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)

MYOP/ToPS/SGEval: A computational framework for gene prediction. - André Yoshiaki Kashiwabara (2012)

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)

Feature extraction from complex networks: A case of study in genomic sequences classification. - Bruno Mendes Moro Conque; André Yoshiaki Kashiwabara; Fabrício Martins Lopes (CoRR, 2014)

Aplicação da otimização por colônia de formigas ao problema de múltiplos caixeiros viajantes no atendimento de ordens de serviço nas empresas de distribuição de energia elétrica [Applying a variation of the ant colony optimization algorithm to solve the multiple traveling salesmen problem to route the teams of the electric power distribution companies]. - Denilson Fagundes Barbosa; Carlos N. Silla; André Y. Kashiwabara (SBSI, 2015)

Adicionando informações estruturadas ao Bulário Eletrônico da ANVISA [Adding structured information to the ANVISA's "Bulario Eletronico"]. - Joao Vitor F. da Silva; Carlos N. Silla; André Y. Kashiwabara (SBSI, 2015)

Aplicação do Rank-Based Ant System ao problema de múltiplos caixeiros viajantes no atendimento de ordens de serviço nas empresas de distribuição de energia elétrica. - Denilson Fagundes Barbosa; Carlos Nascimento Silla Jr.; André Yoshiaki Kashiwabara (Braz. J. Inf. Syst., 2015)

A feature extraction approach based on complex networks for genomic sequences recognition. - Bruno Mendes Moro Conque; André Yoshiaki Kashiwabara; Fabrício Martins Lopes (CISP-BMEI, 2016)

Discovery Biological Motifs Using Heuristics Approaches. - Jader M. Caldonazzo Garbelini; André Yoshiaki Kashiwabara; Danilo Sipoli Sanches (BRACIS, 2016)

Discovery Motifs by Evolutionary Computation. - Jader C. Garbelini; André Yoshiaki Kashiwabara; Danilo Sipoli Sanches (GECCO (Companion), 2016)

Sequence motif finder using memetic algorithm. - Jader M. Caldonazzo Garbelini; André Yoshiaki Kashiwabara; Danilo Sipoli Sanches (BMC Bioinform., 2018)

A Probabilistic Algorithm to Estimate the Spectral Moments of Large Undirected Weighted Graphs. - Gustavo Dias; André Yoshiaki Kashiwabara (BRACIS, 2019)

A Novel Decomposing Model With Evolutionary Algorithms for Feature Selection in Long Non-Coding RNAs. - Robson Parmezan Bonidia; Jaqueline Sayuri Machida; Tatianne da Costa Negri; Wonder Alexandre Luz Alves; André Y. Kashiwabara; Douglas Silva Domingues; André C. P. L. F. de Carvalho; Alexandre Rossi Paschoal; Danilo Sipoli Sanches (IEEE Access, 2020)

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

circTIS: A Weighted Degree String Kernel with Support Vector Machine Tool for Translation Initiation Sites Prediction in circRNA. - Denilson Fagundes Barbosa; Liliane Santana Oliveira; André Yoshiaki Kashiwabara (BSB, 2023)

SMT: A High-Performance Approach for Counting Kmers. - Jader M. Caldonazzo Garbelini; Danilo Sipoli Sanches; André Yoshiaki Kashiwabara; Aurora T. R. Pozo (BIOSTEC (1), 2024)

Identification of SNPs in genomes using GRAMEP, an alignment-free method based on the Principle of Maximum Entropy. - Matheus Henrique Pimenta-Zanon; André Yoshiaki Kashiwabara; André Luís Laforga Vanzela; Fabrício Martins Lopes (CoRR, 2024)

GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs. - Matheus Henrique Pimenta-Zanon; André Yoshiaki Kashiwabara; André Luís Laforga Vanzela; Fabrício Martins Lopes (BMC Bioinform., 2025)