CV Ana Usié

 

Ana Usié   Investigadora de Pós-Doutoramento                    Doutorada em Bioinformática                       Universidade de Lleida     Este endereço de email está protegido contra piratas. Necessita ativar o JavaScript para o visualizar.   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

Fev. 2020 - (Current). Post-Doctoral Researcher

CEBAL -Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo. Project ALT20-03-0145-FEDER-000041 - SelectPinea – Desenvolvimento de marcadores genéticos para características de interesse em Pinheiro manso (Pinus pinea).

Set. 2016 - Jan. 2020. 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. Trindade, A. Usié, B. Meireles, A. M. Fortes, J. Guimarães, F. Simões, R. Costa, A. M. Ramos (2020). Comparative transcriptomic response of two Pinus species to infection with the pine wood nematode Bursaphelenchus xylophilus. Forests 2020, 11(2), 204; https://doi.org/10.3390/f11020204

Capote, T., Usié, A., Barbosa P., Ramos, A.M., Morais-Cecílio, L. and Gonçalves, S. 2. (2019). Transcriptome dynamics of cork oak (Quercus suber) somatic embryogenesis reveals active gene players in transcriptome regulation and phytohormone homeostasis of embryo development. Tree Genetics & Genomes, 15: 52. https://doi.org/10.1007/s11295-019-1353-6

Capote, T., Barbosa, P., Usié, A., Ramos, A.M., Inácio, V., Ordás, R., Gonçalves, S. and Morais-Cecílio, L. (2018). Chip-Seq reveals that QsMYB1 directly targets genes involved in ligning and subering biosynthesis pathways in cork oak (Quercus suber). BMC Plant Biology 2018 Sep 17; 18(1):198.

Ramos , A.M., Usié, A., Barbosa, P., Barros, P.M., Capote, T., Chaves, I., Simões, F., Abreu, I., Carrasquinho, I., Faro, C., Guimarães, J.B., Mendonça, D., Nóbrega, F., Rodrigues, L., Saibo, N., Varela, M.C., Egas, C., Matos, J., Miguel, C.M., Oliveira, M.M., Ricardo, C.P., Gonçalves, S.. (2018). The draft genome sequence of cork oak. Scientific Data, 5, 180069.

B. Meireles, A. Usié, P. Barbosa, A.M. Fortes, A. Folgado. I. Chaves, I. Carrasquinho, R.L. Costa, S. Gonçalves, R.T. Teixeira, A.M. Ramos, F. Nóbrega (2018) Characterization of the cork formation and production transcriptome in Quercus cerris × suber hybrids. Physiology and Molecular Biology of Plants, pp 1-15, doi:10.1007/s12298-018-0526-3  

A. Usié, F. Simões, P. Barbosa, B. Meireles, I. Chaves, S. Gonçalves, A. Folgado  M.H. Almeida, J. Matos and A.M. Ramos (2017). Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting. Forests, vol 8. No. 12. 486, doi:10.3390/f8120486

P. Barbosa, C. Leão, A Usié, A. Amaro, A. Botelho, C. Pinto, J. Inácio, K. Stevenson and A.M. Ramos (2017) Draft Genome Sequence of a Rare Pigmented Mycobacterium avium subsp. paratuberculosis Type C Strain. Genome Announcements, 5(41), e01066–17. http://doi.org/10.1128/genomeA.01066-17

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 xylophilus. Forests, 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

B. Mendes, M. Antunes, A. Usié, C. Leão, A.M. Ramos (2020). “Characterization of the stone pine (Pinus pinea) needle transcriptome: de novo assembly and SNP identification”. Bioinformatics open days. February 19th-21st, 2020, Braga, Portugal.

M. Antunes, B. Mendes, H. Magalhães, A. Usié, T. Sampaio, F. Simões, H. Almeida, A.M. Ramos (2020). “Identification of genetic markers for traits of economic importance in cork oak using high throughput SNP genotyping”. Bioinformatics open days. February 19th-21st, 2020, Braga, Portugal

B. Mendes, T. Sampaio, M. Antunes, H. Magalhães, A. Usié, F. Simões, H. Almeida, A.M. Ramos (2020). “Kinship analysis and Pedigree Reconstruction of a Self-Regenerating Cork Oak Population”. Bioinformatics open days. February 19th-21st, 2020, Braga, Portugal

A. Usié, H. Magalhães, M, Antunes, C. Leão, D. Gaspar, B. Meireles, P. Barbosa, L. Cachucho, A. Albuquerque, R. Charneca, J. Martins, E. Jerónimo, A.M. Ramos (2020). “Whole genome resequencing analysis of Alentejano pigs reveals differences associated with meat quality phenotypes”. Bioinformatics open days. February 19th-21st, 2020, Braga, Portugal

A. Usié, H. Magalhães, C. Leão, D. Gaspar, B. Meireles, P. Barbosa, L. Cachucho, A. Albuquerque, R. Charneca, J. Martins, E. Jerónimo, A.M. Ramos (2020). “Whole Genome Analysis of Alentejano Pigs with Contrasting Meat Quality Phenotypes”. Plant & Animal Genome XXVIII Conference, January 11-15, 2020 in San Diego, CA at the Town & Country Hotel and Convention Center.

C. Leão, A. Usié, M. Antunes, H. Magalhães and A.M. Ramos. (2018). “Identification and characterization of SNPs in stone pine (Pinus pinea) transcriptome”. Bioinformatics open days. March 14th-16th, 2018, Braga, Portugal.

GASPAR, D.; MEIRELES, B.; USIÉ, A.; BARBOSA, P.; SCOTTI, P.; SEMEDO, J.; PAIS, I.; MAÇÃS, B.; ALMEIDA, A.S.; COSTA, R.; COUTINHO, J.; PINHEIRO, N.; MATOS, J.; SIMÕES, F.; MENDONÇA, D.; GUIMARÃES, J.; RAMOS, A.M. (2017) “Comparative analysis of transcriptional response to heat stress in two Triticum durum varieties”. Bioinformatics open days. February 22nd – 24th, 2017, Braga, Portugal

B. MEIRELES, D. GASPAR, A. USIÉ, P. BARBOSA, P. SCOTTI, J. SEMEDO, I. PAIS, B. MAÇÃS, A. S. ALMEIDA, R. COSTA, J. COUTINHO, N. PINHEIRO, J. MATOS, F. SIMÕES, D. MENDONÇA, J. GUIMARÃES, A. M. RAMOS (2017, February). Identification of miRNAs related with the response to heat stress in two Triticum durum varieties. 6th Bioinformatics Open Days, Braga, Portugal.

BARROS, P.M., BARBOSA, P., USIÉ, A., OLIVEIRA, M.M., PESQUITA, C.,  RAMOS, A.M. (2017) “Alternative splicing detection across different tissues in cork oak”. Bioinformatics open days. February 22nd – 24th, 2017, Braga, Portugal

L.CACHUCO, A. USIÉ, A. ALBUQUERQUE, C. LEÃO, B. MEIRELES, P. BARBOSA, D. GASPAR, J.M. MARTINS, R. CHARNECA, A.M. RAMOS, E. JERÓNIMO (2017, November) Characterization of carcass composition and meat quality traits of Alentejano pigs finished under free-range conditions - Preliminary results. Poster presented at 4th Fatty Pig Science & Utilization International Conference, Badajoz, Spain.

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

USIÉ, A., GENOSUBER CONSORTIUM, 2019. Cork oak (Quercus suber L.) genome. Jornadas MED, Pólo da Mitra, Évora, Portugal, 27-28 June

Thesis

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