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TITLE: QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq
AUTHORS: Bruno Cavadas; Joana Ferreira; Rui Camacho ; Nuno A Fonseca ; Luísa Pereira;
PUBLISHED: 2017, SOURCE: 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2017 in 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, Portugal, 21-23 June, 2017, VOLUME: 616

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TITLE: The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data Full Text
AUTHORS: Robert Petryszak; Nuno A Fonseca ; Anja Füllgrabe; Laura Huerta; Maria Keays; Amy A Tang; Alvis Brazma;
PUBLISHED: 2017, SOURCE: Bioinformatics, VOLUME: 33, ISSUE: 14

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TITLE: Transcription factor activities enhance markers of drug response in cancer
AUTHORS: Luz Garcia-Alonso; Francesco Iorio; Angela Matchan; Nuno Fonseca ; Patricia Jaaks; Fiamenta Falcone; Graham Bignell; Simon S McDade; Mathew J Garnett; Julio Saez-Rodriguez;
PUBLISHED: 2017

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TITLE: Two independent modes of chromatin organization revealed by cohesin removal Full Text
AUTHORS: Schwarzer, W; Abdennur, N; Goloborodko, A; Pekowska, A; Fudenberg, G; Loe Mie, Y; Fonseca, NA ; Huber, W; Haering, CH; Mirny, L; Spitz, F;
PUBLISHED: 2017, SOURCE: Nature, VOLUME: 551, ISSUE: 7678

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TITLE: Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements
AUTHORS: Yiqun Zhang; Fengju Chen; Nuno A Fonseca ; Yao He; Masashi Fujita; Hidewaki Nakagawa; Zemin Zhang; Alvis Brazma; Chad J Creighton;
PUBLISHED: 2017

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TITLE: Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants Full Text
AUTHORS: Robert Petryszak; Maria Keays; Amy A Tang; Nuno A Fonseca ; Elisabet Barrera; Tony Burdett; Anja Füllgrabe; Alfonso Muñoz Pomer Fuentes; Simon Jupp; Satu Koskinen; Oliver Mannion; Laura Huerta; Karine Megy; Catherine Snow; Eleanor Williams; Mitra Barzine; Emma Hastings; Hendrik Weisser; James Wright; Pankaj Jaiswal; Wolfgang Huber; Jyoti Choudhary; Helen E Parkinson; Alvis Brazma; ...More
PUBLISHED: 2016, SOURCE: Nucleic Acids Research, VOLUME: 44, ISSUE: Database-Issue

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TITLE: Gramene 2016: comparative plant genomics and pathway resources Full Text
AUTHORS: Tello Ruiz, MK; Stein, J; Wei, S; Preece, J; Olson, A; Naithani, S; Amarasinghe, V; Dharmawardhana, P; Jiao, YP; Mulvaney, J; Kumari, S; Chougule, K; Elser, J; Wang, B; Thomason, J; Bolser, DM; Kerhornou, A; Walts, B; Fonseca, NA ; Huerta, L; Keays, M; Tanga, YA; Parkinson, H; Fabregat, A; McKay, S; Weiser, J; D'Eustachio, P; Stein, L; Petryszak, R; Kersey, PJ; Jaiswal, P; Ware, D; ...More
PUBLISHED: 2016, SOURCE: NUCLEIC ACIDS RESEARCH, VOLUME: 44, ISSUE: D1

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TITLE: Parallel Algorithms for Multirelational Data Mining: Application to Life Science Problems
AUTHORS: Rui Camacho ; Jorge G Barbosa ; Altino M Sampaio ; João Ladeiras; Nuno A Fonseca ; Vítor Santos Costa ;
PUBLISHED: 2016, SOURCE: Resource Management for Big Data Platforms - Algorithms, Modelling, and High-Performance Computing Techniques

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TITLE: Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction Full Text
AUTHORS: Frankish, A; Uszczynska, B; Ritchie, GRS; Gonzalez, JM; Pervouchine, D; Petryszak, R; Mudge, JM; Fonseca, N ; Brazma, A; Guigo, R; Harrow, J;
PUBLISHED: 2015, SOURCE: BMC GENOMICS, VOLUME: 16, ISSUE: 8

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