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Faraz Hach
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Pan-cancer analysis of whole genomes
Nature 578 (7793), 82-93, 2020
1749*2020
Spatial genomic heterogeneity within localized, multifocal prostate cancer
PC Boutros, M Fraser, NJ Harding, R De Borja, D Trudel, E Lalonde, ...
Nature genetics 47 (7), 736-745, 2015
5302015
mrsFAST: a cache-oblivious algorithm for short-read mapping
F Hach, F Hormozdiari, C Alkan, F Hormozdiari, I Birol, EE Eichler, ...
Nature methods 7 (8), 576-577, 2010
3442010
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
F Hormozdiari, I Hajirasouliha, P Dao, F Hach, D Yorukoglu, C Alkan, ...
Bioinformatics 26 (12), i350-i357, 2010
2722010
From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer
AV Lapuk, C Wu, AW Wyatt, A McPherson, BJ McConeghy, S Brahmbhatt, ...
The Journal of Pathology 227 (3), 286-297, 2012
2142012
SCALCE: boosting Sequence Compression Algorithms using Locally Consistent Encoding
F Hach, I Numanagić, C Alkan, SC Sahinalp
Bioinformatics 28 (23), 3051-3057., 2012
1772012
Comparison of high-throughput sequencing data compression tools
I Numanagić, JK Bonfield, F Hach, J Voges, J Ostermann, C Alberti, ...
nature methods 13 (12), 1005-1008, 2016
1162016
Alu repeat discovery and characterization within human genomes
F Hormozdiari, C Alkan, M Ventura, I Hajirasouliha, M Malig, F Hach, ...
Genome Research 21 (6), 840-849, 2011
1162011
BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma
R Shrestha, N Nabavi, YY Lin, F Mo, S Anderson, S Volik, HH Adomat, ...
Genome medicine 11, 1-12, 2019
1052019
An androgen receptor switch underlies lineage infidelity in treatment-resistant prostate cancer
A Davies, S Nouruzi, D Ganguli, T Namekawa, D Thaper, S Linder, ...
Nature cell biology 23 (9), 1023-1034, 2021
862021
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
S Malikic, FR Mehrabadi, S Ciccolella, MK Rahman, C Ricketts, ...
Genome research 29 (11), 1860-1877, 2019
812019
Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer
C Wu, AW Wyatt, AV Lapuk, A McPherson, BJ McConeghy, RH Bell, ...
The Journal of pathology 227 (1), 53-61, 2012
812012
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications
F Hach, I Sarrafi, F Hormozdiari, C Alkan, EE Eichler, SC Sahinalp
Nucleic acids research 42 (W1), W494-W500, 2014
762014
CoLoRMap: correcting long reads by mapping short reads
E Haghshenas, F Hach, SC Sahinalp, C Chauve
Bioinformatics 32 (17), i545-i551, 2016
692016
Fast characterization of segmental duplications in genome assemblies
I Numanagić, AS Gökkaya, L Zhang, B Berger, C Alkan, F Hach
Bioinformatics 34 (17), i706-i714, 2018
632018
DeeZ: reference-based compression by local assembly
F Hach, I Numanagic, SC Sahinalp
Nature methods 11 (11), 1082-1084, 2014
632014
CLIIQ: Accurate comparative detection and quantification of expressed isoforms in a population
YY Lin, P Dao, F Hach, M Bakhshi, F Mo, A Lapuk, C Collins, SC Sahinalp
Algorithms in Bioinformatics: 12th International Workshop, WABI 2012 …, 2012
632012
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA
C Kockan, F Hach, I Sarrafi, RH Bell, B McConeghy, K Beja, A Haegert, ...
Bioinformatics 33 (1), 26-34, 2017
602017
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data
A McPherson, C Wu, I Hajirasouliha, F Hormozdiari, F Hach, A Lapuk, ...
Bioinformatics 27 (11), 1481-1488, 2011
602011
HASLR: fast hybrid assembly of long reads
E Haghshenas, H Asghari, J Stoye, C Chauve, F Hach
Iscience 23 (8), 2020
532020
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