Pedro Lobo Fernandes

Pedro Lobo Fernandes
Instituto Gulbenkian de Ciência (IGC) | IGC · Education and Training Unit

Electronics and Telecommunications Engineering

About

87
Publications
16,490
Reads
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896
Citations
Introduction
Additional affiliations
July 2013 - August 2015
Instituto Gulbenkian de Ciência (IGC)
Position
  • Researcher @ TBomics (NewIndigo project)
January 2005 - present
January 1999 - present
Position
  • Coordinator, Gulbenkian Training Programme in Bioinformatics GTPB (http://gtpb.igc.gulbenkian.pt)
Education
September 1973 - July 1979

Publications

Publications (87)
Article
Full-text available
ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinf...
Preprint
In recent years the volume of biological data has soared. Parallel to this growth, the need for developing data mining strategies has not met sufficiently. Bioinformaticians use different techniques of data mining to obtain the required information they need from genomic, transcriptomic and proteomic databases. One of the simple mining approaches t...
Conference Paper
Full-text available
USA-Europe Data Analysis Training School (USEDAT) is a Multi-center Trans-Atlantic initiative offering hands-on training focused in both Introduction to Experimental Data Recording (NMR, MS, IR, 2DGE, EEG, etc.) and/or posterior Computational Data Analysis (Machine Learning, Complex Networks, etc.). We made emphasis on applications in for Cheminfor...
Poster
Full-text available
The multiple roles of feedback in GTPB bioinformatics training courses In Face-to-Face training courses there are multiple opportunities for collecting valuable feedback. Instant feedback is elicited by questioning the audience during the course to gauge the effectiveness of the learning in various aspects, reflecting on the comfort of the learner...
Article
Full-text available
In the last decade, bioinformatics has become an indispensable branch of modern science research, experiencing an explosion in financial support, developed applications and data collection. The growth of the datasets that are emerging from research laboratories, industry, the health sector, etc., are increasingly raising the levels of demand in com...
Book
Full-text available
A group of fourteen authors came together in February 2018 at the TIB (German National Library of Science and Technology) in Hannover to create an open, living handbook on Open Science training. High-quality trainings are fundamental when aiming at a cultural change towards the implementation of Open Science principles. Teaching resources provide g...
Book
Full-text available
The goal of these resources is to give a bird's eye view of the developments in open scientific research. That is, we cover both social developments (e.g. the culture in various communities) as well as technological ones. As such, no part of the contents are especially in-depth or geared towards advanced users of specific practices or tools. Nevert...
Article
Full-text available
Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), th...
Data
Detailed description of the different modules provided in the IBT_2016 course, including learning objectives and learning outcomes. (PDF)
Article
Full-text available
Demand for training life scientists in bioinformatics methods, tools and resources and computational approaches is urgent and growing. To meet this demand, new trainers must be prepared with effective teaching practices for delivering short hands-on training sessions-a specific type of education that is not typically part of professional preparatio...
Article
Full-text available
One of the main goals of the ELIXIR-EXCELERATE project from the European Union’s Horizon 2020 programme is to support a pan-European training programme to increase bioinformatics capacity and competency across ELIXIR Nodes. To this end, a Train-the-Trainer (TtT) programme has been developed by the TtT subtask of EXCELERATE’s Training Platform, to t...
Poster
Full-text available
Abstract The Global Organisation for Bioinformatics Learning, Education and Training [1] (GOBLET: http://mygoblet.org) was established to provide a global, sustainable support structure to foster international communities of bioinformatics trainers and trainees. The activities of GOBLET are carried out via committees, which have independent but ove...
Article
Full-text available
Presented at the ECCB2016, den Haag, NL, Sept 2016 Africa is not unique in its need for basic bioinformatics training for individuals from a molecular biology background. However, unique logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the conti...
Article
Full-text available
For a synthetic biologist or biohacker to be able to hack, design, create, and engi- neer biological systems, the ability to work with biological data is essential. Basic bioinformatics skills will be required in order to read, interpret, write, and gener- ate files containing DNA, RNA, protein, and other biological information. In this article, we...
Article
Full-text available
Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype pl...
Article
Full-text available
As we move deeper into the digital age, the social praxis of science undergoes fundamental changes, driven by new tools provided by information and communication technologies. Specifically, social networks and computing resources such as online cloud-based infrastructures and applications provide the necessary context for unprecedented innovations...
Article
Full-text available
The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not...
Article
Full-text available
Summary: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently acc...
Article
Full-text available
The idea was raised during a proteomics training course in 2008: Roman Zubarev, Alexander Kel and myself were discussing some ideas about the future of proteomics, and how emerging quantitative proteomics data could find its way into the characterization of pathways and their dynamics. Loads of new ideas were popping up but, in truth, little was be...
Article
The synthesis of di-myo-inositol phosphate (DIP), a common compatible solute in hyperthermophiles, involves the consecutive actions of inositol-1-phosphate cytidylyltransferase (IPCT) and di-myo-inositol phosphate phosphate synthase (DIPPS). In most cases, both activities are present in a single gene product, but separate genes are also found in a...
Article
Full-text available
Bioinformatics, for its very nature, is devoted to a set of targets that constantly evolve. Training is probably the best response to the constant need for the acquisition of bioinformatics skills. It is interesting to assess the effects of training in the different sets of researchers that make use of it. While training bench experimentalists in t...
Article
Full-text available
The 2011 AGM workshop took place at the Instituto Gulbenkian de Ciência (IGC) in Oeiras, Portugal, from 23-25 May (Figure 1). The goal of the workshop was to build on the demonstrable progress made during the previous year, in particular by helping to deliver on some of the plans outlined during the 2010 AGM. It was also an opportunity to build on...
Article
Full-text available
Genetic data have been widely used to reconstruct the demographic history of populations, including the estimation of migration rates, divergence times and relative admixture contribution from different populations. Recently, increasing interest has been given to the ability of genetic data to distinguish alternative models. One of the issues that...
Article
Full-text available
Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the...
Article
Full-text available
As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies s...
Article
Full-text available
The Gulbenkian Training Programme in Bioinformatics has been offering hands-on training courses in Oeiras, PT for more than a decade. This article is a review of its functional organization and evolution. We aim to share our experience with people considering setting-up similar training facilities elsewhere. More than 1600 course attendees, so far,...
Article
Full-text available
The P&PR-PC main goal is to enhance EMBnet visibility and to establish cooperation/collaboration with other (even dissimilar) major groups, networks and societies. This is the report of the Committee's activies from November 2009 to June 2010.
Article
Full-text available
Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological seq...
Article
Full-text available
The cadherin superfamily is a diverse and multifunctional group of proteins with extensive representation across genomes of phylogenetically distant species that is involved in cell-cell communication and adhesion. The mosquito Anopheles gambiae is an emerging model organism for the study of innate immunity and host-pathogen interactions, where the...
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Article
The present study describes the responses of cortisol, prolactin and growth hormone (GH) to emotions elicited during sessions in which an hypnoidal state was induced. The purpose of the study was to provide answers for the following questions: 1) Do sessions with an emotional content have more hormonal surges than baseline, relaxation-only, session...
Book
Full-text available
The acquisition, cultivation, preservation, and storage of objects in biological collections is an integral part of biological research in many sub-disciplines. Field and research notes and specimen labels contain valuable and detailed data and the object itself can be a physical resource for research and industry. This publication reports on the c...
Article
The distribution of vasoactive intestinal peptide (VIP)- and calcitonin gene-related peptide (CGRP)-immunoreactive nerves and 125I-labeled VIP- and CGRP-binding sites was studied in the hamster seminal vesicle of 12-, 30- and 60-day-old animals. In addition, the general innervation of the seminal vesicle was examined using the general neuronal mark...
Article
In the present work we have investigated the effects of medium- (15 days) and long-term (2 months) castration on vasoactive intestinal peptide (VIP)-immunoreactive nerve fibres and 125I-labelled VIP binding sites in the adult hamster seminal vesicle. The density of VIP- and synaptophysin (general neuronal marker)-containing nerve fibres was determi...
Article
The distribution of calcitonin gene-related peptide (CGRP)-immunoreactive nerves and CGRP binding sites, as well as the effect of CGRP on the muscle tension, was studied in the hamster seminal vesicle and coagulating gland. The use of an immunofluorescence staining technique on cryostat sections revealed that in the hamster seminal vesicle and coag...
Article
In the past 5 years, a new approach was developed to evaluate the patient with sporadic symptoms as is the patient with syncope--the long-term ambulatory loop electrocardiogram monitoring. This method allow to assure the heart rate and rhythm at the moment of the symptoms hardly to be able with the other diagnostic tools disposable. The long-term a...
Article
Full-text available
The transport of Na+, K+ and Cl- across the isolated epithelium of the eel intestine was studied using a combination of four experimental strategies: short-circuiting, measurements of intracellular potentials and ion concentrations, application of a variety of transport inhibitors and measurement of unidirectional fluxes with radioactive tracers. W...
Article
Full-text available
Electrical potential differences between the haemolymph and the extrapallial fluid, and between the haemolymph and the mantle cavity fluid, and ionic concentrations of calcium in the haemolymph and in extrapallial fluid were measured in vivo in Anodonta cygnea. The electrochemical potential of ionic calcium in the haemolymph is clearly above the el...
Article
Full-text available
The objectives of the study were to characterize power spectrum pattern of the heart rate variability and assessment of the relative contributions of sympathetic and parasympathetic cardiac nervous system control in athletes. Thirty-three male athletes, swimming (1), canoeing (10), cycling (6), athletics (4), football (3), roller-skating (2) and vo...
Article
The isolated rabbit caecum was studied in vitro. Under our experimental conditions, the rabbit caecum secreted potassium and chloride and absorbed sodium. To characterize the transport properties of the apical and the basolateral barriers, transepithelial electrical and flux (22Na, 36Cl and 86Rb) measurements and their sensitivity to transport inhi...
Article
Sympathovagal interaction was assessed by analysis of spectral components of heart rate variability in patients after acute myocardial infarction. The indices of the time and frequency domain of heart rate variability were compared with some prognostic risk variables like radionuclide left ventricular ejection fraction, New York Heart Association f...
Article
1. The intracellular concentration of ionized calcium was measured with double-barrelled ion-sensitive microelectrodes under short-circuit conditions in the isolated outer mantle epithelium of Anodonta cygnea. 2. When the outside baths contained 1 mmol/l Ca2+ the average intracellular Ca2+ was 5.42 +/- 0.64 mmol/l (N = 41) while the equilibrium con...
Article
The present work is an attempt to provide a general overview on the current methods and applications of heart rate variability (HRV), starting from the underlying mechanisms of cardiac rhythmic automaticity and the influence on heart rate of biological modulators, namely autonomous nervous system. Different evaluation methods for HRV are compared i...
Article
Full-text available
A mathematical version of the cell model of the cortical thick ascending limb of the rabbit proposed by Greger and Schlatter ((1983) Pfügers Arch. 396, 325-334) is described. Available data are sufficient to compute the most important parameters. Simulations of experiments with perfused tubules in which the transepithelial voltage and conductance,...
Article
The signal-averaged ECG became an important noninvasive method for identifying life-threatening ventricular arrhythmias. It is most accurate in patients with coronary artery disease and can be helpful in predicting whether a patient with an unexplained syncope or nonsustained VT is at risk of developing sustained ventricular tachycardia or not. A p...
Article
Characterize power spectrum pattern of the heart rate variability and assessment of the relative contributions of sympathetic and parasympathetic cardiac nervous system control in athletes. Prospective study of athletes and sedentary healthy control group sex and age matched. 8 athletes, 3 female and 5 male, swimming (4), canoeing (2) and cycling (...
Chapter
Spectral analysis of R-R variability has been done in twenty subjects with Familial Amyloidotic Polyneuropathy in order to define intensity, chronology and discriminative capacity of this method in parasympathetic and sympathetic disturbances. The subjects were subdivided in 3 groups. Group I with far advanced disease, group II in early stages of t...
Article
1. When frog skin epithelium was exposed to a chloride-free solution bathing the basolateral side of the frog skin preparation the short-circuit current fell and there was a simultaneous loss of chloride and water from its cells. This effect was partially blocked by furosemide when this drug was added to the basolateral bathing solution. 2. Under c...
Article
1. A method of estimating absolute ionic permeability coefficients which does not depend on the use of impermeant substitutes is reported. 2. The method is based on a pump leak model of the Xenopus laevis oocyte membrane. The procedure consists of measuring, in the same experiment, the pump current and the currents generated under voltage clamp by...