(joint first or last authors are marked with * in case of equal contribution)
Khorsand P, Denti L, Bonizzoni P, Chikhi R, Hormozdiari F. Comparative genome analysis using sample-specific string detection in accurate long reads. Bioinformatics Advances. 2021. [in press].
Khorsand P, Hormozdiari F. Nebula: ultra-efficient mapping-free structural variant genotyper. Nucleic Acids Research. 2021. gkab025, doi: 10.1093/nar/gkab025
Ricketts C, Seidman D, Popic V, Hormozdiari F, Batzoglou S, Hajirasouliha I. Meltos: multi-sample tumor phylogeny reconstruction for structural variants. Bioinformatics. 2020. 36-4:1082-1090.
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. 2019. 11:1-14. doi.org/10.1186/s13073-019-0678-y.
Standage DS, Brown CT, Hormozdiari F. Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants. iScience. 2019 Jul 23;18:28-36. doi: 10.1016/j.isci.2019.07.032.
Chaisson MJP, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communication. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z.
Soylev A, Le T, Amini H, Alkan C, Hormozdiari F. Discovery of tandem and interspersed segmental duplications using high throughput sequencing. Bioinformatics. 2019 Apr 1. pii: btz237. doi: 10.1093/bioinformatics/btz237.
Huynh L, Hormozdiari F. TAD fusion score: discovery and ranking the contribution of deletions to genome structure. Genome Biology. 2019 Mar 21;20(1):60. doi: 10.1186/s13059-019-1666-7.
Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E. How bioinformatics and open data can boost basic science in countries and universities with limited resources. Nature Biotechnology. 2019 Mar;37(3):324-326. doi: 10.1038/s41587-019-0053-y.
Coe BP, Stessman HAF, Sulovari A, Geisheker MR, Bakken TE, Lake AM, Dougherty JD, Lein ES, Hormozdiari F, Bernier RA, Eichler EE. Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nature Genetics. 2019 Jan;51(1):106-116. doi: 10.1038/s41588-018-0288-4. Epub 2018 Dec 17.
Main BJ, Everitt A, Cornel AJ, Hormozdiari F, Lanzaro GC. Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii Parasites & vectors 2018 11 (1), 225.
Kronenberg ZN, et al. High-resolution comparative analysis of great ape genomes Science 2018 Vol. 360, Issue 6393, eaar6343.
Huynh L, Hormozdiari F. Combinatorial Approach for Complex Disorder Prediction: Case Study of Neurodevelopmental Disorders Genetics 2018 vol. 210 no. 4 1483-1495.
Huynh L, Hormozdiari F. Contribution of structural variation to genome structure: TAD fusion discovery and ranking RECOMB 2018 (full version of paper in Biorxiv)
Turner T, et al. Genomic Patterns of De Novo mutation in Autism Simplex. Cell 2017 Vol 171, Issue 3, Oc 2017.
Soylev A, Kockan C, Hormozdiari F*, Alkan C*. Toolkit for automated and rapid discovery of structural variants. METHODS 2017 (joint last author).
Stessman HA, Xiong B, Coe BP, Wang T, et al. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. Nature Genetics 2017 doi:10.1038/ng.3792
Huynh L, Hormozdiari F. Ultra-accurate complex disorder prediction: case study of neurodevelopmental disorders. RECOMB 2017 (full version of paper in Biorxiv).
Hehir-Kwa JY, et al. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications 2016 7: 12989.
Hormozdiari F, Hormozdiari F, Kingsford C, Medvedev P, Vandin P. The second decade of the International Conference on Research Research in Computational Molecular Biology (RECOMB). RECOMB 2016.
Turner TN, Hormozdiari F, Duyzend MH, et al. Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. AJHG 2016 Jan. 98(1):58-74
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, et al. An integrated map of structural variation in 2,504 human genomes. Nature 2015 Oct 1,526(7571) 75-81. doi:10.1038/nature15394
1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 2015 Oct 1; 526(7571):68-74 doi: 10.1038/nature15393
Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, et al. Global diversity, population stratification, and selection of human copy-number variation. Science 2015 Sep 11, 349(6253):aa3761. doi:101126/science.aab3761. Epub 2015 Aug 6
Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, et al. Characteristics of de novo structural changes in the human genome. Genome Research 2015 Jun;25(6):792-801. doi:10.1101/gr.185041.114 Epub 2015 Apr 16
Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 2015 Jan 29;517(7536) 608-11. DOI: 10.1038/Nature 13907. Pub 2014 Nov 10
Hormozdiari F, Penn O, Borenstein E, Eichler EE. The discovery of integrated gene networks for autism and related disorders. Genome Research 2015 Jan; 25(1) 142-54 do:10.1101/gr178855.114 Epub 2014 Nov 5
Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, et al. Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. PLoS One 2014 Aug 12; 9(8) e104396 do:10.1371/journal PONE.0104396 ECOLLECTION 2014.
Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics 2014 Aug; 46(8):818-25
Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, et al. Rates and patterns of great ape retrotransposition. PNAS 2013 Aug 13; 110(33):13457-62 doi: 10.1073/pnas1310914110 Epub 2013 Jul 24
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, et al. Great ape genetic diversity and population history. Nature 2013 Jul 25; 499(7459) 471-5 doi:10.1038/Nature 12228 Epub 2013 Jul 3
Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, et al. The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics 2013 May 31; 14:363. doi: 10.1186/1471-2164-14-363
Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, et al. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. J Pathol 2012 Jul; 227(3):286-97. doi: 10.1002/Path.4047
Wu C, Wyatt AW, Lapuk AV, McPherson A, et al. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. J Pathol 2012 May; 22(1): 53-61 do:10.1002/path 3987 Epub 2012 Mar 21
1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 2012 Nov 1;491(7422):56-65 doi: 10.1038/nature11632
Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome Research 2011 Dec; 21(2):2203-12. doi: 10.1101/gr/ 120501.111 Epub 2011 Nov 2.
Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, et al. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Research 2011 Oct; 21(10):1640-9 do:10.1101/gr.124461.111 Epub 2011 Jun 17
McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Computational Biology 2011 May 7(5):e1001138 doi: 101371/journal.pcei.1001138 Epub 2011 May 19.
McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, et al. Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinformatics 2011 Jun 1; 27(11):1481-8 do:10.1093/bioinformtaics/btr184 Epub 2011 Apr 9.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, et al. Mapping copy number variation by population-scale genome sequencing. Nature 2011 Feb 3; 470)7332):59-65 do:10.1038/nature09708
Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, et al. Alu repeat discovery and characterization within human genomes. Genome Research 2011 Jun; 21(6):840-9 do: 101101/gr115956110 Epub 2010 Dec 3
Hach F, Hormozdiari F, Alkan C, et al. mrsFAST: a cache-oblivious algorithm for short-read mapping. Nature Methods 2010 Aug; 7(8):576-7 doi:10.1038/nmeth0810-576
Hormozdiari F, Hajirasouliha I, Dao P, Hach F, et al. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 2010 Jun 15; 26(12):i350-7 doi:10.1093/bioinformatics/btg216
Hormozdiari F, Salari R, Bafna V, Sahinalp SC. Protein-protein interaction network evaluation for identifying potential drug targets. J Computational Biology 2010 May; 17(5): 669-84 doi: 10.1089/cmb 2009.0032.
Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, et al. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 2010 May 15; 26(10) 1277-83 do:10.1093/bioinformatics/btq152 Epub 2010 Apr 12
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. J. Computational Biology 2010 Jan; 17(1):20 doi:10.1089/cmb.2009.0031
1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 2010 Oct 28; 467(7319):1061-73
Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genetics 2009 Oct; 41(10):1061-7 do:10.1038/ng 437 Epub 2009 Aug 30.
Lee S, Hormozdiari F, Alkan C, Brudno M. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nature Methods 2009 Jul; 6(7):473-4 doi:10.1038/nmeth.f.256 Epub 2009 May 31.
Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Research 2009 Jul; 19(7):1270-8 do: 10.1101/gr.088633.108 Epub 2009 May 15
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. J Computational Biology 2009 Feb; 16(2):159-67 doi:10.1089/cmb.2008.03TT
Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics 2008 Jul; 24(13):32-40 doi:10.1093/bioinformatics/btn173
Alon N, Dao P, Hajirasouliha I, Hormozdiari F, Sahinalp SC. Biomolecular network motif counting and discovery by color coding. Bioinformatics 2008 Jul; 24(13):241-9 doi:10.1093/bioinformatics/btn163
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 2007 Jul; 3(7):e118
Chan SK, Hsing M, Hormozdiari F, Cherkasov A. Relationship between insertion/deletion (indel) frequency of proteins and essentiality. BMC Bioinformatics 2007 Jun 28; 8:227