Silva A - Search Results

1

PetriScape - A plugin for discrete Petri net simulations in Cytoscape.

Almeida D, Azevedo V, Silva A, Baumbach J. Almeida D, et al. Among authors: silva a. J Integr Bioinform. 2016 Jun 4;13(1):284. doi: 10.2390/biecoll-jib-2016-284. J Integr Bioinform. 2016. PMID: 27402693

2

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing.

Almeida D, Skov I, Lund J, Mohammadnejad A, Silva A, Vandin F, Tan Q, Baumbach J, Röttger R. Almeida D, et al. Among authors: silva a. J Integr Bioinform. 2016 Dec 18;13(4):294. doi: 10.2390/biecoll-jib-2016-294. J Integr Bioinform. 2016. PMID: 28187410

3

Efficient detection of differentially methylated regions using DiMmeR.

Almeida D, Skov I, Silva A, Vandin F, Tan Q, Röttger R, Baumbach J. Almeida D, et al. Among authors: silva a. Bioinformatics. 2017 Feb 15;33(4):549-551. doi: 10.1093/bioinformatics/btw657. Bioinformatics. 2017. PMID: 27794558

4

Mature Epitope Density--a strategy for target selection based on immunoinformatics and exported prokaryotic proteins.

Santos AR, Pereira VB, Barbosa E, Baumbach J, Pauling J, Röttger R, Turk MZ, Silva A, Miyoshi A, Azevedo V. Santos AR, et al. Among authors: silva a. BMC Genomics. 2013;14 Suppl 6(Suppl 6):S4. doi: 10.1186/1471-2164-14-S6-S4. Epub 2013 Oct 25. BMC Genomics. 2013. PMID: 24564223 Free PMC article.

5

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

Mariano DC, Pereira FL, Aguiar EL, Oliveira LC, Benevides L, Guimarães LC, Folador EL, Sousa TJ, Ghosh P, Barh D, Figueiredo HC, Silva A, Ramos RT, Azevedo VA. Mariano DC, et al. Among authors: silva a. BMC Bioinformatics. 2016 Dec 15;17(Suppl 18):456. doi: 10.1186/s12859-016-1344-7. BMC Bioinformatics. 2016. PMID: 28105921 Free PMC article.

6

PIPS: pathogenicity island prediction software.

Soares SC, Abreu VA, Ramos RT, Cerdeira L, Silva A, Baumbach J, Trost E, Tauch A, Hirata R Jr, Mattos-Guaraldi AL, Miyoshi A, Azevedo V. Soares SC, et al. Among authors: silva a. PLoS One. 2012;7(2):e30848. doi: 10.1371/journal.pone.0030848. Epub 2012 Feb 15. PLoS One. 2012. PMID: 22355329 Free PMC article.

7

The core stimulon of Corynebacterium pseudotuberculosis strain 1002 identified using ab initio methodologies.

Pinto AC, Ramos RT, Silva WM, Rocha FS, Barbosa S, Miyoshi A, Schneider MP, Silva A, Azevedo V. Pinto AC, et al. Among authors: silva a, silva wm. Integr Biol (Camb). 2012 Jul;4(7):789-94. doi: 10.1039/c2ib00092j. Epub 2012 May 28. Integr Biol (Camb). 2012. PMID: 22641428

8

Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by Piper betel compounds.

Barh D, Gupta K, Jain N, Khatri G, León-Sicairos N, Canizalez-Roman A, Tiwari S, Verma A, Rahangdale S, Shah Hassan S, dos Santos AR, Ali A, Guimarães LC, Thiago Jucá Ramos R, Devarapalli P, Barve N, Bakhtiar M, Kumavath R, Ghosh P, Miyoshi A, Silva A, Kumar A, Misra AN, Blum K, Baumbach J, Azevedo V. Barh D, et al. Among authors: silva a. Integr Biol (Camb). 2013 Mar;5(3):495-509. doi: 10.1039/c2ib20206a. Integr Biol (Camb). 2013. PMID: 23288366

9

An improved interolog mapping-based computational prediction of protein-protein interactions with increased network coverage.

Folador EL, Hassan SS, Lemke N, Barh D, Silva A, Ferreira RS, Azevedo V. Folador EL, et al. Among authors: silva a. Integr Biol (Camb). 2014 Nov;6(11):1080-7. doi: 10.1039/c4ib00136b. Integr Biol (Camb). 2014. PMID: 25209055

10

CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks.

Abreu VA, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Röttger R. Abreu VA, et al. Among authors: silva a. BMC Genomics. 2015 Jun 11;16(1):452. doi: 10.1186/s12864-015-1631-0. BMC Genomics. 2015. PMID: 26062809 Free PMC article.

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