Journal Papers

[1] Nelson Perdigão, Agostinho Rosa, S. O Donoghue, The Dark Proteome Database, BioData Mining, pp. 10-24. Springer Nature. July, 2017
[2] Nelson Perdigão, J. Heinrich, C. Stolte, K. Sabir, M. Buckley, B. Tabor, B. Signal, B. S. Gloss, C. J. Hammang, B. Rost, A. Schafferhans, S. O Donoghue, Unexpected features of the dark proteome, PNAS - Proceedings of the National Academy of Sciences of the United States of America. doi: 10.1073/pnas.1508380112, 2015
[3] T. Soldatos, Nelson Perdigão, N. Brown, K. Sabir, S. ODonoghue, How to learn about gene function: text-mining or ontologies?, Methods, Elsevier, Vol. 74, March 2015, pp. 315, doi:10.1016/j.ymeth.2014.07.004, Epub 2014 Aug 1, 2015
[4] Sean O Donoghue, K. Sabir, M. Kalemanov, C. Stolte, B. Wellmann, V. Ho, M. Roos, Nelson Perdigão, F. Buske, J. Heinrich, B. Rost, A. Schafferhans, Aquaria: simplifying discovery and insight from protein structures, Nature Methods, Vol. 12, pp. 98-99, Nature, doi:10.1038/nmeth.3258, 2015

Book Chapters

[5] J. Tavares, Sobre a geracao de malhas tridimensionais para fins computacionais a partir de imagens medicas, Proc. of Congress of Methods in Engineering, ISBN 84-95999-74-9, pp.217, SEMNI, Granada, Spain, 2005
[6] J. Tavares, Geracao de modelos de malhas de elementos finitos a partir de imagens medicas 2D, Proc. of Encontro 1 Biomecanica, ISBN 972-789-151-9, pp.81-85, Sociedade Portuguesa de Biomecanica, Abrantes, Portugal, 2005
[7] Nelson Perdigão, Agostinho Rosa, Multiple Sequence Alignment by Hybrid Evolutionary Algorithms Applied to BALiBASE, Proc. of ICCB2005 - II International Conference on Computational Bioengineering, Vol. 2, pp. 849-860, ISBN 972-8469-37-3, IST Press, Lisbon, Portugal, 2005

Conference Papers

[8] Nelson Perdigão, J. Heinrich, C. Stolte, K. Sabir, M. Buckley, B. Tabor, B. Signal, B. S. Gloss, C. J. Hammang, B. Rost, A. Schafferhans, S. O Donoghue, Unexpected Features of the ‘Dark’ Proteome of structural biology, Proc. of 3Dsig 2016 - Structural Bioinformatics and Computational Biophysics, Orlando, Florida, USA, pp. 54-55, 2016
[9] Nelson Perdigão, T. Soldatos, K. Sabir, S. O Donoghue, Visual Analytics of Gene Sets Comparison, Proc. of BDVA 2015 - IEEE International Symposium on Big Data Visual Analytics, Hobart, Tasmania, Australia, 2015
[10] S. O Donoghue, K. Sabir, M. Kalemanov, C. Stolte, B. Wellmann, V. Ho, M. Roos, Nelson Perdigão, F. Buske, J. Heinrich, B. Rost, A. Schafferhans, Aquaria: simplifying discovery and insight from protein structures, Proc. of 3Dsig 2015 - Structural Bioinformatics and Computational Biophysics, Dublin, Ireland, pp. 76, 2015
[11] S. O Donoghue, K. Sabir, C. Stolte, Nelson Perdigão, V. Ho, V. P. Satagopam, M. Kalemanov, M. Roos, D. Ma, B. Rost, A. Schafferhans, From SRS 3D to Aquaria, making protein structures discoverable, Proc. of 3Dsig 2013 - Structural Bioinformatics and Computational Biophysics, – Berlin, Germany, pp. 97, 2013
[12] Nelson Perdigão, Java Hidden Markov Model applied to Multiple Sequence Alignment of Proteins, Proc. of ISIB08 5th International Symposium on Integrative Bioinformatics, Leucorea, Lutherstadt Wittenberg, Germany, 2008
[13] Daria Migotina, Evolutionary Algorithm for Phylogenetic Tree Construction, Proc. of MCCMB2007 - 3rd Moscow Conference on Computational Molecular Biology, pp. 248-249, Moscow State University, Russia, 2007
[14] Daria Migotina, Agostinho Rosa, Hybrid Evolutionary Algorithms for Multiple Sequence Alignment, Proc. of MCCMB2005 - 2nd Moscow Conference on Computational Molecular Biology, pp. 291-293, Moscow State University, Russia, 2005
[15] S. Domingues, Surgical correction of scoliosis by the Resina-Alves method: numerical simulation of a clinical case, Proc. of the International Congress on Computacional Bioengineering in Zaragoza Spain, Vol. 2, pp. 471-476, M.Doblare, M. Cerrolaza, H. Rodrigues (Eds.), 2003

PhD Theses

[16] Nelson Perdigão, Illuminating the Dark Proteome, Ph.D. Thesis, Instituto Superior Técnico, Universidade de Lisboa, January, 2017

MSc Theses

[17] Nelson Perdigão, Hybrid Evolutionary Algorithm for Multiple Sequence Alignment, Master Thesis, Instituto Superior Tecnico, Lisbon, Portugal, 2005

Technical Reports

[18] Nelson Perdigão, Alinhamento de Proteinas utilizando Algoritmos Geneticos, Former Report of Project PRODEP III / Take 3 / Action 3.2, 2001
[1] Nelson Perdigão, Agostinho Rosa, S. O Donoghue, The Dark Proteome Database, BioData Mining, pp. 10-24. Springer Nature. July, 2017
[2] Nelson Perdigão, J. Heinrich, C. Stolte, K. Sabir, M. Buckley, B. Tabor, B. Signal, B. S. Gloss, C. J. Hammang, B. Rost, A. Schafferhans, S. O Donoghue, Unexpected features of the dark proteome, PNAS - Proceedings of the National Academy of Sciences of the United States of America. doi: 10.1073/pnas.1508380112, 2015
[3] T. Soldatos, Nelson Perdigão, N. Brown, K. Sabir, S. ODonoghue, How to learn about gene function: text-mining or ontologies?, Methods, Elsevier, Vol. 74, March 2015, pp. 315, doi:10.1016/j.ymeth.2014.07.004, Epub 2014 Aug 1, 2015
[4] Sean O Donoghue, K. Sabir, M. Kalemanov, C. Stolte, B. Wellmann, V. Ho, M. Roos, Nelson Perdigão, F. Buske, J. Heinrich, B. Rost, A. Schafferhans, Aquaria: simplifying discovery and insight from protein structures, Nature Methods, Vol. 12, pp. 98-99, Nature, doi:10.1038/nmeth.3258, 2015
[1] J. Tavares, Sobre a geracao de malhas tridimensionais para fins computacionais a partir de imagens medicas, Proc. of Congress of Methods in Engineering, ISBN 84-95999-74-9, pp.217, SEMNI, Granada, Spain, 2005
[2] J. Tavares, Geracao de modelos de malhas de elementos finitos a partir de imagens medicas 2D, Proc. of Encontro 1 Biomecanica, ISBN 972-789-151-9, pp.81-85, Sociedade Portuguesa de Biomecanica, Abrantes, Portugal, 2005
[3] Nelson Perdigão, Agostinho Rosa, Multiple Sequence Alignment by Hybrid Evolutionary Algorithms Applied to BALiBASE, Proc. of ICCB2005 - II International Conference on Computational Bioengineering, Vol. 2, pp. 849-860, ISBN 972-8469-37-3, IST Press, Lisbon, Portugal, 2005
[1] Nelson Perdigão, J. Heinrich, C. Stolte, K. Sabir, M. Buckley, B. Tabor, B. Signal, B. S. Gloss, C. J. Hammang, B. Rost, A. Schafferhans, S. O Donoghue, Unexpected Features of the ‘Dark’ Proteome of structural biology, Proc. of 3Dsig 2016 - Structural Bioinformatics and Computational Biophysics, Orlando, Florida, USA, pp. 54-55, 2016
[2] Nelson Perdigão, T. Soldatos, K. Sabir, S. O Donoghue, Visual Analytics of Gene Sets Comparison, Proc. of BDVA 2015 - IEEE International Symposium on Big Data Visual Analytics, Hobart, Tasmania, Australia, 2015
[3] S. O Donoghue, K. Sabir, M. Kalemanov, C. Stolte, B. Wellmann, V. Ho, M. Roos, Nelson Perdigão, F. Buske, J. Heinrich, B. Rost, A. Schafferhans, Aquaria: simplifying discovery and insight from protein structures, Proc. of 3Dsig 2015 - Structural Bioinformatics and Computational Biophysics, Dublin, Ireland, pp. 76, 2015
[4] S. O Donoghue, K. Sabir, C. Stolte, Nelson Perdigão, V. Ho, V. P. Satagopam, M. Kalemanov, M. Roos, D. Ma, B. Rost, A. Schafferhans, From SRS 3D to Aquaria, making protein structures discoverable, Proc. of 3Dsig 2013 - Structural Bioinformatics and Computational Biophysics, – Berlin, Germany, pp. 97, 2013
[5] Nelson Perdigão, Java Hidden Markov Model applied to Multiple Sequence Alignment of Proteins, Proc. of ISIB08 5th International Symposium on Integrative Bioinformatics, Leucorea, Lutherstadt Wittenberg, Germany, 2008
[6] Daria Migotina, Evolutionary Algorithm for Phylogenetic Tree Construction, Proc. of MCCMB2007 - 3rd Moscow Conference on Computational Molecular Biology, pp. 248-249, Moscow State University, Russia, 2007
[7] Daria Migotina, Agostinho Rosa, Hybrid Evolutionary Algorithms for Multiple Sequence Alignment, Proc. of MCCMB2005 - 2nd Moscow Conference on Computational Molecular Biology, pp. 291-293, Moscow State University, Russia, 2005
[8] S. Domingues, Surgical correction of scoliosis by the Resina-Alves method: numerical simulation of a clinical case, Proc. of the International Congress on Computacional Bioengineering in Zaragoza Spain, Vol. 2, pp. 471-476, M.Doblare, M. Cerrolaza, H. Rodrigues (Eds.), 2003
[1] Nelson Perdigão, Illuminating the Dark Proteome, Ph.D. Thesis, Instituto Superior Técnico, Universidade de Lisboa, January, 2017
[1] Nelson Perdigão, Hybrid Evolutionary Algorithm for Multiple Sequence Alignment, Master Thesis, Instituto Superior Tecnico, Lisbon, Portugal, 2005
[1] Nelson Perdigão, Alinhamento de Proteinas utilizando Algoritmos Geneticos, Former Report of Project PRODEP III / Take 3 / Action 3.2, 2001

In the same group

Rodolfo Abreu
David Afonso
Gina Caetano
Alexandre Calapez
Janir Cruz
Nuno Fachada
Carlos Fernandes
Patrícia Figueiredo
Andreia Gaspar
Rogério Largo
Fernando Melicio
Rita Gouveia Nunes
Nelson Perdigão
Joana Pinto
Joao Ribeiro
Agostinho Rosa
João Sanches