Raquel Silva

Position	Post-doc researcher
Affiliation	iBiMED / IEETA
Group	Biomedical Informatics and Technologies
Status	Researcher with PhD
Country	Portugal
Students	Sara Pereira
Former PhD students
Former masters students
Courses
Projects
Past projects	NETDIAMOND, NeuroPath
Events
Proposals
ORCID	0000-0001-5926-8042
Personal page

Publications

Articles in international journals listed in the ISI

• Carlos A C Bastos, Vera Afreixo, João M. O. S. Rodrigues, Armando J. Pinho, Raquel Silva. Distribution of Distances Between Symmetric Words in the Human Genome: Analysis of Regular Peaks. Interdisciplinary Sciences: Computational Life Sciences, vol. 11, no. 3, p. 367--372, September 2019 [IF 2018: 1.418 (Q3, 40/59)]
• Mafalda Cavalheiro, Catarina Costa, Ana Silva-Dias, Isabel M. Miranda, Can Wang, Pedro Pais, Sandra N. Pinto, Dalila Mil-Homens, Michiyo Sato-Okamoto, Azusa Takahashi-Nakaguchi, Raquel Silva, Nuno P. Mira, Arsénio M. Fialho, Hiroji Chibana, Acácio G. Rodrigues, Geraldine Butler, Miguel C. Teixeira. Unveiling the mechanisms of in vitro evolution towards fluconazole resistance of a Candida glabrata clinical isolate: a transcriptomics approach. Antimicrobial Agents and Chemotherapy, vol. 63, no. 1, January 2019 [IF 2018: 4.715 (Q1, 27/267)]
• Diogo Pratas, Morteza Hosseini, Gonçalo Grilo, Armando J. Pinho, Raquel Silva, Tânia Caetano, João Carneiro, Filipe Pereira. Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard. Genes, vol. 9, no. 9, p. 445, September 2018 [IF 2018: 3.331 (Q2, 61/174)]
• Diogo Pratas, Raquel Silva, Armando J. Pinho. Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes. Entropy, vol. 20, no. 6, p. 393, May 2018 [IF 2018: 2.419 (Q2, 28/81)]
• Ana H. M. P. Tavares, Jakob Raymaekers, Peter J. Rousseeuw, Raquel Silva, Carlos A C Bastos, Armando J. Pinho, Paula Brito, Vera Afreixo. Comparing reverse complementary genomic words based on their distance distributions and frequencies. Interdisciplinary Sciences: Computational Life Sciences, vol. 10, no. 1, p. 1-11, March 2018 [IF 2018: 1.418 (Q3, 40/59)]
• AF Pedrosa, C Lisboa, I Faria‐Ramos, Raquel Silva, IM Miranda, AG Rodrigues. Malassezia species retrieved from skin with pityriasis versicolor, seborrheic dermatitis and skin free of lesions: a comparison of two sampling methods. British Journal of Dermatology, vol. 179, no. 2, p. 526-527, March 2018
• Joana Branco, Mihaela Ola, Raquel Silva, Elizangela Fonseca, Nuno C. Gomes, Cláudia Martins-Cruz, Ana P. Silva, Ana Silva-Dias, Cidália Pina-Vaz, Claire Erraught, Lorraine Brennan, Acácio G. Rodrigues, Geraldine Butler, Isabel M. Miranda. Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance. Clinical Microbiology and Infection, vol. 23, no. 8, p. 575.e1-575.e8, August 2017
• Ana H. M. P. Tavares, Armando J. Pinho, Raquel Silva, João M. O. S. Rodrigues, Carlos A C Bastos, Paulo J S G Ferreira, Vera Afreixo. DNA word analysis based on the distribution of the distances between symmetric words. Scientific Reports, vol. 7, no. 728, April 2017 [IF 2018: 4.011 (Q1, 15/69)]
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos, Ana H.M.P. Tavares, Raquel Silva. Exceptional symmetry by genomic word. Interdisciplinary Sciences: Computational Life Sciences, vol. 9, no. 1, p. 14-23, March 2017 [IF 2017: 0.796 (Q4, 54/59)] [IF 2018: 1.418 (Q3, 40/59)]
• Luisa Azevedo, Matthew Mort, Antonio C Costa, Raquel Silva, Dulce Quelhas, Antonio Amorim, David N Cooper. Improving the in silico assessment of pathogenicity for compensated variants. European Journal of Human Genetics, vol. 25, no. 1, p. 2-7, January 2017
• Filipe Pereira, Sara Pereira, Raquel Silva, Luis Teixeira da Costa, Isabel Pereira-Castro. Evolution of the NET (NocA, Nlz, Elbow, TLP-1) protein family in metazoans: insights from expression data and phylogenetic analysis. Scientific Reports, vol. 6, p. 38383, December 2016 [IF 2016: 4.259 (Q1, 10/64)] [IF 2018: 4.011 (Q1, 15/69)]
• Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza K. Irin, Lars J. Jensen, Silvia Jimenez, Toni R. Jue, Ingrid Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole Vasilevsky, Xiaodong Wang, Andrew Chatr-Aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna McEntyre, Sandra Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary Schaeffer, Cathy H. Wu, Lynette Hirschman, and Cecilia N. Arighi. Overview of the interactive task in BioCreative V. Database, vol. 2016, p. baw119, September 2016 [IF 2016: 3.290 (Q1, 8/57)] [IF 2018: 3.683 (Q1, 7/59)]
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database, vol. 2016, June 2016 [IF 2016: 3.290 (Q1, 8/57)] [IF 2018: 3.683 (Q1, 7/59)]
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos, Raquel Silva. The exceptional genomic word symmetry along DNA sequences. BMC Bioinformatics, vol. 17, no. 59, p. 1-10, February 2016 [IF 2016: 2.448 (Q1, 10/57)]
• Sara Pereira, Isabel Pereira Castro, Sarah Silva, Mariana Gonçalves Correia, Célia Neto, Luis Teixeira da Costa, António Amorim, Raquel Silva. Extensive regulation of nicotinate phosphoribosyltransferase (NAPRT) expression in human tissues and tumors. Oncotarget, vol. 7, no. 2, p. 1973-1983, December 2015 [IF 2015: 5.008 (Q1, 36/213)]
• Joana Branco, Ana P. Silva, Raquel Silva, Ana Silva-Dias, Cidália Pina-Vaz, Geraldine Bitler, Acacio G. Rodrigues, Isabel Miranda. Fluconazole and Voriconazole Resistance in Candida parapsilosis Is Conferred by Gain-of-Function Mutations in MRR1 Transcription Factor Gene. Antimicrobial Agents and Chemotherapy, vol. 59, no. 10, p. 6629-33, August 2015 [IF 2015: 4.415 (Q1, 34/255)] [IF 2018: 4.715 (Q1, 27/267)]
• Diogo Pratas, Raquel Silva, Armando J. Pinho, Paulo J S G Ferreira. An alignment-free method to find and visualise rearrangements between pairs of DNA sequences. Scientific Reports, vol. 5, p. 10203, May 2015 [IF 2015: 5.228 (Q1, 7/63)] [IF 2018: 4.011 (Q1, 15/69)]
• Raquel Silva, Diogo Pratas, Luísa Castro, Armando J. Pinho, Paulo J S G Ferreira. Three minimal sequences found in Ebola virus genomes and absent from human DNA. Bioinformatics, vol. 31, no. 15, p. 2421-2425, April 2015 [IF 2015: 5.766 (Q1, 3/56)] [IF 2018: 4.531 (Q1, 4/59)]
• Sara Duarte Pereira, Sarah S. Silva, Luísa Azevedo, Luísa Castro, António Amorim, Raquel Silva. Nampt and Naprt1: Novel Polymorphisms and Distribution of Variants between Normal Tissues and Tumor Samples. Scientific Reports, vol. 4, p. 6311, September 2014 [IF 2014: 5.578 (Q1, 5/57)] [IF 2018: 4.011 (Q1, 15/69)]

Other articles in journals

• Ana Marote, Nathalie Barroca, Rui Vitorino, Raquel Silva, Maria H.V. Fernandes, Paula M. Vilarinho, Odete A.B. da Cruz e Silva, Sandra I. Vieira. A proteomic analysis of the interactions between poly(L-Lactic Acid) nanofibers and SH-SY5Y neuronal-like cells. AIMS Molecular Science, vol. 3, no. 4, p. 661-682, November 2016

Articles in conference proceedings

• Ana Teixeira, Diogo Pratas, Armando J. Pinho, Raquel Silva. Evolutionary insights from the comparative analysis of hominid genomes. Proceedings of the 24th Portuguese Conference on Pattern Recognition, RecPad2018, Coimbra, October 2018
• Catarina Figueiredo, Diogo Pratas, Armando J. Pinho, Raquel Silva. Identification of antifungal targets using alignment-free methods. Proceedings of the 24th Portuguese Conference on Pattern Recognition, RecPad2018, Coimbra, October 2018
• Ana H. M. P. Tavares, Jakob Raymaekers, Peter J. Rousseeuw, Raquel Silva, Carlos A C Bastos, Armando J. Pinho, Paula Brito, Vera Afreixo. Dissimilar symmetric word pairs in the human genome. PACBB 2017 - 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, Portugal, vol. AISC 616, p. 248-256, June 2017
• Diogo Pratas, Morteza Hosseini, Raquel Silva, Armando J. Pinho, Paulo J S G Ferreira. Visualization of distinct DNA regions of the modern human relatively to a Neanderthal genome. IbPRIA 2017 - 8th Iberian Conference on Pattern Recognition and Image Analysis, Faro, Portugal, vol. LNCS 10255, p. 235-242, June 2017
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos, Raquel Silva. Exceptional symmetry profile: a genomic word analysis. International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB), Sevilla, Spain, vol. 477 (in Springer series Advances in Intelligent Systems and Computing), p. 151--159, June 2016
• Vera Afreixo, Carlos A C Bastos, João M. O. S. Rodrigues, Raquel Silva. Identification of DNA CpG Islands Using Inter-dinucleotide Distances. Optimization in the Natural Sciences. 30th Euro Mini-Conference, EmC-ONS 2014. Aveiro, Portugal, February 5–9, 2014. Revised Selected Papers. (Series: Communications in Computer and Information Science), Springer International Publishing, Switzerland, vol. 499, p. 162-172, 2015
• Diogo Pratas, Raquel Silva, Armando J. Pinho, Paulo J S G Ferreira. Detection and visualisation of regions of human DNA not present in other primates. Proceedings of the 21st Portuguese Conference on Pattern Recognition, RecPad 2015, Faro, Portugal, October 2015
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Assisted Mining and Curation of Genomic Variants using Egas. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 396-402, September 2015
• Diogo Pratas, Raquel Silva, Armando J. Pinho. Large-scale inversions between human reference assemblies. Proceedings of the 20th Portuguese Conference on Pattern Recognition, RecPad 2014, Covilhã, Portugal, October 2014
• Raquel Silva, Luísa Castro, Diogo Pratas, Armando J. Pinho. Towards personalized medicine: ebola virus absent words in the human genome. Proceedings of the 20th Portuguese Conference on Pattern Recognition, RecPad 2014, Covilhã, Portugal, October 2014
• Luísa Castro, José Luís Oliveira, Raquel Silva. Mutation Analysis in Park2 Gene Uncovers Patterns of Associated Genetic Variants. Advances in Intelligent Systems and Computing, Proc. of the 8th Int. Conf. on Practical Applications of Computational Biology & Bioinformatics (PACBB14), Salamanca, Spain, June 2014