Jonas S. Almeida

Susana Vinga, Alexandra M. Carvalho, Alexandre P. Francisco, Luís M. S. Russo, Jonas S. Almeida: Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis. Algorithms for Molecular Biology 7: 10 (2012)

Jonas S. Almeida, Alexander Grüneberg, Wolfgang Maass, Susana Vinga: Fractal MapReduce decomposition of sequence alignment. Algorithms for Molecular Biology 7: 12 (2012)

Helena F. Deus, Miria C. Correa, Romesh Stanislaus, Maria Miragaia, Wolfgang Maass, Hermínia de Lencastre, Ronan Fox, Jonas S. Almeida: S3QL: A distributed domain specific language for controlled semantic integration of life sciences data. BMC Bioinformatics 12: 285 (2011)

Jonas S. Almeida, Helena F. Deus, Wolfgang Maass: S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics 11: 387 (2010)

Helena F. Deus, Diogo F. Veiga, Pablo R. Freire, John N. Weinstein, Gordon B. Mills, Jonas S. Almeida: Exposing the cancer genome atlas as a SPARQL endpoint. Journal of Biomedical Informatics 43(6): 998-1008 (2010)

Miria C. Correa, Helena F. Deus, Ana Tereza R. Vasconcelos, Yuki Hayashi, Jaffer A. Ajani, Srikrishna V. Patnana, Jonas S. Almeida: AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services. BMC Med. Inf. & Decision Making 10: 65 (2010)

Jonas S. Almeida, Susana Vinga: Biological sequences as pictures - a generic two dimensional solution for iterated maps. BMC Bioinformatics 10 (2009)

Martina Mueller, Sarah N. Taylor, Carol L. Wagner, Jonas S. Almeida: Using an artificial neural network to predict necrotizing enterocolitis in premature infants. IJCNN 2009: 2172-2175

Romesh Stanislaus, John M. Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen, Jonas S. Almeida: An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis. BMC Bioinformatics 9 (2008)

Romesh Stanislaus, Mark Carey, Helena F. Deus, Kevin R. Coombes, Bryan T. J. Hennessy, Gordon B. Mills, Jonas S. Almeida: RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays. BMC Bioinformatics 9 (2008)

Xiaoshu Wang, Jonas S. Almeida, Arlindo L. Oliveira: Ontology Design Principles and Normalization Techniques in the Web. DILS 2008: 28-43

Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida: PrepMS: TOF MS data graphical preprocessing tool. Bioinformatics 23(2): 264-265 (2007)

Francisco R. Pinto, João A. Carriço, Mário Ramirez, Jonas S. Almeida: Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement. BMC Bioinformatics 8 (2007)

Marco Vilela, Carlos Cristiano H. Borges, Susana Vinga, Ana Tereza R. Vasconcelos, Helena Santos, Eberhard O. Voit, Jonas S. Almeida: Automated smoother for the numerical decoupling of dynamics models. BMC Bioinformatics 8 (2007)

Susana Vinga, Jonas S. Almeida: Local Renyi entropic profiles of DNA sequences. BMC Bioinformatics 8 (2007)

Jonas S. Almeida, Susana Vinga: Computing distribution of scale independent motifs in biological sequences. Algorithms for Molecular Biology 1 (2006)

Yian A. Chen, Cheng-Chung Chou, Xinghua Lu, Elizabeth H. Slate, Konan Peck, Wenying Xu, Eberhard O. Voit, Jonas S. Almeida: A multivariate prediction model for microarray cross-hybridization. BMC Bioinformatics 7: 101 (2006)

Yuliya V. Karpievitch, Jonas S. Almeida: mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code. BMC Bioinformatics 7: 139 (2006)

Martina Mueller, Carol L. Wagner, David J. Annibale, Rebecca G. Knapp, Thomas C. Hulsey, Jonas S. Almeida: Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants. BMC Med. Inf. & Decision Making 6: 11 (2006)

Francisco R. Pinto, L. Ashley Cowart, Yusuf A. Hannun, Bärbel Rohrer, Jonas S. Almeida: Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory method. Bioinformatics 21(7): 1037-1045 (2005)

Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John M. Arthur, Jonas S. Almeida: AGML Central: web based gel proteomic infrastructure. Bioinformatics 21(9): 1754-1757 (2005)

Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida: Comparative evaluation of word composition distances for the recognition of SCOP relationships. Bioinformatics 20(2): 206-215 (2004)

Eberhard O. Voit, Jonas S. Almeida: Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics 20(11): 1670-1681 (2004)

Romesh Stanislaus, Liu Hong Jiang, Martha Swartz, John M. Arthur, Jonas S. Almeida: An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. BMC Bioinformatics 5: 9 (2004)

Yian A. Chen, David J. Mckillen, Shuyuan Wu, Matthew J. Jenny, Robert Chapman, Paul S. Gross, Gregory W. Warr, Jonas S. Almeida: Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinformatics 5: 191 (2004)

Susana Vinga, Jonas S. Almeida: Alignment-free sequence comparison-a review. Bioinformatics 19(4): 513-523 (2003)

Sara Silva, Rodrigo Gouveia-Oliveira, António Maretzek, João A. Carriço, Thorolfur Gudnason, Karl G. Kristinsson, Karl Ekdahl, António Brito-Avô, Alexander Tomasz, Ilda Santos Sanches, Hermínia de Lencastre, Jonas S. Almeida: EURISWEB - Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers. BMC Med. Inf. & Decision Making 3: 9 (2003)

Sara Silva, Jonas S. Almeida: Dynamic Maximum Tree Depth. GECCO 2003: 1776-1787

Jonas S. Almeida, Susana Vinga: Universal sequence map (USM) of arbitrary discrete sequences. BMC Bioinformatics 3: 6 (2002)

John Schwacke, Jonas S. Almeida: Efficient Boolean implementation of universal sequence maps (bUSM). BMC Bioinformatics 3: 28 (2002)

Jonas S. Almeida, João A. Carriço, António Maretzek, Peter A. Noble, Madilyn Fletcher: Analysis of genomic sequences by Chaos Game Representation. Bioinformatics 17(5): 429-437 (2001)