immunotherapy Design. - Bruna Moreira da Silva; David B. Ascher; Nicholas Geard; Douglas E. V. Pires (CoRR, 2023)

Explainable Machine Learning for ICU Readmission Prediction. - Alex G. C. de Sá; Daniel Gould; Anna Fedyukova; Mitchell Nicholas; Lucy Dockrell; Calvin Fletcher; David Pilcher; Daniel Capurro; David B. Ascher; Khaled El-Khawas; Douglas E. V. Pires (CoRR, 2023)

Automating reward function configuration for drug design. - Marius Urbonas; Temitope Ajileye; Paul Gainer; Douglas Pires (CoRR, 2023)

Developing a deep learning natural language processing algorithm for automated reporting of adverse drug reactions. - Christopher McMaster; Julia Chan; David F. L. Liew; Elizabeth Su; Albert G. Frauman; Wendy W. Chapman; Douglas E. V. Pires (J. Biomed. Informatics, 2023)

embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. - Raghad Al-Jarf; Simon Tang; Douglas E. V. Pires; David B. Ascher (J. Chem. Inf. Model., 2023)

epitope1D: accurate taxonomy-aware B-cell linear epitope prediction. - Bruna Moreira da Silva; David B. Ascher; Douglas E. V. Pires (Briefings Bioinform., 2023)

DDMut: predicting effects of mutations on protein stability using deep learning. - Yunzhuo Zhou; Qisheng Pan; Douglas E. V. Pires; Carlos H. M. Rodrigues; David B. Ascher (Nucleic Acids Res., 2023)

Data-driven overdiagnosis definitions: A scoping review. - Prabodi Senevirathna; Douglas E. V. Pires; Daniel Capurro (J. Biomed. Informatics, 2023)

Clinical Translation of a Heparin-Induced Thrombocytopenia predictor for Intensive Care Patients. - Prabodi Senevirathna; Douglas Pires; Daniel Capurro (ACSW, 2024)

Large scale paired antibody language models. - Henry Kenlay; Frédéric A. Dreyer; Aleksandr Kovaltsuk; Dom Miketa; Douglas Pires; Charlotte M. Deane (PLoS Comput. Biol., 2024)

piscesCSM: prediction of anticancer synergistic drug combinations. - Raghad Al-Jarf; Carlos H. M. Rodrigues; Yoochan Myung; Douglas E. V. Pires; David B. Ascher (J. Cheminformatics, 2024)

Uncovering digital overdiagnosis - Quantification and mitigation using clinical trajectories: Heparin-induced thrombocytopenia use case. - Prabodi Senevirathna; Douglas E. V. Pires; Daniel Capurro (J. Biomed. Informatics, 2025)