Analysis of Functional Interactions of Enzymes in Mycoplasma pneumoniae. - Adriana Neves dos Reis; Cláudia K. Barcellos; Fabiana Herédia; Jean J. Schmith; José C. M. Mombach; Ney Lemke; Rejane A. Ferreira (WOB, 2002)

A Method to Identify Essential Enzymes in the Metabolism: Application to Escherichia Coli. - Ney Lemke; Fabiana Herédia; Cláudia K. Barcellos; José C. M. Mombach (CMSB, 2003)

An Integrated Model for Cellular Analysis. - Eduardo Battistella; José Souza; Cláudia K. Barcellos; Ney Lemke; José C. M. Mombach (WOB, 2004)

Essentiality and damage in metabolic networks. - Ney Lemke; Fabiana Herédia; Cláudia K. Barcellos; Adriana Neves dos Reis; José C. M. Mombach (Bioinform., 2004)

Modeling and Property Verification of Lactose Operon Regulation. - Marcelo Cezar Pinto; Luciana Foss; José C. M. Mombach; Leila Ribeiro 001 (BSB, 2005)

An Efficient Parallel Algorithm to Evolve Simulations of the Cellular Potts Model. - Éder Gusatto; José C. M. Mombach; Fernando Piccini Cercato; Gerson G. H. Cavalheiro (Parallel Process. Lett., 2005)

High Performance Simulations of the Cellular Potts Model. - Fernando Piccini Cercato; José C. M. Mombach; Gerson G. H. Cavalheiro (HPCS, 2006)

Computer simulation of the influence of cellular adhesion on the morphology of the interface between tissues of proliferating and quiescent cells. - Marcos A. Knewitz; José C. M. Mombach (Comput. Biol. Medicine, 2006)

Bioinformatics analysis of mycoplasma metabolism: Important enzymes, metabolic similarities, and redundancy. - José C. M. Mombach; Ney Lemke; Norma M. da Silva; Rejane A. Ferreira; Eduardo Isaia; Cláudia K. Barcellos (Comput. Biol. Medicine, 2006)

Modelling, property verification and behavioural equivalence of lactose operon regulation. - Marcelo Cezar Pinto; Luciana Foss; José Carlos Merino Mombach; Leila Ribeiro 001 (Comput. Biol. Medicine, 2007)

An Ontology to Integrate Transcriptomics and Interatomics Data Involved in Gene Pathways of Genome Stability. - Giovani Rubert Librelotto; José Carlos Merino Mombach; Marialva Sinigaglia; Éder Simão; Heleno Borges Cabral; Mauro A. A. Castro (BSB, 2009)

ViaComplex: software for landscape analysis of gene expression networks in genomic context. - Mauro A. A. Castro; José L. Rybarczyk Filho; Rodrigo J. S. Dalmolin; Marialva Sinigaglia; José C. F. Moreira; José C. M. Mombach; Rita M. C. de Almeida (Bioinform., 2009)

The R implementation of the CRAN package PATHChange, a tool to study genetic pathway alterations in transcriptomic data. - Carla A. R. S. Fontoura; Gastone C. Castellani; José C. M. Mombach (Comput. Biol. Medicine, 2016)

Towards the contribution of the p38MAPK pathway to the dual role of TGFβ in cancer: A boolean model approach. - Veronica V. Rossato; Daner Acunha Silveira; Shantanu Gupta; José Carlos Merino Mombach (Comput. Biol. Medicine, 2019)

The Wnt pathway can stabilize hybrid phenotypes in the epithelial-mesenchymal transition: A logical modeling approach. - Daner Acunha Silveira; Shantanu Gupta; Marialva Sinigaglia; José Carlos Merino Mombach (Comput. Biol. Chem., 2022)

A differentiable programming framework for spin models. - Tiago de Souza Farias; Vitor Vaz Schultz; José C. M. Mombach; Jonas Maziero (Comput. Phys. Commun., 2024)

Hypoxia-driven hybrid phenotypes in Ewing sarcoma: Insights from computational epithelial-mesenchymal transition modeling. - Daner Acunha Silveira; Shantanu Gupta; André T. Brunetto; José Carlos Merino Mombach; Marialva Sinigaglia (J. Comput. Sci., 2024)

PTEN expression can be used as a switch between senescence and apoptosis in breast cancer cells according to a logical model of the G2/M checkpoint. - Yolanda M. B. Marcello; Daner Acunha Silveira; Shantanu Gupta; José Carlos Merino Mombach (Biosyst., 2024)