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List of works by Jonas Almeida

A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images

scientific article published in November 2017

A Semantic Web management model for integrative biomedical informatics

scientific article

A cDNA microarray for Crassostrea virginica and C. gigas.

scientific article

A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions

scientific article

A multivariate prediction model for microarray cross-hybridization

scientific article

A self-updating road map of The Cancer Genome Atlas

scientific article (publication date: 15 May 2013)

AGML Central: web based gel proteomic infrastructure.

scientific article published on 12 January 2005

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services

scientific article

Accurate discrimination of Barrett's esophagus and esophageal adenocarcinoma using a quantitative three-tiered algorithm and multimarker real-time reverse transcription-PCR.

scientific article published in March 2005

Adapting experimental ontologies for molecular epidemiology

scientific article published on 11 October 2007

Alignment-free sequence comparison-a review

scientific article

Alignment-free sequence comparison: benefits, applications, and tools.

scientific article published on 3 October 2017

An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results

scientific article

An improved method for two-dimensional fluorescence monitoring of complex bioreactors.

scientific article published on 16 January 2007

An innovative microarray strategy identities informative molecular markers for the detection of micrometastatic breast cancer.

scientific article

An introspective comparison of random forest-based classifiers for the analysis of cluster-correlated data by way of RF++.

scientific article

An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis

scientific article (publication date: 7 January 2008)

Automated smoother for the numerical decoupling of dynamics models

scientific article

Benchmarking of alignment-free sequence comparison methods

Benchmarking of alignment-free sequence comparison methods

scientific article published on 25 July 2019

Biological sequences as pictures: a generic two dimensional solution for iterated maps

scientific article

Can Machine Learning Methods Predict Extubation Outcome in Premature Infants as well as Clinicians?

scientific article

Comparative evaluation of word composition distances for the recognition of SCOP relationships.

scientific article

Comparison of variability associated with sample preparation in two-dimensional gel electrophoresis of cardiac tissue

scientific article published on July 2006

Computing distribution of scale independent motifs in biological sequences

scientific article

DASMiner: discovering and integrating data from DAS sources

scientific article

Data Analysis and Modeling

article published in 2003

Data driven semantic integration of translational lung cancer research at MDAnderson Cancer Center.

scientific article

Data integration gets 'Sloppy'

scientific article

Decoupling dynamical systems for pathway identification from metabolic profiles

scientific article published on 26 February 2004

Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS)

article

Diagnostic and prognostic biomarkers in acute renal failure.

scientific article published on January 2008

EURISWEB--Web-based epidemiological surveillance of antibiotic-resistant pneumococci in day care centers

scientific article

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

scientific article

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

scientific article published on 31 December 2018

Entropic Profiler - detection of conservation in genomes using information theory

scientific article

Examining the Effect of Maternal Obesity on Outcome of Labor Induction in Patients with Preeclampsia ⬇️

scientific article published on January 1, 2010

Exploratory analysis of the copy number alterations in glioblastoma multiforme

scientific article

Exposing the cancer genome atlas as a SPARQL endpoint

scientific article (publication date: December 2010)

Fractal MapReduce decomposition of sequence alignment

scientific article

From XML to RDF: how semantic web technologies will change the design of 'omic' standards

scientific article

High rates of transmission of and colonization by Streptococcus pneumoniae and Haemophilus influenzae within a day care center revealed in a longitudinal study

scientific article

Identification of diagnostic urinary biomarkers for acute kidney injury

scientific article

Identification of neutral biochemical network models from time series data

scientific article

Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis

scientific article

ImageBox 2 - Efficient and Rapid Access of Image Tiles from Whole-Slide Images Using Serverless HTTP Range Requests

scientific article published on 10 September 2020

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser ⬇️

scientific article published on July 20, 2012

Impact of Population Growth and Aging on Estimates of Excess U.S. Deaths During the COVID-19 Pandemic, March to August 2020

scientific article published on 15 December 2020

Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge

scientific article

Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data

scientific article published in PLoS ONE

Linked cancer genome atlas database

Local Renyi entropic profiles of DNA sequences

scientific article

Machine learning to predict extubation outcome in premature infants

scientific article published on August 2013

Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms

scientific article

Mechanistic Parameterization of the Kinomic Signal in Peptide Arrays

scientific article published on 24 May 2016

Modelling interactions of acid-base balance and respiratory status in the toxicity of metal mixtures in the American oyster Crassostrea virginica

scientific article

Molecular characterization of methicillin-resistant Staphylococcus epidermidis clones: evidence of geographic dissemination

scientific article

Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling

scientific article

Multivariate phase space reconstruction by nearest neighbor embedding with different time delays

scientific article

Nearest neighbor embedding with different time delays

scientific article published on 29 March 2005

Non-mechanistic modelling of complex biofilm reactors and the role of process operation history.

scientific article published on 25 March 2005

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

scientific article

Normalization and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics.

scientific article published in April 2005

Ontology Design Principles and Normalization Techniques in the Web

article published in Lecture Notes in Computer Science

OpenHealth Platform for Interactive Contextualization of Population Health Open Data

scientific article

Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information

scientific article

Ovarian cancer: linking genomics to new target discovery and molecular markers--the way ahead

scientific article

Parameter optimization in S-system models

scientific article

Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants

scientific article

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

scientific article

Predicting extubation outcome in preterm newborns: a comparison of neural networks with clinical expertise and statistical modeling

scientific article published on 5 May 2004

Prediction of pelvic organ prolapse using an artificial neural network

scientific article published on 04 June 2008

Prediction of urinary protein markers in lupus nephritis

scientific article published on December 2005

Premature atherosclerosis is associated with hypovitaminosis D and angiotensin-converting enzyme inhibitor non-use in lupus patients.

scientific article published in October 2012

PrepMS: TOF MS data graphical preprocessing tool

scientific article

Proteomic Analysis of Plasma from California Sea Lions (Zalophus californianus) Reveals Apolipoprotein E as a Candidate Biomarker of Chronic Domoic Acid Toxicosis

scientific article published on January 2014

RPPAML/RIMS: a metadata format and an information management system for reverse phase protein arrays

scientific article

Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement

scientific article

Roles for Sphingolipid Biosynthesis in Mediation of Specific Programs of the Heat Stress Response Determined through Gene Expression Profiling

scientific article published in Journal of Biological Chemistry

Rényi continuous entropy of DNA sequences

scientific article published on 01 December 2004

S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

scientific article

S3QL: a distributed domain specific language for controlled semantic integration of life sciences data

scientific article

Safe "cloudification" of large images through picker APIs

scientific article published on January 2016

Serum profiling by MALDI-TOF mass spectrometry as a diagnostic tool for domoic acid toxicosis in California sea lions.

scientific article published on 19 March 2012

Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time

article

Sources of variability among replicate samples separated by two-dimensional gel electrophoresis.

scientific article

Techniques for Ontology Visualization

scholarly article

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative

scientific article (publication date: September 2010)

TopFed: TCGA tailored federated query processing and linking to LOD

scientific article

Towards Generation, Management, and Exploration of Combined Radiomics and Pathomics Datasets for Cancer Research

scientific article

Universal sequence map (USM) of arbitrary discrete sequences

scientific article

Urine biomarkers predict the cause of glomerular disease.

scientific article published on 14 February 2007

Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor Infiltrating Lymphocytes in Invasive Breast Cancer

scientific article published on 08 April 2020

Web-based prediction of extubation outcome in premature infants on mechanical ventilation using an artificial neural network.

scientific article published on January 2003

mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

scientific article published on 15 March 2006

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