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Publications

[Last update: February 2022]

* marks first or co-first author

Journal Papers (JCR journals)

  1. Mateo Torres, Haixuan Yang, A. E. Romero*, Alberto Paccanaro, Protein function prediction for newly sequenced organisms, Nature Machine Intelligence, 3(12), 1050-1060, 2021. (link) (pdf)
  2. Naihui Zhou, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee, Balint Z Kacsoh, Alex W Crocker, Kimberley A Lewis, George Georghiou, Huy N Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L Hurto, Peter L Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M Fernández, Branislava Gemovic, Vladimir R Perovic, Radoslav S Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad RK Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A Freitas, Magdalena Antczak, Fabio Fabris, Mark N Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B Roche, Jonas Reeb, David W Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio CE Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S Black, Dane Jo, Erica Suh, Jonathan B Dayton, Dallas J Larsen, Ashton R Omdahl, Liam J McGuffin, Danielle A Brackenridge, Patricia C Babbitt, Jeffrey M Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti EE Tolvanen, Tapio Salakoski, The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens, Genome Biology, 20(1), 1-23, 2019. (link)
  3. F. Manfredini, A. E. Romero, I. Pedroso, A. Paccanaro, S. Sumner, M. J. F. Brown, Neurogenomic signatures of successes and failures in life-history transitions in a key insect pollinator, Genome Biology and Evolution, 9(11), 3059-3072, 2017. (link)
  4. Ö Kafalı, A. E Romero, K. Stathis, Agent‐oriented activity recognition in the event calculus: An application for diabetic patients, Computational Intelligence, 33(4), 899-925, 2017. (link)
  5. M. J Meyer, R. Lapcevic, A. E Romero*, M. Yoon, J. Das, J. F. Beltrán, M. Mort, P. D. Stenson, D. N. Cooper, A. Paccanaro, H. Yu, mutation3D: cancer gene prediction through atomic clustering of coding variants in the structural proteome, Human Mutation, 37(5), 447-456, 2016. (link) (preprint pdf)
  6. B. Cvetković, V. Janko, A. E. Romero, Ö. Kafalı, K. Stathis, M. Luštrek, Activity Recognition for Diabetic Patients Using a Smartphone, Journal of Medical Systems, 40(256), 2016. (link)
  7. Y. Jiang, T. R. Oron, W. T. Clark, A. R. Bankapur, D. D’Andrea, R. Lepore, C. S. Funk, I. Kahanda, K. M. Verspoor, A. Ben-Hur, D. C. E. Koo, D. Penfold-Brown, D. Shasha, N. Youngs, R. Bonneau, A. Lin, S. M. E. Sahraeian, P. L. Martelli, G. Profiti, R. Casadio, R. Cao, Z. Zhong, J. Cheng, A. Altenhoff, N. Skunca, C. Dessimoz, T. Dogan, K. Hakala, S. Kaewphan, F. Mehryary, T. Salakoski, F. Ginter, H. Fang, B. Smithers, M. Oates, J. Gough, P. Törönen, P. Koskinen, L. Holm, C. Chen, W. Hsu, K. Bryson, D. Cozzetto, F. Minneci, D. T. Jones, S. Chapman, D. BKC, I. K. Khan, D. Kihara, D. Ofer, N. Rappoport, A. Stern, E. Cibrian-Uhalte, P. Denny, R. E. Foulger, R. Hieta, D. Legge, R. C. Lovering, M. Magrane, A. N. Melidoni, P. Mutowo-Meullenet, K. Pichler, A. Shypitsyna, B. Li, P. Zakeri, S. ElShal, L. C. Tranchevent, S. Das, N. L. Dawson, D. Lee, J. G. Lees, I. Sillitoe, P. Bhat, T. Nepusz, A. E. Romero, R. Sasidharan, H. Yang, A. Paccanaro, J. Gillis, A. E. Sedeño-Cortés, P. Pavlidis, S. Feng, J. M. Cejuela, T. Goldberg, T. Hamp, L. Richter, A. Salamov, T. Gabaldon, M. Marcet-Houben, F. Supek, Q. Gong, W. Ning, Y. Zhou, W. Tian, M. Falda, P. Fontana, E. Lavezzo, S. Toppo, C. Ferrari, M. Giollo, D. Piovesan, S. C.E. Tosatto, A. del Pozo, J. M. Fernández, P. Maietta, A. Valencia, M. L. Tress, A. Benso, S. Di Carlo, G. Politano, A. Savino, H. U. Rehman, M. Re, M. Mesiti, G. Valentini, J. W. Bargsten, A. D. J. van Dijk, B. Gemovic, S. Glisic, V. Perovic, V. Veljkovic, N. Veljkovic, D. C. Almeida-e-Silva, R. Z. N. Vencio, M. Sharan, J. Vogel, L. Kansakar, S. Zhang, S. Vucetic, Z. Wang, M. J. E. Sternberg, M. N. Wass, R. P. Huntley, M. J. Martin, C. O’Donovan, P. N. Robinson, Y. Moreau, A. Tramontano, P. C. Babbitt, S. E. Brenner, M. Linial, C. A. Orengo, B. Rost, C. S. Greene, S. D. Mooney, I. Friedberg, P. Radivojac, An expanded evaluation of protein function prediction methods shows an improvement in accuracy, Genome Biology, 17(184), 2016. (link)
  8. H. Caniza, A. E. Romero, A. Paccanaro, A network medicine approach to quantify distance between hereditary disease modules on the interactome, Scientific reports, 5: 17658, 2015. (link)
  9. H. Caniza, A. E. Romero*, S. Heron, H. Yang, A. Devoto, M. Frasca, M. Mesiti, G. Valentini, A. Paccanaro, GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology, Bioinformatics, 30(15), 2235-2236, 2014. (link)
  10. G. Valentini, A. Paccanaro, H. Caniza, A. E. Romero, M. Re, An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods, Artif. Intell. Med., 61(2), 63-78, 2014. (link)
  11. E. Ferrara, A. E. Romero, Scientific impact evaluation and the effect of self-citations: mitigating the bias by discounting h-index, J. Am. Soc. Inf. Sci. Technol., 64(11), 2332-2339, 2013. (link) (arXiv preprint)
  12. A. E. Romero*, L. M. de Campos, A probabilistic methodology for multilabel classification, Intell. Data Anal., 18 (5), 2014. (arXiv preprint)
  13. P. Radivojac, W. T. Clark, T. R. Oron, A. M. Schnoes, T. Wittkop, A. Sokolov, K. Graim, C. Funk, K. Verspoor, A. Ben-Hur, G. Pandey, J. M. Yunes, A. S. Talwalkar, S. Repo, M. L. Souza, D. Piovesan, R. Casadio, Z. Wang, J. Cheng, H. Fang, J. Gough, P. Koskinen, P. Törönen, J. Nokso-Koivisto, L. Holm, D. Cozzetto, D. W. A. Buchan, K. Bryson, D. T. Jones, B. Limaye, H. Inamdar, A. Datta, S. K. Manjari, R. Joshi, M. Chitale, D. Kihara, A. M. Lisewski, S. Erdin, E. Venner, O. Lichtarge, R. Rentzsch, H. Yang, A. E. Romero, P. Bhat, A. Paccanaro, T. Hamp, R. Kassner, S. Seemayer, E. Vicedo, C. Schaefer, D. Achten, F. Auer, A. Boehm, T. Braun, M. Hecht, M. Heron, P. Hönigschmid, T. A. Hopf, S. Kaufmann, M. Kiening, D. Krompass, C. Landerer, Y. Mahlich, M. Roos, J. Björne, T. Salakoski, A. Wong, H. Shatkay, F. Gatzmann, I. Sommer, M. N. Wass, M. J. E. Sternberg, N. Škunca, F. Supek, M. Bošnjak, P. Panov, S. Džeroski, T. Šmuc, Y. A. I. Kourmpetis, A. D. J. van Dijk, C. J. F. ter Braak, T. Zhou, Q. Gong, X. Dong, W. Tian, M. Falda, P. Fontana, E. Lavezzo, B. Di Camillo, S. Toppo, L. Lan, N. Djuric, Y. Guo, S. Vucetic, A. Bairoch, M. Linial, P. C. Babbitt, S. E. Brenner, C. Orengo, B. Rost, S. D Mooney & I. Friedberg, A large-scale evaluation of computational protein function prediction, Nat. Methods, 10 (3), 221-227, 2013. (link)
  14. R. Dóczi, L. Ökrész, A. E. Romero, A. Paccanaro, L. Bögre, Exploring the evolutionary path of plant MAPK networks, Trends Plant Sci., 17 (9), 518-525, 2012. (link)
  15. L. M. de Campos, A. E. Romero, Bayesian Network Models for Hierarchical Text Classification from a Thesaurus, Int. J. Approx. Reasoning 50 (7): 932-944, 2009. (pdf)

Journal Papers (other journals)

  1. J. M. Almira, A. E. Romero, How distant is the ideal filter of being a causal one?, Atlantic Electronic Journal of Mathematics, 3 47-56, 2008. (pdf)
  2. J. M. Almira, A. E. Romero, Image Zooming based on sampling theorems, Materials Matematics, 1, 1-22, 2011. (link).

Book chapters

  1. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, An Information Retrieval System for Parliamentary XML Documents based on Probabilistic Graphical Models, book chapter in Bayesian Belief Networks A Practical Guide to Applications. Ed. John Wiley & Sons, 2008, ISBN: 978-0-470-06030-8.
  2. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, Thesaurus Based Automatic Indexing, book chapter in Handbook of Research on Text and Web Mining Technologies. Ed. Idea Group, Inc. USA, 2009, ISBN: 978-1-59904-990-8. (pdf)

International Conferences (published in "Lecture Notes" series)

  1. O. Kafalı, A. E. Romero, K. Stathis, Activity Recognition for an Agent-oriented Personal Health System, Principles and Practice of Multi-Agent Systems - 17th International Conference, PRIMA 2014, 254-269. In: Lecture Notes in Computer Science 8861 Springer 2014, ISBN 978-3-319-13190-0. (preprint pdf)
  2. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. R. Masegosa, A. E. Romero, Link-Based Text Classification Using Bayesian Networks. INEX 2009: 397-406. In: Lecture Notes in Computer Science 6203 Springer 2010, ISBN 978-3-642-14555-1.
  3. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, Probabilistic Methods for Link-Based Classification at INEX 2008. INEX 2008: 453-459. In: Lecture Notes in Computer Science 5631 Springer 2009, ISBN 978-3-642-03760-3. (pdf)
  4. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, C. J. Martín-Dancausa, A. E. Romero, New Utility Models for the Garnata Information Retrieval System at INEX'08. INEX 2008: 39-45. In: Lecture Notes in Computer Science 5631 Springer 2009, ISBN 978-3-642-03760-3. (pdf)
  5. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, C. J. Martín-Dancausa, A. E. Romero, The Garnata Information Retrieval System at INEX'07. INEX 2007: 57-69, In: Lecture Notes in Computer Science 4862 Springer 2008, ISBN 978-3-540-85901-7. (pdf)
  6. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, Probabilistic Methods for Structured Document Classification at INEX'07. INEX 2007: 195-206. In: Lecture Notes in Computer Science 4862 Springer 2008, ISBN 978-3-540-85901-7. (pdf)
  7. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, Automatic Indexing from a Thesaurus Using Bayesian Networks: Application to the Classification of Parliamentary Initiatives. ECSQARU 2007: 865-877. In: Lecture Notes in Computer Science 4724 Springer 2007, ISBN 978-3-540-75255-4. (pdf)
  8. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, Influence Diagrams and Structured Retrieval: Garnata Implementing the SID and CID Models at INEX'06. INEX 2006: 165-177. In: Lecture Notes in Computer Science 4518 Springer 2007, ISBN 978-3-540-73887-9. (pdf)

Other International Conferences

  1. M. Luštrek, B. Cvetković, V. Mirchevska, Ö. Kafalı, A. E. Romero, K. Stathis, Recognising lifestyle activities of diabetic patients with a smartphone, Pervasive Health 2015 : Workshop on Personal Health Systems for Chronic Diseases (PHSCD 2015), 2015. (pdf)
  2. F. J. Ribadas-Peña, L. M. de Campos Ibáñez, V. M. Darriba Bilbao, A. E. Romero, CoLe and UTAI at BioASQ 2015: experiments with similarity based descriptor assignment. Working Notes of CLEF 2015 - Conference and Labs of the Evaluation forum, Toulouse, France, September 8-11, 2015. CEUR Workshop Proceedings 1391, 2015, (pdf).
  3. F. J. Ribadas-Peña, L. M. de Campos Ibáñez, V. M. Darriba Bilbao, A. E. Romero, CoLe and UTAI Participation at the 2014 BioASQ Semantic Indexing Challenge. Working Notes for CLEF 2014 Conference, Sheffield, UK, September 15-18, 1361-1374, 2014, (pdf).
  4. F. J. Ribadas-Peña, L. M. de Campos Ibáñez, V. M. Darriba Bilbao, A. E. Romero, Two Hierarchical Text Categorization Approaches for BioASQ Semantic Indexing Challenge. BioASQ@CLEF 2013, (link).
  5. J. M. Almira, A. E. Romero, A note about Norbert Wiener and his contribution to Harmonic Analysis and Tauberian Theorems, in Mathematical Models in Engineering, Biology and Medicine, American Institute of Physics Conference Proceedings, 1124, (2009) 19-28. ISBN 978-0-7354-0660-5, (link)
  6. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, A flexible object-oriented system for teaching and learning structured IR, First International Workshop on Teaching and Learning of Information Retrieval (TLIR'07), London (UK), 2007. (pdf)
  7. A. E. Romero, Geometry and Information Retrieval, International Seminar on Applied Geometry in Andalusia, Granada 2006 (Satellite of the ICM, Madrid 2006). (pdf)
  8. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, Garnata: An Information Retrieval System for Structured Documents based on Probabilistic Graphical Models, Proc. of the 11th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU 2006), Paris (France). (pdf). ISBN: 88-87242-54-2.

National Conferences

  1. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, Or gate Bayesian networks for text classification: A discriminative alternative approach to multinomial naive Bayes, actas del XIV Congreso Español sobre Tecnologías y Lógica Fuzzy, ESTYLF 2008, Mieres-Langreo (España), 17-19 Septiembre 2008. (pdf). ISBN: 978-84-691-5807-4.
  2. L. M. de Campos, J. M. Fernández-Luna, J. F. Huete, A. E. Romero, Un Prototipo de Motor de Búsqueda para los Diarios de Sesiones del Parlamento de Andalucía basado en Modelos Gráficos Probabilísticos, Actas de las VI Jornadas de Transferencia Tecnológica de Inteligencia Artificial (TTIA'2005), 37-44, ISBN: 84-9732-435-8, 2005. (pdf)

Chapters in textbooks

  1. L. M. de Campos, A. E. Romero, Clasificación Documental, chapter 11 (pp. 359-392) in F. Cacheda, J. M. Fernández-Luna, J. F. Huete (eds.) "Recuperación de Información. Un Enfoque Práctico y Multidisciplinar", RA-MA editorial, ISBN: 978-84-9964-112-6, 2011 (link). In Spanish.
  2. A. E. Romero, Introducción a MATLAB, chapter in J. M. Almira, Matemáticas para la Recuperación de Señales, una Introducción, Grupo Editorial Universitario, (chapter 6: Introducción a MATLAB, 187-200), ISBN: 84-8491-519-0, 2005. In Spanish.

PhD Thesis

  • A. E. Romero, Document Classification Models Based On Bayesian Networks, April 2010. (manuscript) (slides)