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2020 – today
- 2022
[j19]Hamza Iseric, Can Alkan, Faraz Hach
, Ibrahim Numanagic:
Fast characterization of segmental duplication structure in multiple genome assemblies. Algorithms Mol. Biol. 17(1): 4 (2022)- 2021
- [j18]Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye:
Detecting high-scoring local alignments in pangenome graphs. Bioinform. 37(16): 2266-2274 (2021) - [c4]Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic:
BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. WABI 2021: 15:1-15:18 - 2020
- [j17]Hossein Asghari, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, Faraz Hach:
CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme. Bioinform. 36(12): 3703-3711 (2020)
2010 – 2019
- 2019
- [j16]Ehsan Haghshenas, Süleyman Cenk Sahinalp, Faraz Hach:
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. Bioinform. 35(1): 20-27 (2019) - [j15]Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach:
Alignment-free clustering of UMI tagged DNA molecules. Bioinform. 35(11): 1829-1836 (2019) - 2018
- [j14]Yen-Yi Lin, Alexander Gawronski, Faraz Hach, Sujun Li, Ibrahim Numanagic, Iman Sarrafi, Swati Mishra, Andrew W. McPherson, Colin C. Collins, Milan Radovich, Haixu Tang, Süleyman Cenk Sahinalp:
Computational identification of micro-structural variations and their proteogenomic consequences in cancer. Bioinform. 34(10): 1672-1681 (2018) - [j13]Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach:
Fast characterization of segmental duplications in genome assemblies. Bioinform. 34(17): i706-i714 (2018) - [j12]Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach:
Dynamic Alignment-Free and Reference-Free Read Compression. J. Comput. Biol. 25(7): 825-836 (2018) - [i1]Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach:
Fast Characterization of Segmental Duplications in Genome Assemblies. CoRR abs/1807.00205 (2018) - 2017
- [j11]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:
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA. Bioinform. 33(1): 26-34 (2017) - [j10]Pinar Kavak, Yen-Yi Lin, Ibrahim Numanagic, Hossein Asghari, Tunga Güngör, Can Alkan, Faraz Hach:
Discovery and genotyping of novel sequence insertions in many sequenced individuals. Bioinform. 33(14): i161-i169 (2017) - [c3]Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach:
Dynamic Alignment-Free and Reference-Free Read Compression. RECOMB 2017: 50-65 - 2016
- [j9]Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve:
CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinform. 32(17): 545-551 (2016) - 2014
- [j8]Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp:
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinform. 30(5): 644-651 (2014) - [j7]Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res. 42(Webserver-Issue): 494-500 (2014) - 2012
- [j6]Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan:
Sensitive and fast mapping of di-base encoded reads. Bioinform. 28(1): 150 (2012) - [j5]Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp:
Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinform. 28(12): 179-187 (2012) - [j4]Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp:
SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinform. 28(23): 3051-3057 (2012) - [c2]Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp:
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. WABI 2012: 178-189 - 2011
- [j3]Andrew W. McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp:
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinform. 27(11): 1481-1488 (2011) - [j2]Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan:
Sensitive and fast mapping of di-base encoded reads. Bioinform. 27(14): 1915-1921 (2011) - 2010
- [j1]Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinform. 26(12): 350-357 (2010)
2000 – 2009
- 2007
- [c1]David G. Mitchell, Faraz Hach, Raheleh Mohebali:
Faster Phylogenetic Inference with MXG. LPAR 2007: 423-437
Coauthor Index
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