Roqueiro, Damian Sabas, Dr.

Dr.  Damian Sabas Roqueiro

Address

ETH Zürich, D-BSSE

Professur für Data-Mining

Dr. Damian Sabas Roqueiro

Professur für Data-Mining

BSB  G 6.1 

Mattenstrasse 26

4058 Basel

Switzerland

  • phone +41 61 387 32 82 
  • mail
  • vcard V-Card (vcf, 1kb)

Publications

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Felipe Llinares-Lopez*, Laetitia Papaxanthos*, Dean Bodenham, Damian Roqueiro, COPDGene Investigators and Karsten Borgwardt (*=equal contributions)
Genome-wide genetic heterogeneity discovery with categorical covariates
Bioinformatics 2017, 33 (12): 1820-1828. (Online)

Further information and the code can be found on the project page.

@article{Llinares-Lopes-2017-Bioinformatics,
author = {Llinares-López, Felipe and Papaxanthos, Laetitia and Bodenham, Dean and Roqueiro, Damian and {COPDGene Investigators} and Borgwardt, Karsten},
title = {Genome-wide genetic heterogeneity discovery with categorical covariates},
journal = {Bioinformatics},
volume = {33},
number = {12},
pages = {1820},
year = {2017},
doi = {10.1093/bioinformatics/btx071},
URL = {http://dx.doi.org/10.1093/bioinformatics/btx071}
}

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Dominik G. Grimm, Damian Roqueiro, Patrice Salome, Stefan Kleeberger, Bastian Greshake, Wangsheng Zhu, Chang Liu, Christoph Lippert, Oliver Stegle, Bernhard Schölkopf, Detlef Weigel and Karsten Borgwardt
easyGWAS: A Cloud-based Platform for Comparing the Results of Genome-wide Association Studies
The Plant Cell 2017. 29(1):5-19 (Online)

@article{Grimm-2016-Plant_Cell,
author = {Grimm, Dominik G. and Roqueiro, Damian and Salom{\'e}, Patrice A. and Kleeberger, Stefan and Greshake, Bastian and Zhu, Wangsheng and Liu, Chang and Lippert, Christoph and Stegle, Oliver and Sch{\"o}lkopf, Bernhard and Weigel, Detlef and Borgwardt, Karsten M.},
title = {easy{GWAS}: {A} {C}loud-{B}ased {P}latform for {C}omparing the {R}esults of {G}enome-{W}ide {A}ssociation {S}tudies},
volume = {29},
number = {1},
pages = {5-19},
year = {2017},
doi = {10.1105/tpc.16.00551},
URL = {http://www.plantcell.org/content/29/1/5.abstract},
journal = {The Plant Cell}
}

Further information and the code can be found on the project page and directly on easygwas.org.

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Damian Roqueiro, Menno Witteveen, Verneri Anttila, Gisela Terwindt, Arn van den Maagdenberg and Karsten Borgwardt
In silico phenotyping via co-training for improved phenotype prediction from genotype.
ISMB 2015, Bioinformatics (2015) 31 (12): i303-i310. (Online)

The code and further information can be found on the project page.

@article{Roqueiro-2015-Bioinformatics,
author = {Roqueiro, Damian and Witteveen, Menno J. and Anttila, Verneri and Terwindt, Gisela M. and van den Maagdenberg, Arn M.J.M. and Borgwardt, Karsten},
title = {In silico phenotyping via co-training for improved phenotype prediction from genotype},
volume = {31},
number = {12},
pages = {i303-i310},
year = {2015},
doi = "10.1093/bioinformatics/btv254",
URL = {http://bioinformatics.oxfordjournals.org/content/31/12/i303.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/31/12/i303.full.pdf+html},
journal = {Bioinformatics}
}

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Congmao Wang, Chang Liu, Damian Roqueiro, Dominik G. Grimm, Rebecca Schwab, Claude Becker, Christa Lanz and Detlef Weigel
Genome-wide analysis of local chromatin packing in Arabidopsis thaliana,
Genome Research 2015, 25(2):246-256. (Online)

@article{Wang-2015-Genome_Res,
author = {Wang, Congmao and Liu, Chang and Roqueiro, Damian and Grimm, Dominik G. and Schwab, Rebecca and Becker, Claude and Lanz, Christa and Weigel, Detlef},
title = {Genome-wide analysis of local chromatin packing in \textit{{A}rabidopsis thaliana}},
doi = "10.1101/gr.170332.113",
URL = {http://genome.cshlp.org/content/25/2/246.abstract},
eprint = {http://genome.cshlp.org/content/25/2/246.full.pdf+html},
journal = {Genome Research},
volume = {25},
number = {2},
pages = {246-256},
year = {2015},
}

Other publications

L. Montefiori, R. Wuerffel, D. Roqueiro, B. Lajoie, C. Guo, T. Gerasimova, S. De, W. Wood, K.G. Becker, J. Dekker, J. Liang, R. Sen, A.L. Kenter. Extremely long-range chromatin loops link topological domains to facilitate a diverse antibody repertoire. Cell Reports , Volume 14 , Issue 4 , 896-906 (2016). (Online)


M.T. Dyson, D. Roqueiro, D. Monsivais, C.M. Ercan, M.E. Pavone, D.C. Brooks, T. Kakinuma, M. Ono, N. Jafari, Y. Dai, and S.E. Bulun. Genome-wide DNA methylation analysis predicts an epigenetic switch for GATA factor expression in endometriosis. PLoS
Genet, 10(3):e1004158, 03 2014 (Online)


Y. Afshar, J. Hastings, D. Roqueiro, J.W. Jeong, L. Giudice, A.T. Fazleabas. Changes in eutopic endometrial gene expression during the development of experimental endometriosis in the baboon. Biology of Reproduction 2013, doi:10.1095/biolreprod.112.104497. PubMed


W. Mu, D. Roqueiro, Y. Dai. A local genetic algorithm for the identification of condition-specific microRNA-gene modules. The Scientific World Journal, 2013:9, 2013. PubMed


D. Roqueiro, L. Huang, Y. Dai. Identifying Transcription Factors and microRNAs as Key Regulators of Pathways Using Bayesian Inference on Known Pathway Structures. Proteome Science 2012. doi:10.1186/1477-5956-10-S1-S15. PubMed


P. Yin, D. Roqueiro, L. Huang, J.K. Owen, A. Xie, A. Navarro, D. Monsivais, J.S. Coon V, J.J. Kim, Y. Dai, S. E. Bulun. Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells. PLoS ONE, 7(1) (2012): e29021. doi:10.1371/journal.pone.0029021. PubMed


D. Roqueiro, L. Huang, Y. Dai. Identifying Transcription Factors and microRNAs as Key Regulators of Pathways Using Bayesian Inference on Known Pathway Structures. Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference, pp.228-233 (2011) doi: 10.1109/BIBM.2011.120 IEEE Digital Library


Y. Afshar, J.W. Jeong, D. Roqueiro, F. Demayo, J. Lydon, F. Radtke, R. Radnor, L. Miele, A. Fazleabas. Notch1 mediates uterine stromal differentiation and is critical for complete decidualization in the mouse. FASEB Journal, October 11, 2011 fj.11-184663 PubMed


L. Huang, D. Roqueiro, Y. Dai. Analyzing mRNA and microRNA co-expression profiles to identify pathways and their potential regulators in ER+ and ER- breast tumors. Engineering in Medicine and Biology Society,EMBC, 2011 Annual International Conference of the IEEE , pp.932-935 (2011) doi: 10.1109/IEMBS.2011.6090210 IEEE Digital Library


H. Hu, D. Roqueiro, Y. Dai. Prioritizing predicted cis-regulatory elements for co-expressed gene sets based on Lasso regression models. Engineering in Medicine and Biology Society,EMBC, 2011 Annual International Conference of the IEEE , pp.6853-6856 (2011) doi: 10.1109/IEMBS.2011.6091690 IEEE Digital Library


D. Roqueiro, J. Frasor and Y. Dai. "bindSDb: A Binding-information Spatial Database"Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference, pp.573-578 (2010) doi: 10.1109/BIBMW.2010.5703864 IEEE Digital Library


Publications in Computer Science

A. Gershman, R. Ghani, D. Roqueiro and G. Wei. Trade-offs in the Use of Bayesian Filtering for Sensor Fusion. International Workshop on Knowledge Discovery from Sensor Data (Sensor-KDD'07). Held with ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD-2007) (Paper (PDF, 367 KB))


D. Roqueiro, V.A. Petrushin. Counting People using Video Cameras. International Journal of Parallel, Emergent and Distributed Systems (IJPEDS). Taylor & Francis. Volume 22; Issue 3, pages 193-209 (2007). (Online)


V.A. Petrushin, G. Wei, O. Shakil, D. Roqueiro, A. Gershman, Multiple-Sensor Indoor Surveillance System. Proceedings of The 3rd Canadian Conference on Computer and Robot Vision (CRV'06),  crv, p. 40, (2006).


D. Roqueiro, V.A. Petrushin. Counting People using Video Cameras. Workshop for Multimedia and Data Mining (MDM at KDD’06) (2006).


B.P. Allen, V.A. Petrushin, D. Roqueiro, G. Wei. Semantic Web Techniques for Searching and Navigating Video Shots in BBC Rushes. TRECVID 2006 Workshop. (Paper (PDF, 42 KB))

 

 
 
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