2010
 Jose M. Prats-Montalban, Sonia Tarazona, Maria Jose Nueda, Alberto Ferrer and Ana Conesa
"A multiway approach to data integration in Systems Biology"
Chemolab, accepted. 
 
Nueda, Maria; Carbonell, Jose; Medina, Ignacio; Dopazo, Joaquin; Conesa, Ana
"Serial Expression Analysis (SEA): a web tool for the analysis of serial gene expression data"
Nucleic Acids Research 2010, doi:10.1093/nar/gkq488. 
 
Ignacio Medina; Jose Carbonell; Luis Pulido; Sara C. Madeira; Stefan Goetz; Ana Conesa; Joaquin Tarraga; Alberto Pascual-Montano; Ruben Nogales-Cadenas; Javier Santoyo; Francisco Garcia; Martina Marba; David Montaner; Joaquin Dopazo
"Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling "
Nucleic Acids Research 2010; doi: 10.1093/nar/gkq388. 
 
Attila Nemeth, Ana Conesa, Javier Santoyo-Lopez, Ignacio Medina, David Montaner, Balint Peterfia, Irina Solovei, Thomas Cremer, Joaquin Dopazo, Gernot Langst
"Inital genomics of the human nucleolus"
PloS Genetics, 6(3), e1000889. 
 
Sonia Prado, Ana Conesa, Ana Arminan, Magdalena Martinez-Losa, Maria del Carmen Escobedo, Carolina Gandia, Sonia Tarazona, Dario Melguizo, David Montaner, Silvia Sanz-Gonzale, Pilar Sepulveda, Stefan Goetz, Jose Enrique O'Connor, Ruben Moreno, Joaquin Dopazo, Deborah J. Burks and Miodrag Stojkovi
"Hypoxia promotes efficient differentiation of human embryonic stem cells to functional endothelium"
Stem Cells, 2010, doi:10.1002/stem.295. 
 
2009
 Rattei, Thomas; Tischler, Patrick;Goetz, Stefan; Jehl, Marc-Andr��; Hoser, Jonathan; Arnold, Roland; Conesa, Ana; Mewes, Hans W
"SIMAP: a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters"
NAR-02008-Data-E-2009.R1. 
 
Johan H. van Heerden, Conesa, Ana, Dan J. Stein , David Montaner, Vivienne Russell,Nicola Illing
"Parallel changes in gene expression in peripheral blood mononuclear cells and the brain after maternal separation in the mouse"
BMC Research Notes 2009 2:19. 
 
Maria Jose Nueda, Patricia Sebastian, Sonia Tarazona, Francisco Garcia-Garcia, Joaquin Dopazo, Alberto Ferrer, Conesa, Ana
"Functional Assessment of Time Course Microarray Data"
BMC Bioinformatics 2009, 10(Suppl 6):S9 (16 June 2009). 
 
Gotz, Stefan; Arnold, Roland; Sebastian, Patricia; Tischler, Patrick; Jehl, Marc-Andre; Dopazo, Joaquin; Rattei, Thomas; Conesa, Ana
"B2G-FAR: The Blast2GO Functional Annotation Repository"
Submitted. 
   
Javier Brumos, Jose M. Colmenero-Flores, Ana Conesa, Pedro Izquierdo, Guadalupe Sanchez, Domingo Iglesias, Maria F. Lopez-Climent, Aurelio Sanchez-Cadenas and Manuel Talon
"Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstock"
Funct. Integr. Genomics. DOI 10.1007/s10142-008-0107-6. 
 
2008
 Al-Shahrour, Fatima; Carbonell, Jose; Minguez, Pablo; Gotz, Stefan; Conesa, Ana ; Tarraga, Joaquin; Medina, Ignacio; Alloza, Eva; Montaner, David; Dopazo, Joaquin
"Babelomics: advanced functional profiling of transcriptomics, proteomics and genomic experiments"
Nucleic Acid Research 2008 10.1093/nar/gkn318. 
   
Tarraga, Joaquin; Medina, Ignacio; Carbonell, Jose; Huerta-Cepas, Jaime; Minguez, Pablo; Alloza, Eva; Al-Shahrour, Fatima; Vegas-Azcarate, Susana; Gotz, Stefan; Escobar, Pablo; Garcia-Garcia, Francisco; Conesa, Ana ; Montaner, David; Dopazo, Joaquin
"GEPAS, a web-based tool for microarray data analysis and interpretation"
Nucleic Acids Research 2008; 10.1093/nar/gkn303. 
   
Ana Conesa
"Functional Profiling at CIPF: from Blast2GO to Babelomics, all strategies for every species"
EMBnet.news, vol14, Nr.1:40-44. 
   
Robert Stierum, Ana Conesa , Wilbert Heijne, Ben van Ommen, Karin Junker, Mary P. Scott, Roger J. Price, Clive Meredith, Brian G. Lake, John Groten
"Transcriptome analysis provides new insights into liver changes induced in the rat upon dietary administration of the food additives butylated hydroxytoulene, curcumin, propyl gallate and thiabendazole"
Food and Chemical Toxicology, doi:10.1016/j.fct.2008.04.019. 
   
Willemijntje A Hoogerwerf, Mala Sinha, Ana Conesa , Bruce A Luxon, Vincent M Cassone.
"Transcriptional Profiling of mRNA Expression in the Mouse Distal Colon"
Gastroenterology. 2008 Dec;135(6):2019-29. 
   
Ana Conesa, Rasmus Bro, Francisco Garcia-Garcia, Jose Manuel Prats, Stefan Goetz, Karin Kjeldahl, David Montaner and Joaquin Dopazo.
"Direct functional assessment of the composite phenotype through multivariate projection strategies"
Genomics 2008; 92:373:383. 
 
   
Stefan Götz, Tim D. Williams, Shivashankar H. Nagaraj, María José Nueda, Javier Terol, Juan Miguel García-Gómez, Montserrat Robles, Manuel Talón, Joaquín Dopazo and Ana Conesa.
"High-throughput functional annotation with the Blast2GO suite"
Nucleic Acids Research 2008; doi: 10.1093/nar/gkn176 . 
   
Agudo, M, Sobrado, P,  Pérez-Marín, MC, Lönngren, U, Conesa, A , Cánovas, I, Salinas-Navarro, M, Miralles-Imperial, J, Hallböök, F, Vidal-Sanz, M.
"Time course profiling of retinal transcriptome after optic nerve transection and crush"
Molecular Vision 2008; 14:1050-1060.  
 
   
Ana Conesa and Stefan Götz.
"Blast2GO: A comprehensive suite for functional analysis in plant genomics"
Journal of Plant Genomics, vol. 2008, doi:10.1155/2008/619832
 
   
Alessandro Botton, Giulio Galla, Ana Conesa, Christian Bachem, Angelo Ramina and Gianni Barcaccia.
"Large-scale Gene Ontology analysis of plant genome- and transcriptome-derived sequences retrieved by AFLP technology"
BMC Genomics 2008, 9:347
 
   
2007
 Ana M Levin, Ronald P de Vries, Ana Conesa, Charissa de Bekker, Manuel Talon, Hildegard H. Menke, Noel NME van Peij & Han AB Wösten.
"Spatial differentiation in the vegetative mycelium of Aspergillus niger"
Eukaryot Cell. 2007 Dec;6(12):2311-22
   
Gandia M, Conesa A, Ancillo G, Gadea J, Forment J, Pallas V, Flores R, Duran-Vila N, Moreno P, Guerri J.
"Transcriptional response of Citrus aurantifolia to infection by Citrus tristeza virus"
Virology. 2007 Oct 25;367(2):298-306
   
Conesa A, Forment J, Gadea J, van Dijk J.
"Microarray Technology in Agricultural Research."
IN. Microarray Technology Through Applications. 2007. ISBN:0-4153-7853-2. Eds. F. Falciani. Publisher: Taylor and Francis Group. pp: 173-209 
   
Nueda MJ, Conesa A, Westerhuis JA, Hoefsloot HC, Smilde AK, Talon M, Ferrer A.   
"Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA"
Bioinformatics. 2007 Jul 15;23(14):1792-800.  
   
Terol J, Conesa A, Colmenero JM, Cercos M, Tadeo F, Agusti J, Alos E, Andres F, Soler G, Brumos J, Iglesias DJ, Gotz S, Legaz F, Argout X, Courtois B, Ollitrault P, Dossat C, Wincker P, Morillon R, Talon M.
"Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance"
BMC Genomics. 2007 Jan 25;8:31

 
2006
Williams TD, Diab AM, George SG, Godfrey RE, Sabine V, Conesa A, Minchin SD, Watts PC, Chipman JK.
"Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose"
Environ Sci Technol. 2006 Oct 15;40(20):6479-88.   
   
G. Aparicio, S. Götz, A. Conesa, D. Segrelles, I. Blanquer, V. Hernandez, M. Robles, M. Talon
"Blast2go Goes Grid: Developing A Grid-Enabled Prototype For Functional genomics Analysis"
IN:Challenges and Oprtunities in GealthGrids.Eds. VHernandez, I. Balaquer, T. Solomonides, Y. Legr��. IOS Press. ISBN 1-58603-617-3, pgs: 194-204
   
Conesa A, Nueda MJ, Ferrer A, Talon M.  
"maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments"
2006. Bioinformatics. May 1;22(9):1096-102.

 
2005
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. 2005.
"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research"
Bioinformatics. Sep 15;21(18):3674-6.
   
Forment J, Gadea J, Huerta L, Abizanda L, Agusti J, Alamar S, Alos E, Andres F, Arribas R, Beltran JP, Berbel A, Blazquez MA, Brumos J, Canas LA, Cercos M, Colmenero-Flores JM, Conesa A, Estables B, Gandia M, Garcia-Martinez JL, Gimeno J, Gisbert A, Gomez G, Gonzalez-Candelas L, Granell A, Guerri J, Lafuente MT, Madueno F, Marcos JF, Marques MC, Martinez F, Martinez-Godoy MA, Miralles S, Moreno P, Navarro L, Pallas V, Perez-Amador MA, Perez-Valle J, Pons C, Rodrigo I, Rodriguez PL, Royo C, Serrano R, Soler G, Tadeo F, Talon M, Terol J, Trenor M, Vaello L, Vicente O, Vidal Ch, Zacarias L, Conejero V. 2005.   
"Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies"
Plant Mol Biol. Feb;57(3):375-91.

 
2004 - 2000
Yi X, Conesa A, Punt PJ, Hager LP.
"Examining the role of glutamic Acid 183 in chloroperoxidase catalysis"
2003. J Biol Chem Apr 18;278(16):13855-9 
   
Conesa, A., Jeenes, D. Archer, D. B., van den Hondel, C. A. M. J. J. and Punt, P. J.
"2002. Calnexin overexpression increases manganese peroxidase production in Aspergillus niger"
Applied and Environmental Microbiology, 68: 846-851.
   
Punt, P.J., van Biezen, N., Conesa, A., Albers, A., Mangnus, J. and van den Hondel, C.A.M.J.J.
"Filamentous fungi as cell factories for heterologous protein production"
2002 .Trends Biotechnol. May;20(5):200-6  
   
Conesa, A., Punt, P. J. and van den Hondel, C. A. M. J. J. 2002.
"Fungal Peroxidases: Molecular Aspects and Applications"
Journal of Biotechnology 93: 143-158.
pdf
   
Conesa, A., Weelink, G. van den Hondel, C. A. M. J. J. and Punt, P. J. 2001.
"The C-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone?"
FEBS Letters503: 117-20.
pdf
   
Conesa, A., Punt, P. J., van Luijk, N. and van den Hondel, C. A. M. J. J. 2001.
"The secretion pathway in filamentous fungi; a biotechnological view"
Fungal Genetics and Biology 33: 155-71. 
pdf
   
Conesa, A., van de Velde, F., van Rantwijk, F., Sheldon, R. A., Punt,P. J., van den Hondel, C. A. M. J. J.2001.
"Expression of the Caldariomyces fumago chloroperoxidase in Aspergillus niger and characterisation of the recombinant enzyme"
Journal of Biological Chemistry, 276: 17635-40. 
   
Conesa, A., van den Hondel, C. A. M. J. J. and Punt, P. J. 2000.
"Studies on the Production of Fungal Peroxidases in Aspergillus niger"
Applied and Environmental Microbiology, 66: 3016-3023.