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2001
Dopazo J, Mendoza A, Herrero J, et al. Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate. Microb Drug Resist. 2001;7:99-125. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11442348.
Conesa A, Weelink G, van den Hondel CA, Punt PJ. C-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone?. FEBS Lett. 2001;503:117-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11513866.
Conesa A, van De Velde F, van Rantwijk F, Sheldon RA, van den Hondel CA, Punt PJ. Expression of the Caldariomyces fumago chloroperoxidase in Aspergillus niger and characterization of the recombinant enzyme. J Biol Chem. 2001;276:17635-40. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11278701.
Nunez JI, Martin MJ, Piccone ME, et al. Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses. Vet Res. 2001;32:31-45. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11254175.
Conesa A, Punt PJ, van Luijk N, van den Hondel CA. The secretion pathway in filamentous fungi: a biotechnological view. Fungal Genet Biol. 2001;33:155-71. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11495573.
2002
Tamames J, Clark D, Herrero J, et al. Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. J Biotechnol. 2002;98:269-83. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12141992.
Conesa A, Jeenes D, Archer DB, van den Hondel CA, Punt PJ. Calnexin overexpression increases manganese peroxidase production in Aspergillus niger. Appl Environ Microbiol. 2002;68:846-51. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11823227.
Punt PJ, van Biezen N, Conesa A, Albers A, Mangnus J, van den Hondel C. Filamentous fungi as cell factories for heterologous protein production. Trends Biotechnol. 2002;20:200-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11943375.
Conesa A, Punt PJ, van den Hondel CA. Fungal peroxidases: molecular aspects and applications. J Biotechnol. 2002;93:143-58. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11738721.
Conde L, Mateos A, Herrero J, Dopazo J. Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data. In: Neural Networks for Signal Processing XII. 2002 IEEE Signal Processing Society WorkshopProceedings of the 12th IEEE Workshop on Neural Networks for Signal Processing. Neural Networks for Signal Processing XII. 2002 IEEE Signal Processing Society WorkshopProceedings of the 12th IEEE Workshop on Neural Networks for Signal Processing. Martigny, Switzerland: IEEE; 2002. doi:10.1109/NNSP.2002.1030019.
Iverson GM, Reddel S, Victoria EJ, et al. Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol. 2002;169:7097-103. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12471146.
2003
Yi X, Conesa A, Punt PJ, Hager LP. Examining the role of glutamic acid 183 in chloroperoxidase catalysis. J Biol Chem. 2003;278:13855-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12576477.
2004
Martinez-Delgado B, Meléndez B, Cuadros M, et al. Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes. Clinical cancer research : an official journal of the American Association for Cancer Research. 2004;10:4971-82. Available at: http://clincancerres.aacrjournals.org/content/10/15/4971.long.
Martinez-Delgado B, Meléndez B, Cuadros M, et al. Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes. Clinical cancer research : an official journal of the American Association for Cancer Research. 2004;10:4971-82. Available at: http://clincancerres.aacrjournals.org/content/10/15/4971.long.
Martinez-Delgado B, Meléndez B, Cuadros M, et al. Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes. Clinical cancer research : an official journal of the American Association for Cancer Research. 2004;10:4971-82. Available at: http://clincancerres.aacrjournals.org/content/10/15/4971.long.
Melendez B, Diaz-Uriarte R, Cuadros M, et al. Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization. Genes Chromosomes Cancer. 2004;41:353-65. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15382261.
Melendez B, Diaz-Uriarte R, Cuadros M, et al. Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization. Genes Chromosomes Cancer. 2004;41:353-65. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15382261.
Herrero J, Vaquerizas JM, Al-Shahrour F, et al. New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res. 2004;32:W485-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215434.
Conde L, Vaquerizas JM, Santoyo J, et al. PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res. 2004;32:W242-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215388.
2005
Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J. BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 2005;33:W460-4. Available at: http://nar.oxfordjournals.org/content/33/suppl_2/W460.long.
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16081474.
Forment J, Gadea J, Huerta L, et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol. 2005;57:375-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128.
Forment J, Gadea J, Huerta L, et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol. 2005;57:375-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128.
Forment J, Gadea J, Huerta L, et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol. 2005;57:375-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128.
Forment J, Gadea J, Huerta L, et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol. 2005;57:375-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128.