A Framework for Run-Time Systems and its Visual Programming Language. - Alan M. Durham; Ralph E. Johnson (OOPSLA, 1996)

Implementing Run-Time Systems in a Compiler - Alan Mitchell Durham (1997)

A system to implement primitive data types. - Alan M. Durham; Ralph E. Johnson (J. Braz. Comput. Soc., 1999)

A framework for building language interpreters. - Alan M. Durham; Edson Sussumu; Arlindo Flávio da Conceição (OOPSLA Companion, 2003)

EGene: a configurable pipeline generation system for automated sequence analysis. - Alan M. Durham; André Yoshiaki Kashiwabara; Fernando T. G. Matsunaga; Paulo H. Ahagon; Flávia Rainone; Leonardo Varuzza; Arthur Gruber (Bioinform., 2005)

TRAP: automated classification, quantification and annotation of tandemly repeated sequences. - Tiago José P. Sobreira; Alan M. Durham; Arthur Gruber (Bioinform., 2006)

The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria. - Luiz Thibério Rangel; Jeniffer Novaes; Alan M. Durham; Alda Maria B. N. Madeira; Arthur Gruber (Database J. Biol. Databases Curation, 2013)

ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data. - André Yoshiaki Kashiwabara; Ígor Bonadio; Vitor Onuchic; Felipe Amado; Rafael Mathias; Alan Mitchell Durham (PLoS Comput. Biol., 2013)

CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts. - Pedro G. Nachtigall; André Y. Kashiwabara; Alan M. Durham (Briefings Bioinform., 2021)

TSSFinder - fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. - Mauro de Medeiros Oliveira; Ígor Bonadio; Alicia Lie de Melo; Glaucia Mendes Souza; Alan Mitchell Durham (Briefings Bioinform., 2021)

Combined Learning of Neural Network Weights for Privacy in Collaborative Tasks. - Aline R. Ioste; Alan M. Durham; Marcelo Finger (CoRR, 2022)