Research Topics
Species | Carolina Perez-IratxetaSummaryAffiliation: Ottawa Health Research Institute Country: Canada Publications
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Detail Information
Publications
Recent developments in StemBase: a tool to study gene expression in human and murine stem cellsReatha Sandie
Ottawa Health Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
BMC Res Notes 2:39. 2009..CONCLUSION: StemBase can be used to study gene expression in human and murine stem cells and is available at http://www.stembase.ca...- Inconsistencies over time in 5% of NetAffx probe-to-gene annotationsCarolina Perez-Iratxeta
BMC Bioinformatics 6:183. 2005.... 
A protocol for the update of references to scientific literature in biological databasesCarolina Perez-Iratxeta
European Molecular Biology Laboratory, Heidelberg, Germany
Appl Bioinformatics 2:189-91. 2003..Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful...- G2D: a tool for mining genes associated with diseaseCarolina Perez-Iratxeta
Ontario Genomics Innovation Centre, Ottawa Health Research Institute, ON K1H 8L6, Ottawa, Canada
BMC Genet 6:45. 2005..We previously developed an algorithm to prioritize genes on a chromosomal region according to their possible relation to an inherited disease using a combination of data mining on biomedical databases and gene sequence analysis... - Update of the G2D tool for prioritization of gene candidates to inherited diseasesCarolina Perez-Iratxeta
Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON, Canada K1H 8L6
Nucleic Acids Res 35:W212-6. 2007..This means that some of them will correspond to well-known characterized genes, and others will overlap with predicted genes, thus providing a wider analysis. G2D is publicly available at http://www.ogic.ca/projects/g2d_2/.. - K2D2: estimation of protein secondary structure from circular dichroism spectraCarolina Perez-Iratxeta
Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON, K1H 8L6, Canada
BMC Struct Biol 8:25. 2008..Predictive methods use the circular dichroism spectra from proteins of known tertiary structure to assess the secondary structure contents of a protein with unknown structure given its circular dichroism spectrum... - Gene function in early mouse embryonic stem cell differentiationKagnew Hailesellasse Sene
Ontario Genomics Innovation Centre, Ottawa Health Research Institute, Ottawa, ON, Canada
BMC Genomics 8:85. 2007..5) undergoing undirected differentiation into embryoid bodies (EBs) over a period of two weeks... - StemBase: a resource for the analysis of stem cell gene expression dataChristopher J Porter
Ottawa Health Research Institute, Molecular Medicine Program, Ontario, Canada
Methods Mol Biol 407:137-48. 2007.... - Amplification of the Gene Ontology annotation of Affymetrix probe setsEnrique M Muro
Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth Rd, Ottawa ON, K1H 8L6, Canada
BMC Bioinformatics 7:159. 2006..This results in very accurate but incomplete annotations which is not always desirable for microarray experiment evaluation... - Information extraction from full text scientific articles: where are the keywords?Parantu K Shah
Biocomputing, European Molecular Biology Laboratory, Heidelberg, Germany
BMC Bioinformatics 4:20. 2003..Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant... - Association of genes to genetically inherited diseases using data miningCarolina Perez-Iratxeta
European Molecular Biology Laboratory, Meyerhofstr.1, Heidelberg 69012, Germany
Nat Genet 31:316-9. 2002..The scoring also indicates that for some diseases, the chance of identifying the underlying gene is higher... - Computing fuzzy associations for the analysis of biological literatureCarolina Perez-Iratxeta
European Molecular Biology Laboratory, Heidelberg, Germany
Biotechniques 32:1380-2, 1384-5. 2002..Those relations are used to derive ensembles of related words and their associated subsets of abstracts. The algorithm can be used publicly at http:// www.bork.embl-heidelberg.de/xplormed/... - Update on XplorMed: A web server for exploring scientific literatureCarolina Perez-Iratxeta
European Molecular Biology Laboratory, Meyerhofstr 1, 69117 Heidelberg, Germany
Nucleic Acids Res 31:3866-8. 2003..Here we describe new features added to XplorMed during the last 2 years (http://www.bork.embl-heidelberg.de/xplormed/)... - Systematic association of genes to phenotypes by genome and literature miningJan O Korbel
European Molecular Biology Laboratory, Heidelberg, Germany
PLoS Biol 3:e134. 2005..Among the clusters, we observe an enrichment of pathogenicity-related associations, suggesting that the approach reveals many novel genes likely to play a role in infectious diseases... - Resident endothelial precursors in muscle, adipose, and dermis contribute to postnatal vasculogenesisGuillaume Grenier
Sprott Centre for Stem Cell Research, Ottawa Health Research Institute, 501 Smyth Road, Ottawa, Ontario K1H 8L6, Canada
Stem Cells 25:3101-10. 2007..This finding is of particular interest since it could bring new insight in cancer angiogenesis and collateral blood vessels developed following ischemia. Disclosure of potential conflicts of interest is found at the end of this article... - NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteriaMiguel A Andrade
European Molecular Biology Laboratory, Meyerhofstr, 1, 69117 Heidelberg, Germany
Genome Biol 3:RESEARCH0047. 2002..To find potential targets for drugs active against pathogenic bacteria, we have searched all completely sequenced genomes of pathogenic bacteria for genes relevant for iron transport... - Towards completion of the Earth's proteomeCarolina Perez Iratxeta
Department of Molecular Medicine, Ottawa Health Research Institute, 501 Smyth Road, Ottawa, Ontario K1H 8L6, Canada
EMBO Rep 8:1135-41. 2007.... - Evolving research trends in bioinformaticsCarolina Perez Iratxeta
Ottawa Health Research Institute, Ontario, Canada
Brief Bioinform 8:88-95. 2007..Via this analysis, we were able to identify areas of rapid growth in the use of informatics to aid in curriculum planning, development of computational infrastructure and strategies for workforce education and funding... - Exploring MEDLINE abstracts with XplorMedCarolina Perez-Iratxeta
European Molecular Biology Laboratory, Heidelberg, Germany
Drugs Today (Barc) 38:381-9. 2002..XplorMed is available http://www.bork. embl-heidelberg.de/xplormed... - Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineagesCarmen G Palii
The Sprott Center for Stem Cell Research, Department of Regenerative Medicine, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
EMBO J 30:494-509. 2011.... - Study of stem cell function using microarray experimentsCarolina Perez-Iratxeta
Ontario Genomics Innovation Centre, Ottawa Health Research Institute, Molecular Medicine Program, 501 Smyth Road, Ottawa, Canada K1H 8L6
FEBS Lett 579:1795-801. 2005..The data can be accessed online (StemBase; http://www.scgp.ca:8080/StemBase/)... - Oct4 targets regulatory nodes to modulate stem cell functionPearl A Campbell
Sprott Centre for Stem Cell Research, Ottawa Health Research Institute, Ottawa, Ontario, Canada University of Ottawa, Department of Cellular and Molecular Medicine, Ottawa, Ontario, Canada
PLoS ONE 2:e553. 2007..Together, these data define the mechanism by which Oct4 orchestrates cellular regulatory pathways to enforce the stem cell state and provides important insight into stem cell function and cancer... - Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genesNicki Tiffin
South African National Bioinformatics Institute, University of the Western Cape, Bellville, 7535, South Africa
Nucleic Acids Res 34:3067-81. 2006..Two genes, LPL and BCKDHA, are common to these two sets. We also present a set of secondary candidates for T2D (94 genes) and for obesity (116 genes) with 58 genes in common to both diseases... - Gene annotation from scientific literature using mappings between keyword systemsAntonio J Pérez
University of Malaga, Facultad de Ciencias, Departmento de Genetica, Group of Bioinformatics, Campus Universitario de Teatinos, 29071 Malaga, Spain
Bioinformatics 20:2084-91. 2004..However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene... 
Prioritization of candidate disease genes for metabolic syndrome by computational analysis of its defining phenotypesNicki Tiffin
Division of Human Genetics, MRC Human Genetics Research Unit, Institute for Infectious Diseases and Molecular Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
Physiol Genomics 35:55-64. 2008..We propose here that information about the clinical presentation of a complex trait can be used to effectively inform computational prioritization of disease-causing genes for that trait...- The way we writeRebecca Netzel
Institute of Translation and Interpreting, University of Heidelberg, Germany
EMBO Rep 4:446-51. 2003 - Worldwide scientific publishing activityCarolina Perez-Iratxeta
Science 297:519. 2002