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Publications

Publications by LIAAD

2020

A vast resource of allelic expression data spanning human tissues

Authors
Castel S.E.; Aguet F.; Aguet F.; Aguet F.; Mohammadi P.; Mohammadi P.; Anand S.; Anand S.; Ardlie K.G.; Ardlie K.G.; Gabriel S.; Getz G.A.; Graubert A.; Graubert A.; Hadley K.; Hadley K.; Handsaker R.E.; Handsaker R.E.; Huang K.H.; Kashin S.; Kashin S.; Li X.; MacArthur D.G.; Meier S.R.; Meier S.R.; Nedzel J.L.; Nedzel J.L.; Nguyen D.T.; Segrè A.V.; Todres E.; Todres E.; Balliu B.; Barbeira A.N.; Battle A.; Bonazzola R.; Brown A.; Brown C.D.; Castel S.E.; Conrad D.F.; Cotter D.J.; Cox N.; Das S.; De Goede O.M.; Dermitzakis E.T.; Einson J.; Engelhardt B.E.; Eskin E.; Eulalio T.Y.; Ferraro N.M.; Flynn E.D.; Fresard L.; Gamazon E.R.; Garrido-Martín D.; Gay N.R.; Gloudemans M.J.; Guigó R.; Hame A.R.; He Y.; Hoffman P.J.; Hormozdiari F.; Hou L.; Huang K.H.; Im H.K.; Jo B.; Kasela S.; Kellis M.; Kim-Hellmuth S.; Kwong A.; Lappalainen T.; Li X.; Li X.; Liang Y.; Mangul S.; Montgomery S.B.; Muñoz-Aguirre M.; Nachun D.C.; Nguyen D.T.; Nobel A.B.; Oliva M.; Park Y.S.; Park Y.; Parsana P.; Rao A.S.; Reverter F.; Rouhana J.M.; Sabatti C.; Saha A.; Segrè A.V.; Skol A.D.; Stephens M.; Stranger B.E.; Strober B.J.; Teran N.A.; Viñuela A.; Wang G.; Wen X.; Wright F.; Wucher V.; Zou Y.; Ferreira P.G.;

Publication
Genome Biology

Abstract
Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.

2020

IMPACT OF A SHIFT-INVARIANT HARMONIC PHASE MODEL IN FULLY PARAMETRIC HARMONIC VOICE REPRESENTATION AND TIME/FREQUENCY SYNTHESIS

Authors
Ferreira, A; Silva, J; Brito, F; Sinha, D;

Publication
2020 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH, AND SIGNAL PROCESSING

Abstract
Harmonic representation models are widely used, notably in speech coding and synthesis. In this paper, we describe two fully parametric harmonic representation and signal reconstruction alternatives that rely on a shift-invariant harmonic phase model and that implement accurate frame-based synthesis in the frequency-domain, and accurate pitch pulse-based synthesis in the time-domain. We use natural spoken and sung voice signals in order to assess the objective and subjective quality of both alternatives when parameters are exact, and when they are replaced by compact and shift-invariant harmonic phase and magnitude approximation models. We highlight the flexibility of these models and present results indicating that not only does the compact shift-invariant phase model cause a smaller impact than that caused by harmonic magnitude modeling, but it also compares favorably to results presented in the literature.

2020

Manipulation of the Fundamental Frequency Micro-Variations using a Fully Parametric and Computationally Efficient Speech Model

Authors
Silva, JP; Oliveira, MA; Cardoso, CF; Ferreira, AJ;

Publication
IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation

Abstract
In this paper, we present a computationally efficient and fully parametric harmonic speech model that is suitable for real-time flexible frame-based analysis and synthesis implementation in the frequency domain. We carry out a performance comparison between this vocoder and similar ones, such as WORLD and HPMD. Then, a deliberate manipulation of the speaker's fundamental frequency micro-variations is performed in order to understand in which way it conveys prosodic and idiosyncratic information. We conclude our discussion by evaluating the impact of these manipulations through the realization of perceptual tests. © 2020 IEEE.

2020

Classification of HRV using Long Short-Term Memory Networks

Authors
Leite, A; Silva, ME; Rocha, AP;

Publication
2020 11TH CONFERENCE OF THE EUROPEAN STUDY GROUP ON CARDIOVASCULAR OSCILLATIONS (ESGCO): COMPUTATION AND MODELLING IN PHYSIOLOGY NEW CHALLENGES AND OPPORTUNITIES

Abstract
This work focus on detection of diseases from Heart Rate Variability (HRV) series using Long Short-Term Memory (LSTM) networks. First, non-linear models are used to extract sequences of features that characterize the HRV series. These time sequences are then used as input for the LSTM. HRV recordings from the Noltisalis database are used for training and testing this approach. The results indicate that the procedure provides accuracy scores in the range of 86.7% to 90.0% on the test set.

2020

Vector Autoregressive Fractionally Integrated Models to Assess Multiscale Complexity in Cardiovascular and Respiratory Time Series

Authors
Martins, A; Amado, C; Rocha, AP; Silva, ME; Pernice, R; Javorka, M; Faes, L;

Publication
2020 11TH CONFERENCE OF THE EUROPEAN STUDY GROUP ON CARDIOVASCULAR OSCILLATIONS (ESGCO): COMPUTATION AND MODELLING IN PHYSIOLOGY NEW CHALLENGES AND OPPORTUNITIES

Abstract
Cardiovascular variability is the result of the activity of several physiological control mechanisms, which involve different variables and operate across multiple time scales encompassing short term dynamics and long range correlations. This study presents a new approach to assess the multiscale complexity of multivariate time series, based on linear parametric models incorporating autoregressive coefficients and fractional integration. The approach extends to the multivariate case recent works introducing a linear parametric representation of multiscale entropy, and is exploited to assess the complexity of cardiovascular and respiratory time series in healthy subjects studied during postural and mental stress.

2020

MODELLING IRREGULARLY SPACED TIME SERIES UNDER PREFERENTIAL SAMPLING

Authors
Monteiro, A; Menezes, R; Silva, ME;

Publication
REVSTAT-STATISTICAL JOURNAL

Abstract
Irregularly spaced time series are commonly encountered in the analysis of time series. A particular case is that in which the collection procedure over time depends also on the observed values. In such situations, there is stochastic dependence between the process being modeled and the times at which the observations are made. Ignoring this dependence can lead to biased estimates and misleading inferences. In this paper, we introduce the concept of preferential sampling in the temporal dimension and we propose a model to make inference and prediction. The methodology is illustrated using artificial data as well a real data set.

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