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Publicações

Publicações por LIAAD

2018

y Unilateral effects screens for partial horizontal acquisitions: The generalized HHI and GUPPI

Autores
Brito, D; Osorio, A; Ribeiro, R; Vasconcelos, H;

Publicação
INTERNATIONAL JOURNAL OF INDUSTRIAL ORGANIZATION

Abstract
Recent years have witnessed an increased interest, by competition agencies, in assessing the competitive effects of partial acquisitions. We propose a generalization of the two most traditional indicators used to screen unilateral anti-competitive effects - the HerfindahlHirschman Index and the Gross Up- ward Price Pressure Index - to partial horizontal acquisition settings. The proposed generalized indicators are endogenously derived under a probabilistic voting model in which the manager of each firm is elected in a shareholder assembly between two potential candidates who seek to obtain utility from an exogenous rent associated with corporate office. The model (i) can cope with settings involving all types of owners and rights: owners that can be internal to the industry (rival firms) and external to the industry; and rights that can capture financial and corporate control interests, can be direct and indirect, can be partial or full, (ii) yields an endogenous measure of the owners ultimate corporate control rights, and (iii) can also be used - in case the potential acquisition is inferred to likely enhance market power - to devise divestiture structural remedies. We also provide an empirical application of the two proposed generalized indicators to several acquisitions in the wet shaving industry, with the objective of providing practitioners with a step-by-step illustration of how to compute them in antitrust cases.

2018

On the impossibility of a perfect counting method to allocate the credits of multi-authored publications

Autores
Osório, A;

Publicação
Scientometrics

Abstract

2018

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Autores
Ferreira, PG; Munoz Aguirre, M; Reverter, F; Sa Godinho, CPS; Sousa, A; Amadoz, A; Sodaei, R; Hidalgo, MR; Pervouchine, D; Carbonell Caballero, J; Nurtdinov, R; Breschi, A; Amador, R; Oliveira, P; Cubuk, C; Curado, J; Aguet, F; Oliveira, C; Dopazo, J; Sammeth, M; Ardlie, KG; Guigo, R;

Publicação
NATURE COMMUNICATIONS

Abstract
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante-and postmortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.

2018

Bioinformatics algorithms: Design and implementation in python

Autores
Rocha, M; Ferreira, PG;

Publicação
Bioinformatics Algorithms: Design and Implementation in Python

Abstract
Bioinformatics Algorithms: Design and Implementation in Python provides a comprehensive book on many of the most important bioinformatics problems, putting forward the best algorithms and showing how to implement them. The book focuses on the use of the Python programming language and its algorithms, which is quickly becoming the most popular language in the bioinformatics field. Readers will find the tools they need to improve their knowledge and skills with regard to algorithm development and implementation, and will also uncover prototypes of bioinformatics applications that demonstrate the main principles underlying real world applications.

2018

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Autores
Barbeira, AN; Dickinson, SP; Bonazzola, R; Zheng, J; Wheeler, HE; Torres, JM; Torstenson, ES; Shah, KP; Garcia, T; Edwards, TL; Stahl, EA; Huckins, LM; Aguet, F; Ardlie, KG; Cummings, BB; Gelfand, ET; Getz, G; Hadley, K; Handsaker, RE; Huang, KH; Kashin, S; Karczewski, KJ; Lek, M; Li, X; MacArthur, DG; Nedzel, JL; Nguyen, DT; Noble, MS; Segrè, AV; Trowbridge, CA; Tukiainen, T; Abell, NS; Balliu, B; Barshir, R; Basha, O; Battle, A; Bogu, GK; Brown, A; Brown, CD; Castel, SE; Chen, LS; Chiang, C; Conrad, DF; Damani, FN; Davis, JR; Delaneau, O; Dermitzakis, ET; Engelhardt, BE; Eskin, E; Ferreira, PG; Frésard, L; Gamazon, ER; Garrido Martín, D; Gewirtz, ADH; Gliner, G; Gloudemans, MJ; Guigo, R; Hall, IM; Han, B; He, Y; Hormozdiari, F; Howald, C; Jo, B; Kang, EY; Kim, Y; Kim Hellmuth, S; Lappalainen, T; Li, G; Li, X; Liu, B; Mangul, S; McCarthy, MI; McDowell, IC; Mohammadi, P; Monlong, J; Montgomery, SB; Muñoz Aguirre, M; Ndungu, AW; Nobel, AB; Oliva, M; Ongen, H; Palowitch, JJ; Panousis, N; Papasaikas, P; Park, Y; Parsana, P; Payne, AJ; Peterson, CB; Quan, J; Reverter, F; Sabatti, C; Saha, A; Sammeth, M; Scott, AJ; Shabalin, AA; Sodaei, R; Stephens, M; Stranger, BE; Strober, BJ; Sul, JH; Tsang, EK; Urbut, S; Van De Bunt, M; Wang, G; Wen, X; Wright, FA; Xi, HS; Yeger Lotem, E; Zappala, Z; Zaugg, JB; Zhou, YH; Akey, JM; Bates, D; Chan, J; Claussnitzer, M; Demanelis, K; Diegel, M; Doherty, JA; Feinberg, AP; Fernando, MS; Halow, J; Hansen, KD; Haugen, E; Hickey, PF; Hou, L; Jasmine, F; Jian, R; Jiang, L; Johnson, A; Kaul, R; Kellis, M; Kibriya, MG; Lee, K; Li, JB; Li, Q; Lin, J; Lin, S; Linder, S; Linke, C; Liu, Y; Maurano, MT; Molinie, B; Nelson, J; Neri, FJ; Park, Y; Pierce, BL; Rinaldi, NJ; Rizzardi, LF; Sandstrom, R; Skol, A; Smith, KS; Snyder, MP; Stamatoyannopoulos, J; Tang, H; Wang, L; Wang, M; Van Wittenberghe, N; Wu, F; Zhang, R; Nierras, CR; Branton, PA; Carithers, LJ; Guan, P; Moore, HM; Rao, A; Vaught, JB; Gould, SE; Lockart, NC; Martin, C; Struewing, JP; Volpi, S; Addington, AM; Koester, SE; Little, AR; Brigham, LE; Hasz, R; Hunter, M; Johns, C; Johnson, M; Kopen, G; Leinweber, WF; Lonsdale, JT; McDonald, A; Mestichelli, B; Myer, K; Roe, B; Salvatore, M; Shad, S; Thomas, JA; Walters, G; Washington, M; Wheeler, J; Bridge, J; Foster, BA; Gillard, BM; Karasik, E; Kumar, R; Miklos, M; Moser, MT; Jewell, SD; Montroy, RG; Rohrer, DC; Valley, DR; Davis, DA; Mash, DC; Undale, AH; Smith, AM; Tabor, DE; Roche, NV; McLean, JA; Vatanian, N; Robinson, KL; Sobin, L; Barcus, ME; Valentino, KM; Qi, L; Hunter, S; Hariharan, P; Singh, S; Um, KS; Matose, T; Tomaszewski, MM; Barker, LK; Mosavel, M; Siminoff, LA; Traino, HM; Flicek, P; Juettemann, T; Ruffier, M; Sheppard, D; Taylor, K; Trevanion, SJ; Zerbino, DR; Craft, B; Goldman, M; Haeussler, M; Kent, WJ; Lee, CM; Paten, B; Rosenbloom, KR; Vivian, J; Zhu, J; Nicolae, DL; Cox, NJ; Im, HK;

Publicação
Nature Communications

Abstract
Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. Colocalized significant associations in unexpected tissues underscore the need for an agnostic scanning of multiple contexts to improve our ability to detect causal regulatory mechanisms. Monogenic disease genes are enriched among significant associations for related traits, suggesting that smaller alterations of these genes may cause a spectrum of milder phenotypes. © 2018 The Author(s).

2018

Model-Based Classification of Heart Rate Variability.

Autores
Leite, Argentina; Silva, MariaEduarda; Rocha, AnaPaula;

Publicação
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference

Abstract
Several Heart Rate Variability (HRV) based novel methodologies for describing heart rate dynamics have been proposed in the literature with the aim of risk assessment. One such methodology is ARFIMA-EGARCH modeling which allows the quantification of long range dependence and time-varying volatility with the aim of describing non-linear and complex characteristics of HRV. This study applies the ARFIMA-EGARCH modeling of HRV recordings from 30 patients of the Noltisalis database to investigate the discrimination power of a set of features comprising currently used linear HRV features (low and high frequency components) and new measures obtained from the modeling such as, long memory in the mean, and persistence and asymmetry in volatility. A subset of the multidimensional HRV features is selected in a two-step procedure using Principal Components Analysis (PCA). Additionally, supervised classification by quadratic discriminant analysis achieves 93.3% of discrimination accuracy between the groups using the new feature set created by PCA.

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