Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation. - Fereydoun Hormozdiari; Petra Berenbrink; Natasa Przulj; Süleyman Cenk Sahinalp (Systems Biology and Computational Proteomics, 2006)

Relationship between insertion/deletion (indel) frequency of proteins and essentiality. - Simon K. Chan; Michael Hsing; Fereydoun Hormozdiari; Artem Cherkasov (BMC Bioinform., 2007)

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution. - Fereydoun Hormozdiari; Petra Berenbrink; Natasa Przulj; Süleyman Cenk Sahinalp (PLoS Comput. Biol., 2007)

Biomolecular network motif counting and discovery by color coding. - Noga Alon; Phuong Dao; Iman Hajirasouliha; Fereydoun Hormozdiari; Süleyman Cenk Sahinalp (ISMB, 2008)

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. - Iman Hajirasouliha; Fereydoun Hormozdiari; Süleyman Cenk Sahinalp; Inanç Birol (ISMB, 2008)

The Relation between Indel Length and Functional Divergence: A Formal Study. - Raheleh Salari; Alexander Schönhuth; Fereydoun Hormozdiari; Artem Cherkasov; Süleyman Cenk Sahinalp (WABI, 2008)

Dense Graphlet Statistics of Protein Interaction and Random Networks. - Recep Colak; Fereydoun Hormozdiari; Flavia Moser; Alexander Schönhuth; J. Holman; Martin Ester; Süleyman Cenk Sahinalp (Pacific Symposium on Biocomputing, 2009)

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. - Fereydoun Hormozdiari; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (RECOMB, 2009)

Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. - Phuong Dao; Alexander Schönhuth; Fereydoun Hormozdiari; Iman Hajirasouliha; Süleyman Cenk Sahinalp; Martin Ester (WABI, 2009)

The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study. - Fereydoun Hormozdiari; Raheleh Salari; Michael Hsing; Alexander Schönhuth; Simon K. Chan; Süleyman Cenk Sahinalp; Artem Cherkasov (J. Comput. Biol., 2009)

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. - Iman Hajirasouliha; Fereydoun Hormozdiari; Can Alkan; Jeffrey M. Kidd; Inanç Birol; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2010)

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. - Fereydoun Hormozdiari; Iman Hajirasouliha; Phuong Dao; Faraz Hach; Deniz Yörükoglu; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2010)

Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. - Fereydoun Hormozdiari; Raheleh Salari; Vineet Bafna; Süleyman Cenk Sahinalp (J. Comput. Biol., 2010)

Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length. - Alexander Schönhuth; Raheleh Salari; Fereydoun Hormozdiari; Artem Cherkasov; Süleyman Cenk Sahinalp (J. Comput. Biol., 2010)

Session Introduction. - Can Alkan; Emidio Capriotti; Eleazar Eskin; Fereydoun Hormozdiari; Maricel G. Kann (Pacific Symposium on Biocomputing, 2011)

Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. - Fereydoun Hormozdiari; Iman Hajirasouliha; Andrew W. McPherson; Evan E. Eichler; Süleyman Cenk Sahinalp (RECOMB, 2011)

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. - Andrew W. McPherson; Chunxiao Wu; Iman Hajirasouliha; Fereydoun Hormozdiari; Faraz Hach; Anna Lapuk; Stanislav Volik; Sohrab P. Shah; Colin C. Collins; Süleyman Cenk Sahinalp (Bioinform., 2011)

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. - Andrew W. McPherson; Fereydoun Hormozdiari; Abdalnasser Zayed; Ryan Giuliany; Gavin Ha; Mark G. F. Sun; Malachi Griffith; Alireza Heravi Moussavi; Janine Senz; Nataliya Melnyk; Marina Pacheco; Marco A. Marra; et al. (PLoS Comput. Biol., 2011)

The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). - Farhad Hormozdiari; Fereydoun Hormozdiari; Carl Kingsford; Paul Medvedev; Fabio Vandin (RECOMB, 2016)

Ultra-Accurate Complex Disorder Prediction: Case Study of Neurodevelopmental Disorders. - Linh Huynh; Fereydoun Hormozdiari (RECOMB, 2017)

Contribution of Structural Variation to Genome Structure: TAD Fusion Discovery and Ranking. - Linh Huynh; Fereydoun Hormozdiari (RECOMB, 2018)

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing. - Arda Soylev; Thong Minh Le; Hajar Amini; Can Alkan; Fereydoun Hormozdiari (Bioinform., 2019)

Meltos: multi-sample tumor phylogeny reconstruction for structural variants. - Camir Ricketts; Daniel Seidman; Victoria Popic; Fereydoun Hormozdiari; Serafim Batzoglou; Iman Hajirasouliha (Bioinform., 2020)