Computer Science Assistant

Olgert Denas

Resume

Personal

Current position: Ph.D. candidate in Computer Science

Dept. of Math & CS, Emory University,

*** ****** **., *******, ** 30322, USA

******@*****.*** (cell) 678-***-****

Thesis title Deep modeling of functional genome elements and their effect on gene regulation

Under the advise of James Taylor (expected graduation: December 2013)

Positions

from July 2010: RA at the Goizueta Business School, Emory University; Atlanta, GA.

Design and use social network analysis software, data management and cloud computing. Technologies

(Python, numpy/scipy, Amazon Cloud Services, MySQL).

June-August 2012: Research Assistant at the Taylor Lab, Emory University; Atlanta, GA

Collaborator of the Consortia for the Mouse ENCODE project. Design of software for functional

genome human-mouse comparative analysis. Technologies (Python, numpy/scipy, Scala/Java, R,

MySQL, HDF, C/cuda).

June-August 2011: Research Assistant at the Taylor Lab, Emory University; Atlanta, GA

Analysis of symbiotic lifestyle of A. Cephalotes at the gene level. Analysis integrated in published

work. Technologies, (Python, MySQL).

May-July 2008: Visiting Researcher, Partner Institute for Computational Biology between Max Plank G

and the Chinese Academy of Sciences; Shanghai, P. R. China

Analysis, design, and implementation of efficient distance kernels and large scale data indexes. Method

achieves proved best running time and space efficiency. (Python, C, HDF, sqlite3).

January-May 2008: Teaching Assistant for Computability and Algorithms, Georgia Institute of Technol-

ogy and Korea University; Seoul, South Korea

Participant in the joint master program between the Georgia Tech and Korea University.

September-December 2007: Research Trainee, Georgia Institute of Technology; Atlanta, GA

July-August 2006: Exchange Student, the University of Michigan; Ann-Arbor, Dearborn, MI Interna-

tional Summer Program in Management. Courses in Strategic planning and Business management.

Spring 2005: Junior engineer at the C.L.A at the University of Padua

Implementation and integration of an authentication system in a hybrid Windows/Unix environment.

(Windows server, Unix, PHP, JavaScript, Apache).

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Experience

Algorithms and data structures for pattern discovery and mining in text data. Deep Learning architectures

and Probabilistic Graphical Models in genome scale data. Completed Combinatorial Optimization at Work,

ZIB; Berlin, Germany, September 2009.

Commonly use: Python/Cython, Mathematical Programming (SCIP, Gurobi etc.), C (CUDA dialect),

MySQL/HDF, Java/Scala and Octave/Matlab.

Teaching

Co-teaching CS574: Machine Learning with Prof. J. Taylor, Fall 2012.

Teaching CS224: Mathematical Foundations of Computer Science, Fall 2010

Co-teaching CS323: Data Structures and Algorithms with Prof. J. Smith, Spring 2010.

Education

2007, Masters in Computer Science, University of Padua, Padova, Italy (summa cum laude)

2004, B.S in Information Engineering, University of Padua, Padova, Italy

Selected scientific production

A. Conti, O. Denas, and F. Visentin. Knowledge specialization in phd student groups. Transactions on

Engineering Management, 2013. (accepted)

O. Denas and J. Taylor. Deep modeling of gene expression regulation in an erythropoiesis model. In 30th

International Conference on Machine Learning (ICML), 2013.

O. Denas, R. Sandstrom, J. Herrero, Y. Cheng, R. Hardison, and J. Taylor. Genome-wide comparative

analysis reveals human-mouse regulatory landscape. Submitted to Genome Research as a companion of

Mouse ENCODE project, 2013.

Mouse ENCODE Consortium, J. A. Stamatoyannopoulos, M. Snyder, R. Hardison, B. Ren, T. Gingeras,

D. M. Gilbert, O. Denas, J. Taylor, et al. An encyclopedia of mouse dna elements (mouse encode). Genome

Biol, 13(8):418, Aug 2012.

G. Suen, C. Teiling, L. Li, C. Holt, E. Abouheif, E. Bornberg-Bauer, P. Bouffard, E. J. Caldera, E. Cash,

A. Cavanaugh, O. Denas, et al. The genome sequence of the leaf-cutter ant atta cephalotes reveals insights

into its obligate symbiotic lifestyle. PLoS Genet, 7(2):e1002007, 2011.

O. Denas and J. Taylor. Conservation of regulatory region activity between human and mouse. In 8th

International Conference on Bioinformatics. From Genomics to Synthetic Biology, 2011.

A. Apostolico, O. Denas, and A. Dress. Efficient tools for comparative substring analysis. J Biotechnol,

149(3):120–6, Sep 2010.

A. Apostolico and O. Denas. Fast algorithms for computing sequence distances by exhaustive substring

composition. Algorithms for Molecular Biology, 3:13, 2008.

Languages

Albanian (native), English (written and spoken), Italian (written and spoken)

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