Safiye Celik

Address: Paul G. Allen Center for Computer Science & Engineering Box 352350 185 Stevens Way Seattle, WA 98195-2350
Email: safiye [at] cs.washington.edu

Curriculum Vitae: pdf

I am a 4th-year Ph.D. student in Computer Science and Engineering at the University of Washington. I feel very lucky to be supervised by Prof. Su-In Lee. I received my most recent MS degree in Computer Science and Engineering in February 2014 from the University of Washington under the supervision of Prof. Su-In Lee. I got my previous MS degree in Computer Engineering in September 2012 from Bogazici University under the supervision of Prof. Ali Taylan Cemgil. I received my Bachelor's degree in Computer Engineering from Middle East Technical University.

I am interested in developing statistical machine learning algorithms which aim to address the problem of high-dimensionality in systems biology applications. Those include identifying expression features that are conserved across multiple independent gene expression datasets and are likely to represent important molecular events underlying the cancer; and identifying robust biomarkers that can predict sensitivity of cancer patients to different chemotherapy drugs, with the long-term goal of introducing a promising way for personalized therapy. In my PhD thesis, I am proposing to develop a novel network learning framework to discover important molecular events in Alzheimer's disease progression.


Publications

An integrative framework for prioritizing candidate molecular markers reveals a novel driver for sensitivity to topoisomerase II inhibitors
Su-In Lee*, Safiye Celik*, Benjamin A Logsdon, Scott M. Lundberg, Timothy J Martins, Vivian G Oehler, Elihu H Estey, Chris P Miller, Sylvia Chien, Akanksha Saxena, Anthony Blau and Pamela S Becker
(in review) (* means equal contribution)

Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer [pdf]
Safiye Celik, Benjamin A Logsdon, Stephanie Battle, Charles W Drescher, Mara Rendi, David Hawkins and Su-In Lee
Genome Medicine (2016)

Efficient Dimensionality Reduction for High-Dimensional Network Estimation [pdf] [supplement]
Safiye Celik, Benjamin A Logsdon and Su-In Lee
International Conference on Machine Learning (ICML), Beijing, China (2014)

Sparse Estimation of Module Gaussian Graphical Models with Applications to Cancer Systems Biology [pdf]
Safiye Celik, Benjamin A Logsdon and Su-In Lee
NIPS Workshop on Machine Learning in Computational Biology (MLCB), Lake Tahoe, NV (2013)


Professional Experience

Between December 2010 and August 2012, I worked as a researcher at the Scientific and Technological Research Council of Turkey (TUBITAK), where I worked on the design and development of novel efficient data mining and pattern recognition algorithms to be applied on massive spatio-temporal datasets.

Between March 2007 and April 2010, I worked as a software engineer at MilSOFT Software Technologies Inc.. At MilSOFT, I worked for the Turkish Unmanned Air Vehicle (UAV) project where I developed image processing tools to work on the data retrieved from various types of cameras located on the UAV. I also developed a compiler/parser for NATO Message Handling System for Search and Rescue ship communication tasks.