Jonas S. Almeida

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 16

Top Topics

Predictive Modeling

Sequence Analysis

Top Venues

Publications

Aaron Ge, Monjoy Saha, Máire A. Duggan, Petra Lenz, Mustapha Abubakar, Montserrat Garcia-Closas, Jeya Balasubramanian, Jonas S. Almeida, Praphulla M. S. Bhawsar
TMA-Grid: An open-source, zero-footprint web application for FAIR Tissue MicroArray De-arraying. CoRR (2024)
Aaron Ge, Jeya Balasubramanian, Xueyao Wu, Peter Kraft, Jonas S. Almeida
FastImpute: A Baseline for Open-source, Reference-Free Genotype Imputation Methods - A Case Study in PRS313. CoRR (2024)
Lee Mason, Blánaid Hicks, Jonas S. Almeida
ClusterRadar: an Interactive Web-Tool for the Multi-Method Exploration of Spatial Clusters Over Time. CoRR (2024)
Martim Afonso, Praphulla M. S. Bhawsar, Monjoy Saha, Jonas S. Almeida, Arlindo L. Oliveira
Finding Regions of Interest in Whole Slide Images Using Multiple Instance Learning. CoRR (2024)
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
Quest markup for developing FAIR questionnaire modules for epidemiologic studies. BMC Medical Informatics Decis. Mak. 23 (1) (2023)
Erich Bremer, Tammy DiPrima, Joseph Balsamo, Jonas S. Almeida, Rajarsi Gupta, Joel H. Saltz
Halcyon - A Pathology Imaging and Feature analysis and Management System. CoRR (2023)
Wolfgang Maass, Arturo Castellanos, Monica C. Tremblay, Roman Lukyanenko, Veda C. Storey, Jonas S. Almeida
Conceptual Alignment Method. AMCIS (2023)
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
PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project. Bioinform. 38 (18) (2022)
Thomas Villmann, Jonas S. Almeida, Lee John, Susana Vinga
Tutorial - Machine Learning and Information Theoretic Methods for Molecular Biology and Medicine. ESANN (2022)
Praphulla M. S. Bhawsar, Erich Bremer, Máire A. Duggan, Stephen J. Chanock, Montserrat Garcia-Closas, Joel H. Saltz, Jonas S. Almeida
ImageBox3: No-Server Tile Serving to Traverse Whole Slide Images on the Web. CoRR (2022)
Erich Bremer, Jonas S. Almeida, Joel H. Saltz
Representing Whole Slide Cancer Image Features with Hilbert Curves. CoRR (2020)
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
Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor Infiltrating Lymphocytes in Invasive Breast Cancer. CoRR (2019)
Alisha Kamat, Ting Jin, So Yeon Min, Flaminia Talos, Jonas S. Almeida, Daifeng Wang
Interpretable Machine Learning Approach Reveals Developmental Gene Expression Biomarkers for Cancer Patient Outcomes at Early Stages. BCB (2018)
Emanuel Diego S. Penha, Egiebade Iriabho, Alex Dussaq, Diana Magalhaes de Oliveira, Jonas S. Almeida
Isomorphic semantic mapping of variant call format (VCF2RDF). Bioinform. 33 (4) (2017)
Erich Bremer, Tahsin M. Kurç, Yi Gao, Joel H. Saltz, Jonas S. Almeida
Safe "cloudification" of large images through picker APIs. AMIA (2016)
Sarah B. Putney, Andrew White, Janos G. Hajagos, Joel H. Saltz, Jonas S. Almeida, Mary M. Saltz
S2CR3UM: A Solution to the In Silico Relevance, Reliability & Reproducibility Conundrum. AMIA (2016)
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
Integrative Informatics and Predictive Modeling Support for Population Health. AMIA (2015)
Jonas S. Almeida, Janos G. Hajagos, Ivan Crnosija, Tahsin M. Kurç, Mary M. Saltz, Joel H. Saltz
OpenHealth Platform for Interactive Contextualization of Population Health Open Data. AMIA (2015)
Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas S. Almeida, William J. Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder
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. 15 (2014)
Muhammad Saleem, Shanmukha S. Padmanabhuni, Axel-Cyrille Ngonga Ngomo, Aftab Iqbal, Jonas S. Almeida, Stefan Decker, Helena F. Deus
TopFed: TCGA Tailored Federated Query Processing and Linking to LOD. J. Biomed. Semant. 5 (2014)
Jonas S. Almeida
Sequence analysis by iterated maps, a review. Briefings Bioinform. 15 (3) (2014)
Sean R. Wilkinson, Jonas S. Almeida
QMachine: commodity supercomputing in web browsers. BMC Bioinform. 15 (2014)
Martina Mueller, Carol C. Wagner, Romesh Stanislaus, Jonas S. Almeida
Machine learning to predict extubation outcome in premature infants. IJCNN (2013)
Jonas S. Almeida, Andreas W. M. Dress, Titus Kühne, Laxmi Parida
ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342). Dagstuhl Manifestos 3 (1) (2013)
Jonas S. Almeida, Andreas W. M. Dress, Titus Kühne, Laxmi Parida
ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342). Dagstuhl Reports 3 (8) (2013)
David E. Robbins, Alexander Grüneberg, Helena F. Deus, Murat M. Tanik, Jonas S. Almeida
A self-updating road map of The Cancer Genome Atlas. Bioinform. 29 (10) (2013)
David E. Robbins, Alexander Grüneberg, Helena F. Deus, Murat M. Tanik, Jonas S. Almeida
TCGA Toolbox: an Open Web App Framework for Distributing Big Data Analysis Pipelines for Cancer Genomics. BCB (2013)
Muhammad Saleem, Shanmukha S. Padmanabhuni, Axel-Cyrille Ngonga Ngomo, Jonas S. Almeida, Stefan Decker, Helena F. Deus
Linked cancer genome atlas database. I-SEMANTICS (2013)
Jonas S. Almeida, Alexander Grüneberg, Wolfgang Maass, Susana Vinga
Fractal MapReduce decomposition of sequence alignment. Algorithms Mol. Biol. 7 (2012)
Susana Vinga, Alexandra M. Carvalho, Alexandre P. Francisco, Luís M. S. Russo, Jonas S. Almeida
Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis. Algorithms Mol. Biol. 7 (2012)
Helena F. Deus, Miria C. Correa, Romesh Stanislaus, Maria Miragaia, Wolfgang Maass, Hermínia de Lencastre, Ronan Fox, Jonas S. Almeida
S3QL: A distributed domain specific language for controlled semantic integration of life sciences data. BMC Bioinform. 12 (2011)
Jonas S. Almeida, Helena F. Deus, Wolfgang Maass
S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinform. 11 (2010)
Helena F. Deus, Diogo F. Veiga, Pablo R. Freire, John N. Weinstein, Gordon B. Mills, Jonas S. Almeida
Exposing the cancer genome atlas as a SPARQL endpoint. J. Biomed. Informatics 43 (6) (2010)
Miria C. Correa, Helena F. Deus, Ana Tereza Ribeiro de Vasconcelos, Yuki Hayashi, Jaffer A. Ajani, Srikrishna V. Patnana, Jonas S. Almeida
AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services. BMC Medical Informatics Decis. Mak. 10 (2010)
Diogo F. Veiga, Helena F. Deus, Caner Akdemir, Ana Tereza Ribeiro de Vasconcelos, Jonas S. Almeida
DASMiner: discovering and integrating data from DAS sources. BMC Syst. Biol. 3 (2009)
Jonas S. Almeida, Susana Vinga
Biological sequences as pictures - a generic two dimensional solution for iterated maps. BMC Bioinform. 10 (2009)
Martina Mueller, Sarah N. Taylor, Carol L. Wagner, Jonas S. Almeida
Using an artificial neural network to predict necrotizing enterocolitis in premature infants. IJCNN (2009)
Marco Vilela, Susana Vinga, Marco Maia, Eberhard O. Voit, Jonas S. Almeida
Identification of neutral biochemical network models from time series data. BMC Syst. Biol. 3 (2009)
Romesh Stanislaus, Mark Carey, Helena F. Deus, Kevin R. Coombes, Bryan T. J. Hennessy, Gordon B. Mills, Jonas S. Almeida
RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays. BMC Bioinform. 9 (2008)
Romesh Stanislaus, John M. Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen, Jonas S. Almeida
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis. BMC Bioinform. 9 (2008)
Marco Vilela, I-Chun Chou, Susana Vinga, Ana Tereza Ribeiro de Vasconcelos, Eberhard O. Voit, Jonas S. Almeida
Parameter optimization in S-system models. BMC Syst. Biol. 2 (2008)
Xiaoshu Wang, Jonas S. Almeida, Arlindo L. Oliveira
Ontology Design Principles and Normalization Techniques in the Web. DILS (2008)
Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida
PrepMS: TOF MS data graphical preprocessing tool. Bioinform. 23 (2) (2007)
Susana Vinga, Jonas S. Almeida
Local Renyi entropic profiles of DNA sequences. BMC Bioinform. 8 (2007)
Francisco R. Pinto, João A. Carriço, Mário Ramirez, Jonas S. Almeida
Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement. BMC Bioinform. 8 (2007)
Marco Vilela, Carlos Cristiano H. Borges, Susana Vinga, Ana Tereza Ribeiro de Vasconcelos, Helena Santos, Eberhard O. Voit, Jonas S. Almeida
Automated smoother for the numerical decoupling of dynamics models. BMC Bioinform. 8 (2007)
Jonas S. Almeida, Susana Vinga
Computing distribution of scale independent motifs in biological sequences. Algorithms Mol. Biol. 1 (2006)
Yuliya V. Karpievitch, Jonas S. Almeida
mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code. BMC Bioinform. 7 (2006)
Yian Ann Chen, Cheng-Chung Chou, Xinghua Lu, Elizabeth H. Slate, Konan Peck, Wenying Xu, Eberhard O. Voit, Jonas S. Almeida
A multivariate prediction model for microarray cross-hybridization. BMC Bioinform. 7 (2006)
Martina Mueller, Carol L. Wagner, David J. Annibale, Rebecca G. Knapp, Thomas C. Hulsey, Jonas S. Almeida
Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants. BMC Medical Informatics Decis. Mak. 6 (2006)
Francisco R. Pinto, L. Ashley Cowart, Yusuf A. Hannun, Bärbel Rohrer, Jonas S. Almeida
Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory method. Bioinform. 21 (7) (2005)
Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John M. Arthur, Jonas S. Almeida
AGML Central: web based gel proteomic infrastructure. Bioinform. 21 (9) (2005)
Romesh Stanislaus, Liu Hong Jiang, Martha Swartz, John M. Arthur, Jonas S. Almeida
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. BMC Bioinform. 5 (2004)
Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida
Comparative evaluation of word composition distances for the recognition of SCOP relationships. Bioinform. 20 (2) (2004)
Eberhard O. Voit, Jonas S. Almeida
Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinform. 20 (11) (2004)
Yian Ann Chen, David J. Mckillen, Shuyuan Wu, Matthew J. Jenny, Robert Chapman, Paul S. Gross, Gregory W. Warr, Jonas S. Almeida
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinform. 5 (2004)
Martina Mueller, Carol L. Wagner, David J. Annibale, Thomas C. Hulsey, Rebecca G. Knapp, Jonas S. Almeida
Web-based prediction of extubation outcome in premature infants on mechanical ventilation using an artificial neural network. AMIA (2003)
Susana Vinga, Jonas S. Almeida
Alignment-free sequence comparison-a review. Bioinform. 19 (4) (2003)
Sara Silva, Jonas S. Almeida
Dynamic Maximum Tree Depth. GECCO (2003)
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
EURISWEB - Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers. BMC Medical Informatics Decis. Mak. 3 (2003)
Jonas S. Almeida, Susana Vinga
Universal sequence map (USM) of arbitrary discrete sequences. BMC Bioinform. 3 (2002)
John Schwacke, Jonas S. Almeida
Efficient Boolean implementation of universal sequence maps (bUSM). BMC Bioinform. 3 (2002)
Jonas S. Almeida, João A. Carriço, António Maretzek, Peter A. Noble, Madilyn Fletcher
Analysis of genomic sequences by Chaos Game Representation. Bioinform. 17 (5) (2001)