Publications
Publications in cancer and bioinformatics
Castro, M.A.A.; Wang, W; Fletcher, M.N.C; Meyer, K.B.; Markowetz, F. RedeR: bridging the gap between hierarchical network representation and functional analysis. Journal Paper (submitted), 2011.
Dalmolin, R.J.S; Castro, M.A.A.; Rybarczyk-Filho, J.L.; Souza LH; de Almeida, R.M.C; Moreira, J.C.F. Evolutionary plasticity determination by orthologous groups distribution. Biology Direct, v.6, n22, 2011.
PMID: 21586164
Rybarczyk-Filho, J.L.; Castro, M.A.A.; Dalmolin, R.J.S.; Moreira, J.C.F.; Brunnet, L; de Almeida, R.M.C. Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Nucleic Acids Research, v.39, p3005-3016, 2011.
PMID: 21169199
Muller C.B.; de Barros R.L.; Castro, M.A.A.; et al. Validation of cofilin-1 as a biomarker in non-small cell lung cancer: application of quantitative method in a retrospective cohort. J Cancer Res Clin Oncol. , v.137, p1309-1316, 2011.
PMID: 21735353
Castro, M.A.A.; Dal-Pizzol F.; Soares, M.; Müller, C.B.; Lopes, F.; Zanotto-Filho, A.; Meurer, R.; Cruz Fernandes, M.; Zdanov, S.; Moreira, J.C.F.; Shacter, E.; Klamt, F. CFL1 expression levels as a prognostic and drug resistance marker in non-small cell lung cancer. Cancer, v.116, p3645-3655, 2010.
PMID: 20564088
Castro, M.A.A.; Rybarczyk-Filho, J.L.; Dalmolin, R.J.S.; Sinigaglia, M.; Moreira, J.C.F.; Mombach, J.C.M.; de Almeida, R.M.C. ViaComplex: software for landscape analysis of gene expression networks in genomic context. Bioinformatics. v.25, p.1468 – 1469, 2009.
PMID: 19369498
Castro, M.A.A.; Dalmolin, R.J.S.; Moreira, J.C.F.; Mombach, J.C.M.; de Almeida, R.M.C. Evolutionary origins of human apoptosis and genome-stability gene networks. Nucleic Acids Research. v.36, 6269-6283, 2008.
MID: 18832373
Castro, M.A.A.; Mombach, J.C.M.; de Almeida, R.M.C.; Moreira, J.C.F. Impaired expression of NER gene network in sporadic solid tumors. Nucleic Acids Research. v.35, 1859-1867, 2007.
PMID: 17332015
Publications in cancer statistics
Castro, M.A.A.; Onsten, T.G.H.; Moreira, J.C.F.; de Almeida, R.M.C. Chromosome aberrations in solid tumors have a stochastic nature. Mutation Research. v.600, 150-164, 2006.
PMID: 16814328
Castro, M.A.A.; Onsten, T.G.H.; de Almeida, R.M.C.; Moreira, J.C.F. Profiling cytogenetic diversity with entropy-based karyotypic analysis. Journal of Theoretical Biology. v.234, 487-495, 2005.
PMID: 15808870
Castro, M.A.A.; Klamt, F.; Grieneisen, V.A.; Grivicich, I.; Moreira, J.C.F. Gompertzian growth pattern correlated with phenotypic organization of colon carcinoma, malignant glioma and non-small cell lung carcinoma cell lines. Cell Proliferation. v.36, 65-73, 2003.
PMID: 12680874
Publications in cancer, cellular and molecular biology
Gelain, D.P.; Dalmolin, R.J.S.; Belau V.L.; Moreira, J.C.F.; Klant, F.; Castro, M.A.A. A systematic review of human antioxidant genes. Frontiers in Bioscience. v.14, 4457-4463 4457, 2009.
PMID: 19273363
Klant, F.; Castro, M.A.A.; Passos, D.T.; Gelain, D.; Grivicich, I.; Moreira, J.C.F. Inhibition of MDR1 expression by retinol treatment increases sensitivity to etoposide (VP16) in human neoplasic cell line. Toxicology in Vitro. v.22, 873-878, 2008.
PMID: 18282684
Mombach, J.C.M.; Castro, M.A.A.; Moreira, J.C.F., de Almeida, R.M.C. On the absence of mutations in nucleotide excision repair genes in sporadic solid tumors. Genetics and Molecular Research. v.7, 152-160, 2008.
PMID: 18393219
Castro, M.A.A.; Grieneisen, V.A.; de Almeida, R.M.C. Disruption and de novo formation of nanotubular membrane extensions in SW620 colon carcinoma cell line during cell division. Cell Biology International. v.29, 929-931, 2005.
PMID: 1619918
de Oliveira, R.B.; Klamt, F.; Castro, M.A.A.; Polydoro, M.; Zanotto Filho, A.; Gelain, D.; Dal-Pizzol, F.; Moreira, J.C.F. Morphological and oxidative alterations on Sertoli cells cytoskeleton due to retinol-induced reactive oxygen species. Molecular and Cellular Biochemistry.v.271, 189-196, 2005.
PMID: 15881670
Castro, M.A.A.; Moreira, J.C.F. Intercellular contact-dependent survival of human A549, NCI-H596 and NCI-H520 non-small cell lung carcinoma cell lines. Brazilian Journal of Medical and Biological Research.v.34, 1007-1013, 2001.
PMID: 11471039
Castro, M.A.A.; Schwartsmann, G.; Bernard, E.A.; Moreira, J.C.F. Phenotype modulation of cellular UV-sensitivity. Cancer Letters. v.145, 65-72, 1999.
PMID: 10530771
Other publications in bioinformatics and related areas
Simão, E.M. ; Cabral, H.B.; Castro, M.A.A.; Sinigaglia, M.; Mombach, J.C.M. ; Librelotto, G.R. Modeling the human genome maintenance network. Physica. A. p. 4188-4194, 2010. http://dx.doi.org/10.1016/j.physa.2010.05.051
Sinigaglia, M.; Castro, M.A.A.; Pereira, G.A.G.; Echeverrigaray, S.; Mombach, J.C.M. Analysis of expression pathways alterations of Arabidopsis thaliana induced by a Necrosis- and Ethylene-inducing protein. Physica. A, v. 388, p. 4515-4522, 2009.
http://dx.doi.org/10.1016/j.physa.2009.06.045
Librelotto, G.; Mombach, J. C. M.; Sinigaglia, M.; Simão, E.D.; Cabral, H.B.; Castro, M.A.A. An ontology to integrate transcriptomics and interatomics data involved in gene pathways of genome stability. Lecture Notes in Bioinformatics, v. 5676. p. 164-167, 2009.
http://dx.doi.org/10.1007/978-3-642-03223-3_18
Rybarczyk-Filho, J.L; Castro, M.A.A.; Dalmolin, R.J.S.; de Almeida, R.M.C. GNATT: gene/protein network analysis tools for tracing interactome ordering. Journal Paper (in preparation), 2009.
Book Chapter
Sinigaglia, M. ; Rycbarzyck-Filho,J ; Dalmolin, R. ; Moreira, J.C.F. ;de Almeida, R.M.C.; Castro, M.A.A.; Mombach, J. C. M. ; Giovani Librelotto . Bioinformatics analysis of gene networks involved in genomic stability and cancer. In: Helen C. Kristoff. (Org.). Cancer Biomarkers. : Nova Science Publishers, 2010. ISBN: 978-1-61761-302-9
Technical Production
Patents
Castro, M.A.A.; de Almeida, R.M.C.; Onsten, T.G.H.; Moreira, J.C.F. Kit for Karyotypic Diagnosis based on chromosome instability analysis. 2006. Publication number: PI0602793-8; Publication date: 2008-02-26.
European Patent Office No. BRPI0602793
Klant, F.; Castro, M.A.A.; Moreira, J.C.F.; Dal-Pizzol, F.; Shacter, E. Method and kit for diagnosis and/or prognosis of lung cancer. Filed June 26, 2008.
Brazilian Patent Office N. PI0802917-2
Softwares
Wang, X.; Castro, M.A.A.; Markowetz, F. IGIR: The Integrative network Graphic engine Interface for R. 2010 (in preparation).
http://igir.r-forge.r-project.org/
Castro, M.A.A. et al. RedeR: bridging the gap between functional analyses and hierarchical network visualization. 2011. (Bioconductor package)
http://www.markowetzlab.org/software/networks.html
Castro, M.A.A.; Rybarczyk-Filho, J.L.; de Almeida, R.M.C. ViaComplex: software for landscape analysis of gene expression networks in genomic context. 2009. (Published in Bioinformatics, as specified above).
http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex/
Castro, M.A.A.; Rybarczyk-Filho, J.L.; Moreira, J.C.F.; de Almeida, R.M.C. KaryoComplex: software for cytogenetic analysis of complex chromosome aberrations.2008. (Prototype that materializes the patent PI0602793-8)
http://lief.if.ufrgs.br/pub/biosoftwares/karyocomplex/
Rybarczyk-Filho, J.L.; Castro, M.A.A.; de Almeida, R.M.C. GNATT: Gene/protein network analysis tools for tracing interactome ordering. 2010 (in preparation)
http://lief.if.ufrgs.br/pub/biosoftwares/gnatt
Technical Works
Castro, M.A.A. Ad hoc consulting services for Biotech and IT companies in response to the PRIME Program (FINEP – Research and Project Financing, Brazilian Innovation Agency). 2009.
Castro, M.A.A. Ad hoc consulting services in response to the CYTED Program (Latinamerican Science & Technology Development Programme). 2009-.
Other Kinds of Technical Production
Yuan, Y.; Castro, M.A.A.; Markowetz, F. Analysis of Globally-Coherent Data Sets: a two day course for GlaxoSmithKline, Stevenage, 28-29th Oct 2010. (Short Course Taught/Extension).
Castro, M.A.A. Analysis of gene expression networks. Second Brazilian School on Bioinformatics, PUC-RS, 2009. (Short Course Taught/Extension).
Castro, M.A.A. Systems biology applied to the analysis of oxidative pathways. Short Course on Free Radicals, Department of Biochemistry, UFRGS, 2007. (Short Course Taught/Extension).
