Health and Biomedical Informatics

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Information

Description:

LASIGE presents a longstanding record of research contributions in the area of Health & Biomedical Informatics, by providing innovative solutions for processing biological and medical data and for supporting the discovery of new biomedical insights. This research line aims to encompass all the scientific work in LASIGE where Informatics plays a fundamental role to the generation of new knowledge in Life and Health Sciences.

Targeted areas:

Bioinformatics
Chemoinformatics
Text Mining of Biomedical Literature and Multilingual Electronic Medical Records
Biomedical Data Mining, Machine Learning, and Data Analytics
Semantic Web Technologies, Linked Data and Biomedical Ontologies
Health and Biomedical Decision Support systems
Technology adoption in health‐care
Ubiquitous health systems
Physiologic sensing and monitoring
Interaction Design for Healthcare
Biomedical Data Visualization, Media and Wellbeing
Storage and Protection of Large Biomedical Data
Biomedical Data Privacy

Leader:

Francisco Couto

Research Line Members:

Name	Category
Alysson Bessani	Integrated Researcher
André Falcão	Integrated Researcher
Carlos Duarte	Integrated Researcher
Cátia Pesquita	Integrated Researcher
Francisco Couto	Integrated Researcher
João Ferreira	Integrated Researcher
Luís Carriço	Integrated Researcher
Manuel Fonseca	Integrated Researcher
Sara Madeira	Integrated Researcher
Teresa Chambel	Integrated Researcher
Tiago Guerreiro	Integrated Researcher
Catarina Pereira	PhD Student
Márcia Barros	PhD Student
Muhammad Asif	PhD Student
Telma Pereira	PhD Student
Madalena Pavão	MSc Student
Sebastião Almeida	MSc Student
Sofia Pires	MSc Student
Tânia Maldonado	MSc Student
Tiago Pacheco	MSc Student

Software and Tools

Software and Tools:

Title	Short descritption
AgreementMakerLight	An automated and efficient ontology matching system derived from AgreementMaker that has been in development since the beginning of 2013
B3PP	A web application that interfaces a machine learning model designed to predict the Blood-Brain Barrier penetration properties
CESSM	An online tool for the automated evaluation of GO-based semantic similarity measures
CIDS	A user-friendly web tool that calculates different citation statistics
CMPSim	A web tool that implements a novel approach to measure the similarity between chemical compounds and metabolic pathays using semantic similarity
DNA Privacy Detector	A method that systematically detects privacy-sensitive DNA segments coming directly from an input stream
Epidemiology Ontology	Aims at increasing the amount of epidemiological data available, improving disease surveillance systems, and promoting the collaboration among epidemiological researchers
GIN 2.0	Devised to design primers within microbial species or genus as broad as possible, for PCR gene-screening projects
GRYFUN	Allows the visualization, filtering and subsequent analysis of Gene Ontology (GO) annotation profiles
JDNA	A referential compressor for aligned DNA files
Lusica	A project of automatic collection of music quotes of Lusophone artists from the social networks
Missinks	A web application that given a search query identifies the links in the first two pages of a given Google country search engine
NAMS	A free Webtool to calculate similarity between molecules based on the structural/topological relationships of each atom towards all the others within a molecule
O Mundo em Pessoa	A collaboration project with Sapo Labs for the celebration of the 125th year of birth of Fernando Pessoa
Onde e quem vai ver	An app that allow the user to browse, create and share the best events
ProteInOn	A web tool focused on calculating GO-based protein semantic similarity
Rankores	Allows users to vote on news thus helping with their validation and taking advantage of social networks by sharing news we validate
Therminfo	A cheminformatics system designed and built with two main objectives in mind: collecting and retrieving critically evaluated thermochemical values, and estimating new data

Publications

2016

Conference Paper

Rodrigues, A., Nicolau H., Montague K., Carriço L., & Guerreiro T. (2016). Effect of Target Size on Non-visual Text-entry. Proceedings of the 18th International Conference on Human-Computer Interaction with Mobile Devices and Services.

Ivanova, V., Lambrix P., Lohmann S., & Pesquita C. (2016). VOILA! 2016: Proceedings of the 2nd International Workshop on Visualization and Interaction for Ontologies and Linked Data, Co-located with ISWC 2016, Kobe, Japan, October 17, 2016. 2nd International Workshop on Visualization and Interaction for Ontologies and Linked Data, Kobe, Japan, October 17.

Botelho, F., Ribeiro T. A., Ferreira P., Ramos F. M. V., & Bessani A. (2016). Design and Implementation of a Consistent Data Store for a Distributed SDN Control Plane. Dependable Computing Conference (EDCC), 2016 12th European. 169–180.

Cruz, W. Marreiro, Isotani S., Carriço L., & Guerreiro T. (2016). Interface to support caregivers in daily record and information visualization of patients with dementia. Proceedings of the 15th Brazilian Symposium on Human Factors in Computer Systems. 13.

Bernardino, C., Ferreira H. Alexandre, & Chambel T. (2016). Towards Media for Wellbeing. Proceedings of the ACM International Conference on Interactive Experiences for TV and Online Video. 171–177.

Journal Article

Rodrigues, M. J., Falé M., Lamurias A., & Couto F. M. (2016). WS4A: a biomedical question and answering system based on public web services and ontologies. arXiv preprint arXiv:1609.08492.

Henriques, R., & Madeira S. C. (2016). BicNET: Flexible module discovery in large-scale biological networks using biclustering. Algorithms for Molecular Biology. 11, 14.

Sieberts, S. K., Zhu F., García-García J., Stahl E., Pratap A., Pandey G., et al. (2016). Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature communications. 7, 12460.

Barros, M., Couto F. M., & (2016). Knowledge Representation and Management: a linked data perspective. IMIA Yearbook. 178–183.

Journal

Viana, P., Chambel T., V. Bove M., Strover S., & Thomas G. (2016). Special Issue on "Immersive Media Experiences"", MTAPS: Multimedia Tools and Applications.

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