Entropic Profiler – detection of conservation in genomes using information theory (2009)
Fernandes, Francisco, Freitas, Ana T, Almeida, Jonas S, Vinga, Susana
Abstract Background In the last decades, with the successive availability of whole genome sequences, many research efforts have been made to mathematically model DNA. Entropic Profiles (EP) were...
Identification of neutral biochemical network models from time series data (2009)
Vilela, Marco, Vinga, Susana, Maia, Marco, Voit, Eberhard O, Almeida, Jonas S
Abstract Background The major difficulty in modeling biological systems from multivariate time series is the identification of parameter sets that endow a model with dynamical behaviors sufficiently...
Biological sequences as pictures – a generic two dimensional solution for iterated maps (2009)
Almeida, Jonas S, Vinga, Susana
Abstract Background Representing symbolic sequences graphically using iterated maps has enjoyed an enduring popularity since it was first proposed in Jeffrey 1990 as chaos game representation (CGR)....
Stanislaus, Romesh, Carey, Mark, Deus, Helena F, Coombes, Kevin, Hennessy, Bryan T, Mills, Gordon B, ...
Abstract Background Reverse Phase Protein Arrays (RPPA) are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies,...
Parameter optimization in S-system models (2008)
Vilela, Marco, Chou, I-Chun, Vinga, Susana, Vasconcelos, Ana, Voit, Eberhard O, Almeida, Jonas S
Abstract Background The inverse problem of identifying the topology of biological networks from their time series responses is a cornerstone challenge in systems biology. We tackle this challenge...
Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John Arthur, Jonas S. Almeida
Summary: AGML Central is a web-based open-source public infrastructure for dissemination of two-dimensional Gel Electrophoresis (2-DE) proteomics data in AGML format (Annotated Gel Markup Language)....
Stanislaus, Romesh, Arthur, John M, Rajagopalan, Balaji, Moerschell, Rick, McGlothlen, Brian, Almeida, Jonas S
Abstract Background In spite of two-dimensional gel electrophoresis (2-DE) being an effective and widely used method to screen the proteome, its data standardization has still not matured to the...
Bmc Bioinformatics, Romesh Stanislaus, Balaji Rajagopalan, Rick Moerschell, Brian Mcglothlen, ...
Research article An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis
3 Methodology article Universal sequence map (USM) of arbitrary discrete sequences (2007)
Jonas S Almeida, Susana Vinga, Biomed Central
© 2002 Almeida and Vinga; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any purpose, provided this notice is preserved along with...
Efficient Boolean implementation of universal sequence maps (bUSM) (2007)
Bmc Bioinformatics, Jonas S Almeida, John Schwacke, John Schwacke, Jonas S. Almeida
corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available within a few days, from the URL listed below.
Local Renyi entropic profiles of DNA sequences (2007)
Vinga, Susana, Almeida, Jonas S
Abstract Background In a recent report the authors presented a new measure of continuous entropy for DNA sequences, which allows the estimation of their randomness level. The definition therein...
Automated smoother for the numerical decoupling of dynamics models (2007)
Vilela, Marco, Borges, Carlos CH, Vinga, Susana, Vasconcelos, Ana, Santos, Helena, Voit, Eberhard O, ...
Abstract Background Structure identification of dynamic models for complex biological systems is the cornerstone of their reverse engineering. Biochemical Systems Theory (BST) offers a particularly...
Pinto, Francisco R, Carriço, João A, Ramirez, Mário, Almeida, Jonas S
Abstract Background Biological information is commonly used to cluster or classify entities of interest such as genes, conditions, species or samples. However, different sources of data can be used...
PrepMS: TOF MS data graphical preprocessing tool (2007)
Karpievitch, Yuliya V., Hill, Elizabeth G., Smolka, Adam J., Morris, Jeffrey S., Coombes, Kevin R., Baggerly, Keith A., ...
Summary: We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides...
BioMed Central Open Access (2007)
Susana Vinga, Jonas S Almeida, R. Alves Redol
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Computing distribution of scale independent motifs in biological sequences (2006)
Almeida, Jonas S, Vinga, Susana
Abstract The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of...
Garcia, Sara P., Almeida, Jonas S.
A recently proposed nearest neighbor based selection of time delays for phase space reconstruction is extended to multivariate time series, with an iterative selection of variables and time delays. A...
Karpievitch, Yuliya V, Almeida, Jonas S
Abstract Background Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large...
A multivariate prediction model for microarray cross-hybridization (2006)
Chen, Yian A, Chou, Cheng-Chung, Lu, Xinghua, Slate, Elizabeth H, Peck, Konan, Xu, Wenying, ...
Abstract Background Expression microarray analysis is one of the most popular molecular diagnostic techniques in the post-genomic era. However, this technique faces the fundamental problem of...
Mueller, Martina, Wagner, Carol L, Annibale, David J, Knapp, Rebecca G, Hulsey, Thomas C, Almeida, Jonas S
Abstract Background Approximately 30% of intubated preterm infants with respiratory distress syndrome (RDS) will fail attempted extubation, requiring reintubation and mechanical ventilation. Although...
Mueller, Lukas N, De Brouwer, Jody FC, Almeida, Jonas S, Stal, Lucas J, Xavier, João B
Abstract Background Confocal laser scanning microscopy (CLSM) is the method of choice to study interfacial biofilms and acquires time-resolved three-dimensional data of the biofilm structure. CLSM...
Mueller, Lukas N., De Brouwer, Jody, Almeida, Jonas S., Stal, Lucas J., Xavier, João B.
In: BMC Ecology 2006,6
Bmc Bioinformatics, Yuliya V Karpievitch, Yuliya V Karpievitch, Jonas S Almeida
Software mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code
Yian A Chen, Cheng-chung Chou, Xinghua Lu, Elizabeth H Slate, Konan Peck, Wenying Xu, ...
© 2006Chen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
BIOINFORMATICS APPLICATIONS NOTE Data and text mining (2006)
Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, ...
doi:10.1093/bioinformatics/btl583
Algorithms for Molecular Biology (2006)
Jonas S Almeida, Susana Vinga, Biomed Central, Jonas S Almeida, Susana Vinga
Computing distribution of scale independent motifs in biological sequences
A multivariate prediction model for microarray cross-hybridization (2006)
Chen, Yian A., Chou, Cheng-Chung, Lu, Xinghua, Slate, Elizabeth H., Peck, Konan, Xu, Wenying, ...
© 2006 Chen et al; licensee BioMed Central Ltd.
Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms (2005)
McKillen, David J, Chen, Yian A, Chen, Chuming, Jenny, Matthew J, Trent, Harold F, Robalino, Javier, ...
Abstract Background The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs) and gene expression microarray...
AGML Central: web based gel proteomic infrastructure (2005)
Stanislaus, Romesh, Chen, Chuming, Franklin, Jennifer, Arthur, John, Almeida, Jonas S.
Summary: AGML Central is a web-based open-source public infrastructure for dissemination of two-dimensional Gel Electrophoresis (2-DE) proteomics data in AGML format (Annotated Gel Markup Language)....
AGML central: web based gel proteomic infrastructure (2005)
Stanislaus, Romesh, Chen, Chuming, Franklin, Jennifer, Arthur, John, Almeida, Jonas S.
Summary: AGML Central is a web-based open-source public infrastructure for dissemination of 2-D Gel Electrophoresis (2-DE) proteomics data in AGML format (Annotated Gel Markup Language). It includes...
David J Mckillen, Yian A Chen, Chuming Chen, Matthew J Jenny, Javier Robalino, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Chen, Yian A, Mckillen, David J, Wu, Shuyuan, Jenny, Matthew J, Chapman, Robert, Gross, Paul S, ...
Abstract Background Expression microarrays are increasingly used to characterize environmental responses and host-parasite interactions for many different organisms. Probe selection for cDNA...
Nearest neighbor embedding with different time delays (2004)
Garcia, Sara P., Almeida, Jonas S.
A nearest neighbor based selection of time delays for phase space reconstruction is proposed and compared to the standard use of time delayed mutual information. The possibility of using different...
Priming nonlinear searches for pathway identification (2004)
Veflingstad, Siren R., Almeida, Jonas S., Voit, Eberhard O.
©2004 Veflingstad et al; licensee BioMed Central Ltd. This is an open-access article distributed under the terms of the Creative Commons Attribution License...
Stanislaus, Romesh, Jiang, Liu, Swartz, Martha, Arthur, John, Almeida, Jonas S
Abstract Background Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to...
BMC Medical Informatics and Decision Making (2004)
Biomed Central, Martina Mueller, Carol L Wagner, David J Annibale, Thomas C Hulsey, ...
Research article Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants
Bmc Bioinformatics, Yian A Chen, David J Mckillen, Shuyuan Wu, Matthew J Jenny, Robert Chapman, ...
Research article Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information
Vinga, Susana, Gouveia-Oliveira, Rodrigo, Almeida, Jonas S.
Motivation: Alignment-free metrics were recently reviewed by the authors, but have not until now been object of a comparative study. This paper compares the classification accuracy of word...
XML4MAT: Inter-conversion between MatlabTM (2003)
Almeida, Jonas S., Wu, Shuyuan, Voit, Eberhard O.
The MatlabTM programming environment and related public license environments such as Octave are gaining in popularity for the identification of algorithms and the rapid prototyping of applications in...
XML4MAT: Inter-conversion between MatlabTM structured variables and the markup language MbML (2003)
Almeida, Jonas S., Wu, Shuyuan, Voit, Eberhard O.
The MatlabTM programming environment and related public license environments such as Octave are gaining in popularity for the identification of algorithms and the rapid prototyping of applications in...
Neural-network-based parameter estimation in s-system models of biological networks (2003)
Jonas S. Almeida, Eberhard O. Voit
The genomic and post-genomic eras have been blessing us with overwhelming amounts of data that are of increasing quality. The challenge is that most of these data alone are mere snapshots of the...
W-metric for protein sequence comparison in SCOP database (2003)
Susana Vinga Rodrigo, Rodrigo Gouveia-oliveira, Jonas S. Almeida
Introduction Alignment-free metrics for sequence comparison were recently reviewed by the authors [1], but have not until now been object of a comparative quantitative study. In order to complement...
XML4MAT: Inter-conversion between Matlab TM structured variables and the markup language MbML (2003)
Jonas S Almeida, Shuyuan Wu, Eberhard O. Voit
The Matlab TM programming environment and related public license environments such as Octave are gaining in popularity for the identification of algorithms and the rapid prototyping of applications...
Efficient Boolean implementation of universal sequence maps (bUSM) (2002)
Schwacke, John, Almeida, Jonas S
Abstract Background Recently, Almeida and Vinga offered a new approach for the representation of arbitrary discrete sequences, referred to as Universal Sequence Maps (USM), and discussed its...
Universal sequence map (USM) of arbitrary discrete sequences (2002)
Almeida, Jonas S, Vinga, Susana
Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any...
Analysis of genomic sequences by Chaos Game Representation (2001)
Almeida, Jonas S., Carriço, João A., Maretzek, António, Noble, Peter A., Fletcher, Madilyn
Motivation: Chaos Game Representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to find...
Phospholipid Fatty Acid Profiles of Natural Microbial Communities† (1999)
Peter A. Noble, Jonas S. Almeida, Charles R. Lovell
The microbial community compositions of surface and subsurface marine sediments and sediments lining burrows of marine polychaetes and hemichordates from the North Inlet estuary (near Georgetown,...
Noble, Peter A., Almeida, Jonas S., Lovell, Charles R.
The microbial community compositions of surface and subsurface marine sediments and sediments lining burrows of marine polychaetes and hemichordates from the North Inlet estuary (near Georgetown,...
Blehert, David S., Palmer, Robert J., Xavier, Joao B., Almeida, Jonas S., Kolenbrander, Paul E.
The luxS gene, present in many bacterial genera, encodes the autoinducer 2 (AI-2) synthase. AI-2 has been implicated in bacterial signaling, and this study investigated its role in biofilm formation...
Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms
McKillen, David J, Chen, Yian A, Chen, Chuming, Jenny, Matthew J, Trent, Harold F, Robalino, Javier, ...
A multivariate prediction model for microarray cross-hybridization
Chen, Yian A, Chou, Cheng-Chung, Lu, Xinghua, Slate, Elizabeth H, Peck, Konan, Xu, Wenying, ...
Mueller, Martina, Wagner, Carol L, Annibale, David J, Knapp, Rebecca G, Hulsey, Thomas C, Almeida, Jonas S
Mueller, Martina, Wagner, Carol L., Annibale, David J., Hulsey, Thomas C., Knapp, Rebecca G., Almeida, Jonas S.
The web-based implementation of a decision-support tool for the prediction of extubation outcome in mechanically ventilated premature infants enables the integration of advanced and computationally...
Computing distribution of scale independent motifs in biological sequences
Almeida, Jonas S, Vinga, Susana
The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of the...
Noble, Peter A., Almeida, Jonas S., Lovell, Charles R.
The microbial community compositions of surface and subsurface marine sediments and sediments lining burrows of marine polychaetes and hemichordates from the North Inlet estuary (near Georgetown,...
Blehert, David S., Palmer, Robert J., Xavier, Joao B., Almeida, Jonas S., Kolenbrander, Paul E.
The luxS gene, present in many bacterial genera, encodes the autoinducer 2 (AI-2) synthase. AI-2 has been implicated in bacterial signaling, and this study investigated its role in biofilm formation...
Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms
McKillen, David J, Chen, Yian A, Chen, Chuming, Jenny, Matthew J, Trent, Harold F, Robalino, Javier, ...
A multivariate prediction model for microarray cross-hybridization
Chen, Yian A, Chou, Cheng-Chung, Lu, Xinghua, Slate, Elizabeth H, Peck, Konan, Xu, Wenying, ...
Mueller, Martina, Wagner, Carol L, Annibale, David J, Knapp, Rebecca G, Hulsey, Thomas C, Almeida, Jonas S
Mueller, Martina, Wagner, Carol L., Annibale, David J., Hulsey, Thomas C., Knapp, Rebecca G., Almeida, Jonas S.
The web-based implementation of a decision-support tool for the prediction of extubation outcome in mechanically ventilated premature infants enables the integration of advanced and computationally...
Computing distribution of scale independent motifs in biological sequences
Almeida, Jonas S, Vinga, Susana
The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of the...
Automated smoother for the numerical decoupling of dynamics models
Vilela, Marco, Borges, Carlos CH, Vinga, Susana, Vasconcelos, Ana Tereza R, Santos, Helena, Voit, Eberhard O, ...
Stanislaus, Romesh, Arthur, John M, Rajagopalan, Balaji, Moerschell, Rick, McGlothlen, Brian, Almeida, Jonas S
Parameter optimization in S-system models
Vilela, Marco, Chou, I-Chun, Vinga, Susana, Vasconcelos, Ana Tereza R, Voit, Eberhard O, Almeida, Jonas S
Sá-Leão, Raquel, Nunes, Sónia, Brito-Avô, António, Alves, Carla R., Carriço, João A., Saldanha, Joana, ...
Day care centers (DCCs) are unique settings where young children are at increased risk for colonization by pneumococci and Haemophilus influenzae. Although point prevalence studies in DCCs are...
Bland, Alison M., D’Eugenio, Louis R., Dugan, Melissa A., Janech, Michael G., Almeida, Jonas S., Zile, Michael R., ...
Variability is a major complicating factor in analysis by two-dimensional gel electrophoresis. Improvements in methodologies have focused on improving individual gel quality rather than...
A Semantic Web Management Model for Integrative Biomedical Informatics
Deus, Helena F., Stanislaus, Romesh, Veiga, Diogo F., Behrens, Carmen, Wistuba, Ignacio I., Minna, John D., ...
Exploratory Analysis of the Copy Number Alterations in Glioblastoma Multiforme
Freire, Pablo, Vilela, Marco, Deus, Helena, Kim, Yong-Wan, Koul, Dimpy, Colman, Howard, ...
RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays
Stanislaus, Romesh, Carey, Mark, Deus, Helena F, Coombes, Kevin, Hennessy, Bryan T, Mills, Gordon B, ...
Entropic Profiler – detection of conservation in genomes using information theory
Fernandes, Francisco, Freitas, Ana T, Almeida, Jonas S, Vinga, Susana
Identification of neutral biochemical network models from time series data
Vilela, Marco, Vinga, Susana, Voit, Eberhard O, Almeida, Jonas S
Karpievitch, Yuliya V., Hill, Elizabeth G., Leclerc, Anthony P., Dabney, Alan R., Almeida, Jonas S.
Many mass spectrometry-based studies, as well as other biological experiments produce cluster-correlated data. Failure to account for correlation among observations may result in a classification...