@article {19127482,
	title = {Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups},
	journal = {Leuk Lymphoma},
	volume = {50},
	number = {1},
	year = {2009},
	note = {<p>Jantus Lewintre, Eloisa Reinoso Martin, Cristina Montaner, David Marin, Miguel Jose Terol, Maria Farras, Rosa Benet, Isabel Calvete, Juan J Dopazo, Joaquin Garcia-Conde, Javier Research Support, Non-U.S. Gov{\textquoteright}t England Leukemia \&amp; lymphoma Leuk Lymphoma. 2009 Jan;50(1):68-79.</p>},
	pages = {68-79},
	abstract = {<p>B cell chronic lymphocytic leukemia (CLL) is a lymphoproliferative disorder with a variable clinical course. Patients with unmutated IgV(H) gene show a shorter progression-free and overall survival than patients with immunoglobulin heavy chain variable regions (IgV(H)) gene mutated. In addition, BCL6 mutations identify a subgroup of patients with high risk of progression. Gene expression was analysed in 36 early-stage patients using high-density microarrays. Around 150 genes differentially expressed were found according to IgV(H) mutations, whereas no difference was found according to BCL6 mutations. Functional profiling methods allowed us to distinguish KEGG and gene ontology terms showing coordinated gene expression changes across subgroups of CLL. We validated a set of differentially expressed genes according to IgV(H) status, scoring them as putative prognostic markers in CLL. Among them, CRY1, LPL, CD82 and DUSP22 are the ones with at least equal or superior performance to ZAP70 which is actually the most used surrogate marker of IgV(H) status.</p>},
	keywords = {cancer, microarray data analysis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=19127482},
	author = {Jantus Lewintre, E. and Reinoso Martin, C. and Montaner, D. and Marin, M. and Jose Terol, M. and Farras, R. and Benet, I. and Calvete, J. J. and Dopazo, J. and Garcia-Conde, J.}
}
@article {17570147,
	title = {The AnnoLite and AnnoLyze programs for comparative annotation of protein structures},
	journal = {BMC Bioinformatics},
	volume = {8 Suppl 4},
	year = {2007},
	note = {Marti-Renom, Marc A Rossi, Andrea Al-Shahrour, Fatima Davis, Fred P Pieper, Ursula Dopazo, Joaquin Sali, Andrej Research Support, Non-U.S. Gov{\textquoteright}t England BMC bioinformatics BMC Bioinformatics. 2007 May 22;8 Suppl 4:S4.},
	pages = {S4},
	abstract = {BACKGROUND: Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited by the structural genomics consortia have little or no information about their biological function. Therefore, there is a need for tools for automatically and comprehensively annotating the function of protein structures. We aim to provide such tools by applying comparative protein structure annotation that relies on detectable relationships between protein structures to transfer functional annotations. Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database. DESCRIPTION: AnnoLite predicts the SCOP, CATH, EC, InterPro, PfamA, and GO terms with an average sensitivity of  90\% and average precision of  80\%. AnnoLyze predicts ligand binding site and domain interaction patches with an average sensitivity of  70\% and average precision of  30\%, correctly localizing binding sites for small molecules in  95\% of its predictions. CONCLUSION: The AnnoLite and AnnoLyze programs for comparative annotation of protein structures can reliably and automatically annotate new protein structures. The programs are fully accessible via the Internet as part of the DBAli suite of tools at http://salilab.org/DBAli/.},
	keywords = {*Algorithms Amino Acid Sequence Confidence Intervals Data Interpretation, Amino Acid *Software Structure-Activity Relationship, Protein Information Storage and Retrieval/methods Molecular Sequence Data Proteins/*chemistry/classification/*metabolism Sensitivity and Specificity Sequence Alignment/*methods Sequence Analysis, Protein/*methods Sequence Homology, Statistical *Databases},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17570147},
	author = {M. A. Marti-Renom and Rossi, A. and Fatima Al-Shahrour and Davis, F. P. and Pieper, U. and Dopazo, J. and Sali, A.}
}
@article {17909067,
	title = {Association study of 69 genes in the ret pathway identifies low-penetrance loci in sporadic medullary thyroid carcinoma},
	journal = {Cancer Res},
	volume = {67},
	number = {19},
	year = {2007},
	note = {Ruiz-Llorente, Sergio Montero-Conde, Cristina Milne, Roger L Moya, Christian M Cebrian, Arancha Leton, Rocio Cascon, Alberto Mercadillo, Fatima Landa, Inigo Borrego, Salud Perez de Nanclares, Guiomar Alvarez-Escola, Cristina Diaz-Perez, Jose Angel Carracedo, Angel Urioste, Miguel Gonzalez-Neira, Anna Benitez, Javier Santisteban, Pilar Dopazo, Joaquin Ponder, Bruce A Robledo, Mercedes Medullary Thyroid Carcinoma Clinical Group Research Support, Non-U.S. Gov{\textquoteright}t United States Cancer research Cancer Res. 2007 Oct 1;67(19):9561-7.},
	pages = {9561-7},
	abstract = {To date, few association studies have been done to better understand the genetic basis for the development of sporadic medullary thyroid carcinoma (sMTC). To identify additional low-penetrance genes, we have done a two-stage case-control study in two European populations using high-throughput genotyping. We selected 417 single nucleotide polymorphisms (SNP) belonging to 69 genes either related to RET signaling pathway/functions or involved in key processes for cancer development. TagSNPs and functional variants were included where possible. These SNPs were initially studied in the largest known series of sMTC cases (n = 266) and controls (n = 422), all of Spanish origin. In stage II, an independent British series of 155 sMTC patients and 531 controls was included to validate the previous results. Associations were assessed by an exhaustive analysis of individual SNPs but also considering gene- and linkage disequilibrium-based haplotypes. This strategy allowed us to identify seven low-penetrance genes, six of them (STAT1, AURKA, BCL2, CDKN2B, CDK6, and COMT) consistently associated with sMTC risk in the two case-control series and a seventh (HRAS) with individual SNPs and haplotypes associated with sMTC in the Spanish data set. The potential role of CDKN2B was confirmed by a functional assay showing a role of a SNP (rs7044859) in the promoter region in altering the binding of the transcription factor HNF1. These results highlight the utility of association studies using homogeneous series of cases for better understanding complex diseases.},
	keywords = {80 and over Carcinoma, Adolescent Adult Aged Aged, Genetic, Genetic Proto-Oncogene Proteins c-ret/*genetics/metabolism Signal Transduction Thyroid Neoplasms/*genetics/metabolism Transcription, Medullary/*genetics/metabolism Case-Control Studies Cyclin-Dependent Kinase Inhibitor p15/biosynthesis/genetics Female Genetic Predisposition to Disease Germ-Line Mutation Haplotypes Humans Male Middle Aged Penetrance Polymorphism, Single Nucleotide Promoter Regions},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17909067},
	author = {Ruiz-Llorente, S. and Montero-Conde, C. and Milne, R. L. and Moya, C. M. and Cebrian, A. and Leton, R. and Cascon, A. and Mercadillo, F. and Landa, I. and Borrego, S. and Perez de Nanclares, G. and Alvarez-Escola, C. and Diaz-Perez, J. A. and Carracedo, A. and Urioste, M. and Gonzalez-Neira, A. and Benitez, J. and Santisteban, P. and Dopazo, J. and Ponder, B. A. and M. Robledo}
}
@article {18629097,
	title = {An approach to inferring transcriptional regulation among genes from large-scale expression data},
	journal = {Comp Funct Genomics},
	volume = {4},
	number = {1},
	year = {2003},
	note = {Herrero, Javier Diaz-Uriarte, Ramon Dopazo, Joaquin Egypt Comparative and functional genomics Comp Funct Genomics. 2003;4(1):148-54.},
	pages = {148-54},
	abstract = {The use of DNA microarrays opens up the possibility of measuring the expression levels of thousands of genes simultaneously under different conditions. Time-course experiments allow researchers to study the dynamics of gene interactions. The inference of genetic networks from such measures can give important insights for the understanding of a variety of biological problems. Most of the existing methods for genetic network reconstruction require many experimental data points, or can only be applied to the reconstruction of small subnetworks. Here we present a method that reduces the dimensionality of the dataset and then extracts the significant dynamic correlations among genes. The method requires a number of points achievable in common time-course experiments.},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18629097},
	author = {Herrero, J. and Diaz-Uriarte, R. and Dopazo, J.}
}
@article {11442348,
	title = {Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate},
	journal = {Microb Drug Resist},
	volume = {7},
	number = {2},
	year = {2001},
	note = {Dopazo, J Mendoza, A Herrero, J Caldara, F Humbert, Y Friedli, L Guerrier, M Grand-Schenk, E Gandin, C de Francesco, M Polissi, A Buell, G Feger, G Garcia, E Peitsch, M Garcia-Bustos, J F United States Microbial drug resistance (Larchmont, N.Y.) Microb Drug Resist. 2001 Summer;7(2):99-125.},
	pages = {99-125},
	abstract = {The public availability of numerous microbial genomes is enabling the analysis of bacterial biology in great detail and with an unprecedented, organism-wide and taxon-wide, broad scope. Streptococcus pneumoniae is one of the most important bacterial pathogens throughout the world. We present here sequences and functional annotations for 2.1-Mbp of pneumococcal DNA, covering more than 90\% of the total estimated size of the genome. The sequenced strain is a clinical isolate resistant to macrolides and tetracycline. It carries a type 19F capsular locus, but multilocus sequence typing for several conserved genetic loci suggests that the strain sequenced belongs to a pneumococcal lineage that most often expresses a serotype 15 capsular polysaccharide. A total of 2,046 putative open reading frames (ORFs) longer than 100 amino acids were identified (average of 1,009 bp per ORF), including all described two-component systems and aminoacyl tRNA synthetases. Comparisons to other complete, or nearly complete, bacterial genomes were made and are presented in a graphical form for all the predicted proteins.},
	keywords = {Bacterial Molecular Sequence Data Pneumococcal Infections/*microbiology Prokaryotic Cells RNA, Bacterial/chemistry/genetics Genes, Bacterial/genetics *Genome, DNA, Transfer/metabolism Streptococcus pneumoniae/*genetics},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=11442348},
	author = {Dopazo, J. and Mendoza, A. and Herrero, J. and Caldara, F. and Humbert, Y. and Friedli, L. and Guerrier, M. and Grand-Schenk, E. and Gandin, C. and de Francesco, M. and Polissi, A. and Buell, G. and Feger, G. and Garcia, E. and Peitsch, M. and Garcia-Bustos, J. F.}
}
