Publications :
Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco Marra, Martin Hirst, Torsten Nielsen, S.Cenk Sahinalp, David Huntsman, Sohrab P. Shah
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
PLoS Computational Biology (
Mario Ventura, Claudia Catacchio, Can Alkan, Tomas Bonet-Marques, Saba Sajadian, Tina Graves, Fereydoun Hormozdiari, Arcadi Navarro, Maika Malig, Carl Baker, Choo Lee, Emily Turner, Lin Chen, Jeffrey Kidd, Nicoletta Archidiacono, Jay Shendure, Richard Wilson, Evan Eichler
Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee
Genome Research (
Andrew McPherson*, Chunxiao Wu*, Iman Hajirasouliha, * Fereydoun Hormozdiari * ,Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, S.Cenk Sahinalp .
Comrad: a novel algorithm framework for the integrated analysis of RNA-Seq and WGSS data
HiTSeq 2011: Conference on High Throughput Sequencing Analysis and Algorithms .
Also: Bioinformatics 2011 27(11):1481-8
(* joint first author)
Fereydoun Hormozdiari*, Iman Hajirasouliha*, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp
Simultaneous structural variation discovery in multiple paired-end sequenced genomes
Recomb 2011 (
(* joint first author)
Fereydoun Hormozdiari*, Can Alkan*, Mario Ventura*, Iman Hajirasouliha, Maika Malig, Faraz Hach, Deniz Yorukoglu, Phuong Dao, Marzieh Bakhshi, S. Cenk Sahinalp, Evan E. Eichler
Genome Research (
(* joint first author)
Mills, R. E.*, K. Walter*, D. A. Stewart*, R. Handsaker*, K. Chen*, C. Alkan*, A. Abyzov*, S. C. Yoon*, K. Ye*, R. K. Cheetham, A. Chinwalla, D. F. Conrad, Y. Fu, F. Grubert., I. Hajirasouliha, F. Hormozdiari, Z. Iqbal, J. M. Kidd, M. K. Konkel, J. Korn, E. Khurana, D. Kura, H. J. K. Lam, J. Leng, R. Li, Y. Li, C.-Y. Lin, R. Luo, X. J. Mu, J. Nemesh, H. E. Peckham, T. Rausch, A. Scally, X. Shi, M. P. Stromberg, A. M. Stutz, A. E. Urban, J. A. Walker, J. Wu, Y. Zhang, Z. Zhang, M. A. Batzer, L. Ding, G. T. Marth, G. McVean, J. Sebat, M. Snyder, J. Wang, K. Ye, K. Ye, E. E. Eichler, M. B. Gerstein, M. E. Hurles, C. Lee, S. A. McCarroll and J. O. Korbel on behalf of the 1000 Genomes Project.
Mapping copy number variation at fine-scale by population-scale genome sequencing
Nature (
The 1000 Genome Project Consortium
A map of human genome variation from population-scale sequencing
Nature 2010 467:1061-1073
Fereydoun Hormozdiari , Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yorukoglu, Can Alkan, Evan E. Eichler and S.Cenk Sahinalp.
Next Generation VariationHunter: Combinatorial Algorithms for Transposon Insertion Discovery
18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010).
Also: Bioinformatics 2010 26(12):i350-i357; doi:10.1093/bioinformatics/btq216
Iman Hajirasouliha * Fereydoun Hormozdiari * ,Can Alkan *,Jeffrey M. Kidd ,Inanc Birol, Evan E. Eichler and S.Cenk Sahinalp.
Detection and characterization of sequence insertions using paired-end next-generation sequencing
HiTSeq 2010: Conference on High Throughput Sequencing Analysis and Algorithms .
Also: Bioinformatics 2010 26(10):1277-1283; doi:10.1093/bioinformatics/btq152
(* joint first author)
Fereydoun Hormozdiari*, Raheleh Salari*, Vineet Bafna, and S. Cenk Sahinalp.
Protein protein interaction network evaluation for identifying potential drug targets
Journal of Computational Biology 2010.
(* joint first author)
Faraz Hach ,Fereydoun Hormozdiari, Can Alkan, Farhad Hormozdiari, Inanc Birol, Evan E. Eichler, and S.Cenk Sahinalp
mrsFAST : a cache-oblivious algorithm for short-read mapping
Nature Methods 2010.
Can Alkan, Jeffrey M. Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O. Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs and Evan E. Eichler.
Personalized copy number and segmental duplication maps using next-generation sequencing.
Nature Genetics 2009.
Alexander Schonhuth, Raheleh Salari, Fereydoun Hormozdiari, Artem cherkasov, S. Cenk Sahinalp.
Towards improved assessment of functional similarity in large-scale screens:an indel study"
Journal of Computational Biology 2009.
Seunghak Lee,Fereydoun Hormozdiari, Can Alkan, Michael Brudno.
MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions.
Nature Methods 2009.
Phuong Dao, Alexander Schonhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, S.Cenk Sahinalp and Martin Ester.
Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Network.
9th Workshop on Algorithms on Bioinformatics (WABI 2009).
Fereydoun Hormozdiari*, Can Alkan*, Evan E. Eichler and S.Cenk Sahinalp.Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes.
13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009).
Also: Genome Research 2009.
(* joint first author)
Recep Colak*, Fereydoun Hormozdiari*, Flavia Moser*, Alexander Schonhuth, Jeremy Holman, Martin Ester and S.Cenk Sahinalp.
Dense graphlet statistics of protein interaction networks and random networks.
14th Pacific Symposium on Biocomputing (PSB 2009).
(* joint first author)
Fereydoun Hormozdiari*, Raheleh Salari*, Michael Hsing*, Alexander Schonuth and S.Cenk Sahinalp.
The effect of insertion and deletions (indels) on wirings in protein interaction networks: a large scale study.
proceedings:RECOMB satellite conference on Systems Biology (2008).
Also: Journal of computational Biology 2009
(* joint first author)
Raheleh Salari, Alexander Schonhuth,
Fereydoun Hormozdiari, Artem Cherkasov and S.Cenk
Sahinalp. The relation between indel length and functional divergence: a formal study
8th Workshop on Algorithms in Bioinformatics (WABI 2008). abstract
Iman Hajirasouliha*, Fereydoun Hormozdiari *, S.Cenk Sahinalp and Inanc Biroil.
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies
16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008)
Also: Bioinformatics 2008 24: i32-i40; doi:10.1093/bioinformatics/btn173 abstract
(* joint first author)
Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari and S.Cenk Sahinalp.
Biomolecular Network Motif Counting and Discovery by Color Coding.
16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008).
Also: Bioinformatics 2008 24: i32-i40; doi:10.1093/bioinformatics/btn173 abstract
Simon K. Chan, Michael Hsing, Fereydoun Hormozdiari and Artem Cherkasov.
Relationship between insertion/deletion (indel) frequency of proteins and essentiality.
BMC Bioinformatics 2007.abstract
Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj and S.Cenk Sahinalp.
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution.
journal: PLoS Computational Biology 2007 abstract
proceedings: RECOMB satellite conference on Systems Biology 2006 abstract
Recent Presentations:
