Blaz Zupan

Summary

Affiliation: University of Ljubljana
Country: Slovenia

Publications

  1. ncbi Conserved developmental transcriptomes in evolutionarily divergent species
    Anup Parikh
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Genome Biol 11:R35. 2010
  2. ncbi Does replication groups scoring reduce false positive rate in SNP interaction discovery?
    Marko Toplak
    Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI 1000 Ljubljana, Slovenia
    BMC Genomics 11:58. 2010
  3. ncbi New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data
    Anup Parikh
    Graduate Program in Structural Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Bioinformatics 11:163. 2010
  4. ncbi GenePath: a system for inference of genetic networks and proposal of genetic experiments
    Blaz Zupan
    Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI 1000 Ljubljana, Slovenia
    Artif Intell Med 29:107-30. 2003
  5. ncbi Machine learning for survival analysis: a case study on recurrence of prostate cancer
    B Zupan
    Faculty of Computer and Information Science, University of Ljubliana, and J Stefan Institute, Slovenia
    Artif Intell Med 20:59-75. 2000
  6. ncbi Decisions at hand: a decision support system on handhelds
    B Zupan
    Faculty of Computer and Information Science, University of Ljubljana, SI 1000 Ljubljana, Slovenia
    Stud Health Technol Inform 84:566-70. 2001
  7. ncbi Open-source tools for data mining
    Blaz Zupan
    University of Ljubljana, Trzaska 25, SI 1000 Ljubljana, Slovenia
    Clin Lab Med 28:37-54, vi. 2008
  8. ncbi Predicting patient's long-term clinical status after hip arthroplasty using hierarchical decision modelling and data mining
    B Zupan
    Faculty of Computer and Information Sciences, University of Ljubljana, Slovenia
    Methods Inf Med 40:25-31. 2001
  9. ncbi VizRank: finding informative data projections in functional genomics by machine learning
    Gregor Leban
    University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, Slovenia
    Bioinformatics 21:413-4. 2005
  10. ncbi dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
    Gregor Rot
    Faculty of Computer and Information Science, University of Ljubljana, SI 1000 Ljubljana, Slovenia
    BMC Bioinformatics 10:265. 2009

Collaborators

Detail Information

Publications26

  1. ncbi Conserved developmental transcriptomes in evolutionarily divergent species
    Anup Parikh
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Genome Biol 11:R35. 2010
    ..The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish...
  2. ncbi Does replication groups scoring reduce false positive rate in SNP interaction discovery?
    Marko Toplak
    Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI 1000 Ljubljana, Slovenia
    BMC Genomics 11:58. 2010
    ..Because Gayan et al. do not compare their approach to the standard interaction analysis techniques, we here investigate if replication groups indeed reduce the number of reported false positive interactions...
  3. ncbi New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data
    Anup Parikh
    Graduate Program in Structural Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Bioinformatics 11:163. 2010
    ..However, these algorithms are computationally demanding, so novel techniques that allow targeted exploration for discovering new members of known pathways are essential...
  4. ncbi GenePath: a system for inference of genetic networks and proposal of genetic experiments
    Blaz Zupan
    Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI 1000 Ljubljana, Slovenia
    Artif Intell Med 29:107-30. 2003
    ..We illustrate GenePath's approach and utility on analysis of data on aggregation and sporulation of the soil amoeba Dictyostelium discoideum...
  5. ncbi Machine learning for survival analysis: a case study on recurrence of prostate cancer
    B Zupan
    Faculty of Computer and Information Science, University of Ljubliana, and J Stefan Institute, Slovenia
    Artif Intell Med 20:59-75. 2000
    ....
  6. ncbi Decisions at hand: a decision support system on handhelds
    B Zupan
    Faculty of Computer and Information Science, University of Ljubljana, SI 1000 Ljubljana, Slovenia
    Stud Health Technol Inform 84:566-70. 2001
    ..A use case where LogReg has been applied to clinical outcome prediction in crush injury is presented...
  7. ncbi Open-source tools for data mining
    Blaz Zupan
    University of Ljubljana, Trzaska 25, SI 1000 Ljubljana, Slovenia
    Clin Lab Med 28:37-54, vi. 2008
    ..The approaches we review are diverse in data mining methods and user interfaces and also demonstrate that the field and its tools are ready to be fully exploited in biomedical research...
  8. ncbi Predicting patient's long-term clinical status after hip arthroplasty using hierarchical decision modelling and data mining
    B Zupan
    Faculty of Computer and Information Sciences, University of Ljubljana, Slovenia
    Methods Inf Med 40:25-31. 2001
    ..Although applied to hip endoprosthesis domain, the proposed schema is general and can be used for the construction of other prognostic models where both follow-up data and human expertise is available...
  9. ncbi VizRank: finding informative data projections in functional genomics by machine learning
    Gregor Leban
    University of Ljubljana, Faculty of Computer and Information Science, Ljubljana, Slovenia
    Bioinformatics 21:413-4. 2005
    ..AVAILABILITY: http://www.ailab.si/supp/bi-vizrank SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-vizrank...
  10. ncbi dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
    Gregor Rot
    Faculty of Computer and Information Science, University of Ljubljana, SI 1000 Ljubljana, Slovenia
    BMC Bioinformatics 10:265. 2009
    ....
  11. ncbi Visualization-based cancer microarray data classification analysis
    Minca Mramor
    Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, 1000 Ljubljana, Slovenia
    Bioinformatics 23:2147-54. 2007
    ....
  12. ncbi GenePath: from mutations to genetic networks and back
    Peter Juvan
    Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
    Nucleic Acids Res 33:W749-52. 2005
    ..GenePath is available at http://www.genepath.org/genepath2...
  13. ncbi FreeViz--an intelligent multivariate visualization approach to explorative analysis of biomedical data
    Janez Demsar
    Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI 1000 Ljubljana, Slovenia
    J Biomed Inform 40:661-71. 2007
    ..The paper gives mathematical foundations of FreeViz, and presents its utility on various biomedical data sets...
  14. ncbi GenePath: a system for automated construction of genetic networks from mutant data
    Blaz Zupan
    University of Ljubljana, Faculty of Computer and Information Science Jozef Stefan Institute, Ljubljana, Slovenia
    Bioinformatics 19:383-9. 2003
    ..AVAILABILITY: GenePath can be accessed at http://genepath.org. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://genepath.org/bi-.supp...
  15. ncbi Microarray data mining with visual programming
    Tomaz Curk
    Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
    Bioinformatics 21:396-8. 2005
    ..AVAILABILITY: http://www.ailab.si/supp/bi-visprog SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-visprog...
  16. ncbi FragViz: visualization of fragmented networks
    Miha Stajdohar
    Faculty of Computer and Information Science, University of Ljubljana, Slovenia
    BMC Bioinformatics 11:475. 2010
    ..This can lead to misinterpretations due to the proximity of otherwise unrelated elements...
  17. ncbi SNPsyn: detection and exploration of SNP-SNP interactions
    Tomaz Curk
    Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, SI 1000 Ljubljana, Slovenia
    Nucleic Acids Res 39:W444-9. 2011
    ..The user can explore details on identified synergistic pairs of SNPs, perform gene set enrichment analysis and interact with the constructed SNP synergy network...
  18. ncbi GenePath: a computer program for genetic pathway discovery from mutant data
    J Demsar
    Faculty of Computer and Information Sciences, Ljubljana, Slovenia
    Stud Health Technol Inform 84:956-9. 2001
    ..elegans confirmed the usefulness of the proposed schema. Our results suggest that GenePath is a valuable tool that can be used as an intelligent assistant to support genetic reasoning...
  19. ncbi Feature mining and predictive model construction from severe trauma patient's data
    J Demsar
    Faculty of Computer and Information Sciences, University of Ljubljana, Tr aska 25, SI 1000 Ljubljana, Slovenia
    Int J Med Inform 63:41-50. 2001
    ..This finding is pathophysiologically reasonable and represents two of three major problems with severe trauma patients, metabolic acidosis, hypothermia, and coagulopathy...
  20. ncbi Rule-based clustering for gene promoter structure discovery
    Tomaz Curk
    Tomaz Curk, University of Ljubljana, Faculty of Comp and Inf Science, Trzaska c 25, 1000 Ljubljana, Slovenija
    Methods Inf Med 48:229-35. 2009
    ..The genetic cellular response to internal and external changes is determined by the sequence and structure of gene-regulatory promoter regions...
  21. ncbi Stage prediction of embryonic stem cell differentiation from genome-wide expression data
    Lan Zagar
    Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
    Bioinformatics 27:2546-53. 2011
    ..Recent findings suggest that such profiles provide sufficient information to reliably predict the cell's developmental stage...
  22. ncbi Towards knowledge-based gene expression data mining
    Riccardo Bellazzi
    Dipartimento di Informatica e Sistemistica, Universita di Pavia, Via Ferrata 1, I 27100 Pavia, Italy
    J Biomed Inform 40:787-802. 2007
    ..In particular, we discuss recent developments in gene expression-based analysis methods used in association and classification studies, phenotyping and reverse engineering of gene networks...
  23. ncbi TA-clustering: cluster analysis of gene expression profiles through Temporal Abstractions
    Lucia Sacchi
    Dipartimento di Informatica e Sistemistica, Universita di Pavia, Via Ferrata 1, 27100 Pavia, Italy
    Int J Med Inform 74:505-17. 2005
    ..We demonstrate the utility of the proposed algorithm on a set of two simulated data sets and on a study of gene expression data from S. cerevisiae...
  24. ncbi Developmentally regulated DNA methylation in Dictyostelium discoideum
    Mariko Katoh
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Eukaryot Cell 5:18-25. 2006
    ..Our findings establish a role for a Dnmt2 methyltransferase in eukaryotic development...
  25. ncbi Epistasis analysis with global transcriptional phenotypes
    Nancy Van Driessche
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nat Genet 37:471-7. 2005
    ..This work shows that microarray data can provide a uniform, quantitative tool for large-scale genetic network analysis...
  26. ncbi Knowledge-based data analysis and interpretation
    Blaz Zupan
    Artif Intell Med 37:163-5. 2006