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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.
Mas JM, Aloy P, Marti-Renom MA, et al. Classification of protein disulphide-bridge topologies. J Comput Aided Mol Des. 2001;15:477-87. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11394740.
Mas JM, Aloy P, Marti-Renom MA, et al. Classification of protein disulphide-bridge topologies. J Comput Aided Mol Des. 2001;15:477-87. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11394740.
Marti-Renom MA, Ilyin VA, Sali A. DBAli: a database of protein structure alignments. Bioinformatics. 2001;17:746-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11524379.
Eyrich VA, Marti-Renom MA, Przybylski D, et al. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001;17:1242-3. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751240.
Eyrich VA, Marti-Renom MA, Przybylski D, et al. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001;17:1242-3. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751240.
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.
Elena SF, Dopazo J, de la Pena M, Flores R, Diener TO, Moya A. Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment. J Mol Evol. 2001;53:155-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11479686.
2002
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.
Mateos A, Herrero J, Tamames J, Dopazo J. Methods of Microarray Data Analysis IISupervised Neural Networks for Clustering Conditions in DNA Array Data After Reducing Noise by Clustering Gene Expression Profiles. (Lin SM, Johnson KF, eds.). Boston: Kluwer Academic Publishers; 2002:91 - 103. doi:10.1007/b11298210.1007/0-306-47598-7_7.
Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure. 2002;10:435-40. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12005441.
Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure. 2002;10:435-40. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12005441.
Mateos A, Herrero J, Tamames J, Dopazo J. Supervised Neural Networks For Clustering Conditions In DNA Array Data After Reducing Noise By Clustering Gene Expression Profiles. In: Microarray data analysis II. Microarray data analysis II. Kluwer Academic; 2002:91-103.
Mateos A, Dopazo J, Jansen R, Tu Y, Gerstein M, Stolovitzky G. Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Res. 2002;12:1703-15. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12421757.
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.
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.
Mateos A, Herrero J, Dopazo J. Using perceptrons for supervised classification of DNA microarray samples: obtaining the optimal level of information and finding differentially expressed genes. In: ICANN 2002, LNCS 2415. ICANN 2002, LNCS 2415. J.R. Dorronsoro; 2002:577-582.
2003
Martin MJ, Herrero J, Mateos A, Dopazo J. Comparing bacterial genomes through conservation profiles. Genome Res. 2003;13:991-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12695324.
Martin MJ, Herrero J, Mateos A, Dopazo J. Comparing bacterial genomes through conservation profiles. Genome Res. 2003;13:991-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12695324.
Koh IY, Eyrich VA, Marti-Renom MA, et al. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003;31:3311-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824315.
Koh IY, Eyrich VA, Marti-Renom MA, et al. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003;31:3311-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824315.
Herrero J, Al-Shahrour F, Diaz-Uriarte R, et al. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res. 2003;31:3461-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824345.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A. ModView, visualization of multiple protein sequences and structures. Bioinformatics. 2003;19:165-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12499313.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A. ModView, visualization of multiple protein sequences and structures. Bioinformatics. 2003;19:165-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12499313.