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publications
2006
Oliveira DC, Milheirico C, Vinga S, de Lencastre H. (2006). Assessment of allelic variation in the ccrAB locus in methicillin-resistant Staphylococcus aureus clones. J Antimicrob Chemother. 2006 Jul;58(1):23-30. Epub 2006 May 30. PMID: 16735433 [PubMed - in process]
Carriço J.A., Silva-Costa C., Melo-Cristino J., Pinto F.R., de Lencastre H., Almeida J.S., and Ramirez M. 2006. Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes. Clinical Microbilogy and Infection 12(4):338-44.
2005
Almeida JS, R Stanislaus, E Krug, J Arthur (2005). Normalization and Analysis of residual variation in 2D Gel Electrophoresis for quantitative differential proteomics. Proteomics 5(5) : 1242-9.
Mitas M, JS Almeida, K Mikhitarian, WE Gillanders, DN Lewin, DD Spyropoulos, L Hoover, A Graham, T Glenn, P King, DJ Cole, R Hawes, CE Reed, BJ Hoffman (2005). Accurate discrimination of Barrett’s esophagus and esophageal adenocarcinoma using a quantitative three-tiered algorithm and multi-marker real-time RT-PCR. Clin Cancer Res. 2005 Mar 15;11(6):2205-14.
Stanislaus R, C Chen, J Franklin, J Arthur, JS Almeida (2005). AGML Central: AGML Compatible Proteomic Database. Bioinformatics, 21(9):1754-7.
Mikhitarian, K., Gillanders, W.E., Almeida, J.S., Hebert Martin R., Varela J.C., Metcalf, J.S., Cole, D.J., and Mitas, M. (2005). Relative levels of gene expression are correlated with the ability to detect micrometastatic breast cancer: statistical analysis of data from a multi-institutional prospective cohort study and development of an innovative microarray strategy. Clinical Cancer Research 11(10):3697-704.
McKillen DJ, YA Chen, C Chen, MJ Jenny, HF Trent, J Robalino, DC McLean, PS Gross, RW Chapman, GW Warr, JS Almeida (2005). Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms. BMC Genomics 2005, 6:34.
Almeida JS, DJ McKillen, YA Chen, PS Gross, RW Chapman, G Warr (2005). Design and Calibration of Microarrays as Universal Transcriptomic Environmental Biosensors. Comparative and Functional Genomics, 6(3):132-137(6).
Wolf G, JS Almeida, MAM Reis and JG Crespo (2005). Modelling of the extractive membrane bioreactor process based on natural fluorescence fingerprints and process operation history. Water Science and Technology, 51 (6-7): 51-58.
Wolf G, JS Almeida, MAM Reis and JG Crespo (2005). Non-mechanistic modelling of complex biofilm reactors and the role of process operation history. Journal of Biotechnology, 117 (4): 367-383.
Wang X, R Gorlitsky, and JS Almeida (2005). From XML to RDF: How Semantic Web Technologies Will Change the Design of ‘Omic’ Standards. Nature Biotechnology, Sep;23(9):1099-103.
Oates JC, Varghese S, Bland AM, Taylor TP, Self SE, Stanislaus R, Almeida JS, Arthur JM (2005). Prediction of urinary protein markers in lupus nephritis. Kidney Int. Dec;68(6):2588-92.
Sara P. Garcia and Jonas S. Almeida, Nearest neighbor embedding with different time delays, Physical Review E 71, 037204 (2005). Selected for reprinting in Volume 9, Issue 7 (April 1, 2005) of the Virtual Journal of Biological Physics Research.
Sara P. Garcia and Jonas S. Almeida, Multivariate phase space reconstruction by nearest neighbor embedding with different time delays, Physical Review E 72, 027205 (2005). Selected for reprinting in Volume 10, Issue 5 (September 1, 2005) of the Virtual Journal of Biological Physics Research.
L. N. Mueller, J. F.C. de Brouwer, J. S. Almeida, L. J., J. B. Xavier (accepted for publication in BMC Ecology) Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP.
Mato R, Sanches IS, Simas C, Nunes S, Carrico JA, Sousa NG, Frazao N, Saldanha J, Brito-Avo A, Almeida JS, Lencastre HD. Natural History of Drug-Resistant Clones of Streptococcus pneumoniae Colonizing Healthy Children in Portugal. Microb Drug Resist. 2005 Winter;11(4):309-22.
Carriço, J.A. , F.R. Pinto, C. Simas, S. Nunes, N. G. Sousa, N. Frazão, H. de Lencastre, and J.S. Almeida. 2005. Assessment of band-based similarity coefficients for automatic Type/Subtype classification ofmicrobial isolates analyzed by Pulsed-Field Gel Electrophoresis. J Clin Microbiol. 2005 Nov;43(11):5483-90.
Sousa N. G., R. Sá-Leão, M.I. Crisóstomo, C. Simas, S. Nunes, N. Frazão, J. Carriço, R. Mato, I. Santos-Sanches, and H. de Lencastre. 2005. Properties of novel international drug-resistant pneumococcal clones identified in day-care centers (DCCs) of Lisbon, Portugal. J Clin Microbiol. 2005 Sep;43(9):4696-703.
I. Serrano, J. Melo-Cristino, J. Carriço and M. Ramirez, Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal, J Clinical Microbiology,2005 Apr;43(4):1706-15.
Nelson Frazão; António Brito-Avô; Carla Simas; Joana Saldanha; Rosario Mato; Sónia Nunes; Natacha Gonçalves Sousa; João Carriço; Jonas Almeida; Ilda Santos-Sanches; Hermínia de Lencastre, Effect of the 7-valent conjugate pneumococcal vaccine on carriage and drug resistance of Streptococcus pneumoniae in healthy children attending day-care centers in Lisbon. Pediatr Infect Dis J. 2005 Mar;24(3):243-52.
Gomes, A. R., Vinga, S., Zavolan, M. and de Lencastre, H, Analysis of the Genetic Variability of Virulence-related Loci in Epidemic Clones of Methicillin-resistant Staphylococcus aureus, Antimicrobial Agents and Chemotherapy 2005, 49(1):366-379.
Pinto F.R., L Ashley Cowart, Yusuf A. Hannun, B. Roher, J.S.Almeida (2005). Local correlation of expression profiles with gene annotations – proof of concept for a general conciliatory method. Bioinformatics, 21(7):1037-45.
Pina C., Pinto F.R., Feijó J.A., Becker J.D. (2005) A genomic view of the commitment to cell growth, cell division control and regulation of gene expression in Arabidopsis pollen. Plant Physiology, 138(2): 744-56.
Pinto F.R., Carriço J.A., Ramirez M., Almeida J.S. (2005).Evaluating the agreement between clusterings. Submitted.
Pinto F.R., Almeida J.S. (2005). When two are more than three: a probabilistic approach to study yeast’s gene regulatory network. Submitted.
Sara P. Garcia and Jonas S. Almeida, Multivariate phase space reconstruction by nearest neighbor embedding with different time delays. Physical Review E 72 (2005) 027205 [doi:10.1103/PhysRevE.72.027205].
Almeida JS, DJ McKillen, YA Chen, PS Gross, RW Chapman, G Warr (2005) Design and Calibration of Microarrays as Universal Transcriptomic Environmental Biosensors. Comparative and Functional Genomics, in press.
McKillen DJ, YA Chen, C Chen, MJ Jenny, HF Trent, J Robalino, DC McLean, PS Gross, RW Chapman, GW Warr, JS Almeida (2005) Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms. BMC Genomics 2005, 6:34.
Almeida JS, Nowotny H. (2005) The emergence of the ERC. Science. 307(5713):1200.
Mikhitarian, K., Gillanders, W.E., Almeida, J.S., Hebert Martin R., Varela J.C., Metcalf, J.S., Cole, D.J., and Mitas, M. (2005) Relative levels of gene expression are correlated with the ability to detect micrometastatic breast cancer: statistical analysis of data from a multi-institutional prospective cohort study and development of an innovative microarray strategy. Clinical Cancer Research, in press.
I. Serrano, J. Melo-Cristino, J. Carriço and M. Ramirez. Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal. J Clinical Microbiology, in press.
Nelson Frazão, António Brito-Avô, Carla Simas, Joana Saldanha, Rosario Mato, Sónia Nunes, Natacha Gonçalves Sousa, João Carriço, Jonas Almeida, Ilda Santos-Sanches, Hermínia de Lencastre. Effect of the 7-valent conjugate pneumococcal vaccine on carriage and drug resistance of Streptococcus pneumoniae in healthy children attending day-care centers in Lisbon J.Ped.Infec.Dis., in press
Stanislaus R, C Chen, J Franklin, J Arthur, JS Almeida (2005) AGML Central: AGML Compatible Proteomic Database. Bioinformatics, advance print 2005 Jan 12.
Nunes S, R Sá-Leão, J Carriço, CR Alves, R Mato, A Brito Avô, J Saldanha, JS Almeida, I Santos Sanches, and H de Lencastre. Trends in drug resistance, serotypes and molecular types of Streptococcus pneumoniae colonizing pre-school age children attending day care centers in Lisbon, Portugal – a summary of four years of annual surveillance. J. Clin. Microbiol. 2005, 43 1285-1293.
Sara P. Garcia and Jonas S. Almeida. Nearest neighbor embedding with different time delays. Physical Review E 71 (2005) 037204 [doi:10.1103/PhysRevE.71.037204]. Selected for reprinting in the Vol. 9, Issue 7 of the Virtual Journal of Biological Physics Research.
Pina C., Pinto F.R., Feijó J.A., Becker J.D. A genomic view of the commitment to cell growth, cell division control and regulation of gene expression in Arabidopsis pollen. Plant Physiology (accepted for publication)
Mitas M, JS Almeida, K Mikhitarian, WE Gillanders, DN Lewin, DD Spyropoulos, L Hoover, A Graham, T Glenn, P King, DJ Cole, R Hawes, CE Reed, BJ Hoffman (2005) Accurate discrimination of Barrett’s esophagus and esophageal adenocarcinoma using a quantitative three-tiered algorithm and multi-marker real-time RT-PCR. Clinical Cancer Research, in press.
Almeida JS, R Stanislaus, E Krug, J Arthur (2005) Normalization and Analysis of residual variation in 2D Gel Electrophoresis for quantitative differential proteomics. Proteomics (Epub ahead of print).
2004
YA Chen, DJ Mckillen, S Wu, MJ Jenny, R Chapman, PS Gross, GW Warr, JS Almeida (2004) Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinformatics 5(1):191.
Veflingstad, S.R., J.S. Almeida, and E.O. Voit, Priming nonlinear searches for pathway identification, BMC Theoretical Biology and Medical Modelling, 1:8 doi:10.1186.
Pinto FR, Cowart LA, Hannun YA, Rohrer B, Almeida JS. Local correlation of expression profiles with gene annotations - proof of concept for a general conciliatory method. Bioinformatics. 2004 Oct 28. [Epub ahead of print]
Rohrer B, Pinto FR, Hulse KE, Lohr HR, Zhang L, Almeida JS. Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling. J Biol Chem. 2004 Oct 1;279(40):41903-10. Epub 2004 Jun 24.
Mueller LN, de Brouwer JFC, Almeida JS, Stal LJ, Xavier JB (2004), Confocal laser scanning microscopy analysis of marine phototrophic biofilm development using PHLIP. (submitted)
Mueller LN, de Brouwer JFC, Xavier JB, Almeida JS (2004), PHLIP: Image bioinformatics for the quantitative analysis of confocal laser scanning microscopy data, Proceedings IWA Biofilm symposium. Las Vegas, Montana. (accepted for publication)
GrayMerod R, Hendrickx L, Mueller LN, Xavier JB, Wuertz S (2004), Effect of nucleic acid stain Syto 9 on nascent biofilm architecture of Acinetobacter.
Susana Vinga and Jonas Almeida. Rényi continuous entropy of DNA sequences. Journal of Theoretical Biology 2004 vol.231(3): 377-388.
Almeida, J.S., Wu, S., and Voit, E.O. (2004). XML4MAT: Inter-conversion between MatlabTM structured variables and the markup language MbML. Elsevier Computer Science Preprint Server CSPS: Data/0312002, submitted Data & Knowledge Engineering.
Stanislaus, R., Jiang, L.H., Swartz, M., Arthur, J., and Almeida, J.S. (2004) An XML standard for the computation and dissemination of annotated 2D gel electrophoresis complemented with Mass spectrometry results. BMC Bioinformatics 2004, 5:9.
Mueller M, Wagner CL, Annibale DJ, Hulsey TC, Knapp RG, Almeida JS. (2004) Predicting Extubation Outcome in Preterm Newborns: a Comparison of Neural Networks with Clinical Expertise and Statistical Modeling. Pediatric Research. In Press.
Voit, E.O., J.S. Almeida (2004) Decoupling Dynamical Systems for Pathway Identification from Metabolic Profiles. Bioinformatics, in press.
Susana Vinga, Rodrigo Gouveia-Oliveira and Jonas S Almeida. Comparative evaluation of word composition distances for the recognition of SCOP relationships. Bioinformatics 2004 20: 206-215.
2003
Freitas F., Temudo M., Almeida J.S., Reis M.A. (2003) Nutrient removal in a sequencing batch reactor operated with short anaerobic/aerobic cycles. Commun Agric Appl Biol Sci. 68(2PtA):85-92.
Silva S, Almeida J (2003) GPLAB - A Genetic Programming Toolbox for MATLAB. In Gregersen L (ed), Proceedings of the Nordic MATLAB Conference (NMC-2003), 273-278.
Almeida, J.S., E.O.Voit (2003) Neural-Network-Based Parameter Estimation in S-System Models of Biological Networks. Genome Informatics, 14:114-123.
D.S.Blehert, R.J.Palmer Jr.,J.B.Xavier, J.S.Almeida, P.E.Kolenbrander (2003) Autoinducer 2 Production by Streptococcus gordonii DL1 and the Biofilm Phenotype of a luxS Mutant Are Influenced by Nutritional Conditions. J.Bacteriol., 185(16):4851-4860.
Cowart LA, Okamoto Y, Pinto FR, Gandy JL, Almeida J, Hannun YA. Roles for sphingolipid biosynthesis in mediation of specific programs of the heat stress response determined through gene expression profiling. J Biol Chem. 2003 May 9.
Sara Silva, Rodrigo Gouveia-Oliveira, Antonio Maretzek, Joao Carrico, Thorolfur Gudnason, Karl G Kristinsson, Karl Ekdahl, Antonio Brito-Avo, Alexander Tomasz, Ilda S Sanches, Herminia de Lencastre and Jonas S Almeida. EURISWEB - Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers.BMC Medical Informatics and Decision Making 2003, 3:9.
Mueller M, Wagner CL, Annibale DJ, Hulsey TC, Knapp RG, Almeida JS. (2003) Web-based Prediction of Extubation Outcome in Premature Infants on Mechanical Ventilation Using an Artificial Neural Network. Proc AMIA Symp.
Wolf G, Almeida JS, Crespo JG, Reis MA. (2003) Monitoring of biofilm reactors using natural fluorescence fingerprints. Water Sci Technol. 2003;47(5):161-7.
Voit EO, and Almeida JS. (2003) Dynamic Profiling and Canonical Modeling: Powerful Partners in Metabolic Pathway Identification, in: R. Goodacre and G.G. Harrigan (Eds): Metabolite Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Kluwer Academic Publishing, Dordrecht, The Netherlands.
Tony Solomonides, Mohammed Odeh, Richard McClatchey,Jean-Marie Le Goff, Joao Carrico,Jonas Almeida. Conceptual Modelling of an Epidemiological Information System, IADIS International Conference e-Society 2003, ISBN:972-98947-0-1.
Silva, S. and J. Almeida Dynamic Maximum Tree Depth - A Simple Technique for Avoiding Bloat in Tree-Based GP. In Cantú-Paz E, Foster JA, Deb K, et al. (eds), Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2003), 1776-1787.
Vinga, Susana, Almeida, Jonas (2003) Alignment-free sequence comparison—a review Bioinformatics 2003 19: 513-523. link
Xavier, JB, DC White, JS Almeida (2003) Automated Biofilm Morphology Quantification from Confocal Laser Scanning Microscopy Imaging. Water Science and Technology 47(5):317.
2002
Schwacke J, Almeida JS. (2002) Efficient Boolean implementation of universal sequence maps (bUSM). BMC Bioinformatics, 3(1):28.
Almeida JS (2002) Data Analysis and Modeling, in Encyclopedia of Environmental Microbiology ISBN047136049X.
Miragaia,Maria, Couto,Isabel, Pereira,Sandro, Kristinsson.Karl, Westh,Henrik , Jarløv,Jens O.,Carriço,João, Almeida, Jonas, Santos-Sanches,Ilda, de Lencastre,Hermínia (2002) Molecular Characterization of Methicillin-Resistant Staphylococcus epidermidis Clones: Evidence of Geographic Dissemination J. Clin.Microbiol, Feb. 2002, Vol. 40( 2), 430-438.
Almeida, Jonas; Vinga, Susana (2002) Universal sequence map (USM) of arbitrary discrete sequences , Bioinformatics 3:6, (5 February 2002). link @ BMC
Almeida, JS (2002) Predictive non-linear modeling of complex data by artificial neural networks. Curr. Op. Biotech. 13(1) 72-76.
2001
Chapman, R.W., Almeida, J.S. (2001) Ecogenomics - Response to the Editors., Comparative Biochemistry and Physiology Part B 130:133-134.
Xavier, J.B., A. Schnell, S. Wuertz, R Palmer, D.C. White, J.S. Almeida (2001) Objective Threshold Selection Procedure (OTS) for segmentation of scanning laser confocal microscope images. J Microb. Methods 47:169-180.
Almeida, JS, JA Carriço, A Maretzek, PA.Noble, M Fletcher (2001) Analysis of Genomic Sequences by Chaos Game Representation. Bioinformatics 17(5):429-437.
Cruz PE, Gonçalves D, Almeida JS, Moreira JL, Carrondo MJT(2001); Modeling Retrovirus Production for Gene Therapy. 2. Integrated Optimization of Bioreaction and Downstream Processing. Biotechnol. Progr.
Wolf G. Almeida JS. Pinheiro C. Correia V. Rodrigues C. Reis MAM. Crespo JG. (2001) Two-dimensional fluorometry coupled with artificial neural networks: A novel method for on-line monitoring of complex biological processes. Biotechnology & Bioengineering. 72(3):297-306.
2000
Santos Sanches, I., R. Mato, H. de Lencastre, A. Tomasz, CEM/NET collaborators: S. Nunes, C. R. Alves, M. Miragaia, J. Carriço, I. Couto, I. Bonfim, M. A. de Sousa, D. Oliveira, A. Gomes, M. Vaz, S. Fernandes, S. C. Verde, S. Ávila, F. Antunes, R. Sá-Leão, J. Almeida, and International collaborators: O. Melter, M. Chung, M. C. Brandileone, E. Castañeda, I. Heitmann, M. Hortal, W. Hryniewicz, F. Jia, K. Kikuchi, K. G. Kristinsson, J. Liñares, A. Rossi, E. Z. Savov, J. Schindler, F. Solorzano-Santos, K. Totsuka, M. Venditti, P. Villari, H. Westh, J. S. Wu, and R. C. Zanella. (2000). Patterns of multidrug resistance among methicillin-resistant hospital isolates of coagulase-positive and coagulase-negative staphylococci collected in the international multicenter study RESIST in 1997 and 1998. Microb. Drug Resist. 6:199-211.
Almeida, JS, PA Noble (2000) Neural Computing in Microbiology. Journal of Microbiological Methods 43:1-2.
Cruz PE, Almeida JS, Murphy PN, Moreira JL, Carrondo MJT (2000) Modeling retrovirus production for gene therapy. 1. Determination of optimal bioreaction mode and harvest strategy. Biotechnol. Progr. 16: (2) 213-221.
Neves, AR, A. Ramos, C. Shearman, M. J. Gasson, J. S. Almeida & H. Santos (2000) Metabolic Characterization of Lactococcus lactis deficient in lactate dehydrogenase using 13C NMR. European Journal of Biochemistry, 267 (12) 3859-3868.
Wolf,G., J.S.Almeida, A.M.Reis, J.G.Crespo (2000). Monitoring of Membrane Bioreactors, in "Integration of Membrane Processes Into Bioconversions, part III". Editors: K Belafi-Bako, L Gubicza, M Mulder, Kluwer Academic Publishers (ISBN: 0306464373).
Noble, PA, Almeida JS, Lovell CR (2000) Application of neural computing methods for phospholipid fatty acid profiles of natural microbial communities. Applied and Environmental Microbiology 66 (2) 694/699.
Almeida JS, Noble PA (2000) Neural computing in microbiology. J Microbiol Methods. 43(1):1-2.
Fonseca, A, JPSG Crespo, JS Almeida, MAM Reis (2000) Achieving biological denitrification without secondary pollution. Environmental Science and Technology 34: (8) 1557-1562.
Xavier, JB, R Malhó, MAM Reis, JS Almeida (2000) Description of Biofilm formation by determination of developmental axis. Water Science and Technology 41(4-5):121-127.
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biomathematics group