Recent News

·         May 2015, Our  joint work with Cem Orhan is accepted to ICML Workshop on "Advances in Active Learning - Bridging Theory and Practice".

·         Feb 2015 Paper titled Integrated Analysis of Genetic Variation and Gene Expression Identifies Networks for Cardiovascular Disease Phenotypes” is published in Circulation.

·         Jan 2015 Paper titled “Refining Literature Curated Protein Interactions Using Expert Opinions” is presented at PSB 2015.

·         May 2014 Paper titled "Distinct regulation of tonsillar immune response in virus infections" has been published in Allergy and it is on May’s cover.

·         Our work titled “Retinal proteins as model systems for membrane protein folding has been published in Biochimica et Biophysica Acta. 

·         Received 2014 BAGEP Young Scientist Award.

·         Received 2013 L’ORÉAL Türkiye Research Award for Young Women in Life Sciences.

 

Research Interests

My research lies at the boundary of applied machine learning and computational biology. Advances in molecular profiling technologies have resulted in large quantities of data turning biology into a data rich field. A key challenge is to systematically analyze these diverse datasets to deepen our understanding of the molecular basis of diseases, and to improve diagnosis and prognosis. My research focuses on developing methodologies towards this aim. Note that although my main research focus is computational biology, other exciting applications of machine learning also piques my interest.

 

To Students:

·         There are open positions for graduate students! Please send me an email if you are interested.

 

Education

·         Post-doctoral researcher at Microsoft Research New England, Cambridge, MA. 2010 – 2012

·         Ph.D. LTI,, School of Computer Science, Carnegie Mellon University, 2011

·         Prediction of Host-Virus Protein-Protein Interactions

·         Supervisors: Prof. Jaime G. Carbonell and Prof. Judith Klein-Seetharaman

·         M.Sc. (in parallel with PhD) LTI, School of Computer Science, Carnegie Mellon University, 2007

·         B.Sc., Biological Sciences and Bioengineering, Sabanci University, 2004

 

Teaching

·         Spring 2015

·         CS464: Introduction to Machine Learning

·         CS557: Computational Systems Biology

·         Fall 2014

·         CS464: Introduction to Machine Learning

·         CS102:  Algorithms & Programming II

·         Spring 2014

·         CS464: Introduction to Machine Learning

·         CS557: Computational Systems Biology

·         Fall 2013

·         CS101:  Algorithms & Programming I

·         CS464: Introduction to Machine Learning

·         CS590 / CS690: Advanced Research Topics

·         Spring 2013

·         CS114: Introduction to Programming for Engineers

·         Fall 2012

·         CS114: Introduction to Programming for Engineers

·         CS557: Computational Systems Biology

·         CS590 / CS690: Advanced Research Topics

·         CS491: Senior Design Projects

·         CS490: Introduction to Research in Computer Engineering and Science

·         IE477: Production Systems Design-Synthesis

 

Publications

 

Journal Publications

·         Comparison of stability predictions and simulated unfolding of rhodopsin structures.

Tastan O, Yu E, Ganapathiraju M, Aref A, Rader AJ and Klein-Seetharaman J. Photochemistry and Photobiology 83, p351-62, 2007.

 

·         The effect of loops on the structural organization of alpha-helical membrane proteins.

Tastan O, Klein-Seetharaman J and Meirovitch H. Biophysical Journal 96, p2299-312, 2009.

 

·         Alternative paths in HIV-1 targeted human signal transduction pathways.

Balakrishnan S, Tastan O, Carbonell JG and Klein-Seetharaman J. BMC Genomics 10 Suppl 3, S30, 2009.

 

·         Oligomerization of HIV-1 Vpr: Identification of essential domains/residues using structure based approaches and evaluation of its relevance to Vpr functions.

Venkatachari NJ, Le T, Tastan O, Timothy MD,Walker L, Ricciuti A, Yanamala N, Srinivasan A, Klein-Seetharaman J, Ramachandran, M, Montelaro RC and Ayyavoo V. Virology Journal,7,119, 2010.

 

·         Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins.

Qi Y, Tastan O, Carbonell JG, Klein-Seetharaman J and Weston J. Bioinformatics 26(18), p645-52, 2010.

[Supp. Web]

 

·         Virus interactions with human signal transduction pathways.

Zhao Z, Xia J, Tastan O, Singh I, Kshirsagar M, Carbonell JG and Klein-Seetharaman J. International Journal of Computational Biology and Drug Design. 4(1), p83-105, 2011.

 

·         Identification of potentially relevant citeable articles using association rule mining.

Uguroglu S, Tastan O, Klein-Seetharaman J and Leuba SH. Medicinal Chemistry. Editorial. 1:e101, 2011.

 

·         Retinal proteins as model systems for membrane protein folding.

Tastan O, Dutta A, Booth P and Klein-Seetharaman J., Biochimica et Biophysica Acta, 2014; 1837(5):656-663.

 

·         Distinct regulation of tonsillar immune response in virus infections.

Jartti T, Palomares O, Waris M, Tastan O, Nieminen R, Puhakka T, Rückert B, Aab A, Vuorinen T,  Vahlberg T, Akdis M and Akdis C, Allergy. 2014; 69(5):658-67. (Cover)

 

·         Integrated Analysis of Genetic Variation and Gene Expression Identifies Networks for Cardiovascular Disease Phenotypes.

Yao C, Chen BH, Joehanes R, Otlu B, Zhang X, Liu C,  Huan T, Tastan O, Cupples A, Meigs JB, Fox CS,  Freedman JE, Courchesne P,  O’Donnell CJ, Munson PJ, Keles S, Levy D. 2015;131(6):536-49.

 

 

Peer Reviewed Conference Publications

·         Prediction of interactions between HIV-1 and human proteins by information integration.

Tastan O, Qi Y, Carbonell JG and Klein-Seetharaman J. Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii, 13, p516-27, 2009. [Supp. Web]

 

·         Comparison of virus interactions with human signal transduction pathways.

Singh I, Tastan O and Klein-Seetharaman J. ACM International Conference on Bioinformatics and Computational Biology. p17-24, 2010.

 

·         Refining literature curated protein interactions using expert opinions.

Tastan O, Qi Y, Carbonell JG and Klein-Seetharaman J. Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii, 2015.

 

Book Chapter

·         Human Immunodeficiency Virus (HIV-1) Vpr polymorphism and disease progression: Mutagenesis approach to study structure-function relationship of HIV-1 Vpr.

Hadi K, Tastan O, Srinivasan A and Ayyavoo V.  Book Chapter in Directed Mutagenesis, 2013.