Peer-Reviewed Conference Publications
Note: In CS disciplines papers in highly ranked conferences are fully refereed and are regarded as highly
as the top journal papers. In computational molecular biology RECOMB is generally accepted as the top
conference, with 10-15% acceptance rate. Joint first authors are marked with * in case of equal contribution.
Joint last authors are marked with ‡.
Can you really anonymize the donors of genomic data in today’s digital world?
M. Alser,
N. Almadhoun, A. Nouri, C. Alkan
‡
, and E. Ayday
‡
.
10
th
International Workshop on Data Privacy
Management (DPM 2015), September 21-22, 2015, Vienna, Austria.
Accelerating read mapping with FastHASH. H. Xin, D. Lee, F. Hormozdiari, S. Yedkar, O. Mutlu
‡
,
C. Alkan
‡
. Proc. of the 11
th
Asia Pacific Bioinformatics Conference, Jan. 21-23, 2013, Vancouver, BC,
Canada
Detection of characterization of novel sequence insertions using paired-end next-generation
sequencing, I. Hajirasouliha*, F. Hormozdiari*, C. Alkan*, J.M. Kidd, I. Birol, E.E. Eichler, S.C. Sahi-
nalp. Proc. of the 11
th
Conference on High Throughput Sequencing Analysis and Algorithms, Special Interest
Group of ISMB 2010 (HiTSeq 2010): July 9-10 2010, Boston, MA, USA
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discov-
ery.
F. Hormozdiari, I. Hajirasouliha, P. Dao, F. Hach, D. Yorukoglu, C. Alkan, E.E. Eichler, S.C.
Sahinalp. Proc. of the 18
th
Annual International Conference on Intelligent Systems for Molecular Biology
(ISMB 2010), July 11-13, 2010, Boston, MA, USA
Combinatorial algorithms for structural variation detection in high throughput sequenced
genomes. F. Hormozdiari*, C. Alkan*, E.E. Eichler, S.C. S
¸ahinalp. Proc. of the Thirteenth Annual
International Conference on Research in Computational Molecular Biology (RECOMB 2009), May 18-21,
2009 Tucson, AZ, USA
RNA secondary structure prediction via energy density minimization. C. Alkan*, E. Karako¸
c*,
S.C. S
¸ahinalp, P. Unrau, H. A. Ebhardt, K. Zhang, J. Buhler. Proc. of the Tenth Annual International
Conference on Research in Computational Molecular Biology (RECOMB 2006 - LNBI 3909), pp. 130-142,
April 2-5, 2006 Venice, Italy, 2006.
RNA-RNA interaction prediction and antisense RNA target search. C. Alkan, E. Karako¸
c, J.
Nadeau, S.C. S
¸ahinalp, K. Zhang. Proc. of the Ninth Annual International Conference on Research in
Computational Molecular Biology (RECOMB 2005 - LNBI 3500), pp 152-171, May 14-18, 2005 Cambridge,
MA, USA, 2005.
An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution.
C. Alkan, J.A. Bailey, E.E. Eichler, S.C. S
¸ahinalp, E. T¨
uz¨
un.
The 13th International Conference on
Genome Informatics, December 16-18, 2002, Tokyo, Japan, vol.18 pp 93-102, 2002.
Unpublished Conference Talks and Posters
Massively Parallel Mapping of Next Generation Sequence Reads Using GPUs.. A. Nouri, R.O.
Selvitopi, O. Ozturk, O. Mutlu
‡
, C. Alkan
‡
. The 20
th
International Conference on Architectural Support
for Programming Languages and Operating Systems (ASPLOS 2015), March 14-18, 2015, ˙Istanbul, Turkey.
Short talk and poster presented by Azita Nouri.
BioPeer: A Fast and Secure Peer-to-Peer Data Sharing Tool.. C. Oge, F.T. Dogan, G. Goktepe,
F. Koc, C. Sevim, C. Alkan. The 6
th
Conference on High Throughput Sequencing Analysis and Algorithms
(HiTSeq 2015), July 10-11, 2015, Dublin, Ireland. Poster presented by Cihad ¨
Oge.
Coinami: A Cryptocurrency with DNA Sequence Alignment as Proof-of-work., A.M. Ileri, H.I.
Ozercan, A. Gundogdu, A.K. Senol, M.Y. Ozkaya, C. Alkan. The 6
th
Conference on High Throughput
Sequencing Analysis and Algorithms (HiTSeq 2015), July 10-11, 2015, Dublin, Ireland. Oral and poster
presentation by H. ˙Ibrahim ¨
Ozercan.
Discovery of large genomic inversions using pooled clone sequencing. M.E. Rasekh, G. Chiatante,
M. Miroballo, J. Tang, M. Ventura, C.T. Amemiya, E.E. Eichler, F. Antonacci
‡
, C. Alkan
‡
. The 6
th
Conference on High Throughput Sequencing Analysis and Algorithms (HiTSeq 2015), July 10-11, 2015,
Dublin, Ireland. Poster presentation by Marzieh Eslami Rasekh.
A new inference attack against kin genomic privacy. F. Balci, H. Kulan, C. Alkan
‡
, and E. Ayday
‡
.
Privacy-aware computational genomics (PRIVAGEN 2015), September 8, 2015, Tokyo, Japan. Oral and
poster presentation by Fatma Balcı.
Identifying anonymous donors of genetic information. M. Alser, N. Almadhoun, A. Nouri, C. Alkan
‡
,
and E. Ayday
‡
. Privacy-aware computational genomics (PRIVAGEN 2015), September 8, 2015, Tokyo,
Japan. Poster presentation by Mohammed Alser.
Teaching
• CS 476 Automata Theory and Formal Languages, Spring 2014, Fall 2014, Spring 2015, Fall 2015, Spring
2016.
• CS 481 Bioinformatics Algorithms, Fall 2012, Fall 2013.
• CS 319 Object Oriented Software Engineering, Summer 2012, Spring 2013, Fall 2013, Fall 2014, Fall
2015.
• CS 681 Advanced Topics in Computational Biology, Spring 2012, Spring 2013.
• CS 202 Fundamental Structures of Computer Science II, Spring 2013.
• CS 590/690 Research Topics (coordinator), Spring 2012, Spring 2014.
Senior Project
Supervision
• BioPeer: Secure research data sharing platform, 2014-2015.
• Coinami: Cryptocurrency mining system for scientific computation, 2014-2015.
• Anotice: Anonymized social network platform, 2014-2015.
• Touravel: Travel logging application, 2014-2015.
• SUN (Social University Network): Study group game application, 2014-2015.
• SmartVote: Electronic Voting System for Mobile Devices, 2013-2014.
Recipient of the Best Senior Project Award in 2014.
• Daycept: Concept-based idea sharing platform, 2013-2014.
• Betcha: Social platform that enables betting among friends, 2013-2014.
Recipient of the Usability Award in 2014.
• SocioDiary: Digital diary system, 2013-2014.
• CMPS101: Activity planning for university students, 2013-2014.
• chkDNA: Genomic variant analysis tool, 2012-2013.
Software
• Multiple alignment Manipulator (MaM).
http://mam-bio.sourceforge.net
• taveRNA: RNA suite for RNA folding, RNA-RNA interaction prediction and search.
http://compbio.cs.sfu.ca/taverna
• micro-read Fast Alignment Search Tools (mrFAST, mrsFAST, drFAST, and sirFAST).
http://mrfast.sourceforge.net, http://mrsfast.sourceforge.net, http://drfast.sourceforge.net,
http://sirfast.sourceforge.net
• mrCaNaVaR: characterization of segmental duplications and absolute copy number prediction from read
depth.
http://mrcanavar.sourceforge.net
• VariationHunter: Structural variation calling algorithm for paired-end, next generation sequencing data.
http://variationhunter.sourceforge.net
• NovelSeq: computational pipeline fo detect novel sequence insertions using second generation sequencing.
http://novelseq.sourceforge.net
• RepeatNet: algorithm to characterize centromeric satellite sequences from paired end sequence data.
http://eichlerlab.gs.washington.edu/software/repeatnet
• SCALCE: Tool to compress FASTQ files.
http://scalce.sourceforge.net
Supervised Students
and Interns
Current Graduate Students (Ph.D.)
• Pınar Kavak: Ph.D. student, Computer Engineering, Fall 2010 - present. Bo˘
gazi¸
ci University, ˙Istanbul,
Turkey. Co-supervised with Tunga G¨
ung¨
or.
• Shatlyk Asyralyyev: Ph.D. student, Computer Engineering, Fall 2013 - present. Bilkent University,
Ankara, Turkey. Co-supervised with Cevdet Aykanat.
• Volkan Yazar: Ph.D. student, Molecular Biology and Genetics, Fall 2013 - present. Bilkent University,
Ankara, Turkey. Co-supervised with ˙Ihsan G¨
ursel.
• Fatma Kahveci: Ph.D. student, Computer Engineering, Fall 2014 - present. Bilkent University, Ankara,
Turkey.
• Mohammed Alser: Ph.D. student, Computer Engineering, Fall 2014 - present. Bilkent University,
Ankara, Turkey. Co-supervised with ¨
Ozcan ¨
Ozt¨
urk.
• Handan Kulan: Ph.D. student, Computer Engineering, Fall 2014 - present. Bilkent University, Ankara,
Turkey.