You are surfing Adrin Jalali‘s page, who works as a data scientist/engineer and has spent his PhD (not finished yet) doing research in the field of Computational Biology.
Area of research
I use/design machine learning tools to classify samples. The datasets I work on vary from microarray to DNA methylation data. I am mostly focused on using gene/protein networks in order to help the classification task, while keeping in mind I need to interpret my results for a biologist. Therefore my goal at the moment is to have a method which directly uses or is inspired by the biological networks, classifies my samples, and can be interpreted on the biological level.
- [Poster] Adrin Jalali, Nico Pfeifer, “Analyzing How Protein Interaction Networks Improve Classification Performance in Gene Expression Data Analysis“, ISMB/ECCB 2013, Berlin, Germany.
- Jalali A., and Pfeifer N., “Interpretable per Case Weighted Ensemble Method for Cancer Associations“, BMC Genomics, volume 17, no. 1, 2016.
I also worked on flow-cytometry data which is a single cell level data. I did it mostly when I was for 15 months in Vancouver, Canada, and I was doing research in British Columbia Cancer Research Center and The University of British Columbia. As a result of this part of my research, I can refer you to:
- Kieran O’Neill†, Adrin Jalali†, Nima Aghaeepour†, Holger Hoos, and Ryan R. Brinkman. “Enhanced flowType/RchyOptimyx: A Bioconductor pipeline for discovery in high-dimensional cytometry data.” Bioinformatics (2014), doi: 10.1093/bioinformatics/btt770
- Nima Aghaeepour†, Adrin Jalali†, Kieran O’Neill, Pratip K. Chattopadhyay, Mario Roederer, Holger H. Hoos, and Ryan R. Brinkman. “RchyOptimyx: Cellular hierarchy optimization for flow cytometry.” Cytometry Part A 81, no. 12 (2012): 1022-1030, doi: 10.1002/cyto.a.22209
- Nima Aghaeepour, Pratip K. Chattopadhyay, Anuradha Ganesan, Kieran O’Neill, Habil Zare, Adrin Jalali, Holger H. Hoos, Mario Roederer, and Ryan R. Brinkman. “Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.” Bioinformatics 28, no. 7 (2012): 1009-1016, doi: 10.1093/bioinformatics/bts082
- [Poster] Adrin Jalali, Nima Aghaeepour, Kieran O’Neill, Andrew P. Weng, Ryan R. Brinkman, “Analysis and Classification of Lymphoma Sub-types“, British Columbia Cancer Agency Annual Conference, Victoria, BC, Canada, 2012.
†: equal contribution
List of publications available on Google Scholar.