Carolina Perez-Iratxeta

Summary

Affiliation: Ottawa Health Research Institute
Country: Canada

Publications

  1. pmc Recent developments in StemBase: a tool to study gene expression in human and murine stem cells
    Reatha Sandie
    Ottawa Health Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
    BMC Res Notes 2:39. 2009
  2. pmc Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
    Carolina Perez-Iratxeta
    BMC Bioinformatics 6:183. 2005
  3. ncbi request reprint A protocol for the update of references to scientific literature in biological databases
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Appl Bioinformatics 2:189-91. 2003
  4. pmc G2D: a tool for mining genes associated with disease
    Carolina Perez-Iratxeta
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, ON K1H 8L6, Ottawa, Canada
    BMC Genet 6:45. 2005
  5. pmc Update of the G2D tool for prioritization of gene candidates to inherited diseases
    Carolina Perez-Iratxeta
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON, Canada K1H 8L6
    Nucleic Acids Res 35:W212-6. 2007
  6. pmc K2D2: estimation of protein secondary structure from circular dichroism spectra
    Carolina Perez-Iratxeta
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON, K1H 8L6, Canada
    BMC Struct Biol 8:25. 2008
  7. pmc Gene function in early mouse embryonic stem cell differentiation
    Kagnew Hailesellasse Sene
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, Ottawa, ON, Canada
    BMC Genomics 8:85. 2007
  8. doi request reprint StemBase: a resource for the analysis of stem cell gene expression data
    Christopher J Porter
    Ottawa Health Research Institute, Molecular Medicine Program, Ontario, Canada
    Methods Mol Biol 407:137-48. 2007
  9. pmc Amplification of the Gene Ontology annotation of Affymetrix probe sets
    Enrique M Muro
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth Rd, Ottawa ON, K1H 8L6, Canada
    BMC Bioinformatics 7:159. 2006
  10. pmc 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

Collaborators

Detail Information

Publications27

  1. pmc Recent developments in StemBase: a tool to study gene expression in human and murine stem cells
    Reatha 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...
  2. pmc Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
    Carolina Perez-Iratxeta
    BMC Bioinformatics 6:183. 2005
    ..However, it is frequent that the reported results of microarray analyses are given just as lists of genes without any reference to the underlying probes...
  3. ncbi request reprint A protocol for the update of references to scientific literature in biological databases
    Carolina 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...
  4. pmc G2D: a tool for mining genes associated with disease
    Carolina 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...
  5. pmc Update of the G2D tool for prioritization of gene candidates to inherited diseases
    Carolina 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/..
  6. pmc K2D2: estimation of protein secondary structure from circular dichroism spectra
    Carolina 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...
  7. pmc Gene function in early mouse embryonic stem cell differentiation
    Kagnew 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...
  8. doi request reprint StemBase: a resource for the analysis of stem cell gene expression data
    Christopher J Porter
    Ottawa Health Research Institute, Molecular Medicine Program, Ontario, Canada
    Methods Mol Biol 407:137-48. 2007
    ....
  9. pmc Amplification of the Gene Ontology annotation of Affymetrix probe sets
    Enrique 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...
  10. pmc 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...
  11. ncbi request reprint Association of genes to genetically inherited diseases using data mining
    Carolina 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...
  12. ncbi request reprint Computing fuzzy associations for the analysis of biological literature
    Carolina 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/...
  13. pmc Update on XplorMed: A web server for exploring scientific literature
    Carolina 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/)...
  14. pmc Systematic association of genes to phenotypes by genome and literature mining
    Jan 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...
  15. ncbi request reprint Resident endothelial precursors in muscle, adipose, and dermis contribute to postnatal vasculogenesis
    Guillaume 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...
  16. pmc NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria
    Miguel 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...
  17. pmc Towards completion of the Earth's proteome
    Carolina Perez-Iratxeta
    Department of Molecular Medicine, Ottawa Health Research Institute, 501 Smyth Road, Ottawa, Ontario K1H 8L6, Canada
    EMBO Rep 8:1135-41. 2007
    ....
  18. ncbi request reprint Evolving research trends in bioinformatics
    Carolina 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...
  19. ncbi request reprint Exploring MEDLINE abstracts with XplorMed
    Carolina 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...
  20. pmc Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages
    Carmen 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
    ....
  21. ncbi request reprint Study of stem cell function using microarray experiments
    Carolina 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/)...
  22. pmc Oct4 targets regulatory nodes to modulate stem cell function
    Pearl 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...
  23. pmc Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes
    Nicki 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...
  24. ncbi request reprint Gene annotation from scientific literature using mappings between keyword systems
    Antonio 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...
  25. doi request reprint Prioritization of candidate disease genes for metabolic syndrome by computational analysis of its defining phenotypes
    Nicki 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...
  26. pmc The way we write
    Rebecca Netzel
    Institute of Translation and Interpreting, University of Heidelberg, Germany
    EMBO Rep 4:446-51. 2003
  27. ncbi request reprint Worldwide scientific publishing activity
    Carolina Perez-Iratxeta
    Science 297:519. 2002