PUBLICATIONS IN SCIENTIFIC JOURNALS

E.Viguera, O.Trelles-Salazar, J.L.Urdiales, J.M.Mates, F.Sanchez-Jimenez. Mammalian L-amino acid decarboxylases producing 1,4-diamines : Analogies among differences. Trends in Biochemical Sciences (TIBS), 19, 318-319 (1994).

M.A.Trelles, W.Verkruysse, O.Trelles-Salazar,  J.Sanchez and M.Vélez. Enhancing Precision of Dermal Lesions Elimination by Laser. Lasers in the Life Sciences 6(1) 1994 pp. 163 – 172.

O.Trelles-Salazar, E.L.Zapata, J.M.Carazo. On an efficient parallelization of exhaustive sequence comparison algorithms. Computer Applications in BioSciences (1994) 10(5):509-511.

O.Trelles-Salazar, E.L.Zapata, J.Dopazo, A.W.F Coulson y J.M.Carazo. An Image processing approach to DotPlots : An X window-based program for interactive analysis of dotplots derived from sequence and structural data. Computer Applications in BioSciences (1995) (11) 3: 301-308.

Trelles, M.A.,  Coates, J.; Trelles,O., Trelles K., Curto, M and Clark A. Histological correlation in Laser Skin Resfurfacing. Lasers in Medical Science 10 (4) pp:279-282, Dec.1995.

Trelles, M.A, Trelles, K., J.L.Cisneros and Trelles, O. Soins Post-Opératoires après un resurfacing au laser. Journal Méd.Esth.et Chir.Derm. Vol.XXIII.90 Juin’96, 99-103.

Trelles M.A., Trelles O.,  Romero L.F. New approaches in the use of CO2 laser in dermatological cosmetic surgery. Journal of the European Academic of Dermatology and Veneorology, Elsevier (1996) vol 7, supp.2.

Ceron, C., Dopazo, J., Zapata, E.L., Carazo, J.M. and Trelles, O. Parallel Implementation for DNAml Program on Message-Passing Architectures. Parallel Computing and Applications, vol 24 (5-6),June 98 pp.701-716.

Trelles O., Andrade M.A., Valencia A., Zapata E.L., and Carazo J.M. Computational Space Reduction and Parallelization of a new Clustering Approach for Large Groups of Sequences. BioInformatics vol.14 no.5 1998 (pp.439-451).

Trelles, O.; Ceron, C., Wang, H.C; Dopazo, and Carazo, J.M. New phylogenetic venues opened by a novel implementation of the DNAml Algorithm. BioInformatics vol.14 no.6 1998 (pp.544-545) (formerly Computer Applications in the Biosciences).

Viguera E.; Rodriguez A.; Hernandez P.; Krimer D.B., Trelles, O. and Schvartzman J.B. A computer model for the analysis of DNA replication intermediates by two-dimensional agarose gel electrophoresis. Gene 217/14 (Sept.98) pp.41-49.

Trelles, M.A; Pardo, L.; Trelles, O., Vélez, M.; García-Solana, L; Rigau, J and Chamorro, J. Seguimiento comparativo clínico e histológico del rejuvenecimiento de la piel con láser Coherent-Sharplan. Cirugía Plástica Ibero-Latinoamericana, (1999) vol. 25-I pag.33-44.

Trelles O. On the parallelisation of bioinformatics applications. Briefings in bioinformatics (May, 2001) vol.2 (2) pp. 181-194.

M.A. Trelles; L.Pardo; O. Trelles; M. Vélez; L.García-Solana; J.Rigau and J.J. Chamorro. Clinical and Histological Effects of Facial Skin Rejuvenation with Pulsed- and Continuous-wave Flash-scanned CO2 Lasers. Aesthetic Surgery Journal (Sep-Oct, 2001) pp. 399-411.

Shotton,D.; Rodríguez, A.; Guil, N. and Trelles, O. A metadata classification schema for semantic content analysis of videos. Journal of Microscopy (January 2002) vol.205, pp.33-42.

C.O.S.Sorzano, J.M. Carazo and Trelles O. Command line interfaces can be efficiently brought to graphics: COLIMATE (the COmmand LIne MATE). Software-Practice and Experience Vol: 32, Issue:9 (July 2002, pp:873-887).

Pérez A.J., Rodríguez, A., Trelles O., Thode G. A computational strategy for protein function assignment which addresses the multidomain problem. Comparative and Functional Genomics , 2002, (3) pag.423-440.

Jorge García de la Nava, Daniel Franco Santaella, Jesús Cuenca Alba, José María Carazo, Oswaldo Trelles, Alberto Pascual-Montano. Engene: The processing and exploratory analysis of gene expression data. Bioinformatics vol.19 no.5 (2003) pp.657-658.

Jorge García de la Nava, Sacha van Hijum and Oswaldo Trelles. PreP: gene expression data pre-processing. Bioinformatics 2003 Nov 22; 19 (17): 2328-2329.

A.J. Pérez, G. Thode, and O. Trelles. AnaGram: protein function assignment. Bioinformatics Vol. 20 no. 2 2004, pages 291-292.

Rodríguez, A.; Shotton,D.; Guil, N. and Trelles, O. Automatic analysis of the content of cell biological video and database organization of their metadata descriptors. IEEE Transactions in Multimedia (February 2004) Vol 6, No. 1, pages 119-128.

Sacha A.F.T. van Hijum, Jorge García de la Nava, Oswaldo Trelles, Jan Kok and Oscar P. Kuipers. MicroPrep: A cDNA microarray data preprocessing framework. Applied Bioinformatics, 2004, 2(4)241-244.

MA Trelles, I Allones, MJ Martín-Vázquez, O. Trelles, M Vélez and S Mordon. Long pulse Nd:YAG laser for treatment of leg veins in 40 patients with assessments at 6 and 12 months. Lasers in Surgery and Medicine (nº 35, pag. 68-76, 2004).

MA Trelles, I Allones, O. Trelles. An 810 nm diode laser in the treatment of small (<= 1.0 nm ) leg veins: a preliminary assessment. Lasers in Medical Sciences 19:21-26 (2004).

Jorge García de la Nava, Sacha A.F.T. van Hijum and  Oswaldo Trelles. Saturation and quantization reduction in microaray experiments using two scans at different sensitivities. Statistical application in genetics and molecular biology; Vol 3. Issue 1, article 11 (2004).

Rodríguez, A.; Carazo, J.M. and A., Trelles O. Mining Association Rules from Biological Databases. Journal of the American Society for Information Science and Technology 56(5):493–504, 2005.

Rodríguez, A.; Shotton,D.; Guil, N. and Trelles, O. Analysis and Description of the Semantic Content of Cell Biological Videos. Multimedia Tools and Applications, 25, 37-58, 2005.

J.F. Aldana, M. Roldán-Castro, I. Navas, M.M. Roldán-García, M. Hidalgo-Conde, and O.Trelles. Bio-Broker: a tool for integration of biological data sources and data analysis tools. Software, Practice and Experience, vol 36, Issue 14, pp. 1585 – 1604 (2006).

Manuel J. Martín-Vázquez; Mario A. Trelles; Alejandro Sola; R. Glen Calderhead and Oswaldo Trelles. A new user-friendly software platform for systematic classification of skin lesions to aid in their diagnosis and prognosis. J.of Laser in Medical Science (2006) 21: 54–60.

M.A.Trelles, M.D, PhD; X.Alvarez, M.J.Martín-Vázquez, O.Trelles, M.Velez, J.L. Levy and I.Allones M.D. Assessment of the Efficacy of Nonablative Long-Pulsed 1064-nn Nd:YAG Laser Treatment of Wrinkles Compared at 2, 4 and 6 Months. Facial Plastic Surgery; vol. 21, num. 2, pp.145-153, 2005.

Ismael Navas-Delgado, Maria del Mar Rojano-Muñoz, Sergio Ramírez, Antonio J. Pérez, Eduardo Andrés León; Jose F. Aldana-Montes, and Oswaldo Trelles. Intelligent client for integrating bioinformatics services. Bioinformatics, vol.22 no.1 2006 pages 106-111.

P. Carmona-Sáez, M. Chagoyen, A. Rodríguez, O. Trelles, J. M. Carazo and A. Pascual-Montano. Integrated analysis of gene expression by association rules discovery. BMC Bioinformatics, 2006, 7:54; 1471-2105.

José María Sayagués, María Dolores Tabernero, Angel Maíllo, Oswaldo Trelles, Ana Belén Espinosa, Maria Eugenia Sarasquete, Ana Rasillo, Marta Merino, Angel Santos-Briz and Alberto Orfao. Microarray-based analysis of Spinal vs intracranial meningiomas: different clinical, biological and genetic characteristics associated with distinct patterns of gene expression. Journal of Neuropathology and Experimental Neurology, vol.65, No. 5:445-454, May 2006.

Mario A. Trelles, Ines Allones, Xavier Alvarez, Mariano Velez, Carmen Buil, Ricardo Luna and Oswaldo Trelles. Long-pulsed Nd:YAG 1064 nm in the treatment of leg veins: Check up of results at 6 months in 100 patients. Medical Laser Application 20 (4) 255-266 (2005).

Mario A. Trelles; Manuel Martín-Vázquez; Oswaldo Trelles and Serge R. Mordon. Treatment Effects of Combined Radio-Frequency Current and a 900 nm Diode Laser on Leg Blood Vessels. Lasers in Surgery and Medicine, vol. 38, pp. 185-195 Mar.2006.

Trelles M.A., Allones I., Alvarez J., Velez M., Martin-Vázquez M., Trelles O., Luna R., Buil C., Mordon S.R. The 800-nm diode laser in the treatment of leg veins: assessment at 6 months. Journal of the American Academy of Dermatology 2006 Feb; 54 (2) :282-289.

Xavier Alvarez, Mariano Vélez, Oswaldo Trelles y Mario A. Trelles. Intensificación de la absorción del láser en el tratamiento de lesiones vasculares: radio frecuencia (RF) y láser de diodo. Revista Científica de la Sociedad Española de Medicina Estética (SEME), vol.10 pág 46-53; Enero 2007.

M. A. Medina, J. F. Aldana, F. R. Villatoro, G. Claros, J. L. Urdiales, O. Trelles and F. Sánchez-Jiménez. Amine System Project. Inflammation Research; ISSN: 1023-3830; vol.56.

Van Hijum,Sacha AFT; Baerends, Richard JS; Zomer, Aldert L; Karsens, Harma A; Martin-Requena, Victoria; Trelles, Oswaldo; Kok, Jan and Kuipers, Oscar P. Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons. BMC Bioinformatics, 2008, 9:93 (11 Feb 2008).

The BioMoby Consortium: Mark Wilkinson et al. (including O. Trelles). Interoperability with Moby 1.0 – It’s better than sharing your toothbrush!. Briefings in Bioinformatics; 2008 May; 9(3):220-31.

María Antúnez-Lamas, Ezequiel Cabrera Ordóñez, Emilia López-Solanilla, Oswaldo Trelles, Andrés Rodríguez and Pablo Rodríguez-Palenzuela. Role of motility and chemotaxis in the pathogenesis of Dickeya dadantii 3937 (ex Erwinia chrysanthemi 3937). Applied and Environmental Microbiology; Microbiology (2009), 155; 434 – 442.

Victoria Martín-Requena; Antonio Muñóz-Merida; M.Gonzalo Claros,  and Oswaldo Trelles. Prep+07: improvements of a user friendly tool to preprocess and analyse microarray data. BMC-Bioinformatics 10:16 (DOI: 10.1186/1471-2105-10-16) (Jan.2009) Article URL http://www.biomedcentral.com/1471-2105/10/16.

Rios, Javier ; Karlsson Johan and Trelles Oswaldo. Magallanes: a web services discovery and automatic workflow composition tool. BMC-Bioinformatics (doi:10.1186/1471-2105-10-334; 15 Oct. 2009).

Martín-Requena Victoria, Rios Javier; García Maximiliano, Ramírez Sergio, and Trelles Oswaldo. jORCA: Easily integrating bioinformatics Web Services. Bioinformatics 2010 26(4):553-559.

Sergio Ramírez, Antonio Muñoz, Johan Karlsson, Maximiliano García, Antonio J. Pérez-Pulido, M.Gonzalo Claros and Oswaldo Trelles. MOWServ: a web client for integration of bioinformatic resources. Nucleic Acid Research, 2010 1-6. DOI 10.1093/nar/gkq497.

Steve Pettifer, et al. (including O.Trelles as INB-Partners). The EMBRACE Web Service Collection. Nucleic Acids Research, 2010, Vol. V, No. I 1–5.

Toshiaki Katayama, et al. (includes O.Trelles). The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. Journal of Biomedical Semantics 1:8; 2010.

Elisabeth Tamayo, Antonio Muñoz, Rafael Fernandez-Muñoz, Antonio Granell-Richart, Oswaldo Trelles. Mixing samples before or after expression analysis determines the final outcome. EBMnet.journal 16 Suppl.A (2010).

Oswaldo Trelles, Pjotr Prins, Marc Snir and Ritsert C. Jansen. Big data, but are we ready? Nature Reviews Genetics 2011 Feb 8. PMID: 21301471.

Toshiaki Katayama, et al. (includes O.Trelles). The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. Journal of Biomedical Semantics 2011, 2:4.

Sergio Ramirez; Johan Karlsson and Oswaldo Trelles. MAPI: towards the integrated exploitation of bioinformatics Web Services. BMC-Bioinformatics 2011, 12:419.

Antonio Muñoz-Mérida, Javier Ríos, Hicham Benzekri and Oswaldo Trelles. Statistical significance for NGS reads similarities. A.T. Freitas and A. Navarro (Eds.): JBI 2010, LNBI 6620, pp. 1–7. Springer, Heidelberg (2012).

Johan Karlsson and Oswaldo Trelles. jORCA and Magallanes sailing together towards Web Services Integration. A.T. Freitas and A. Navarro (Eds.): JBI 2010, LNBI 6620, pp. 94–101. Springer, Heidelberg (2012).

Viviana Lima-Silva, Abel Rosado, Vitor Amorim-Silva, Antonio Muñoz-Mérida, Clara Pons, Aureliano Bombarely, Oswaldo Trelles, Rafael Fernández-Muñoz, Antonio Granell, Victoriano Valpuesta, Miguel Ángel Botella. Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit. BMC Genomics 2012, 13(1):187.

M. Carmen García-López, Isabel Vidoy, Jaime Jiménez-Ruiz, Antonio Muñoz-Mérida, Ana Fernández-Ocaña, Raul de la Rosa, Juan B Barroso, Francisco Navarro, Oswaldo Trelles, Carmen R Beuzón, Araceli Barceló, Victoriano Valpuesta and Francisco Luque. Genetic changes involved in the juvenile-to-adult transition in the shoot apex of Olea europaea L. occurs years before the first flowering. Tree Genetics & Genomes, June 2014, Volume 10, Issue 3, pp 585-603.

Antonio Munoz-Merida; Juan Jose Gonzalez-Plaza; Andres Canada; Ana Maria Blanco; Maria del Carmen Garcia-Lopez; Jose Manuel Rodriguez; Laia Pedrola; M. Dolores Sicardo; M. Luisa Hernandez; Raul De la Rosa; Angjelina Belaj; Mayte Gil-Borja; Francisco Luque; Jose Manuel Martinez-Rivas; David G. Pisano; Oswaldo Trelles; Victoriano Valpuesta; Carmen R. Beuzon. De novo assembly and functional annotation of the olive (Olea europaea) transcriptome. DNA Research (2013). doi: 10.1093/dnares/dss036.

Johan Karlsson and Oswaldo Trelles. MAPI: a software framework for distributed biomedical applications. Journal of Biomedical Semantics (ISSN: 2041-1480). 2013 4:4. DOI: 10.1186 / 2041-1480-4-4.  (2013).

Raúl De la Rosa, Angjelina Belaj, Antonio Muñoz-Mérida, Oswaldo Trelles, Inmaculada Ortíz-Martín, Juan José González-Plaza, Victoriano Valpuesta, Carmen R. Beuzón. Development of EST-derived SSR markers with long core repeat in olive and their utility for paternity testing. Journal of the American Society for Horticultural Science. 138(4) 290-296 (2013).

Martinez-Aranguren Ruben, Lizaso M.T, Goikoetxea M.J., Garcia-Figueroa Blanca, Cabrera-Freitag Paula, Trelles Oswaldo, Sanz María L. Is the determination of specific IgE against components using ISAC 112 a reproducible technique? PLOS ONE, Feb.2014; vol. 9, Issue 2, e88394.

Amil-Ruiz, Francisco; Garrido-Gala, José; Gadea, José; Blanco-Portales, Rosario; Muñoz-Mérida, Antonio; Trelles, Oswaldo; de los Santos, Berta; Romero, Fernando; Mercado, José; Pliego-Alfaro, Fernando; Muñoz-Blanco, Juan; Caballero, José Luis. Incomplete Activation of Both SA- and JA-pathways by Colletotrichum acutatum Provides Clues on the Inaccurate Defense Response in Strawberry. Plant and Cell Physiology; submitted: 02-Apr-2014 -PCP-2014-E-00150.

Antonio Muñoz-Mérida, Enrique Viguera, M. Gonzalo Claros, Oswaldo Trelles and Antonio J. Pérez-Pulido. SMA3S: a three-step modular annotator for large sequence datasets. DNA Research-2014 Aug;21(4):341-53.

María de la O Leyva-Pérez; Antonio Valverde-Corredor; Raquel Valderrama; Jaime Jiménez-Ruiz; Antonio Muñoz-Merida; Oswaldo Trelles; Juan Bautista Barroso; Jesús Mercado-Blanco; Francisco Luque. Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves. DNA Research 2015, 22(1) 1-11 DOI: 10.1093/dnares/dsu033.

Gonzalez Plaza, Juan Jose; Ortiz Martín, Inmaculada; Muñoz Mérida, Antonio; García López, Carmen; Sánchez Sevilla, José Federico; Luque, Francisco; Trelles Salazar, Oswaldo; Rodríguez Bejarano, Eduardo; de la Rosa, Raúl; Valpuesta, Victoriano; Beuzon Lopez, Carmen. Transcriptomic analysis using olive varieties and breeding progenies identify candidate genes involved in plant architecture. Frontiers in Plant Science. | doi: 10.3389/fpls.2016.00240. http://journal.frontiersin.org/article/10.3389/fpls.2016.00240/abstract.

Óscar Torreño and Oswaldo Trelles. Breaking computational barriers in pairwise genome comparison. BMC Bioinformatics, 2015, 16:250. DOI: 10.1186/s12859-015-0679-9.

Alex Upton, Oswaldo Trelles, José Antonio Cornejo-Garcia, James Richard Perkins. High Performance Computing to Detect Epistasis in Genome Scale Datasets. Briefings in bioinformatics. 2015, Aug 13. PMID: 26272945.

Krieger, M. T., Torreno, O., Trelles, O., & Kranzlmüller, D. (2016). “Building an open source cloud environment with auto-scaling resources for executing bioinformatics and biomedical workflows”. Future Generation Computer Systems.

Jose Antonio Arjona-Medina and Oswaldo Trelles, “Computational Synteny Block: A Framework to Identify Evolutionary Events,” in IEEE Transactions on NanoBioscience, vol. 15, no. 4, pp. 343-353, June 2016. doi: 10.1109/TNB.2016.2554150

Pérez-Wohlfeil, E., Arjona-Medina, J. A., Torreno, O., Ulzurrun, E., & Trelles, O. (2016). Computational workflow for the fine-grained analysis of metagenomic samples. BMC genomics, 17(8), 351.

Arjona-Medina, J. A., & Trelles, O. (2016). Refining borders of genome-rearrangements including repetitions. BMC genomics, 17(8), 433.

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