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Publications

Publications by LIAAD

2018

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

Authors
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;

Publication
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.

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

Publication
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.

2018

Wavelet-Based Detection of Outliers in Poisson INAR(1) Time Series

Authors
Silva, I; Silva, ME;

Publication
Contributions to Statistics - Recent Studies on Risk Analysis and Statistical Modeling

Abstract

2018

A Comprehensive Workflow for Enhancing Business Bankruptcy Prediction

Authors
Sarmento, R; Trigo, L; Fonseca, L;

Publication
Intelligent Systems

Abstract
Forecasting enterprise bankruptcy is a critical area for Business Intelligence. It is a major concern for investors and credit institutions on risk analysis. It may also enable the sustainability assessment of critical suppliers and clients, as well as competitors and the business environment. Data Mining may deliver a faster and more precise insight about this issue. Widespread software tools offer a broad spectrum of Artificial Intelligence algorithms and the most difficult task may be the decision of selecting that algorithm. Trying to find an answer for this decision in the relatively large amount of available literature in this area with so many options, advantages, and pitfalls may be as informative as distracting. In this chapter, the authors present an empirical study with a comprehensive Knowledge Discovery and Data Mining (KDD) workflow. The proposed classifier selection automation selects an algorithm that has better prediction performance than the most widely documented in the literature.

2018

DSL-based configuration of solid referential management system: A case study

Authors
Figueiredo, E; Maio, P; Silva, N; Lopes, R;

Publication
Proceedings - 2018 International Conference on Computational Science and Computational Intelligence, CSCI 2018

Abstract
For the last decade, uebe.Q is being adopted by companies in different business areas and countries for managing compliance with solid referential information systems, such as ISO 9000 (for quality) and ISO 1400 (for environment). This is a long-term developed software, encompassing extensive, solid and valuable business logic. When it is deployed for/on a company, it usually demands an extensive and specific adaptation (i.e. software refinement) and configuration process involving DigitalWind's ISO 9000 and ISO 1400 experts as well as software development and operation teams. However, a recent business model change imposed that the evolution and configuration of the software, shifts from DigitalWind (and especially from the development team) to external consultants and to other business partners, along with the fact that different third-party's systems and respective data/information need to be integrated with minimal intervention of the development team. This paper presents and overview of the re-engineering process taken to handle this business model change by adopting (i) ontologies for the specification of business concepts, (ii) closed-world assumption (CWA) rules for the specification of the dynamics of the system and (iii) Domain Specific Language (DSL) for the configuration of the system by domain/business experts. The DSL approach is further described in detail. © 2018 IEEE.

2018

Simplified Mapreduce Mechanism for Large Scale Data Processing

Authors
Tahsir Ahmed Munna, M; Muhammad Allayear, S; Mohtashim Alam, M; Shah Mohammad Motiur Rahman, S; Samadur Rahman, M; Mesbahuddin Sarker, M;

Publication
International Journal of Engineering & Technology

Abstract
MapReduce has become a popular programming model for processing and running large-scale data sets with a parallel, distributed paradigm on a cluster. Hadoop MapReduce is needed especially for large scale data like big data processing. In this paper, we work to modify the Hadoop MapReduce Algorithm and implement it to reduce processing time.  

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