CV Ana Usié

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  Ana Usié

  Investigadora de Pós-Doutoramento                 

  Doutorada em Bioinformática                    

  Universidade de Lleida

 

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  Tel: +351 284314399

  Ext: 01107

 

  

Education and Training

Ph.D. in Bioinformatics, University of Lleida, Lleida, Spain (2014).

Master in Engineering of Free Software, Polytechnic School, University of Lleida, Lleida, Spain (2010)

Senior Computer Engineering, Polytechnic School, University of Lleida, Lleida, Spain (2010)

Technical Engineering in Computer Management, Polytechnic School, University of Lleida, Lleida, Spain (2007)

Research and Professional Experience

Set. 2016 - (Current). Post-Doctoral Researcher

CEBAL -Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo. Project ALT20-03-0145-FEDER-000032 - SelectPorAl - Seleção e melhoramento genómico de características produtivas do Porco Alentejano.

Nov. 2015 - Ago.2016. Post-Doctoral Researcher

CEBAL -Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo. Project IF/01015/2013/CP1209/CT0001 - Genomics and Bioinformatics applied to Portuguese plant and animal genetic resources.

Mar. 2014 - Out. 2015. Post-Doctoral Researcher

CEBAL -Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo. Project ALENT-07- 0224-FEDER-001754 - Genosuber - Cork Oak Genome Sequencing. Sequencing and annotation the cork oak genome, using data generated with several high-throughput sequencing technologies.

Oct. 2009 - Jan. 2014. Ph.D. Student / Researcher

University of Lleida.
Project BFU2010-17704– MetReS (Metabolic Reconstruction Server): desarollo y aplicación en estudio de principios de diseño biológico.
Project - Desarrollo y aplicación de metodologías computacionales integradas para Biología Molecular de Sistemas.

2008 – 2014. Web Manager

University of Lleida.
Administration and management of the website for the Master of Integrated Production Crops (PIC), at University of Lleida.

Jul. - Dec. 2011. Short stay as a Ph.D Student / Researcher

CNIO (Spanish National Cancer Research Centre).

Jul. - Dec. 2011. Researcher

University of Lleida.
Support tasks in the research work of the Distributed Computing Group.

Current interests of research

Bioinformatics, Genome Sequencing, Genome assembly, Genome annotation, Protein-Protein Interactions

Selected Publications

Papers in peer reviewed journals

D. Gaspar, C. Trinidade, A. Usié, B. Meireles, P. Barbosa, A. Fortes, C. Pesquita, R. Costa and A.M. Ramos (2017) Expression Profiling in Pinus Pinaster in Response to Infection with the Pine Wood Nematode Bursaphelenchus xylophilusForest, vol 9. No. 8. 279, doi: 10.3390/f8080279

A Usié, J. Cruz, J. Comas, F. Solsona and R. Alves (2015) CheNER: A tool for the identification of chemical entities and their classes in biomedical literature. ChemInformatics, 7 (Suppl 1) S15 doi:10.1186/1758-2946-7-S1S15

M. Krallinger, O. Rabal, F. Leitner, M. Vazquez, D. Salgado, Z. Lu, R. Leaman, Y. Lu, D. Ji, D. M Lowe, R.A. Sayle, R. Theresa Batista-Navarro, R. Rak, T. Huber, T. Rocktäschel, S. Matos, D. Campos, B. Tang, H. Xu, T. Munkhdalai, K. Ho Ryu, SV Ramanan, S. Nathan, S. Žitnik, M. Bajec, L. Weber, M. Irmer, S.A. Akhondi, J.A. Kors, S. Xu, X. An, U. K. Sikdar, A. Ekbal, M. Yoshioka, T. M. Dieb, M. Choi, K. Verspoor, M. Khabsa, C.L. Giles, H. Liu, K.E. Ravikumar, A. Lamurias, F.M. Couto, H. Dai, R.T. Tsai, C. Ata, T. Can, A. Usié, R. Alves, I. Segura-Bedmar, P. Martínez, J. Oyarzabal and A. Valencia (2015) The CHEMDNER corpus of chemicals and drugs and its annotation principles. Journal of Cheminformatics, 7(Suppl 1):S15 doi: 10.1186/1758-2946-7-S1-S2.

J.Vilaplana, F. Solsona, I. Teixidó, A. Usié, H. Karathia, R. Alves and J. Mateo (2014) Database Constraints Applied to Metabolic Pathway Reconstrution Tools. The Scientific World Journal 08/2014

A. Usié, H. Karathia, I. Teixidó, R. Alves and F. Solsona (2014). Biblio-MetReS for literature mining. PeerJ 01/2014; 2:e276.

A. Usié, R. Alves, F. Solsona, M. Vázquez and A. Valéncia. (2013) CheNER: Chemical Named Entity Recognizer. Bioinformatics 11/2013; doi:10.1093/bioinformatics/btt639

A. Usié, H. Karathia, I. Teixidó, X. Faus, R. Alves and F. Solsona. (2011) Biblo-MetReS: A bibliometric network reconstruction application and server." BMC Bioinformatics, 12:387 doi:10.11.1186/1471-2105-12-387

B. Salvado, H. Karathia, A. Usié, E. Vilaprinyó, S. Omholt, A. Sorribas and R. Alves. (2011) Methods for and results from the study of design principle in moleculars systems. Mathematical Biosciences, Volume 231, Issue 1, Special issue on biological desing principles May 2011, Pages 3-18, ISSN 0025-5564, DOI: 10.1016/j.mbs.2011.02.005.

Papers in Proceedings

I. Teixidó, A. Usié, J. Lérida, F. Solsona, J. Comas, N. Torres, H. Karathia and R. Alves (2013) P-Biblio-MetReS a parallel data-mining tool for the reconstruction of molecular networks. Proceedings of the 20th European MPI Users’ Group Meeting.

A. Usié, J. Cruz, J. Comas, F. Solsona and R. Alves (2013) A tool for the identification of chemical entities (CheNER-BioC). Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2, Pages 66-69.

O. Abdelli, A. Usié, H. Karathia, J. Vilaplana, F. Solsona and R. Alves (2011) Parallelizing Biblio-MetReS, a data mining tool. Actas XXII Jornadas de Paralelismo (JP2011)

Posters in Conferences

USIÉ, A., SIMÕES, F., BARBOSA, P., MEIRELES, B., CHAVES, I., ALMEIDA, M.H., MATOS, J., RAMOS, A.M., 2016. Comprehensive analysis of the cork oak (Quercus suber) transcriptome involved in the regulation of bud sprouting and foliar development. 5th Bioinformatics Open Days, Braga, Portugal, 18-19 February

BARBOSA, P., LEÃO, C., USIÉ, A., CHAVES, I., AMARO, A., BOTELHO, A., PINTO, C., STEVENSON, K., INÁCIO, J., RAMOS, A.M., 2016. Genome wide comparison between Mycobacterium avium subsp. paratuberculosis non-pigmented and pigmented isolates. 5th Bioinformatics Open Days, Braga, Portugal, 18-19 February

GASPAR, D., TRINDADE, C., USIÉ, A., BARBOSA, P., FORTES, A., PESQUITA, C., COSTA, R., RAMOS, A.M., 2016. Characterization of the maritime pine (Pinus pinaster) transcriptome in the response to infection with Bursaphelenchus xylophilus, the causal agent of pine wilt disease. 5th Bioinformatics Open Days, Braga, Portugal, 18-19 February

LEÃO, C., BARBOSA, P., USIÉ, A., CHAVES, I., AMARO, A., BOTELHO, A., PINTO, C., INÁCIO, J., STEVENSON, K., RAMOS, A.M., 2016. Molecular characterization of a rare pigmented Mycobacterium avium subsp. paratuberculosis Type C strain. 13th International Colloquium on Paratuberculosis, Nantes, France, 20-24 June

GONÇALVES, S., GENOSUBER CONSORTIUM, 2014. GENOSUBER – Cork Oak (Quercus suber) Genome Sequencing Project. 2nd Plant Genomics Congress. London, UK, 11-12 May.

VARELA, M.C., GENOSUBER CONSORTIUM, 2014. Controlled pollination in cork oak (Quercus suber L.) to support its genome sequencing project 23rd International Congress on Sexual Plant Reproduction, Porto, Portugal, 13-18 July

A. USIÉ, J. CRUZ, J. COMAS, F. SOLSONA and R. ALVES. A tool for the identification of chemical entities (CheNER-BioC). Fourth BioCreative Challenge Evaluation Workshop. 

A. USIÉ, I. TEIXIDÓ, H. KRATHIA, F. SOLSONA and R. ALVES. Biblio-MetReS: A Bibliometric Network Reconstruction Server. Student Symposium of the XIth Spanish Symposium on Bioinformatics · JBI2012 23-25 Jan 2012.

H. KARATHIA, A. USIÉ, E. VILAPRINYÓ, A. SORRIBAS, F. SOLSONA and R. ALVES. Proteome-MetReS: Network Reconstruction Based on Whole Proteome Comparisons. The XII internation Congress on Molecular Systems Biology: Biological Desing Principle · ICMSB 8-12 May 2011

A. USIÉ, H. KARATHIA, F. SOLSONA and R. ALVES. Biblio-MetReS: A Bibliometric Network Reconstruction Server. The XII internation Congress on Molecular Systems Biology: Biological Desing Principle · ICMSB 8-12 May 2011.

H. BLANCO, J.L. LÉRIDA, F. GUIRADO and A. USIÉ. Modelo de asignación de tareas en entornos multicluster heterogéneos y no dedicados."XX Jornadas del paralelismo, A Coruña 16-18 Sep, 2009.

Oral presentations

RAMOS, A.M., GENOSUBER CONSORTIUM, 2016. The draft assembly and annotation of the cork oak (Quercus suber L.) genome. 5th Bioinformatics Open Days, Braga, Portugal, 18-19 February

RAMOS, A.M., GENOSUBER CONSORTIUM, 2015. The draft assembly and annotation of the cork oak (Quercus suber L.) genome. Fisiologia Vegetal, XXI Meeting of the Spanish Society of Plant Physiology, XIV Iberian Meeting of Plant Physiology, Toledo, Spain, 14-17 June

O. ABDELLI, A. USIÉ, H. KARATHIA, J. VILAPLANA, F. SOLSONA and R. ALVES. Parallelizing Biblio-MetReS, a data mining tool. XXII Jornadas del paralelismo, La Laguna 7-9 Sep, 2011 

R. HARATIA, H., USIÉ, A., VILAPRINYÓ, E., SOLSONA, F., TEIXIDÓ, I., SORRIBAS, A. and ALVES, R. (2012) Homol-MetReS: A web application for integration between molecular systems biology and evolutionary biology, Student Symposium of the XIth Spanish Symposium on Bioinformatics · JBI2012 23-25 Jan 2012. 

Thesis

Usié, A. (2014) Development of computational tools to assist in the reconstruction of molecular networks. Ph.D Thesis. University of Lleida. Pp 195

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