PhD in Computing Science, Simon Fraser University, 2013
- Computational Genomics/Transcriptomics
- Data Structures
- Bioinformatics Algorithms
- HTS Sequence Mapping and Compression
Recently taught courses
Selected recent publications
- Hach F, Sarrafi I, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp, "mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications", Nucl. Acids Res. (1 July 2014) 42 (W1): W494-W500.
- Hach F, Numanagic I, Alkan C, Sahinalp SC, "SCALCE: boosting Sequence Compression Algorithms using Locally Consistent Encoding", Bioinformatics (2012) 28 (23): 3051-3057.
Also Presented at RECOMB-Seq’12 (2nd Annual RECOMB Satellite Workshop on Massively Parallel Sequencing), Barcelona, Spain, April 19-20 2012
- Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC, "Dissect: detection and characterization of novel structural alterations in transcribed sequences", Bioinformatics. 2012 Jun 15;28(12):i179-87
Also presented at ISMB’12 (20th Annual International Conference on Intelligent Systems for Molecular Biology), Long Beach, USA, July 19-23 2012
Won Ian Lawson Van Toch Memorial Award for Outstanding Student Paper
McPherson A, Wu C, Hajirasouliha I, Hormozdiari Fe, Hach F, Lapuk AV, Volik S, Shah SP, Collins CC, Sahinalp SC, "Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data", Bioinformatics (2011) 27 (11): 1481-1488Also presented at ISMB-HitSeq’11 (High Throughput Sequencing Analysis and Algorithms, Special Interest Group of ISMB’11), Vienna, Austria, July 15-16 2011
Won Best Paper Award
- Hach F, Hormozdiari Fe, Alkan C, Hormozdiar Fa, Birol I, Eichler EE, Sahinalp SC, "mrsFAST: a cache-oblivious algorithm for short-read mapping", Nature Methods, 2010 Aug;7(8):576-7