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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. |
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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 |
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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 |
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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. ·
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. |