J. C. Mombach

发表

Network integration of multi-tumour omics data suggests novel targeting strategies

Giulia Menichetti, Gastone Castellani, Daniel Remondini, 2017, bioRxiv.

Modeling the role of microRNA-449a in the regulation of the G2/M cell cycle checkpoint in prostate LNCaP cells under ionizing radiation

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2018, PloS one.

Systems biology approach suggests new miRNAs as phenotypic stability factors in the epithelial–mesenchymal transition

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2020, Journal of the Royal Society Interface.

Bioinformatics analysis of mycoplasma metabolism: Important enzymes, metabolic similarities, and redundancy

Ney Lemke, Cláudia K. Barcellos, José C. M. Mombach, 2006, Comput. Biol. Medicine.

Analysis of expression pathways alterations of Arabidopsis thaliana induced by a Necrosis- and Ethylene-inducing protein

G. Pereira, J. C. Mombach, S. Echeverrigaray, 2009 .

Evolutionary origins of human apoptosis and genome-stability gene networks

J. C. Mombach, José C. F. Moreira, R. D. de Almeida, 2008, Nucleic acids research.

The Wnt pathway can stabilize hybrid phenotypes in the epithelial-mesenchymal transition: A logical modeling approach

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2022, Comput. Biol. Chem..

Dynamics of the feedback loops required for the phenotypic stabilization in the epithelial‐mesenchymal transition

J. C. Mombach, D. A. Silveira, 2020, The FEBS journal.

p53/E2F1/miR-25 axis regulates apoptosis induction in glioblastoma cells: a qualitative model

J. C. Mombach, D. A. Silveira, S. Gupta, 2020, Journal of Physics: Complexity.

A simple stochastic model for the feedback circuit between p16INK4a and p53 mediated by p38MAPK: implications for senescence and apoptosis.

G. Castellani, J. C. Mombach, L. D. de Oliveira, 2015, Molecular bioSystems.

Integrative data modeling from lung and lymphatic cancer predicts functional roles for miR-34a and miR-16 in cell fate regulation

F. Barbé-Tuana, J. C. Mombach, Shantanu Gupta, 2020, Scientific Reports.

Towards DNA-damage induced autophagy: A Boolean model of p53-induced cell fate mechanisms.

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2020, DNA repair.

Induced genome maintenance pathways in pre-cancer tissues describe an anti-cancer barrier in tumor development.

G. Librelotto, J. C. Mombach, Ronnie Alves, 2012, Molecular bioSystems.

ERRATUM: A mean-field theory of cellular growth

Marco Idiart, Ney Lemke, Marco Idiart, 2002 .

ViaComplex: software for landscape analysis of gene expression networks in genomic context

Mauro A. A. Castro, Marialva Sinigaglia, José L. Rybarczyk Filho, 2009, Bioinform..

A Boolean Model of the Proliferative Role of the lncRNA XIST in Non-Small Cell Lung Cancer Cells

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2022, Biology.

Modeling the Human Genome Maintenance network

G. Librelotto, J. C. Mombach, M. Sinigaglia, 2010 .

On the absence of mutations in nucleotide excision repair genes in sporadic solid tumors.

J. C. Mombach, José C. F. Moreira, M. A. Castro, 2008, Genetics and molecular research : GMR.

Impaired expression of NER gene network in sporadic solid tumors

José C. M. Mombach, J. C. Mombach, Mauro A. A. Castro, 2007, Nucleic acids research.

Integrative data modeling from lung and lymphatic cancer predicts functional roles for miR-34a and miR-16 in cell fate regulation

F. Barbé-Tuana, J. C. Mombach, Shantanu Gupta, 2020, Scientific Reports.

ATM/miR‐34a‐5p axis regulates a p21‐dependent senescence‐apoptosis switch in non‐small cell lung cancer: a Boolean model of G1/S checkpoint regulation

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2019, FEBS letters.

Modelling, property verification and behavioural equivalence of lactose operon regulation

Leila Ribeiro, Luciana Foss, Marcelo Cezar Pinto, 2007, Comput. Biol. Medicine.

Modeling and Property Verification of Lactose Operon Regulation

Leila Ribeiro, Luciana Foss, José C. M. Mombach, 2005, BSB.

Towards the contribution of the p38MAPK pathway to the dual role of TGFβ in cancer: A boolean model approach

Shantanu Gupta, José C. M. Mombach, Veronica V. Rossato, 2019, Comput. Biol. Medicine.

MicroRNA-16 feedback loop with p53 and Wip1 can regulate cell fate determination between apoptosis and senescence in DNA damage response

J. C. Mombach, Maria Vitória C Issler, José Carlos M Mombach, 2017, PloS one.

In silico network topology-based prediction of gene essentiality

Renata Vieira, Ney Lemke, Marialva Sinigaglia, 2007, 0709.4206.

A Method to Identify Essential Enzymes in the Metabolism: Application to Escherichia Coli

Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos, 2003, CMSB.

Essentiality and damage in metabolic networks

Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos, 2004, Bioinform..

A mean-field theory of cellular growth

Ney Lemke, Marco Idiart, José C. M. Mombach, 2002 .

The lncRNA DLX6-AS1/miR-16-5p axis regulates autophagy and apoptosis in non-small cell lung cancer: A Boolean model of cell death

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2023, Non-coding RNA research.

Damage, connectivity and essentiality in protein–protein interaction networks

Ney Lemke, Guilherme Balestieri Bedin, Jean Schmith, 2005 .

PseudoCell: A collaborative network for in silico prediction of regulatory pathways

Patrícia Lavandoski, F. Barbé-Tuana, J. C. Mombach, 2023 .

Exploring molecular networks using MONET ontology.

Renata Vieira, João Paulo Müller da Silva, Ney Lemke, 2006, Genetics and molecular research : GMR.

An Integrated Model for Cellular Analysis

Ney Lemke, Cláudia K. Barcellos, José C. M. Mombach, 2005, WOB.

Using Protégé to build a Molecular Network Ontology

José G. C. de Souza, N. Lemke, J. C. Mombach, 2005 .

PseudoCell: A Multi-Valued Logical Regulatory Network to Investigate Premature Senescence Dynamics and Heterogeneity

Patrícia Lavandoski, F. Barbé-Tuana, J. C. Mombach, 2024, bioRxiv.

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

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2023, Biosyst..

A logical model of Ewing sarcoma cell epithelial‐to‐mesenchymal transition supports the existence of hybrid cellular phenotypes

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2023, FEBS Letters.

A dynamic Boolean network reveals that the BMI1 and MALAT1 axis is associated with drug resistance by limiting miR-145-5p in non-small cell lung cancer

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2023, Non-coding RNA research.

Hypoxia-driven hybrid phenotypes in Ewing sarcoma: Insights from computational epithelial-mesenchymal transition modeling

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2024, Journal of Computational Science.

LncRNA PTENP1/miR-21/PTEN Axis Modulates EMT and Drug Resistance in Cancer: Dynamic Boolean Modeling for Cell Fates in DNA Damage Response

J. C. Mombach, Shantanu Gupta, D. A. Silveira, 2024, International journal of molecular sciences.