Dr. Damian Sabas Roqueiro

Lecturer at the Department of Health Sciences and Technology

ETH Zürich, D-BSSE

BSD G 230

Mattenstrasse 26

4058 Basel

Switzerland

Research Statement

My research goal is to apply machine learning techniques in the creation of probabilistic models to better understand the association between specific diseases and the genetic markup of individuals who are affected by those diseases.

Academic Degrees

12/2013

Ph.D. in Bioinformatics.
University of Illinois-Chicago.
Chicago, USA.

07/2003

Master of Science in Computer Science.
University of Illinois-Chicago.
Chicago, USA.

03/1997

Engineer in Information Systems (Dipl.-Ing.)
Universidad Tecnológica Nacional.
Buenos Aires, Argentina.

Academic Experience

Teaching

Assistantships and Tutoring

I held various teaching assistantships (TA), research assistantships (RA) and graduate assistantships (GA).

Industry Experience

Honors & Awards

Books

Anja C. Gumpinger, Damian Roqueiro, Dominik G. Grimm and Karsten M. Borgwardt
Methods and Tools in Genome-wide Association Studies
In Computational Cell Biology, Editors Louise von Stechow L. and Alberto Santos Delgado, volume 1819 of Methods in Molecular Biology, pages 93-136. Humana Press, New York, NY, 2018. (external pageOnline)

Publications

Michael Moor, Max Horn, Bastian Rieck, Damian Roqueiro and Karsten Borgwardt
Early Recognition of Sepsis with Gaussian Process Temporal Convolutional Networks and Dynamic Time Warping
Machine Learning for Healthcare Conference (MLHC) 2019. (external pageOnline)

Xiao He, Thomas Gumbsch, Damian Roqueiro and Karsten Borgwardt
Kernel Conditional Clustering and Kernel Conditional Semi-supervised Learning
Knowledge and Information Systems, 2019, https://doi.org/10.1007/s10115-019-01334-5. (external pageOnline)

Felipe Llinares-Lopez, Laetitia Papaxanthos, Damian Roquiero, Dean Bodenham and Karsten Borgwardt
CASMAP: Detection of statistically significant combinations of SNPs in association mapping
Bioinformatics, 2018, bty1020, https://doi.org/10.1093/bioinformatics/bty1020. (external pageOnline)

Matteo Togninalli, Damian Roqueiro, COPDGene Investigators and Karsten Borgwardt
Accurate and Adaptive Imputation of Summary Statistics in Mixed-Ethnicity Cohorts
ECCB 2018 and Bioinformatics 2018, 35 (17): i687-i696. (external pageOnline)

Christian Bock, Thomas Gumbsch, Michael Moor, Bastian Rieck, Damian Roquiero and Karsten Borgwardt
Association Mapping in Biomedical Time Series via Statistically Significant Shapelet Mining
ISMB 2018 and Bioinformatics 2018, 43 (13): i438–i446. (external pageOnline)

Xiao He, Thomas Gumbsch, Damian Roqueiro and Karsten Borgwardt
Kernel conditional clustering
2017 IEEE International Conference on Data Mining (ICDM), New Orleans, LA, 2017, pp. 157-166. (external pageOnline)

Xiao He, Limin Li, Damian Roqueiro and Karsten Borgwardt
Multi-view spectral clustering on conflicting views.
In: Ceci M., Hollmén J., Todorovski L., Vens C., Džeroski S. (eds) Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2017. Lecture Notes in Computer Science, v. 10535. Springer, Cham. (external pageOnline)

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. (external pageOnline)

Yuanlong Liu, Myriam Brossard, Damian Roqueiro, Patricia Margaritte-Jeannin, Chloé Sarnowski, Emmanuelle Bouzigon, Florence Demenais
SigMod: an exact and efficient method to identify a strongly interconnected disease-associated module in a gene network.
Bioinformatics 2017, 33(10): 1536-1544. (external pageOnline)

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 (external pageOnline)

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. (external pageOnline)

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. (external pageOnline)

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). (external pageOnline)

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 (external pageOnline)

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. external pagePubMed

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. external pagePubMed

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. external pagePubMed

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. external pagePubMed

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 external pageIEEE 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 external pagePubMed

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 external pageIEEE 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 external pageIEEE 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 external pageIEEE 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) (DownloadPaper (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). (external pageOnline)

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. (DownloadPaper (PDF, 42 KB))