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Faraz Hach, Ph.D. - Publications

Affiliations: 
2013 Simon Fraser University, Burnaby, British Columbia, Canada 
Area:
Bioinformatics Biology, Molecular Biology
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Orabi B, Xie N, McConeghy B, Dong X, Chauve C, Hach F. Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing. Nucleic Acids Research. PMID 36478271 DOI: 10.1093/nar/gkac1112  0.328
2020 Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F. HASLR: Fast Hybrid Assembly of Long Reads. Iscience. 23: 101389. PMID 32781410 DOI: 10.1016/J.Isci.2020.101389  0.341
2020 Asghari H, Lin YY, Xu Y, Haghshenas E, Collins CC, Hach F. CircMiner: Accurate and Rapid Detection of Circular RNA through Splice-Aware Pseudo-Alignment Scheme. Bioinformatics (Oxford, England). PMID 32259207 DOI: 10.1093/Bioinformatics/Btaa232  0.368
2020 D'Costa NM, Cina D, Shrestha R, Bell RH, Lin YY, Asghari H, Monjaras-Avila CU, Kollmannsberger C, Hach F, Chavez-Munoz CI, So AI. Identification of gene signature for treatment response to guide precision oncology in clear-cell renal cell carcinoma. Scientific Reports. 10: 2026. PMID 32029828 DOI: 10.1038/S41598-020-58804-Y  0.617
2019 Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC. PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. Genome Research. PMID 31628256 DOI: 10.1101/Gr.234435.118  0.377
2019 Shrestha R, Nabavi N, Lin YY, Mo F, Anderson S, Volik S, Adomat HH, Lin D, Xue H, Dong X, Shukin R, Bell RH, McConeghy B, Haegert A, Brahmbhatt S, ... ... Hach F, et al. BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma. Genome Medicine. 11: 8. PMID 30777124 DOI: 10.1186/S13073-019-0620-3  0.616
2019 Gawronski AR, Lin YY, McConeghy B, LeBihan S, Asghari H, Koçkan C, Orabi B, Adra N, Pili R, Collins CC, Sahinalp SC, Hach F. Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA. Nucleic Acids Research. PMID 30759232 DOI: 10.1093/Nar/Gkz067  0.403
2019 Haghshenas E, Sahinalp SC, Hach F. lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. Bioinformatics (Oxford, England). 35: 20-27. PMID 30561550 DOI: 10.1093/Bioinformatics/Bty544  0.427
2018 Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics (Oxford, England). 34: i706-i714. PMID 30423092 DOI: 10.1093/Bioinformatics/Bty586  0.391
2018 Orabi B, Erhan E, McConeghy B, Volik SV, Le Bihan S, Bell R, Collins CC, Chauve C, Hach F. Alignment-free Clustering of UMI Tagged DNA Molecules. Bioinformatics (Oxford, England). PMID 30351359 DOI: 10.1093/Bioinformatics/Bty888  0.386
2018 Holley G, Wittler R, Stoye J, Hach F. Dynamic Alignment-Free and Reference-Free Read Compression. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 25: 825-836. PMID 30011247 DOI: 10.1089/Cmb.2018.0068  0.382
2018 Davies A, Bostock C, Ahmed M, Lin Y, Johnson F, Nip KM, Ketola K, Bishop J, Fazli L, Goodrich D, Hach F, He H, Beltran H, Zoubeidi A. Abstract A033: Identity fraud: Lineage plasticity as a mechanism of antiandrogen resistance and target for therapy Cancer Research. 78. DOI: 10.1158/1538-7445.Prca2017-A033  0.417
2017 Lin YY, Gawronski A, Hach F, Li S, Numanagic I, Sarrafi I, Mishra S, McPherson A, Collins C, Radovich M, Tang H, Sahinalp SC. Computational identification of micro-structural variations and their proteogenomic consequences in cancer. Bioinformatics (Oxford, England). PMID 29267878 DOI: 10.1093/Bioinformatics/Btx807  0.42
2017 Kalina JL, Neilson DS, Lin YY, Hamilton PT, Comber AP, Loy EMH, Sahinalp SC, Collins CC, Hach F, Lum JJ. Mutational Analysis of Gene Fusions Predicts Novel MHC Class I-Restricted T cell Epitopes & Immune Signatures in a Subset of Prostate Cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 28954787 DOI: 10.1158/1078-0432.Ccr-17-0618  0.405
2017 Kavak P, Lin YY, Numanagic I, Asghari H, Güngör T, Alkan C, Hach F. Discovery and genotyping of novel sequence insertions in many sequenced individuals. Bioinformatics (Oxford, England). 33: i161-i169. PMID 28881988 DOI: 10.1093/Bioinformatics/Btx254  0.415
2016 Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J, Alberti C, Mattavelli M, Sahinalp SC. Comparison of high-throughput sequencing data compression tools. Nature Methods. PMID 27776113 DOI: 10.1038/Nmeth.4037  0.313
2016 Haghshenas E, Hach F, Sahinalp SC, Chauve C. CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinformatics (Oxford, England). 32: i545-i551. PMID 27587673 DOI: 10.1093/Bioinformatics/Btw463  0.359
2016 Kockan C, Hach F, Sarrafi I, Bell RH, McConeghy B, Beja K, Haegert A, Wyatt AW, Volik SV, Chi KN, Collins CC, Sahinalp SC. SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA. Bioinformatics (Oxford, England). PMID 27531099 DOI: 10.1093/Bioinformatics/Btw536  0.478
2015 Kavak P, Yüksel B, Aksu S, Kulekci MO, Güngör T, Hach F, Şahinalp SC, Alkan C, Sağıroğlu MŞ. Robustness of Massively Parallel Sequencing Platforms. Plos One. 10: e0138259. PMID 26382624 DOI: 10.1371/Journal.Pone.0138259  0.413
2015 Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, ... ... Hach F, et al. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nature Genetics. 47: 736-45. PMID 26005866 DOI: 10.1038/Ng.3315  0.645
2015 Lee D, Hormozdiari F, Xin H, Hach F, Mutlu O, Alkan C. Fast and accurate mapping of Complete Genomics reads. Methods (San Diego, Calif.). 79: 3-10. PMID 25461772 DOI: 10.1016/J.Ymeth.2014.10.012  0.402
2014 Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Research. 42: W494-500. PMID 24810850 DOI: 10.1093/Nar/Gku370  0.355
2012 Hach F, Numanagic I, Alkan C, Sahinalp SC. SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinformatics (Oxford, England). 28: 3051-7. PMID 23047557 DOI: 10.1093/Bioinformatics/Bts593  0.355
2012 Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Cenk Sahinalp S. Dissect: Detection and characterization of novel structural alterations in transcribed sequences Bioinformatics. 28: i179-i187. PMID 22689759 DOI: 10.1093/Bioinformatics/Bts214  0.405
2012 Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, ... ... Hach F, et al. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. The Journal of Pathology. 227: 286-97. PMID 22553170 DOI: 10.1002/Path.4047  0.414
2012 Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, ... ... Hach F, et al. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. The Journal of Pathology. 227: 53-61. PMID 22294438 DOI: 10.1002/Path.3987  0.466
2011 Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C. Sensitive and fast mapping of di-base encoded reads. Bioinformatics (Oxford, England). 27: 1915-21. PMID 21586516 DOI: 10.1093/Bioinformatics/Btr303  0.386
2011 McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC. Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinformatics (Oxford, England). 27: 1481-8. PMID 21478487 DOI: 10.1093/Bioinformatics/Btr184  0.429
2011 Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE. Alu repeat discovery and characterization within human genomes. Genome Research. 21: 840-9. PMID 21131385 DOI: 10.1101/Gr.115956.110  0.389
2010 Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. mrsFAST: a cache-oblivious algorithm for short-read mapping. Nature Methods. 7: 576-7. PMID 20676076 DOI: 10.1038/Nmeth0810-576  0.354
2010 Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics (Oxford, England). 26: i350-7. PMID 20529927 DOI: 10.1093/Bioinformatics/Btq216  0.367
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