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Author Details

Jonas S Almeida
National Cancer Institute (NCI)
1990
133
35
PMIDPaper TitleJournal TitlePublished Year
37608772Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: A report of the International Immuno-Oncology Biomarker Working Group on Breast CancerJ Pathol2023
33163255ImageBox 2 - Efficient and Rapid Access of Image Tiles from Whole-Slide Images Using Serverless HTTP Range Requests.J Pathol Inform2020
30671301Serverless OpenHealth at data commons scale-traversing the 20 million patient records of New York's SPARCS dataset in real-time.PeerJ2019
31345254Benchmarking of alignment-free sequence comparison methods.Genome Biol2019
30130366Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data.PLoS One2018
27797761Isomorphic semantic mapping of variant call format (VCF2RDF).Bioinformatics2017
28269829Safe "cloudification" of large images through picker APIs.AMIA Annu Symp Proc2017
28178722Differential Gene Expression in Ductal Carcinoma In Situ of the Breast Based on ERBB2 Status.Cancer Control2017
29092946A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images.Cancer Res2017
28974235Alignment-free sequence comparison: benefits, applications, and tools.Genome Biol2017
26098131Computational Pathology: A Path Ahead.Arch Pathol Lab Med2016
27601856Mechanistic Parameterization of the Kinomic Signal in Peptide Arrays.J Proteomics Bioinform2016
25701882Coming into focus: computational pathology as the new big data microscope.Am J Pathol2015
26958160OpenHealth Platform for Interactive Contextualization of Population Health Open Data.AMIA Annu Symp Proc2015
25919366Proteomic Analysis of Plasma from California Sea Lions (Zalophus californianus) Reveals Apolipoprotein E as a Candidate Biomarker of Chronic Domoic Acid Toxicosis.PLoS One2015
25634794Development of novel software to generate anthropometric norms at perinatal autopsy.Pediatr Dev Pathol2015
24162172Sequence analysis by iterated maps, a review.Brief Bioinform2014
25937882TopFed: TCGA tailored federated query processing and linking to LOD.J Biomed Semantics2014
24913605QMachine: commodity supercomputing in web browsers.BMC Bioinformatics2014
24672738Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology.J Pathol Inform2014
24467687Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.BMC Bioinformatics2014
23502430Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis.Neuro Oncol2013
25419493Can Machine Learning Methods Predict Extubation Outcome in Premature Infants as well as Clinicians?J Neonatal Biol2013
25485175Machine learning to predict extubation outcome in premature infants.Proc Int Jt Conf Neural Netw2013
23595662A self-updating road map of The Cancer Genome Atlas.Bioinformatics2013
22429742Serum profiling by MALDI-TOF mass spectrometry as a diagnostic tool for domoic acid toxicosis in California sea lions.Proteome Sci2012
22934238ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.J Pathol Inform2012
22551205Fractal MapReduce decomposition of sequence alignment.Algorithms Mol Biol2012
22551152Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis.Algorithms Mol Biol2012
22222338Premature atherosclerosis is associated with hypovitaminosis D and angiotensin-converting enzyme inhibitor non-use in lupus patients.Am J Med Sci2012
21756325S3QL: a distributed domain specific language for controlled semantic integration of life sciences data.BMC Bioinformatics2011
19958840Modelling interactions of acid-base balance and respiratory status in the toxicity of metal mixtures in the American oyster Crassostrea virginica.Comp Biochem Physiol A Mol Integr Physiol2010
20851208Exposing the cancer genome atlas as a SPARQL endpoint.J Biomed Inform2010
20818957Examining the effect of maternal obesity on outcome of labor induction in patients with preeclampsia.Hypertens Pregnancy2010
20977768AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.BMC Med Inform Decis Mak2010
20854645Computational ecosystems for data-driven medical genomics.Genome Med2010
20877445A nonparametric approach to detect nonlinear correlation in gene expression.J Comput Graph Stat2010
20677327The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.Proteomics2010
20646315S3DB core: a framework for RDF generation and management in bioinformatics infrastructures.BMC Bioinformatics2010
20224435Identification of diagnostic urinary biomarkers for acute kidney injury.J Investig Med2010
20357976Sources of variability among replicate samples separated by two-dimensional gel electrophoresis.J Biomol Tech2010
19416537Identification of neutral biochemical network models from time series data.BMC Syst Biol2009
19919683DASMiner: discovering and integrating data from DAS sources.BMC Syst Biol2009
19763254An introspective comparison of random forest-based classifiers for the analysis of cluster-correlated data by way of RF++.PLoS One2009
19335894Biological sequences as pictures: a generic two dimensional solution for iterated maps.BMC Bioinformatics2009
19416538Entropic Profiler - detection of conservation in genomes using information theory.BMC Res Notes2009
18179696An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.BMC Bioinformatics2008
19115005Exploratory analysis of the copy number alterations in glioblastoma multiforme.PLoS One2008
19102773RPPAML/RIMS: a metadata format and an information management system for reverse phase protein arrays.BMC Bioinformatics2008
18999102Data driven semantic integration of translational lung cancer research at MDAnderson Cancer Center.AMIA Annu Symp Proc2008
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Collaborators

Helena F Deus
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Joel Saltz
Stony Brook University
Co-authored papers 7
Kevin R Coombes
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Co-authored papers 6
Gordon B Mills
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Co-authored papers 5
Ana Tereza Ribeiro de Vasconcelos
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Co-authored papers 5
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Co-authored papers 4
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Co-authored papers 3
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Stony Brook University
Co-authored papers 3
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Baylor College of Medicine
Co-authored papers 3
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University of Campinas (UNICAMP)
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College of Medicine, University of Florida
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Stony Brook University
Co-authored papers 2
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Co-authored papers 2
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Co-authored papers 2
John D Minna
University of Texas Southwestern Medical Center at Dallas
Co-authored papers 2
Wei Yang
Co-authored papers 1
David N Louis
Co-authored papers 1
Thomas Walter
PSL University
Co-authored papers 1
Xinghua Lu
Co-authored papers 1
Frank Gibson
Newcastle University
Co-authored papers 1
Burkhard Morgenstern
Institute of Microbiology and Genetics
Co-authored papers 1
Konstantinos Krampis
Co-authored papers 1
William M Gallagher
All-Island Cancer Research Institute, UCD Conway Institute, University College Dublin
Co-authored papers 1
Lynn Bry
Co-authored papers 1
David L Rimm
Yale University School of Medicine
Co-authored papers 1
Release 1.2