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Jonas Almeida

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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TOP 3
Fernandes Francisco; Freitas Ana T; Almeida Jonas S; Vinga Susana
Entropic Profiler - detection of conservation in genomes using information theory.
Vilela Marco; Vinga Susana; Maia Marco A Grivet Mattoso; Voit Eberhard O; Almeida Jonas S
Identification of neutral biochemical network models from time series data.
Almeida Jonas S; Vinga Susana
Biological sequences as pictures: a generic two dimensional solution for iterated maps.

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2009: Fernandes Francisco; Freitas Ana T; Almeida Jonas S; Vinga Susana
Entropic Profiler - detection of conservation in genomes using information theory.
BMC research notes 2009;2():72.
2009: Vilela Marco; Vinga Susana; Maia Marco A Grivet Mattoso; Voit Eberhard O; Almeida Jonas S
Identification of neutral biochemical network models from time series data.
BMC systems biology 2009;3():47.
2009: Almeida Jonas S; Vinga Susana
Biological sequences as pictures: a generic two dimensional solution for iterated maps.
BMC bioinformatics 2009;10():100.
2008: Robinson Christopher J; Swift Steven; Johnson Donna D; Almeida Jonas S
Prediction of pelvic organ prolapse using an artificial neural network.
American journal of obstetrics and gynecology 2008;199(2):193.e1-6.
2008: Sá-Leão Raquel; Nunes Sónia; Brito-Avô António; Alves Carla R; Carriço João A; Saldanha Joana; Almeida Jonas S; Santos-Sanches Ilda; de Lencastre Hermíniade
High rates of transmission of and colonization by Streptococcus pneumoniae and Haemophilus influenzae within a day care center revealed in a longitudinal study.
Journal of clinical microbiology 2008;46(1):225-34.
2008: Freire Pablo; Vilela Marco; Deus Helena; Kim Yong-Wan; Koul Dimpy; Colman Howard; Aldape Kenneth D; Bogler Oliver; Yung W K Alfred; Coombes Kevin; Mills Gordon B; Vasconcelos Ana T; Almeida Jonas S
Exploratory analysis of the copy number alterations in glioblastoma multiforme.
PloS one 2008;3(12):e4076.
2008: Stanislaus Romesh; Carey Mark; Deus Helena F; Coombes Kevin; Hennessy Bryan T; Mills Gordon B; Almeida Jonas S
RPPAML/RIMS: a metadata format and an information management system for reverse phase protein arrays.
BMC bioinformatics 2008;9():555.
2008: Deus Helena F; Stanislaus Romesh; Behrens Carmen; Wistuba Ignacio I; Minna John D; Garner Harold R; Swisher Stephen G; Roth Jack A; Correa Arlene M; Broom Bradley; Coombes Kevin; Almeida Jonas S
Data driven semantic integration of translational lung cancer research at MDAnderson Cancer Center.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2008;():927.
2008: Deus Helena F; Stanislaus Romesh; Veiga Diogo F; Behrens Carmen; Wistuba Ignacio I; Minna John D; Garner Harold R; Swisher Stephen G; Roth Jack A; Correa Arlene M; Broom Bradley; Coombes Kevin; Chang Allen; Vogel Lynn H; Almeida Jonas S
A Semantic Web management model for integrative biomedical informatics.
PloS one 2008;3(8):e2946.
2008: Vilela Marco; Chou I-Chun; Vinga Susana; Vasconcelos Ana Tereza R; Voit Eberhard O; Almeida Jonas S
Parameter optimization in S-system models.
BMC systems biology 2008;2():35.
2008: Arthur John M; Janech Michael G; Varghese Sanju A; Almeida Jonas S; Powell T Brian
Diagnostic and prognostic biomarkers in acute renal failure.
Contributions to nephrology 2008;160():53-64.
2008: Stanislaus Romesh; Arthur John M; Rajagopalan Balaji; Moerschell Rick; McGlothlen Brian; Almeida Jonas S
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.
BMC bioinformatics 2008;9():4.
2007: Jenny Matthew J; Chapman Robert W; Mancia Annalaura; Chen Yian A; McKillen David J; Trent Hal; Lang Paul; Escoubas Jean-Michel; Bachere Evelyne; Boulo Viviane; Liu Z John; Gross Paul S; Cunningham Charles; Cupit Pauline M; Tanguy Arnaud; Guo Ximing; Moraga Dario; Boutet Isabelle; Huvet Arnaud; De Guise Sylvain; Almeida Jonas S; Warr Gregory W
A cDNA microarray for Crassostrea virginica and C. gigas.
Marine biotechnology (New York, N.Y.) 2007;9(5):577-91.
2007: Varghese Sanju A; Powell T Brian; Budisavljevic Milos N; Oates Jim C; Raymond John R; Almeida Jonas S; Arthur John M
Urine biomarkers predict the cause of glomerular disease.
Journal of the American Society of Nephrology : JASN 2007;18(3):913-22.
2007: Wolf Gundula; Almeida Jonas S; Crespo João G; Reis Maria A M
An improved method for two-dimensional fluorescence monitoring of complex bioreactors.
Journal of biotechnology 2007;128(4):801-12.
2007: Robalino Javier; Almeida Jonas S; McKillen David; Colglazier Joan; Trent Harold F; Chen Yian Ann; Peck Megan E T; Browdy Craig L; Chapman Robert W; Warr Gregory W; Gross Paul S
Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge.
Physiological genomics 2007;29(1):44-56.
2007: Karpievitch Yuliya V; Hill Elizabeth G; Smolka Adam J; Morris Jeffrey S; Coombes Kevin R; Baggerly Keith A; Almeida Jonas S
PrepMS: TOF MS data graphical preprocessing tool.
Bioinformatics (Oxford, England) 2007;23(2):264-5.
2007: Deus Helena F; Sousa Marta Aires de; Carrico Joao A; Lencastre Herminia de; Almeida Jonas S
Adapting experimental ontologies for molecular epidemiology.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2007;():935.
2007: Vinga Susana; Almeida Jonas S
Local Renyi entropic profiles of DNA sequences.
BMC bioinformatics 2007;8():393.
2007: Vilela Marco; Borges Carlos C H; Vinga Susana; Vasconcelos Ana Tereza R; Santos Helena; Voit Eberhard O; Almeida Jonas S
Automated smoother for the numerical decoupling of dynamics models.
BMC bioinformatics 2007;8():305.
2007: Bohn A; Zippel B; Almeida J S; Xavier J B
Stochastic modeling for characterisation of biofilm development with discrete detachment events (sloughing).
Water science and technology : a journal of the International Association on Water Pollution Research 2007;55(8-9):257-64.
2007: Pinto Francisco R; Carriço João A; Ramirez Mário; Almeida Jonas S
Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement.
BMC bioinformatics 2007;8():44.
2007: Mancia Annalaura; Lundqvist Mats L; Romano Tracy A; Peden-Adams Margie M; Fair Patricia A; Kindy Mark S; Ellis Blake C; Gattoni-Celli Sebastiano; McKillen David J; Trent Harold F; Chen Yian Ann; Almeida Jonas S; Gross Paul S; Chapman Robert W; Warr Gregory W
A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions.
Developmental and comparative immunology 2007;31(5):520-9.
2006: Almeida Jonas S; Chen Chuming; Gorlitsky Robert; Stanislaus Romesh; Aires-de-Sousa Marta; Eleutério Pedro; Carriço João; Maretzek António; Bohn Andreas; Chang Allen; Zhang Fan; Mitra Rahul; Mills Gordon B; Wang Xiaoshu; Deus Helena F
Data integration gets 'Sloppy'.
Nature biotechnology 2006;24(9):1070-1.
2006: Bland Alison M; D'Eugenio Louis R; Dugan Melissa A; Janech Michael G; Almeida Jonas S; Zile Michael R; Arthur John M
Comparison of variability associated with sample preparation in two-dimensional gel electrophoresis of cardiac tissue.
Journal of biomolecular techniques : JBT 2006;17(3):195-9.
2006: Carriço J A; Silva-Costa C; Melo-Cristino J; Pinto F R; de Lencastre H; Almeida J S; Ramirez M
Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes.
Journal of clinical microbiology 2006;44(7):2524-32.
2006: Almeida Jonas S; Vinga Susana
Computing distribution of scale independent motifs in biological sequences.
Algorithms for molecular biology : AMB 2006;1():18.
2006: Karpievitch Yuliya V; Almeida Jonas S
mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.
BMC bioinformatics 2006;7():139.
2006: Mueller Martina; Wagner Carol L; Annibale David J; Knapp Rebecca G; Hulsey Thomas C; Almeida Jonas S
Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants.
BMC medical informatics and decision making 2006;6():11.
2006: Chen Yian A; Chou Cheng-Chung; Lu Xinghua; Slate Elizabeth H; Peck Konan; Xu Wenying; Voit Eberhard O; Almeida Jonas S
A multivariate prediction model for microarray cross-hybridization.
BMC bioinformatics 2006;7():101.
2006: Mueller Lukas N; de Brouwer Jody F C; Almeida Jonas S; Stal Lucas J; Xavier João B
Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP.
BMC ecology 2006;6():1.
2005: Oates Jim C; Varghese Sanju; Bland Alison M; Taylor Timothy P; Self Sally E; Stanislaus Romesh; Almeida Jonas S; Arthur John M
Prediction of urinary protein markers in lupus nephritis.
Kidney international 2005;68(6):2588-92.
2005: Carriço J A; Pinto F R; Simas C; Nunes S; Sousa N G; Frazão N; de Lencastre H; Almeida J S
Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis.
Journal of clinical microbiology 2005;43(11):5483-90.
2005: Wang Xiaoshu; Gorlitsky Robert; Almeida Jonas S
From XML to RDF: how semantic web technologies will change the design of 'omic' standards.
Nature biotechnology 2005;23(9):1099-103.
2005: Garcia Sara P; Almeida Jonas S
Multivariate phase space reconstruction by nearest neighbor embedding with different time delays.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;72(2 Pt 2):027205.
2005: Wolf Gundula; Almeida Jonas S; Reis Maria A M; Crespo João G
Non-mechanistic modelling of complex biofilm reactors and the role of process operation history.
Journal of biotechnology 2005;117(4):367-83.
2005: Mikhitarian Kaidi; Gillanders William E; Almeida Jonas S; Hebert Martin Renee; Varela Juan C; Metcalf John S; Cole David J; Mitas Michael
An innovative microarray strategy identities informative molecular markers for the detection of micrometastatic breast cancer.
Clinical cancer research : an official journal of the American Association for Cancer Research 2005;11(10):3697-704.
2005: Stanislaus Romesh; Chen Chuming; Franklin Jennifer; Arthur John; Almeida Jonas S
AGML Central: web based gel proteomic infrastructure.
Bioinformatics (Oxford, England) 2005;21(9):1754-7.
2005: Almeida Jonas S; Stanislaus Romesh; Krug Ed; Arthur John M
Normalization and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics.
Proteomics 2005;5(5):1242-9.
2005: Pinto F R; Cowart L Ashley; Hannun Yusuf A; Rohrer B; Almeida J S
Local correlation of expression profiles with gene annotations--proof of concept for a general conciliatory method.
Bioinformatics (Oxford, England) 2005;21(7):1037-45.
2005: Garcia Sara P; Almeida Jonas S
Nearest neighbor embedding with different time delays.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;71(3 Pt 2B):037204.
2005: Mitas Michael; Almeida Jonas S; Mikhitarian Kaidi; Gillanders William E; Lewin David N; Spyropoulos Demetri D; Hoover Loretta; Graham Amanda; Glenn Tammy; King Peter; Cole David J; Hawes Robert; Reed Carolyn E; Hoffman Brenda J
Accurate discrimination of Barrett's esophagus and esophageal adenocarcinoma using a quantitative three-tiered algorithm and multimarker real-time reverse transcription-PCR.
Clinical cancer research : an official journal of the American Association for Cancer Research 2005;11(6):2205-14.
2005: Frazão Nelson; Brito-Avô António; Simas Carla; Saldanha Joana; Mato Rosario; Nunes Sónia; Sousa Natacha G; Carriço João A; Almeida Jonas S; Santos-Sanches Ilda; de Lencastre Hermínia
Effect of the seven-valent conjugate pneumococcal vaccine on carriage and drug resistance of Streptococcus pneumoniae in healthy children attending day-care centers in Lisbon.
The Pediatric infectious disease journal 2005;24(3):243-52.
2005: Nunes S; Sá-Leão R; Carriço J; Alves C R; Mato R; Avô A Brito; Saldanha J; Almeida J S; Sanches I Santos; de Lencastre H
Trends in drug resistance, serotypes, and molecular types of Streptococcus pneumoniae colonizing preschool-age children attending day care centers in Lisbon, Portugal: a summary of 4 years of annual surveillance.
Journal of clinical microbiology 2005;43(3):1285-93.
2005: Almeida Jonas S; Nowotny Helga
The emergence of the ERC.
Science (New York, N.Y.) 2005;307(5713):1200; author reply 1200.
2005: Almeida J S; McKillen D J; Chen Y A; Gross P S; Chapman R W; Warr G
Design and calibration of microarrays as universal transcriptomic environmental biosensors.
Comparative and functional genomics 2005;6(3):132-7.
2005: Mato R; Sanches I Santos; Simas C; Nunes S; Carriço J A; Sousa N G; Frazão N; Saldanha J; Brito-Avô A; Almeida J S; Lencastre H De
Natural history of drug-resistant clones of Streptococcus pneumoniae colonizing healthy children in Portugal.
Microbial drug resistance (Larchmont, N.Y.) 2005;11(4):309-22.
2005: Wolf G; Almeida J S; Reis M A M; Crespo J G
Modelling of the extractive membrane bioreactor process based on natural fluorescence fingerprints and process operation history.
Water science and technology : a journal of the International Association on Water Pollution Research 2005;51(6-7):51-8.
2005: McKillen David J; Chen Yian A; Chen Chuming; Jenny Matthew J; Trent Harold F; Robalino Javier; McLean David C; Gross Paul S; Chapman Robert W; Warr Gregory W; Almeida Jonas S
Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms.
BMC genomics 2005;6(1):34.
2004: Chen Yian A; McKillen David J; Wu Shuyuan; Jenny Matthew J; Chapman Robert; Gross Paul S; Warr Gregory W; Almeida Jonas S
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information.
BMC bioinformatics 2004;5():191.
2004: Vinga Susana; Almeida Jonas S
Rényi continuous entropy of DNA sequences.
Journal of theoretical biology 2004;231(3):377-88.
2004: Rohrer Baerbel; Pinto Francisco R; Hulse Kathryn E; Lohr Heather R; Zhang Li; Almeida Jonas S
Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling.
The Journal of biological chemistry 2004;279(40):41903-10.
2004: Mueller Martina; Wagner Carol L; Annibale David J; Hulsey Thomas C; Knapp Rebecca G; Almeida Jonas S
Predicting extubation outcome in preterm newborns: a comparison of neural networks with clinical expertise and statistical modeling.
Pediatric research 2004;56(1):11-8.
2004: Stanislaus Romesh; Jiang Liu Hong; Swartz Martha; Arthur John; Almeida Jonas S
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.
BMC bioinformatics 2004;5():9.
2004: Vinga Susana; Gouveia-Oliveira Rodrigo; Almeida Jonas S
Comparative evaluation of word composition distances for the recognition of SCOP relationships.
Bioinformatics (Oxford, England) 2004;20(2):206-15.
2003: Blehert David S; Palmer Robert J; Xavier Joao B; Almeida Jonas S; Kolenbrander Paul E
Autoinducer 2 production by Streptococcus gordonii DL1 and the biofilm phenotype of a luxS mutant are influenced by nutritional conditions.
Journal of bacteriology 2003;185(16):4851-60.
2003: Cowart L Ashley; Okamoto Yasuo; Pinto Francisco R; Gandy Jason L; Almeida Jonas S; Hannun Yusuf A
Roles for sphingolipid biosynthesis in mediation of specific programs of the heat stress response determined through gene expression profiling.
The Journal of biological chemistry 2003;278(32):30328-38.
2003: Almeida Jonas S; Voit Eberhard O
Neural-network-based parameter estimation in S-system models of biological networks.
Genome informatics. International Conference on Genome Informatics 2003;14():114-23.
2003: Freitas F; Temudo M; Almeida J S; Reis M A M
Nutrient removal in a sequencing batch reactor operated with short anaerobic/aerobic cycles.
Communications in agricultural and applied biological sciences 2003;68(2 Pt A):85-92.
2003: Mueller Martina; Wagner Carol L; Annibale David J; Hulsey Thomas C; Knapp Rebecca G; Almeida Jonas S
Web-based prediction of extubation outcome in premature infants on mechanical ventilation using an artificial neural network.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2003;():945.
2003: Wolf G; Almeida J S; Crespo J G; Reis M A M
Monitoring of biofilm reactors using natural fluorescence fingerprints.
Water science and technology : a journal of the International Association on Water Pollution Research 2003;47(5):161-7.
2003: Xavier J B; White D C; Almeida J S
Automated biofilm morphology quantification from confocal laser scanning microscopy imaging.
Water science and technology : a journal of the International Association on Water Pollution Research 2003;47(5):31-7.
2002: Schwacke John; Almeida Jonas S
Efficient Boolean implementation of universal sequence maps (bUSM).
BMC bioinformatics 2002;3():28.
2002: Almeida Jonas S
Predictive non-linear modeling of complex data by artificial neural networks.
Current opinion in biotechnology 2002;13(1):72-6.
2002: Almeida Jonas S; Vinga Susana
Universal sequence map (USM) of arbitrary discrete sequences.
BMC bioinformatics 2002;3():6.
2001: Xavier J B; Schnell A; Wuertz S; Palmer R; White D C; Almeida J S
Objective threshold selection procedure (OTS) for segmentation of scanning laser confocal microscope images.
Journal of microbiological methods 2001;47(2):169-80.
2001: Almeida J S; Carriço J A; Maretzek A; Noble P A; Fletcher M
Analysis of genomic sequences by Chaos Game Representation.
Bioinformatics (Oxford, England) 2001;17(5):429-37.
2001: Wolf G; Almeida J S; Pinheiro C; Correia V; Rodrigues C; Reis M A; Crespo J G
Two-dimensional fluorometry coupled with artificial neural networks: a novel method for on-line monitoring of complex biological processes.
Biotechnology and bioengineering 2001;72(3):297-306.
2001: Freitas F; Pires T; Barqueiro R; Almeida J S; Reis M A
Carbon, nitrogen and phosphorus removal in a sequential batch reactor operated with high frequency oxygen oscillations.
Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen) 2001;66(3a):155-8.
2000: Almeida J S; Noble P A
Neural computing in microbiology.
Journal of microbiological methods 2000;43(1):1-2.
2000: Neves A R; Ramos A; Shearman C; Gasson M J; Almeida J S; Santos H
Metabolic characterization of Lactococcus lactis deficient in lactate dehydrogenase using in vivo 13C-NMR.
European journal of biochemistry / FEBS 2000;267(12):3859-68.
2000: Cruz P E; Almeida J S; Murphy P N; Moreira J L; Carrondo M J
Modeling retrovirus production for gene therapy. 1. Determination Of optimal bioreaction mode and harvest strategy.
Biotechnology progress 2000;16(2):213-21.
2000: Noble P A; Almeida J S; Lovell C R
Application of neural computing methods for interpreting phospholipid fatty acid profiles of natural microbial communities.
Applied and environmental microbiology 2000;66(2):694-9.
1999: Lopes M F; Pereira C I; Rodrigues F M; Martins M P; Mimoso M C; Barros T C; Figueiredo Marques J J; Tenreiro R P; Almeida J S; Barreto Crespo M T
Registered designation of origin areas of fermented food products defined by microbial phenotypes and artificial neural networks.
Applied and environmental microbiology 1999;65(10):4484-9.
1999: Palmqvist E; Almeida J S; Hahn-Hägerdal B
Influence of furfural on anaerobic glycolytic kinetics of Saccharomyces cerevisiae in batch culture.
Biotechnology and bioengineering 1999;62(4):447-54.
1996: Sijbesma W F; Almeida J S; Reis M A; Santos H
Uncoupling effect of nitrite during denitrification by Pseudomonas fluorescens: An in vivo (31)P-NMR study.
Biotechnology and bioengineering 1996;52(1):176-82.
1995: Almeida J S; Reis M A; Carrondo M J
Competition between nitrate and nitrite reduction in denitrification by Pseudomonas fluorescens.
Biotechnology and bioengineering 1995;46(5):476-84.
1995: Almeida J S; Júlio S M; Reis M A; Carrondo M J
Nitrite inhibition of denitrification by Pseudomonas fluorescens.
Biotechnology and bioengineering 1995;46(3):194-201.
1992: Reis M A; Almeida J S; Lemos P C; Carrondo M J
Effect of hydrogen sulfide on growth of sulfate reducing bacteria.
Biotechnology and bioengineering 1992;40(5):593-600.
1990: Crespo J P; Almeida J S; Moura M J; Carrondo M J
Modeling of immobilized cell reactor for propionic acid fermentation.
Biotechnology and bioengineering 1990;36(7):705-16.

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