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ORCIDJonas S. Almeida
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2020 – today
- 2024
[i10]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 abs/2404.01446 (2024)- [i9]Lee Mason, Blánaid Hicks, Jonas S. Almeida:
ClusterRadar: an Interactive Web-Tool for the Multi-Method Exploration of Spatial Clusters Over Time. CoRR abs/2404.05897 (2024) - [i8]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 abs/2407.09355 (2024) - [i7]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 abs/2407.21233 (2024) - [i6]Lee Mason, Blánaid Hicks, Jonas S. Almeida:
Demystifying Spatial Dependence: Interactive Visualizations for Interpreting Local Spatial Autocorrelation. CoRR abs/2408.02418 (2024) - 2023
- [j40]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): 238 (2023) - [c14]Wolfgang Maass, Arturo Castellanos, Monica C. Tremblay, Roman Lukyanenko, Veda C. Storey, Jonas S. Almeida:
Conceptual Alignment Method. AMCIS 2023 - [i5]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 abs/2304.10612 (2023) - 2022
- [j39]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): 4434-4436 (2022) - [c13]Thomas Villmann, Jonas S. Almeida, John A. Lee, Susana Vinga:
Tutorial - Machine Learning and Information Theoretic Methods for Molecular Biology and Medicine. ESANN 2022 - [i4]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 abs/2207.01734 (2022) - 2020
- [i3]Erich Bremer, Jonas S. Almeida, Joel H. Saltz:
Representing Whole Slide Cancer Image Features with Hilbert Curves. CoRR abs/2005.06469 (2020)
2010 – 2019
- 2019
- [i2]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 abs/1905.10841 (2019) - 2018
- [c12]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: 510 - 2017
- [j38]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): 547-548 (2017) - 2016
- [c11]Erich Bremer, Tahsin M. Kurç, Yi Gao, Joel H. Saltz, Jonas S. Almeida:
Safe "cloudification" of large images through picker APIs. AMIA 2016 - [c10]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 - 2015
- [c9]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 - [c8]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 - 2014
- [j37]Jonas S. Almeida:
Sequence analysis by iterated maps, a review. Briefings Bioinform. 15(3): 369-375 (2014) - [j36]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: 47 (2014) - [j35]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: 28 (2014) - [j34]Sean R. Wilkinson, Jonas S. Almeida:
QMachine: commodity supercomputing in web browsers. BMC Bioinform. 15: 176 (2014) - 2013
- [j33]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): 1333-1340 (2013) - [j32]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): 31-50 (2013) - [c7]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: 62 - [c6]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: 129-134 - [c5]Martina Mueller, Carol C. Wagner, Romesh Stanislaus, Jonas S. Almeida:
Machine learning to predict extubation outcome in premature infants. IJCNN 2013: 1-6 - [i1]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): 87-135 (2013) - 2012
- [j31]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: 10 (2012) - [j30]Jonas S. Almeida, Alexander Grüneberg, Wolfgang Maass, Susana Vinga:
Fractal MapReduce decomposition of sequence alignment. Algorithms Mol. Biol. 7: 12 (2012) - 2011
- [j29]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: 285 (2011) - 2010
- [j28]Jonas S. Almeida, Helena F. Deus, Wolfgang Maass:
S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinform. 11: 387 (2010) - [j27]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): 998-1008 (2010) - [j26]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: 65 (2010)
2000 – 2009
- 2009
- [j25]Jonas S. Almeida, Susana Vinga:
Biological sequences as pictures - a generic two dimensional solution for iterated maps. BMC Bioinform. 10 (2009) - [j24]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: 47 (2009) - [j23]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: 109 (2009) - [c4]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: 2172-2175 - 2008
- [j22]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) - [j21]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) - [j20]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: 35 (2008) - [c3]Xiaoshu Wang, Jonas S. Almeida, Arlindo L. Oliveira:
Ontology Design Principles and Normalization Techniques in the Web. DILS 2008: 28-43 - 2007
- [j19]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): 264-265 (2007) - [j18]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) - [j17]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) - [j16]Susana Vinga, Jonas S. Almeida:
Local Renyi entropic profiles of DNA sequences. BMC Bioinform. 8 (2007) - 2006
- [j15]Jonas S. Almeida, Susana Vinga:
Computing distribution of scale independent motifs in biological sequences. Algorithms Mol. Biol. 1 (2006) - [j14]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: 101 (2006) - [j13]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: 139 (2006) - [j12]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: 11 (2006) - 2005
- [j11]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): 1037-1045 (2005) - [j10]Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John M. Arthur, Jonas S. Almeida:
AGML Central: web based gel proteomic infrastructure. Bioinform. 21(9): 1754-1757 (2005) - 2004
- [j9]Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida:
Comparative evaluation of word composition distances for the recognition of SCOP relationships. Bioinform. 20(2): 206-215 (2004) - [j8]Eberhard O. Voit, Jonas S. Almeida:
Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinform. 20(11): 1670-1681 (2004) - [j7]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: 9 (2004) - [j6]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: 191 (2004) - 2003
- [j5]Susana Vinga, Jonas S. Almeida:
Alignment-free sequence comparison-a review. Bioinform. 19(4): 513-523 (2003) - [j4]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: 9 (2003) - [c2]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 - [c1]Sara Silva, Jonas S. Almeida:
Dynamic Maximum Tree Depth. GECCO 2003: 1776-1787 - 2002
- [j3]Jonas S. Almeida, Susana Vinga:
Universal sequence map (USM) of arbitrary discrete sequences. BMC Bioinform. 3: 6 (2002) - [j2]John Schwacke, Jonas S. Almeida:
Efficient Boolean implementation of universal sequence maps (bUSM). BMC Bioinform. 3: 28 (2002) - 2001
- [j1]Jonas S. Almeida, João A. Carriço, António Maretzek, Peter A. Noble, Madilyn Fletcher:
Analysis of genomic sequences by Chaos Game Representation. Bioinform. 17(5): 429-437 (2001)
Coauthor Index
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