Deniz Yorukoglu

Computer Science and Artificial Intelligence Laboratory
Address:
32-G572 Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology
32 Vassar Street
Cambridge, MA 02139
Email: denizy AT mit.edu

I am currently a PhD student in the Computation and Biology Group in CSAIL at MIT.

My advisor is Prof. Bonnie Berger.


Selected honors and awards

- HHMI International Student Research Fellowship, 2014-2016

- IBM Ph.D. Fellowship Award, 2014-2015

- Ian Lawson van Toch Memorial Award for Outstanding Student Paper at ISMB 2012

- PIMS IGTC Fellowship in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Canada, 2010-2011

- President's PhD Scholarship, Simon Fraser University, Canada, 2011-2014 (Declined)

- First place graduation from Sabanci University BSc Computer Science and Engineering Program.

- Excellence Merit Scholarship, Sabanci University, Istanbul, Turkey, 2005 - 2009

- Listed within the top 20 students in the National University Entrance Exam among more than 1.6 million candidates, Turkey, 2005

- National Olympiads in Informatics 1. Level Examination, 1st place in northwestern Turkey and 2. Level Examination, 3rd place in Turkey, 2004.


Selected publications

- Yorukoglu, D.*, Yu, Y.W., Peng, J., Berger, B.A.
Compressive Mapping for Next-generation Sequencing
Nature Biotechnology 34, 374-376 (2016)

- Berger, E.*, Yorukoglu, D.*, Berger, B.A. (* Co-first authors)
HapTree-X: An integrative Bayesian framework for haplotype reconstruction from transcriptome and genome sequencing data
RECOMB 2015 Proceedings, Full pre-print: http://groups.csail.mit.edu/cb/haptreex/haptreex_recomb2015.pdf

- Parida, L., Filippo, U., Yorukoglu, D., Carrieri, A.P., Kuhn, D., Basu, S.
Topological Signatures for Population Admixture
RECOMB 2015 Proceedings

- Yu, Y.W., Yorukoglu, D., Peng, J., Berger, B.A.
Quality score compression improves genotyping accuracy
Nature Biotechnology 33, 240-243 (2015)

- Berger, E.R., Yorukoglu, D. *, Peng, J., Berger, B.A.*
HapTree: A novel Bayesian framework for single individual polyplotyping using next-generation sequencing data
International Conference on Research in Computational Biology (RECOMB) 2014, Pittsburgh, Pennsylvania (Also accepted to Plos Computational Biology) (* Co-corresponding authors)

- Yu W.W., Yorukoglu, D., Berger, B.A.
Traversing the k-mer landscape of next-generation sequencing read datasets for quality score sparsification
International Conference on Research in Computational Biology (RECOMB) 2014, Pittsburgh, Pennsylvania

- Yorukoglu, D. *^, Hach, F. *^, Swanson, L., Collins, C.C., Birol, I., Sahinalp, S.C. * (2012)
Dissect: detection and characterization of novel structural alterations in transcribed sequences
Bioinformatics 25(12): i179-87 (Received Best Student Paper Award at ISMB 2012) (* Co-corresponding authors) (^ Co-first authors)

- Hormozdiari, F., Alkan, C., Ventura, M., Hajirasouliha, I., Malig, M., Hach, F., Yorukoglu, D., Dao, P., Bakhshi, M., Sahinalp, S.C., Eichler, E.E. (2011)
Alu Repeat Discovery and Characterization within Human Genomes
Genome Research 21(6):840-9

- Hormozdiari, F., Hajirasouliha, I., Dao, P., Hach, F., Yorukoglu, D., Alkan, C., Eichler E.E., Sahinalp, S.C. (2010)
Next Generation VariationHunter: Combinatorial Algorithms for Transposon Insertion Discovery
Bioinformatics 26(12): i350-i357. (Journal version of ISMB 2010 paper)

- Yorukoglu, D., Bakis, Y., Sezerman, U. (2009)
An Entropy Based Heuristic Model for Predicting Functional Sub-type Divisions of Protein Families
Proceedings of the 11th Annual Genetic and Evolutionary Computation Conference (GECCO .09), July 8-12, 2009, Montreal, Canada. Pages: 2173-2178.