Faster Phylogenetic Inference with MXG. - David G. Mitchell; Faraz Hach; Raheleh Mohebali (LPAR, 2007)

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)

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)

CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. - Yen-Yi Lin; Phuong Dao; Faraz Hach; Marzieh Bakhshi; Fan Mo; Anna Lapuk; Colin C. Collins; Süleyman Cenk Sahinalp (WABI, 2012)

SCALCE: boosting sequence compression algorithms using locally consistent encoding. - Faraz Hach; Ibrahim Numanagic; Can Alkan; Süleyman Cenk Sahinalp (Bioinform., 2012)

Sensitive and fast mapping of di-base encoded reads. - Farhad Hormozdiari; Faraz Hach; Süleyman Cenk Sahinalp; Evan E. Eichler; Can Alkan (Bioinform., 2012)

Dissect: detection and characterization of novel structural alterations in transcribed sequences. - Deniz Yörükoglu; Faraz Hach; Lucas Swanson; Colin C. Collins; Inanç Birol; Süleyman Cenk Sahinalp (Bioinform., 2012)

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. - Phuong Dao; Ibrahim Numanagic; Yen-Yi Lin; Faraz Hach; Emre Karakoç; Nilgun Donmez; Colin C. Collins; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2014)

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. - Faraz Hach; Iman Sarrafi; Farhad Hormozdiari; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (Nucleic Acids Res., 2014)

CoLoRMap: Correcting Long Reads by Mapping short reads. - Ehsan Haghshenas; Faraz Hach; Süleyman Cenk Sahinalp; Cédric Chauve (Bioinform., 2016)

Discovery and genotyping of novel sequence insertions in many sequenced individuals. - Pinar Kavak; Yen-Yi Lin; Ibrahim Numanagic; Hossein Asghari; Tunga Güngör; Can Alkan; Faraz Hach (Bioinform., 2017)

SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA. - Can Kockan; Faraz Hach; Iman Sarrafi; Robert H. Bell; Brian McConeghy; Kevin Beja; Anne Haegert; Alexander W. Wyatt; Stanislav Volik; Kim N. Chi; Colin C. Collins; Süleyman Cenk Sahinalp (Bioinform., 2017)

Computational identification of micro-structural variations and their proteogenomic consequences in cancer. - Yen-Yi Lin; Alexander Gawronski; Faraz Hach; Sujun Li; Ibrahim Numanagic; Iman Sarrafi; Swati Mishra 006; Andrew W. McPherson; Colin C. Collins; Milan Radovich; Haixu Tang; Süleyman Cenk Sahinalp (Bioinform., 2018)

Fast characterization of segmental duplications in genome assemblies. - Ibrahim Numanagic; Alim S. Gökkaya; Lillian Zhang; Bonnie Berger; Can Alkan; Faraz Hach (Bioinform., 2018)

Dynamic Alignment-Free and Reference-Free Read Compression. - Guillaume Holley; Roland Wittler; Jens Stoye; Faraz Hach (J. Comput. Biol., 2018)

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. - Ehsan Haghshenas; Süleyman Cenk Sahinalp; Faraz Hach (Bioinform., 2019)

Alignment-free clustering of UMI tagged DNA molecules. - Baraa Orabi; Emre Erhan; Brian McConeghy; Stanislav V. Volik; Stephane Le Bihan; Robert Bell; Colin C. Collins; Cédric Chauve; Faraz Hach (Bioinform., 2019)

CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme. - Hossein Asghari; Yen-Yi Lin; Yang Xu; Ehsan Haghshenas; Colin C. Collins; Faraz Hach (Bioinform., 2020)

BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. - Hamza Iseric; Can Alkan; Faraz Hach; Ibrahim Numanagic (WABI, 2021)

Detecting high-scoring local alignments in pangenome graphs. - Tizian Schulz; Roland Wittler; Sven Rahmann; Faraz Hach; Jens Stoye (Bioinform., 2021)

Fast characterization of segmental duplication structure in multiple genome assemblies. - Hamza Iseric; Can Alkan; Faraz Hach; Ibrahim Numanagic (Algorithms Mol. Biol., 2022)