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The road of excess
. . . leads to the palace of wisdom (William Blake - 1790)
David Montaner
2014-06-19
David Montaner Computational Genomics @ CIPF 1/15
About
Statistician working in genomic research
Computational Genomics Department
(Bioinformatics - Ximo Dopazo)
Massive (high-throughput) data analysis - Genomics
methods
software and tools
practical application
Teaching . . . bioStat-coaching
short courses in bioinformatics
University of Valencia
student tutoring
e-learning materials
CEO at Genometra: bioinformatics consultancy
David Montaner Computational Genomics @ CIPF 2/15
Publications 2013
Di?erential gene-expression analysis de?nes a molecular
pattern related to olive pollen allergy.
Aguerri M, Calzada D, Montaner D, Mata M, Florido F,
Quiralte J, Dopazo J, Lahoz C, Cardaba B.
J Biol Regul Homeost Agents. 2013 Apr-Jun;27(2):337-50.
De?ning the genomic signature of totipotency and
pluripotency during early human development.
Galan A, Diaz-Gimeno P, Poo ME, Valbuena D, Sanchez E,
Ruiz V, Dopazo J, Montaner D, Conesa A, Simon C.
PLoS One. 2013 Apr 17;8(4):e62135. doi:
10.1371/journal.pone.0062135. Print 2013.
Thesis
Methodological advances in the functional pro?ling of genomic
studies.
David Montaner Computational Genomics @ CIPF 3/15
Publications 2014
A novel locus for a hereditary recurrent neuropathy on
chromosome 21q21.
E Calpena, D Mart¨ªnez-Rubio, J Arpa, JJ Garc¨ªa-Pe?as, D
Montaner, J Dopazo, F Palau, C Espin¨®s.
Neuromuscular Disorders, 2014.
Pathway network inference from gene expression data.
Ignacio Ponzoni, Mar¨ªa Jos¨¦ Nueda, Sonia Tarazona, Stefan
G?tz, David Montaner, Julieta Sol Dussaut, Joaqu¨ªn
Dopazo, Ana Conesa.
BMC Systems Biology, 2014. 8 (2), 1-17.
Quantitative modeling of clinical, cellular, and
extracellular matrix variables suggest prognostic
indicators in cancer: a model in neuroblastoma.
Tadeo I, Piqueras M, Montaner D, Villam¨®n E, Berbegall
AP, Ca?ete A, Navarro S, Noguera R.
Pediatr Res. 2014 Feb;75(2):302-14.
David Montaner Computational Genomics @ CIPF 4/15
Research: Gene Set Analysis
Experimental data results + Database information: GO, KEGG. . .
David Montaner Computational Genomics @ CIPF 5/15
PhD Dissertation
Logistic regression models applied to GSA
log
¦Ð(x)
1 ? ¦Ð(x)
= ¦Ê + ¦Áx
Improvements
Including weights to account for gene importance
Estimate of weights from experimental data in repositories
Extension to multiple genomic dimension
log
¦Ð
1 ? ¦Ð
= ¦Ê + ¦Á x1 + ¦Â x2 + ¦Ã x1x2
David Montaner Computational Genomics @ CIPF 6/15
Multi Dimensional Gene Set Analysis
David Montaner Computational Genomics @ CIPF 7/15
Multi Dimensional Gene Set Analysis
David Montaner Computational Genomics @ CIPF 8/15
Multi Dimensional Gene Set Analysis
David Montaner Computational Genomics @ CIPF 9/15
Multi Dimensional Gene Set Analysis
David Montaner Computational Genomics @ CIPF 10/15
Multi Dimensional Gene Set Analysis
David Montaner Computational Genomics @ CIPF 11/15
Ongoing Work
Improving software implementation: R package, Babelomics
tool
Adjust the methods to NGS data
Extend to genomic features other than genes
miRNAs
SNPs
Functional Meta-analysis: combine GSA results from several
datasets
New research interests:
Topological pathway analysis
Metagenomics: genomic analysis of microbial communities
David Montaner Computational Genomics @ CIPF 12/15
Pathways Topology
David Montaner Computational Genomics @ CIPF 13/15
Ongoing work
Improving software implementation: R package, Babelomics
Tool
Adjust the methods to NGS data
Extend to genomic features other than genes
miRNAs
SNPs
Functional Meta-analysis: combine GSA results from several
datasets
New research interests:
Topological pathway analysis
Metagenomics: genomic analysis of microbial communities
David Montaner Computational Genomics @ CIPF 14/15
Thank You
Further reading . . .
www.dmontaner.com
bioinfo.cipf.es/dmontaner
www.linkedin.com/in/dmontaner
twitter.com/david_montaner
David Montaner Computational Genomics @ CIPF 15/15

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dmontaner at cipf_2014

  • 1. The road of excess . . . leads to the palace of wisdom (William Blake - 1790) David Montaner 2014-06-19 David Montaner Computational Genomics @ CIPF 1/15
  • 2. About Statistician working in genomic research Computational Genomics Department (Bioinformatics - Ximo Dopazo) Massive (high-throughput) data analysis - Genomics methods software and tools practical application Teaching . . . bioStat-coaching short courses in bioinformatics University of Valencia student tutoring e-learning materials CEO at Genometra: bioinformatics consultancy David Montaner Computational Genomics @ CIPF 2/15
  • 3. Publications 2013 Di?erential gene-expression analysis de?nes a molecular pattern related to olive pollen allergy. Aguerri M, Calzada D, Montaner D, Mata M, Florido F, Quiralte J, Dopazo J, Lahoz C, Cardaba B. J Biol Regul Homeost Agents. 2013 Apr-Jun;27(2):337-50. De?ning the genomic signature of totipotency and pluripotency during early human development. Galan A, Diaz-Gimeno P, Poo ME, Valbuena D, Sanchez E, Ruiz V, Dopazo J, Montaner D, Conesa A, Simon C. PLoS One. 2013 Apr 17;8(4):e62135. doi: 10.1371/journal.pone.0062135. Print 2013. Thesis Methodological advances in the functional pro?ling of genomic studies. David Montaner Computational Genomics @ CIPF 3/15
  • 4. Publications 2014 A novel locus for a hereditary recurrent neuropathy on chromosome 21q21. E Calpena, D Mart¨ªnez-Rubio, J Arpa, JJ Garc¨ªa-Pe?as, D Montaner, J Dopazo, F Palau, C Espin¨®s. Neuromuscular Disorders, 2014. Pathway network inference from gene expression data. Ignacio Ponzoni, Mar¨ªa Jos¨¦ Nueda, Sonia Tarazona, Stefan G?tz, David Montaner, Julieta Sol Dussaut, Joaqu¨ªn Dopazo, Ana Conesa. BMC Systems Biology, 2014. 8 (2), 1-17. Quantitative modeling of clinical, cellular, and extracellular matrix variables suggest prognostic indicators in cancer: a model in neuroblastoma. Tadeo I, Piqueras M, Montaner D, Villam¨®n E, Berbegall AP, Ca?ete A, Navarro S, Noguera R. Pediatr Res. 2014 Feb;75(2):302-14. David Montaner Computational Genomics @ CIPF 4/15
  • 5. Research: Gene Set Analysis Experimental data results + Database information: GO, KEGG. . . David Montaner Computational Genomics @ CIPF 5/15
  • 6. PhD Dissertation Logistic regression models applied to GSA log ¦Ð(x) 1 ? ¦Ð(x) = ¦Ê + ¦Áx Improvements Including weights to account for gene importance Estimate of weights from experimental data in repositories Extension to multiple genomic dimension log ¦Ð 1 ? ¦Ð = ¦Ê + ¦Á x1 + ¦Â x2 + ¦Ã x1x2 David Montaner Computational Genomics @ CIPF 6/15
  • 7. Multi Dimensional Gene Set Analysis David Montaner Computational Genomics @ CIPF 7/15
  • 8. Multi Dimensional Gene Set Analysis David Montaner Computational Genomics @ CIPF 8/15
  • 9. Multi Dimensional Gene Set Analysis David Montaner Computational Genomics @ CIPF 9/15
  • 10. Multi Dimensional Gene Set Analysis David Montaner Computational Genomics @ CIPF 10/15
  • 11. Multi Dimensional Gene Set Analysis David Montaner Computational Genomics @ CIPF 11/15
  • 12. Ongoing Work Improving software implementation: R package, Babelomics tool Adjust the methods to NGS data Extend to genomic features other than genes miRNAs SNPs Functional Meta-analysis: combine GSA results from several datasets New research interests: Topological pathway analysis Metagenomics: genomic analysis of microbial communities David Montaner Computational Genomics @ CIPF 12/15
  • 13. Pathways Topology David Montaner Computational Genomics @ CIPF 13/15
  • 14. Ongoing work Improving software implementation: R package, Babelomics Tool Adjust the methods to NGS data Extend to genomic features other than genes miRNAs SNPs Functional Meta-analysis: combine GSA results from several datasets New research interests: Topological pathway analysis Metagenomics: genomic analysis of microbial communities David Montaner Computational Genomics @ CIPF 14/15
  • 15. Thank You Further reading . . . www.dmontaner.com bioinfo.cipf.es/dmontaner www.linkedin.com/in/dmontaner twitter.com/david_montaner David Montaner Computational Genomics @ CIPF 15/15