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• Arda S¨ oylev: Ph.D. student, Computer Engineering, Fall 2014 - present. Bilkent University, Ankara, Turkey. • Marzieh Eslami Rasekh: Ph.D. student, Computer Engineering, Fall 2015 - present. Bilkent Univer- sity, Ankara, Turkey. Current Graduate Students (M.Sc.) • Azita Nouri: M.Sc. student, Computer Engineering, Spring 2014 - present. Bilkent University, Ankara, Turkey. Co-supervised with ¨ Ozcan ¨ Ozt¨
urk. • G¨
ulfem Demir: M.Sc. student, Computer Engineering, Fall 2014 - present. Bilkent University, Ankara, Turkey.
• Can Fırtına: M.Sc. student, Computer Engineering, Fall 2015 - present. Bilkent University, Ankara, Turkey.
• Dilek Gen¸ c: M.Sc. student, Computer Engineering, Fall 2015 - present. Bilkent University, Ankara, Turkey. • F. Tu˘
gba Do˘ gan: M.Sc. student, Computer Engineering, Fall 2015 - present. Bilkent University, Ankara, Turkey. Graduate Students (Alumni) • Mustafa Korkmaz: M.Sc., Computer Engineering, graduated in Fall 2012. Bilkent University, Ankara, Turkey. Co-supervised with Cevdet Aykanat. Thesis Title: “Massively parallel mapping of next generation sequence reads using GPU” now: Ph.D. student at University of Waterloo. • Fatma Kahveci (n´ ee Balcı): M.Sc., Computer Engineering, graduated in Spring 2014. Bilkent Uni- versity, Ankara, Turkey. Thesis Title: “Bias correction in finding copy number variation using read depth based methods in exome sequencing data” now: Ph.D. student at Bilkent University • Elif Dal: M.Sc., Computer Engineering, graduated in Fall 2014. Bilkent University, Ankara, Turkey. Thesis Title: “Genome scaffolding using pooled clone sequencing” now: software engineer at T ¨ UB ˙ITAK Software Technologies Research Institute • Marzieh Eslami Rasekh: M.Sc., Computer Engineering, graduated in Spring 2015. Bilkent University, Ankara, Turkey. Thesis Title: “Algorithms for the discovery of large genomic inversions using pooled clone sequencing” now: Ph.D. student at Bilkent University Thesis Committees (Current) • Arif Yılmaz: Ph.D. candidate, Bioinformatics, since December 2012. Advisor: Ye¸sim Aydın Son. Middle East Technical University, Ankara, Turkey. • Evrim Tekeli: Ph.D. candidate, Anthropology, since Fall 2013. Advisor: Timur G¨ ultekin. Ankara University, Ankara, Turkey. • Fahrettin Can Koyuncu: Ph.D. candidate, Computer Engineering, since Spring 2014. Advisor:
C ¸ i˘
gdem G¨ und¨
uz Demir. Bilkent University, Ankara, Turkey. • Abdullah Atmaca: Ph.D. candidate, Computer Engineering, since Spring 2015. Advisors: Yavuz Oru¸c and Cevdet Aykanat. Bilkent University, Ankara, Turkey. Thesis Committees (Alumni) • Fahrettin Can Koyuncu: M.Sc. Computer Engineering, completed in Fall 2012. Advisor: C ¸ i˘
gdem G¨ und¨ uz Demir. Bilkent University, Ankara, Turkey. now: Ph.D. student at Bilkent University, Ankara, Turkey.
• Merve C ¸ akır: M.Sc. Computer Engineering, completed in Spring 2013. Advisor: U˘ gur Do˘ grus¨
oz. Bilkent University, Ankara, Turkey. now: Ph.D. student at Duke University, Durham, NC, USA. • Mehmet Ba¸ saran: M.Sc. Computer Engineering, completed in Fall 2014. Advisor: Cevdet Aykanat. Bilkent University, Ankara, Turkey. • G¨
ul¸ sah Merve Dal: Ph.D. candidate, Molecular Biology and Genetics, completed in Fall 2014. Advisor: Tayfun ¨ Oz¸
celik. Bilkent University, Ankara, Turkey. now: Postdoctoral fellow at National Nanotechnol- ogy Research Center, Ankara, Turkey. • Yogesh Paudel: Ph.D. candidate, Biostatistics and Informatics, completed in January 2015. Advi- sor: Martien A.M. Groenen. Institut f¨ ur Biostatistik und Informatik in Medizin und Alternsforschung, Wageningen University, Wageningen, The Netherlands. • ¨ Ozlem Tufanlı: Ph.D. candidate, Molecular Biology and Genetics, since Fall 2013. Left the committee in Spring 2015. Advisor: Ebru Erbay. Bilkent University, Ankara, Turkey. Undergraduate Volunteers (Current) • Abdullah Alperen: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. Since Spring 2015. • Halil ˙Ibrahim ¨ Ozercan: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. Since Fall 2015. Undergraduate Volunteers (Alumni) • Serhat Kıyak: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. 2013-2014. now: Ph.D. student at Carnegie Mellon University. • Yi˘
git K¨ u¸ c¨ uk: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. 2012-2014. now: Ph.D. student at Case Western Reserve University. • Can Ko¸ ckan: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. 2012-2014. now: M.Sc. student at Simon Fraser University. • G¨
ulfem Demir: B.Sc. student in Computer Engineering, Middle East Technical University, Ankara, Turkey. 2013-2014. now: M.Sc. student at Bilkent University. • Atalay Mert ˙Ileri: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. 2014. now: Ph.D. student at MIT. • Can Fırtına: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. Spring 2015. now: M.Sc. student at Bilkent University. • Damla S ¸enol: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. Spring 2015. now: Ph.D. student at Carnegie Mellon University. • Ayhun Tekat: B.Sc. student in Computer Engineering, Bilkent University, Ankara, Turkey. Summer 2015. now: M.Sc. student at Technische Universit¨ at M¨
unchen. Others
• Kerry Hall: Intern at UW in 2006. • Fereydoun Hormozdiari: Intern between February to July 2008 at UW. now: Postdoctoral Fellow at University of Washington. • Iman Hajirasouliha: Intern UW between February to July 2009 at UW. now: Postdoctoral Fellow at Brown University. • Jacob O. Kitzman: Rotation student at the Eichler Lab between January to April 2009. now: Assistant Professor at University of Michigan. • Peter H. Sudmant: Ph.D. student at the Eichler Lab between May 2009 to December 2011. now: Postdoctoral Fellow at University of Washington. • Pietro D’Addabbo: Visiting scientist at the Eichler Lab between August to November 2009. now: Staff scientist at University of Bari. • Michael Duyzend: Rotation student at the Eichler Lab between June to August 2010. now: Ph.D. student at University of Washington. • Farhad Hormozdiari: Research Scientist at the Eichler Lab between February to September 2010. now: Ph.D. student at University of California, Los Angeles. • S`
onia Casillas: Visiting scientist at the Eichler Lab between February to July 2011. • Vineet Bhakhar: Intern between May to July 2014 at Bilkent. • Farnush Farhadi: Intern between July to September 2014 at Bilkent. Conference and Invited Talks • Workshop Talk, RNA-RNA interactions and miRNA target prediction. MITACS-PIMS Pacific Northwest Bioinformatics Day, Simon Fraser University, Burnaby, BC, Canada, May 20, 2004. • Conference Talk, RNA-RNA interaction prediction and antisense RNA target search. Ninth Annual Conference on Research in Computational Molecular Biology (RECOMB 2005), Cambridge, MA, USA, May 14, 2005. • Invited Speaker, Towards a model for the evolution of alpha-satellite DNA. BC Genome Sciences Centre, Vancouver, BC, Canada April 12, 2006. • Invited Speaker, Organization and evolution of primate centromeric DNA from whole genome shotgun sequence data. Bilkent University Center for Bioinformatics, Ankara, Turkey, July 20, 2007. • Workshop Talk, Personalized copy-number and segmental duplication maps using next-gen sequencing technology. Special Interest Group on Algorithms for Short Read Assembly, Alignment & Variation Analysis at the 16 th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, ON, Canada, July 19, 2008. • Conference Talk, Organization and evolution of primate centromeric DNA from whole genome shotgun sequence data. 16 th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2008), Highlights Track, Toronto, ON, Canada, July 22, 2008. • Invited Speaker, Characterization of structural variation and segmental duplications using next-gen sequencing technology. The Mediterranean Medical Genetics Meeting 2009, Ankara, Turkey, June 30, 2009. • Keynote Speaker, Structural variation discovery and characterization of segmental Duplica- tions with next-gen sequencing technologies. Spanish and Portuguese Bioinformatics Conference (Jornadas de Bioinform´ atica), Lisbon, Portugal, November 6, 2009. • Invited Speaker, Structural variation discovery and characterization of segmental duplications with next-gen sequencing technologies. Universit` a degli Studi di Bari, Bari, Italy, November 9, 2009.
• Invited Speaker, Structural variation discovery and characterization of segmental duplications with next-gen sequencing technologies. Universit` a di Bologna, Bologna, Italy, November 11, 2009. • Invited Speaker, Structural variation discovery and characterization of segmental duplications with next-gen sequencing technologies. Universitat Pompeu Fabra, Barcelona, Spain, November 16, 2009. • Invited Speaker, Structural variation discovery and characterization of segmental duplica- tions with next-gen sequencing technologies. Simon Fraser University, Vancouver, BC, Canada, November 19, 2009. • Tutorial Presenter, Session tutorial: Personal Genomics. Pacific Symposium for Biocomputing (PSB 2010), January 4, 2010, The Big Island of Hawaii, USA. • Invited Speaker, Characterization of novel sequence insertions through both clone-based and clone-free sequencing. Illumina Sequencing Expert Panel Meeting, Toronto, ON, Canada, July 22, 2010.
• Invited Speaker, Discovery and characterization of copy-number variants with next-gen se- quencing technologies. T ¨ UB´ITAK Marmara Research Center, Gebze, Turkey, August 6, 2010. • Tutorial Presenter, Session tutorial: Personal Genomics. Pacific Symposium for Biocomputing (PSB 2011), The Big Island of Hawaii, USA, January 3, 2011. • Invited Speaker, Next-generation sequence characterization of complex genome structural variation. Keystone Symposium on Functional Consequences of Structural Variation in the Genome, Steamboat Springs, CO, USA, January 10, 2011. • Invited Speaker, Next-generation sequence characterization of complex genome structural variation. Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, February 22, 2011. • Invited Speaker, Dark side of genomes: what is missing in current sequence assemblies? Genome 10K Project Genome Assembly Workshop, Santa Cruz, CA, USA, March 16, 2011. • Invited Speaker, Next-generation sequence characterization of complex genome structural variation. Department of Genetics, Yale University, New Haven, CT, USA, May 11, 2011. • Invited Speaker, Alu repeat discovery and characterization within human genomes. FASEB Meeting on Mobile DNA in Mammalian Genomes, Snowmass Village, CO, USA, August 12, 2011. • Invited Speaker, Initial analysis results of the Turkish Genome Project. Bo˘ gazi¸ ci University, ˙Istanbul, Turkey, January 20-21, 2012. • Invited Speaker, Next-generation sequence characterization of complex genome structural variation. Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey, March 14, 2012. • Invited Speaker, Next-generation sequence characterization of complex genome structural variation. School of Medicine, Ko¸ c University, ˙Istanbul, Turkey, May 21, 2012. • Invited Speaker, Characterization of mobile element insertions using high throughput se- quencing. 63rd Fujihara Seminar: A new horizon of retroposon research, Kyoto, Japan, August 2, 2012.
• Invited Speaker, Next-generation sequence characterization of complex genome structural variation. Swiss Institute of Allergy and Asthma Research (SIAF), Davos, Switzerland, September 3, 2012. • Invited Speaker, Genetik Hastalıkların Ke¸ sfinde Y¨ uksek ¨
Ol¸ cekli Dizileme ve Biyoinformatik. (in Turkish), 10 th National Medical Genetics Congress, Bursa, Turkey, December 20, 2012. • Invited Speaker, Yeni nesil dizileme ile karma¸ sık genom yapısal farklılıkların karakterizasyonu. (in Turkish), MBG Weekend Seminars VIII, Bo˘ gazi¸
ci University, March 23, 2013. • Invited Speaker, Next-generation sequence characterization of complex genome structural variation. Sabancı University, Tuzla, ˙Istanbul, Turkey. April 17, 2013. • Instructor, EMBO Practical Course: Computational biology: From genomes to cells and systems. Cappadocia, Nev¸sehir, Turkey. September 29 - October 4, 2013. • Invited Speaker, Next-generation sequence characterization of complex genome structural variation. ˙Izmir Biomedicine and Genome Center, Dokuz Eyl¨ ul University, ˙Izmir, Turkey, October 8, 2014. • Invited Lecturer, Characterization of mobile element insertions using NGS. ALLBIO Course on Next Generation Sequencing (NGS) methods for identification of mutations and large structural variants, Lausanne, Switzerland, March 11-12, 2014. • Conference Talk, Characterization of large inversions using pooled clone sequencing. European Molecular Biology Organization, Young Investigator Meeting, Heidelberg, Germany, May 14-16, 2014. • Invited Speaker, Characterization of genome structural variation and large inversions using NGS. IU Bioinformatics Clinic, July 17, 2014. • Invited Speaker, Genetik Hastalıkların Karakterizasyonunda Y¨ uksek ¨
Ol¸ cekli Dizileme ve Biy- oenformatik. (in Turkish), ˙Izmir Biomedicine and Genome Center, Dokuz Eyl¨ ul University, ˙Izmir, Turkey, October 8, 2014. • Invited Speaker, High Throughput Sequencing and Bioinformatics for characterization of diseases of genomic origin., 24 th Conference of the Asian Pacific Associaton for the Study of the Liver (APASL 2015), ˙Istanbul, Turkey, March 11, 2015. • Invited Speaker, Discovery of large genomic inversions using pooled clone sequencing., ˙Izmir Biomedicine and Genome Center, Dokuz Eyl¨ ul University, ˙Izmir, Turkey, April 20, 2015. • Conference Talk, Coinami: A cryptocurrency with DNA Sequence Alignment as Proof-of- work. High Throughput Sequencing Algorithms and Applications (HiTSeq 2015), Dublin, Ireland, July 10, 2015. • Invited Speaker, Discovery of large genomic inversions using pooled clone sequencing., Georgia Institute of Technology, Atlanta, GA, USA, August 26, 2015. • Workshop Short Talk, Characterization of structural variation and segmental duplications for the GiaB Project., Genome in a Bottle Workshop, National Institute of Standards and Technology, Gaithersburg, MD, USA, August 27, 2015. Honors and Awards • T ¨
UB˙ITAK Incentive Award, 2015. • Thomson Reuters Highly Cited Researcher, 2014. • Young Investigator Award (BAGEP), Science Academy of Turkey, 2013. • AAAS Newcomb Cleveland Prize for the Most Outstanding Paper Published in Science, American As- sociation for the Advancement of Science, USA, 2010. • Case Prime Fellowship, Case Western Reserve University, Cleveland, Ohio, USA, 2000. • Full Scholarship Awarded by Bilkent University, 1996-2000. Service Activities University Duties • Academic Coordinator for Erasmus+ and International Exchange Programs, Department of Computer Engineering, Bilkent University, since Summer 2014. Editorial • Associate Editor, BMC Bioinformatics, 2010-present • PC and OC Member, 7 th Conference on High Throughput Sequencing Analysis and Algorithms (HiTSeq 2016), July 6-7, 2016, Orlando, FL, USA. • PC Member, the 20 th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2016), April 17-21, 2015, Santa Monica, CA, USA. • PC Member, 6 th Conference on High Throughput Sequencing Analysis and Algorithms (HiTSeq 2015), July 10-11, 2015, Dublin, Ireland. • Chair, Bertinoro Computational Biology Meeting, June 14-17, 2015, Bertinoro, Italy. • PC Member, 23 rd Annual International Conference on Intelligent Systems for Molecular Biology and 14 th European Conference on Computational Biology (ISMB/ECCB 2013), July 10-14, 2015, Dublin, Ireland. • PC Member, 22 nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2014), July 13-15, 2014, Boston, MA, USA. • PC and OC Member, 8 th International Symposium on Health Informatics and Bioinformatics, (HIBIT), September 25-27, 2013, Ankara, Turkey. • PC Member, 21 st Annual International Conference on Intelligent Systems for Molecular Biology and 12 th European Conference on Computational Biology (ISMB/ECCB 2013), July 19-23, 2013, Berlin, Germany. • PC Member, Third Annual RECOMB Workshop on Massively Parallel Sequencing (RECOMB-seq), April 11-12, 2013, Beijing, China. • PC Member, 20 th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2012), July 15-17, 2012, Long Beach, CA, USA. • PC Member, Second Annual RECOMB Workshop on Massively Parallel Sequencing (RECOMB-seq), April 19-20, 2012, Barcelona, Spain. • PC Member, 19 th Annual International Conference on Intelligent Systems for Molecular Biology and 10 th European Conference on Computational Biology (ISMB/ECCB 2011), July 15-19, 2011, Vienna, Austria. • Chair, First Annual RECOMB Workshop on Massively Parallel Sequencing (RECOMB-seq), March 26-27, 2011, Vancouver, BC, Canada. • PC Member, the 15 th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011), March 28-31, 2011, Vancouver, BC, Canada. • Session Co-Chair, Session on Personal Genomics at the Pacific Symposium for Biocomputing (PSB 2011), January 3-7, 2011, The Big Island of Hawaii, USA. • PC Member, 18 th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), July 9-14, 2010, Boston, MA, USA. • Session Co-Chair, Session on Personal Genomics at the Pacific Symposium for Biocomputing (PSB 2010), January 4-8, 2010, The Big Island of Hawaii, USA. • PC Member, The IEEE 22nd International Conference on Advanced Information Networking and Ap- plications 2008 (AINA-08). • PC Member, The IEEE 21st International Conference on Advanced Information Networking and Appli- cations 2007 (AINA-07). Consortium Memberships • 1000 Genomes Project Structural Variation Analysis Group, 2008-present • Bonobo Genome Consortium, 2008-2012. • Orangutan Genome Consortium, 2008-2011. • Neandertal Genome Consortium, 2009-2012. • Gorilla Genome Consortium, 2009-2013. • Denisovan Genome Consortium, 2010-2012. • Great Ape Diversity Project, 2011-2014. • Genome in a Bottle Consortium, 2015-present Ad-hoc Reviewer • Nature Genetics, Nucleic Acids Research, Nature Reviews Genetics, Genome Research, PLoS Genet- ics, PLoS Computational Biology, Nature Biotechnology, BMC Genomics, Genome Biology, Methods, Transactions of Computational Biology and Bioinformatics, Bioinformatics, Briefings in Bioinformatics, RECOMB, RECOMB-seq, SODA, FOCS, ICDE, CPM, AINA, PSB, ISMB, HiTSeq. Other
• Member of the Scientific Advisory Board for the Center for Advanced Genomics and Bioinformatics (˙IGBAM) in T ¨ UB˙ITAK Marmara Research Center, Gebze, Turkey. October 2012 - present. • Observer to ELIXIR for Turkey. April 2013 - present. • Individual Member, Global Alliance for Genomic Health. November 2014 - present. Professional Memberships • Member of the International Society for Computational Biology since 2002. Yüklə 170,05 Kb. Dostları ilə paylaş:
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