Farhad Hormozdiari, B.S. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 

102 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
2021 LaPierre N, Taraszka K, Huang H, He R, Hormozdiari F, Eskin E. Identifying causal variants by fine mapping across multiple studies. Plos Genetics. 17: e1009733. PMID 34543273 DOI: 10.1371/journal.pgen.1009733  1
2021 Alipanahi B, Hormozdiari F, Behsaz B, Cosentino J, McCaw ZR, Schorsch E, Sculley D, Dorfman EH, Foster PJ, Peng LH, Phene S, Hammel N, Carroll A, Khawaja AP, McLean CY. Large-scale machine learning-based phenotyping significantly improves genomic discovery for optic nerve head morphology. American Journal of Human Genetics. PMID 34077760 DOI: 10.1016/j.ajhg.2021.05.004  0.01
2021 Hormozdiari F, Jung J, Eskin E, J Joo JW. MARS: leveraging allelic heterogeneity to increase power of association testing. Genome Biology. 22: 128. PMID 33931127 DOI: 10.1186/s13059-021-02353-8  1
2021 Barbeira AN, Bonazzola R, Gamazon ER, Liang Y, Park Y, Kim-Hellmuth S, Wang G, Jiang Z, Zhou D, Hormozdiari F, Liu B, Rao A, Hamel AR, Pividori MD, Aguet F, et al. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biology. 22: 49. PMID 33499903 DOI: 10.1186/s13059-020-02252-4  0.04
2020 Weissbrod O, Hormozdiari F, Benner C, Cui R, Ulirsch J, Gazal S, Schoech AP, van de Geijn B, Reshef Y, Márquez-Luna C, O'Connor L, Pirinen M, Finucane HK, Price AL. Functionally informed fine-mapping and polygenic localization of complex trait heritability. Nature Genetics. 52: 1355-1363. PMID 33199916 DOI: 10.1038/s41588-020-00735-5  1
2020 Gay NR, Gloudemans M, Antonio ML, Abell NS, Balliu B, Park Y, Martin AR, Musharoff S, Rao AS, Aguet F, Barbeira AN, Bonazzola R, Hormozdiari F, Ardlie KG, et al. Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx. Genome Biology. 21: 233. PMID 32912333 DOI: 10.1186/S13059-020-02113-0  0.01
2019 Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E. Leveraging allelic imbalance to refine fine-mapping for eQTL studies. Plos Genetics. 15: e1008481. PMID 31834882 DOI: 10.1371/Journal.Pgen.1008481  1
2019 Kim SS, Dai C, Hormozdiari F, van de Geijn B, Gazal S, Park Y, O'Connor L, Amariuta T, Loh PR, Finucane H, Raychaudhuri S, Price AL. Genes with High Network Connectivity Are Enriched for Disease Heritability. American Journal of Human Genetics. 105: 1302. PMID 31809749 DOI: 10.1016/j.ajhg.2019.11.009  1
2019 Chow J, Jensen M, Amini H, Hormozdiari F, Penn O, Shifman S, Girirajan S, Hormozdiari F. Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. Genome Medicine. 11: 65. PMID 31653223 DOI: 10.1186/S13073-019-0678-Y  1
2019 van de Geijn B, Finucane H, Gazal S, Hormozdiari F, Amariuta T, Liu X, Gusev A, Loh PR, Reshef Y, Kichaev G, Raychauduri S, Price AL. Annotations capturing cell-type-specific TF binding explain a large fraction of disease heritability. Human Molecular Genetics. PMID 31595288 DOI: 10.1093/Hmg/Ddz226  1
2019 Hormozdiari F, van de Geijn B, Nasser J, Weissbrod O, Gazal S, Ju CJ, Connor LO, Hujoel MLA, Engreitz J, Hormozdiari F, Price AL. Functional disease architectures reveal unique biological role of transposable elements. Nature Communications. 10: 4054. PMID 31492842 DOI: 10.1038/S41467-019-11957-5  1
2019 O'Connor LJ, Schoech AP, Hormozdiari F, Gazal S, Patterson N, Price AL. Extreme Polygenicity of Complex Traits Is Explained by Negative Selection. American Journal of Human Genetics. PMID 31402091 DOI: 10.1016/J.Ajhg.2019.07.003  1
2019 Kim SS, Dai C, Hormozdiari F, van de Geijn B, Gazal S, Park Y, O'Connor L, Amariuta T, Loh PR, Finucane H, Raychaudhuri S, Price AL. Genes with High Network Connectivity Are Enriched for Disease Heritability. American Journal of Human Genetics. 104: 896-913. PMID 31051114 DOI: 10.1016/J.Ajhg.2019.03.020  1
2019 Hujoel MLA, Gazal S, Hormozdiari F, van de Geijn B, Price AL. Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species. American Journal of Human Genetics. PMID 30905396 DOI: 10.1016/J.Ajhg.2019.02.008  1
2018 Wu Y, Hormozdiari F, Joo JWJ, Eskin E. Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 30272994 DOI: 10.1089/cmb.2018.0139  1
2018 Reshef YA, Finucane HK, Kelley DR, Gusev A, Kotliar D, Ulirsch JC, Hormozdiari F, Nasser J, O'Connor L, van de Geijn B, Loh PR, Grossman SR, Bhatia G, Gazal S, Palamara PF, et al. Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. Nature Genetics. PMID 30177862 DOI: 10.1038/S41588-018-0196-7  1
2018 Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J, Nicolae DL, Eskin E, Kellis M, et al. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Nature Genetics. PMID 29955180 DOI: 10.1038/S41588-018-0154-4  1
2018 Hormozdiari F, Gazal S, van de Geijn B, Finucane HK, Ju CJ, Loh PR, Schoech A, Reshef Y, Liu X, O'Connor L, Gusev A, Eskin E, Price AL. Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits. Nature Genetics. PMID 29942083 DOI: 10.1038/S41588-018-0148-2  1
2017 Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, et al. Loci associated with skin pigmentation identified in African populations. Science (New York, N.Y.). PMID 29025994 DOI: 10.1126/Science.Aan8433  1
2017 Hormozdiari F, Zhu A, Kichaev G, Ju CJ, Segrè AV, Joo JWJ, Won H, Sankararaman S, Pasaniuc B, Shifman S, Eskin E. Widespread Allelic Heterogeneity in Complex Traits. American Journal of Human Genetics. 100: 789-802. PMID 28475861 DOI: 10.1016/J.Ajhg.2017.04.005  1
2017 Buckley MT, Racimo F, Allentoft ME, Jensen MK, Jonsson A, Huang H, Hormozdiari F, Sikora M, Marnetto D, Eskin E, Jørgensen ME, Grarup N, Pedersen O, Hansen T, Kraft P, et al. Selection in Europeans on fatty acid desaturases associated with dietary changes. Molecular Biology and Evolution. PMID 28333262 DOI: 10.1093/Molbev/Msx103  1
2017 Mangul S, Yang HT, Hormozdiari F, Dainis A, Tseng E, Ashley EA, Zelikovsky A, Eskin E. HapIso : An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads. Ieee Transactions On Nanobioscience. PMID 28328508 DOI: 10.1109/Tnb.2017.2675981  1
2016 Hormozdiari F, van de Bunt M, Segrè AV, Li X, Joo JW, Bilow M, Sul JH, Sankararaman S, Pasaniuc B, Eskin E. Colocalization of GWAS and eQTL Signals Detects Target Genes. American Journal of Human Genetics. PMID 27866706 DOI: 10.1016/J.Ajhg.2016.10.003  1
2016 Joo JW, Kang EY, Org E, Furlotte N, Parks B, Hormozdiari F, Lusis AJ, Eskin E. Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure. Genetics. PMID 27770036 DOI: 10.1534/Genetics.116.189712  1
2016 Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DH. Chromosome conformation elucidates regulatory relationships in developing human brain. Nature. PMID 27760116 DOI: 10.1038/Nature19847  1
2016 Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Bruemmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. Elife. 5. PMID 27623010 DOI: 10.7554/Elife.15614  1
2016 Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E. Using genomic annotations increases statistical power to detect eGenes. Bioinformatics (Oxford, England). 32: i156-i163. PMID 27307612 DOI: 10.1093/Bioinformatics/Btw272  1
2016 Hormozdiari F, Kang EY, Bilow M, Ben-David E, Vulpe C, McLachlan S, Lusis AJ, Han B, Eskin E. Imputing Phenotypes for Genome-wide Association Studies. American Journal of Human Genetics. PMID 27292110 DOI: 10.1016/J.Ajhg.2016.04.013  1
2016 Joo JW, Hormozdiari F, Han B, Eskin E. Multiple testing correction in linear mixed models. Genome Biology. 17: 62. PMID 27039378 DOI: 10.1186/S13059-016-0903-6  1
2016 Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, et al. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. Plos Genetics. 12: e1005851. PMID 26943675 DOI: 10.1371/Journal.Pgen.1005851  1
2016 Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Brümmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ. Author response: Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes Elife. DOI: 10.7554/Elife.15614.024  1
2016 Mangul S, Taegyun Yang H, Hormozdiari F, Tseng E, Zelikovsky A, Eskin E. HapIso: An accurate method for the haplotype-specific isoforms reconstruction from long single-molecule reads Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9683: 80-92. DOI: 10.1007/978-3-319-38782-6_7  1
2015 Turner TN, Hormozdiari F, Duyzend MH, McClymont SA, Hook PW, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman HA, Zody MC, Nelson BJ, Huddleston J, Sandstrom R, Smith JD, et al. Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. American Journal of Human Genetics. PMID 26749308 DOI: 10.1016/J.Ajhg.2015.11.023  1
2015 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... Hormozdiari F, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/Nature15394  1
2015 Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, et al. Global diversity, population stratification, and selection of human copy number variation. Science (New York, N.Y.). PMID 26249230 DOI: 10.1126/Science.Aab3761  1
2015 Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E. Identification of causal genes for complex traits. Bioinformatics (Oxford, England). 31: i206-i213. PMID 26072484 DOI: 10.1093/Bioinformatics/Btv240  1
2015 Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer EW, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, et al. Characteristics of de novo structural changes in the human genome. Genome Research. 25: 792-801. PMID 25883321 DOI: 10.1101/Gr.185041.114  1
2015 Park DS, Baran Y, Hormozdiari F, Eng C, Torgerson DG, Burchard EG, Zaitlen N. PIGS: improved estimates of identity-by-descent probabilities by probabilistic IBD graph sampling. Bmc Bioinformatics. 16: S9. PMID 25860540 DOI: 10.1186/1471-2105-16-S5-S9  1
2015 Hormozdiari F, Eskin E. Memory efficient assembly of human genome. Journal of Bioinformatics and Computational Biology. 13: 1550008. PMID 25603998 DOI: 10.1142/S0219720015500080  1
2015 Yang WY, Hormozdiari F, Eskin E, Pasaniuc B. A spatial haplotype copying model with applications to genotype imputation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 451-62. PMID 25526526 DOI: 10.1089/Cmb.2014.0151  1
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  1
2015 Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE. Resolving the complexity of the human genome using single-molecule sequencing. Nature. 517: 608-11. PMID 25383537 DOI: 10.1038/Nature13907  1
2015 Hormozdiari F, Penn O, Borenstein E, Eichler EE. The discovery of integrated gene networks for autism and related disorders. Genome Research. 25: 142-54. PMID 25378250 DOI: 10.1101/Gr.178855.114  1
2014 Kichaev G, Yang WY, Lindstrom S, Hormozdiari F, Eskin E, Price AL, Kraft P, Pasaniuc B. Integrating functional data to prioritize causal variants in statistical fine-mapping studies. Plos Genetics. 10: e1004722. PMID 25357204 DOI: 10.1371/Journal.Pgen.1004722  1
2014 Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, et al. Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. Plos One. 9: e104396. PMID 25116239 DOI: 10.1371/Journal.Pone.0104396  1
2014 Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E. Identifying causal variants at loci with multiple signals of association. Genetics. 198: 497-508. PMID 25104515 DOI: 10.1534/Genetics.114.167908  1
2014 Francioli LC, Menelaou A, Pulit SL, Van Dijk F, Palamara PF, Elbers CC, Neerincx PBT, Ye K, Guryev V, Kloosterman WP, Deelen P, Abdellaoui A, Van Leeuwen EM, Van Oven M, Vermaat M, ... Hormozdiari F, et al. Whole-genome sequence variation, population structure and demographic history of the Dutch population Nature Genetics. 46: 818-825. PMID 24974849 DOI: 10.1038/Ng.3021  1
2014 Hormozdiari F, Joo JW, Wadia A, Guan F, Ostrosky R, Sahai A, Eskin E. Privacy preserving protocol for detecting genetic relatives using rare variants. Bioinformatics (Oxford, England). 30: i204-11. PMID 24931985 DOI: 10.1093/Bioinformatics/Btu294  1
2014 Hasin-Brumshtein Y, Hormozdiari F, Martin L, van Nas A, Eskin E, Lusis AJ, Drake TA. Allele-specific expression and eQTL analysis in mouse adipose tissue. Bmc Genomics. 15: 471. PMID 24927774 DOI: 10.1186/1471-2164-15-471  1
2014 Orozco LD, Rubbi L, Martin LJ, Fang F, Hormozdiari F, Che N, Smith AD, Lusis AJ, Pellegrini M. Intergenerational genomic DNA methylation patterns in mouse hybrid strains. Genome Biology. 15: R68. PMID 24887417 DOI: 10.1186/Gb-2014-15-5-R68  1
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  1
2014 He D, Furlotte NA, Hormozdiari F, Joo JW, Wadia A, Ostrovsky R, Sahai A, Eskin E. Identifying genetic relatives without compromising privacy. Genome Research. 24: 664-72. PMID 24614977 DOI: 10.1101/Gr.153346.112  1
2014 Ohmen J, Kang EY, Li X, Joo JW, Hormozdiari F, Zheng QY, Davis RC, Lusis AJ, Eskin E, Friedman RA. Genome-wide association study for age-related hearing loss (AHL) in the mouse: a meta-analysis. Journal of the Association For Research in Otolaryngology : Jaro. 15: 335-52. PMID 24570207 DOI: 10.1007/S10162-014-0443-2  1
2014 Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, et al. Genome sequencing highlights the dynamic early history of dogs. Plos Genetics. 10: e1004016. PMID 24453982 DOI: 10.1371/Journal.Pgen.1004016  1
2014 Frésard L, Leroux S, Servin B, Gourichon D, Dehais P, Cristobal MS, Marsaud N, Vignoles F, Bed'hom B, Coville JL, Hormozdiari F, Beaumont C, Zerjal T, Vignal A, Morisson M, et al. Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Research. 42: 3768-82. PMID 24452801 DOI: 10.1093/Nar/Gkt1390  1
2014 Yang WY, Hormozdiari F, Eskin E, Pasaniuc B. A spatial-aware haplotype copying model with applications to genotype imputation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8394: 371-384. DOI: 10.1007/978-3-319-05269-4_30  1
2013 Eskin I, Hormozdiari F, Conde L, Riby J, Skibola CF, Eskin E, Halperin E. eALPS: estimating abundance levels in pooled sequencing using available genotyping data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 861-77. PMID 24144111 DOI: 10.1089/cmb.2013.0105  1
2013 Lagarrigue S, Martin L, Hormozdiari F, Roux PF, Pan C, van Nas A, Demeure O, Cantor R, Ghazalpour A, Eskin E, Lusis AJ. Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage. Genetics. 195: 1157-66. PMID 24026101 DOI: 10.1534/Genetics.113.153882  1
2013 Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C, et al. Rates and patterns of great ape retrotransposition. Proceedings of the National Academy of Sciences of the United States of America. 110: 13457-62. PMID 23884656 DOI: 10.1073/Pnas.1310914110  1
2013 Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E. Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data. Bioinformatics (Oxford, England). 29: 2245-52. PMID 23825370 DOI: 10.1093/Bioinformatics/Btt386  1
2013 Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, ... Hormozdiari F, et al. Great ape genetic diversity and population history. Nature. 499: 471-5. PMID 23823723 DOI: 10.1038/Nature12228  1
2013 Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, et al. The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. Bmc Genomics. 14: 363. PMID 23721540 DOI: 10.1186/1471-2164-14-363  1
2013 Wang Z, Hormozdiari F, Yang WY, Halperin E, Eskin E. CNVeM: copy number variation detection using uncertainty of read mapping. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 224-36. PMID 23421794 DOI: 10.1089/Cmb.2012.0258  1
2013 Lagarrigue S, Hormozdiari F, Martin LJ, Lecerf F, Hasin Y, Rau C, Hagopian R, Xiao Y, Yan J, Drake TA, Ghazalpour A, Eskin E, Lusis AJ. Limited RNA editing in exons of mouse liver and adipose. Genetics. 193: 1107-15. PMID 23410828 DOI: 10.1534/Genetics.112.149054  1
2013 Xin H, Lee D, Hormozdiari F, Yedkar S, Mutlu O, Alkan C. Accelerating read mapping with FastHASH. Bmc Genomics. 14: S13. PMID 23369189 DOI: 10.1186/1471-2164-14-S1-S13  1
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, ... Hormozdiari 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  1
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, ... Hormozdiari 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  1
2012 Xin H, Lee D, Hormozdiari F, Alkan C, Mutlu O. FastHASH: a new algorithm for fast and comprehensive next-generation sequence mapping F1000research. 3. DOI: 10.7490/F1000Research.1089776.1  1
2012 Dao P, Hormozdiari F, Hajirasouliha I, Ester M, Sahinalp SC. Proteome network emulating models Functional Coherence of Molecular Networks in Bioinformatics. 2147483647: 69-95. DOI: 10.1007/978-1-4614-0320-3_4  1
2011 Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome Research. 21: 2203-12. PMID 22048523 DOI: 10.1101/Gr.120501.111  1
2011 Parrish N, Hormozdiari F, Eskin E. Assembly of non-unique insertion content using next-generation sequencing. Bmc Bioinformatics. 12: S3. PMID 21989261 DOI: 10.1186/1471-2105-12-S6-S3  1
2011 Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, Lee C, Turner EH, Chen L, Kidd JM, Archidiacono N, et al. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Research. 21: 1640-9. PMID 21685127 DOI: 10.1101/Gr.124461.111  1
2011 McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. Plos Computational Biology. 7: e1001138. PMID 21625565 DOI: 10.1371/Journal.Pcbi.1001138  1
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  1
2011 He D, Hormozdiari F, Furlotte N, Eskin E. Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions. Bioinformatics (Oxford, England). 27: 1513-20. PMID 21505028 DOI: 10.1093/Bioinformatics/Btr169  1
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  1
2011 Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/Nature09708  1
2011 Cherkasov A, Hsing M, Zoraghi R, Foster LJ, See RH, Stoynov N, Jiang J, Kaur S, Lian T, Jackson L, Gong H, Swayze R, Amandoron E, Hormozdiari F, Dao P, et al. Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus. Journal of Proteome Research. 10: 1139-50. PMID 21166474 DOI: 10.1021/Pr100918U  1
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  1
2011 Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. Simultaneous structural variation discovery in multiple paired-end sequenced genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 104-105. DOI: 10.1007/978-3-642-20036-6_11  1
2011 Bebek G, Chance M, Koyuturk M, Price ND, De La Vega FM, Bustamante CD, Leal SM, Foster J, Moore J, Bernauer J, Flores S, Huang X, Shin S, Zhou R, Alkan C, ... Hormozdiari F, et al. Pacific symposium on biocomputing 2011 Pacific Symposium On Biocomputing 2011, Psb 2011. v.  1
2010 Sushko I, Novotarskyi S, Körner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen K, Schroeter T, Müller KR, Xi L, Liu H, Yao X, Öberg T, Hormozdiari F, et al. Applicability domains for classification problems: Benchmarking of distance to models for Ames mutagenicity set. Journal of Chemical Information and Modeling. 50: 2094-111. PMID 21033656 DOI: 10.1021/Ci100253R  1
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  1
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  1
2010 Hormozdiari F, Salari R, Bafna V, Sahinalp SC. Protein-protein interaction network evaluation for identifying potential drug targets. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 669-84. PMID 20500021 DOI: 10.1089/Cmb.2009.0032  1
2010 Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics (Oxford, England). 26: 1277-83. PMID 20385726 DOI: 10.1093/Bioinformatics/Btq152  1
2010 Schönhuth A, Salari R, Hormozdiari F, Cherkasov A, Sahinalp SC. Towards improved assessment of functional similarity in large-scale screens: a study on indel length. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1-20. PMID 20078394 DOI: 10.1089/Cmb.2009.0031  1
2009 Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genetics. 41: 1061-7. PMID 19718026 DOI: 10.1038/Ng.437  1
2009 Lee S, Hormozdiari F, Alkan C, Brudno M. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nature Methods. 6: 473-4. PMID 19483690 DOI: 10.1038/Nmeth.F.256  1
2009 Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Research. 19: 1270-8. PMID 19447966 DOI: 10.1101/Gr.088633.108  1
2009 Colak R, Hormozdiari F, Moser F, Schönhuth A, Holman J, Ester M, Sahinalp SC. Dense graphlet statistics of protein interaction and random networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 178-89. PMID 19213135  1
2009 Hormozdiari F, Salari R, Hsing M, Schönhuth A, Chan SK, Sahinalp SC, Cherkasov A. The effect of insertions and deletions on wirings in protein-protein interaction networks: a large-scale study. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 159-67. PMID 19193143 DOI: 10.1089/Cmb.2008.03Tt  1
2009 Dao P, Schönhuth A, Hormozdiari F, Hajirasouliha I, Sahinalp SC, Ester M. Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5724: 37-48. DOI: 10.1007/978-3-642-04241-6_4  1
2009 Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. Combinatorial algorithms for structural variation detection in high throughput sequenced genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: 218-219. DOI: 10.1007/978-3-642-02008-7_16  1
2008 Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics (Oxford, England). 24: i32-40. PMID 18586730 DOI: 10.1093/bioinformatics/btn173  1
2008 Alon N, Dao P, Hajirasouliha I, Hormozdiari F, Sahinalp SC. Biomolecular network motif counting and discovery by color coding. Bioinformatics (Oxford, England). 24: i241-9. PMID 18586721 DOI: 10.1093/bioinformatics/btn163  1
2008 Rajabi A, Dadlani A, Hormozdiari F, Khonsari A, Kianrad A, Razi HS. Analysis of the impact of wavelength converters on contention resolution in optical burst switching Proceedings - 2nd Asia International Conference On Modelling and Simulation, Ams 2008. 259-264. DOI: 10.1109/AMS.2008.15  1
2008 Salari R, Schönhuth A, Hormozdiari F, Cherkasov A, Sahinalp SC. The relation between indel length and functional divergence: A formal study Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5251: 330-341. DOI: 10.1007/978-3-540-87361-7_28  1
2007 Hormozdiari F, Berenbrink P, Przulj N, Sahinalp SC. Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. Plos Computational Biology. 3: e118. PMID 17616981 DOI: 10.1371/journal.pcbi.0030118  1
2007 Chan SK, Hsing M, Hormozdiari F, Cherkasov A. Relationship between insertion/deletion (indel) frequency of proteins and essentiality. Bmc Bioinformatics. 8: 227. PMID 17598914 DOI: 10.1186/1471-2105-8-227  1
2007 Hormozdiari F, Rajabi A, Khonsari A. Mathematical analysis of delay line to wavelength allocation algorithms in optical networking Ieee International Workshop On Modeling, Analysis, and Simulation of Computer and Telecommunication Systems - Proceedings. 418-423. DOI: 10.1109/MASCOTS.2007.32  1
2007 Hormozdiari F, Berenbrink P, Pržulj N, Sahinalp C. Not all scale free networks are born equal: The role of the seed graph in PPI network emulation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4532: 1-13.  1
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