Jonas S. Almeida

70 papers A 2B 3Misc 5Journal 55Unranked 5
YearRankTypeTitle / Venue / Authors
2026 J jnl
Engineering FAIR Privacy-preserving Applications that Learn Histories of Disease.
CoRR
Ines Duarte, Praphulla M. S. Bhawsar, Lee Mason, Jeya Balaji Balasubramanian, Daniel E. Russ, Arlindo L. Oliveira, Jonas S. Almeida
2025 J jnl
Fractal Language Modelling by Universal Sequence Maps (USM).
CoRR
Jonas S. Almeida, Daniel E. Russ, Susana Vinga, Ines Duarte, Lee Mason, Praphulla M. S. Bhawsar, Aaron Ge, Arlindo L. Oliveira, Jeya Balaji Balasubramanian
2025 J jnl
Leveraging large language models for structured information extraction from pathology reports.
CoRR
Jeya Balaji Balasubramanian, Daniel Adams, Ioannis Roxanis, Amy Berrington de González, Penny Coulson, Jonas S. Almeida, Montserrat Garcia-Closas
2024 J jnl
A Simplified Positional Cell Type Visualization using Spatially Aggregated Clusters.
CoRR
Lee Mason, Jonas S. Almeida
2024 J jnl
ClusterRadar: an Interactive Web-Tool for the Multi-Method Exploration of Spatial Clusters Over Time.
CoRR
Lee Mason, Blánaid Hicks, Jonas S. Almeida
2024 A conf
Demystifying Spatial Dependence: Interactive Visualizations for Interpreting Local Spatial Autocorrelation.
IEEE VIS
Lee Mason, Blánaid Hicks, Jonas S. Almeida
2024 J jnl
Demystifying Spatial Dependence: Interactive Visualizations for Interpreting Local Spatial Autocorrelation.
CoRR
Lee Mason, Blánaid Hicks, Jonas S. Almeida
2024 J jnl
FastImpute: A Baseline for Open-source, Reference-Free Genotype Imputation Methods - A Case Study in PRS313.
CoRR
Aaron Ge, Jeya Balasubramanian, Xueyao Wu, Peter Kraft, Jonas S. Almeida
2024 J jnl
Finding Regions of Interest in Whole Slide Images Using Multiple Instance Learning.
CoRR
Martim Afonso, Praphulla M. S. Bhawsar, Monjoy Saha, Jonas S. Almeida, Arlindo L. Oliveira
2024 J jnl
TMA-Grid: An open-source, zero-footprint web application for FAIR Tissue MicroArray De-arraying.
CoRR
Aaron Ge, Monjoy Saha, Máire A. Duggan, Petra Lenz, Mustapha Abubakar, Montserrat Garcia-Closas, Jeya Balasubramanian, Jonas S. Almeida, Praphulla M. S. Bhawsar
2023 — conf
Conceptual Alignment Method.
AMCIS
Wolfgang Maass, Arturo Castellanos, Monica C. Tremblay, Roman Lukyanenko, Veda C. Storey, Jonas S. Almeida
2023 J jnl
Halcyon - A Pathology Imaging and Feature analysis and Management System.
CoRR
Erich Bremer, Tammy DiPrima, Joseph Balsamo, Jonas S. Almeida, Rajarsi Gupta, Joel H. Saltz
2023 J jnl
Quest markup for developing FAIR questionnaire modules for epidemiologic studies.
BMC Medical Informatics Decis. Mak.
Daniel E. Russ, Nicole M. Gerlanc, Brian Shen, Bhaumik Patel, Amy Berrington de González, Neal D. Freedman, Julie M. Cusack, Mia M. Gaudet, Montserrat Garcia-Closas, Jonas S. Almeida
2022 J jnl
ImageBox3: No-Server Tile Serving to Traverse Whole Slide Images on the Web.
CoRR
Praphulla M. S. Bhawsar, Erich Bremer, Máire A. Duggan, Stephen J. Chanock, Montserrat Garcia-Closas, Joel H. Saltz, Jonas S. Almeida
2022 J jnl
PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project.
Bioinform.
Eric Ruan, Erika Nemeth, Richard A. Moffitt, Lorena Sandoval, Mitchell J. Machiela, Neal D. Freedman, Wen-Yi Huang, Wendy Wong, Kai-Ling Chen, Brian Park, Kevin Jiang, Belynda Hicks, Jia Liu, Daniel E. Russ, Lori M. Minasian, Paul F. Pinsky, Stephen J. Chanock, Montserrat Garcia-Closas, Jonas S. Almeida
2022 B conf
Tutorial - Machine Learning and Information Theoretic Methods for Molecular Biology and Medicine.
ESANN
Thomas Villmann, Jonas S. Almeida, John A. Lee, Susana Vinga
2021 J jnl
Mortality Tracker: the COVID-19 case for real time web APIs as epidemiology commons.
Bioinform.
Jonas S. Almeida, Meredith Shiels, Praphulla M. S. Bhawsar, Bhaumik Patel, Erika Nemeth, Richard A. Moffitt, Montserrat Garcia-Closas, Neal D. Freedman, Amy Berrington de González
2020 J jnl
Representing Whole Slide Cancer Image Features with Hilbert Curves.
CoRR
Erich Bremer, Jonas S. Almeida, Joel H. Saltz
2019 J jnl
Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor Infiltrating Lymphocytes in Invasive Breast Cancer.
CoRR
Han Le, Rajarsi R. Gupta, Le Hou, Shahira Abousamra, Danielle Fassler, Tahsin M. Kurç, Dimitris Samaras, Rebecca Batiste, Tianhao Zhao, Alison L. Van Dyke, Ashish Sharma, Erich Bremer, Jonas S. Almeida, Joel H. Saltz
2018 — conf
Interpretable Machine Learning Approach Reveals Developmental Gene Expression Biomarkers for Cancer Patient Outcomes at Early Stages.
BCB
Alisha Kamat, Ting Jin, So Yeon Min, Flaminia Talos, Jonas S. Almeida, Daifeng Wang
2017 J jnl
Isomorphic semantic mapping of variant call format (VCF2RDF).
Bioinform.
Emanuel Diego S. Penha, Egiebade Iriabho, Alex Dussaq, Diana Magalhaes de Oliveira, Jonas S. Almeida
2016 Misc conf
S2CR3UM: A Solution to the In Silico Relevance, Reliability & Reproducibility Conundrum.
AMIA
Sarah B. Putney, Andrew White, Janos G. Hajagos, Joel H. Saltz, Jonas S. Almeida, Mary M. Saltz
2016 Misc conf
Safe "cloudification" of large images through picker APIs.
AMIA
Erich Bremer, Tahsin M. Kurç, Yi Gao, Joel H. Saltz, Jonas S. Almeida
2015 Misc conf
Integrative Informatics and Predictive Modeling Support for Population Health.
AMIA
Mary M. Saltz, Joel H. Saltz, Janos G. Hajagos, Andrew White, Charles Boicey, Jim Murry, Ivan Crnosija, Tahsin M. Kurç, Erich Bremer, Jonas S. Almeida
2015 Misc conf
OpenHealth Platform for Interactive Contextualization of Population Health Open Data.
AMIA
Jonas S. Almeida, Janos G. Hajagos, Ivan Crnosija, Tahsin M. Kurç, Mary M. Saltz, Joel H. Saltz
2014 J jnl
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.
BMC Bioinform.
Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas S. Almeida, William J. Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder
2014 J jnl
QMachine: commodity supercomputing in web browsers.
BMC Bioinform.
Sean R. Wilkinson, Jonas S. Almeida
2014 J jnl
Sequence analysis by iterated maps, a review.
Briefings Bioinform.
Jonas S. Almeida
2014 J jnl
TopFed: TCGA Tailored Federated Query Processing and Linking to LOD.
J. Biomed. Semant.
Muhammad Saleem, Shanmukha S. Padmanabhuni, Axel-Cyrille Ngonga Ngomo, Aftab Iqbal, Jonas S. Almeida, Stefan Decker, Helena F. Deus
2013 J jnl
A self-updating road map of The Cancer Genome Atlas.
Bioinform.
David E. Robbins, Alexander Grüneberg, Helena F. Deus, Murat M. Tanik, Jonas S. Almeida
2013 J jnl
ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342).
Dagstuhl Reports
Jonas S. Almeida, Andreas W. M. Dress, Titus Kühne, Laxmi Parida
2013 J jnl
ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342).
Dagstuhl Manifestos
Jonas S. Almeida, Andreas W. M. Dress, Titus Kühne, Laxmi Parida
2013 — conf
Linked cancer genome atlas database.
I-SEMANTICS
Muhammad Saleem, Shanmukha S. Padmanabhuni, Axel-Cyrille Ngonga Ngomo, Jonas S. Almeida, Stefan Decker, Helena F. Deus
2013 B conf
Machine learning to predict extubation outcome in premature infants.
IJCNN
Martina Mueller, Carol C. Wagner, Romesh Stanislaus, Jonas S. Almeida
2013 — conf
TCGA Toolbox: an Open Web App Framework for Distributing Big Data Analysis Pipelines for Cancer Genomics.
BCB
David E. Robbins, Alexander Grüneberg, Helena F. Deus, Murat M. Tanik, Jonas S. Almeida
2012 J jnl
Fractal MapReduce decomposition of sequence alignment.
Algorithms Mol. Biol.
Jonas S. Almeida, Alexander Grüneberg, Wolfgang Maass, Susana Vinga
2012 J jnl
Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis.
Algorithms Mol. Biol.
Susana Vinga, Alexandra M. Carvalho, Alexandre P. Francisco, Luís M. S. Russo, Jonas S. Almeida
2011 J jnl
S3QL: A distributed domain specific language for controlled semantic integration of life sciences data.
BMC Bioinform.
Helena F. Deus, Miria C. Correa, Romesh Stanislaus, Maria Miragaia, Wolfgang Maass, Hermínia de Lencastre, Ronan Fox, Jonas S. Almeida
2010 J jnl
AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.
BMC Medical Informatics Decis. Mak.
Miria C. Correa, Helena F. Deus, Ana Tereza Ribeiro de Vasconcelos, Yuki Hayashi, Jaffer A. Ajani, Srikrishna V. Patnana, Jonas S. Almeida
2010 J jnl
Exposing the cancer genome atlas as a SPARQL endpoint.
J. Biomed. Informatics
Helena F. Deus, Diogo F. Veiga, Pablo R. Freire, John N. Weinstein, Gordon B. Mills, Jonas S. Almeida
2010 J jnl
S3DB core: a framework for RDF generation and management in bioinformatics infrastructures.
BMC Bioinform.
Jonas S. Almeida, Helena F. Deus, Wolfgang Maass
2009 J jnl
Biological sequences as pictures - a generic two dimensional solution for iterated maps.
BMC Bioinform.
Jonas S. Almeida, Susana Vinga
2009 J jnl
DASMiner: discovering and integrating data from DAS sources.
BMC Syst. Biol.
Diogo F. Veiga, Helena F. Deus, Caner Akdemir, Ana Tereza Ribeiro de Vasconcelos, Jonas S. Almeida
2009 J jnl
Identification of neutral biochemical network models from time series data.
BMC Syst. Biol.
Marco Vilela, Susana Vinga, Marco Maia, Eberhard O. Voit, Jonas S. Almeida
2009 B conf
Using an artificial neural network to predict necrotizing enterocolitis in premature infants.
IJCNN
Martina Mueller, Sarah N. Taylor, Carol L. Wagner, Jonas S. Almeida
2008 J jnl
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.
BMC Bioinform.
Romesh Stanislaus, John M. Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen, Jonas S. Almeida
2008 — conf
Ontology Design Principles and Normalization Techniques in the Web.
DILS
Xiaoshu Wang, Jonas S. Almeida, Arlindo L. Oliveira
2008 J jnl
Parameter optimization in S-system models.
BMC Syst. Biol.
Marco Vilela, I-Chun Chou, Susana Vinga, Ana Tereza Ribeiro de Vasconcelos, Eberhard O. Voit, Jonas S. Almeida
2008 J jnl
RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays.
BMC Bioinform.
Romesh Stanislaus, Mark Carey, Helena F. Deus, Kevin R. Coombes, Bryan T. J. Hennessy, Gordon B. Mills, Jonas S. Almeida
2007 J jnl
Automated smoother for the numerical decoupling of dynamics models.
BMC Bioinform.
Marco Vilela, Carlos Cristiano H. Borges, Susana Vinga, Ana Tereza Ribeiro de Vasconcelos, Helena Santos, Eberhard O. Voit, Jonas S. Almeida
2007 J jnl
Local Renyi entropic profiles of DNA sequences.
BMC Bioinform.
Susana Vinga, Jonas S. Almeida
2007 J jnl
PrepMS: TOF MS data graphical preprocessing tool.
Bioinform.
Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida
2007 J jnl
Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement.
BMC Bioinform.
Francisco R. Pinto, João A. Carriço, Mário Ramirez, Jonas S. Almeida
2006 J jnl
A multivariate prediction model for microarray cross-hybridization.
BMC Bioinform.
Yian Ann Chen, Cheng-Chung Chou, Xinghua Lu, Elizabeth H. Slate, Konan Peck, Wenying Xu, Eberhard O. Voit, Jonas S. Almeida
2006 J jnl
Computing distribution of scale independent motifs in biological sequences.
Algorithms Mol. Biol.
Jonas S. Almeida, Susana Vinga
2006 J jnl
Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants.
BMC Medical Informatics Decis. Mak.
Martina Mueller, Carol L. Wagner, David J. Annibale, Rebecca G. Knapp, Thomas C. Hulsey, Jonas S. Almeida
2006 J jnl
mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.
BMC Bioinform.
Yuliya V. Karpievitch, Jonas S. Almeida
2005 J jnl
AGML Central: web based gel proteomic infrastructure.
Bioinform.
Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John M. Arthur, Jonas S. Almeida
2005 J jnl
Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory method.
Bioinform.
Francisco R. Pinto, L. Ashley Cowart, Yusuf A. Hannun, Bärbel Rohrer, Jonas S. Almeida
2004 J jnl
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.
BMC Bioinform.
Romesh Stanislaus, Liu Hong Jiang, Martha Swartz, John M. Arthur, Jonas S. Almeida
2004 J jnl
Comparative evaluation of word composition distances for the recognition of SCOP relationships.
Bioinform.
Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida
2004 J jnl
Decoupling dynamical systems for pathway identification from metabolic profiles.
Bioinform.
Eberhard O. Voit, Jonas S. Almeida
2004 J jnl
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information.
BMC Bioinform.
Yian Ann Chen, David J. Mckillen, Shuyuan Wu, Matthew J. Jenny, Robert Chapman, Paul S. Gross, Gregory W. Warr, Jonas S. Almeida
2003 J jnl
Alignment-free sequence comparison-a review.
Bioinform.
Susana Vinga, Jonas S. Almeida
2003 A conf
Dynamic Maximum Tree Depth.
GECCO
Sara Silva, Jonas S. Almeida
2003 J jnl
EURISWEB - Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers.
BMC Medical Informatics Decis. Mak.
Sara Silva, Rodrigo Gouveia-Oliveira, António Maretzek, João A. Carriço, Thorolfur Gudnason, Karl G. Kristinsson, Karl Ekdahl, António Brito-Avô, Alexander Tomasz, Ilda Santos Sanches, Hermínia de Lencastre, Jonas S. Almeida
2003 Misc conf
Web-based prediction of extubation outcome in premature infants on mechanical ventilation using an artificial neural network.
AMIA
Martina Mueller, Carol L. Wagner, David J. Annibale, Thomas C. Hulsey, Rebecca G. Knapp, Jonas S. Almeida
2002 J jnl
Efficient Boolean implementation of universal sequence maps (bUSM).
BMC Bioinform.
John Schwacke, Jonas S. Almeida
2002 J jnl
Universal sequence map (USM) of arbitrary discrete sequences.
BMC Bioinform.
Jonas S. Almeida, Susana Vinga
2001 J jnl
Analysis of genomic sequences by Chaos Game Representation.
Bioinform.
Jonas S. Almeida, João A. Carriço, António Maretzek, Peter A. Noble, Madilyn Fletcher