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20072021

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  • 2021

    Nebula: Ultra-efficient mapping-free structural variant genotyper

    Khorsand, P. & Hormozdiari, F., May 7 2021, In: Nucleic acids research. 49, 8, p. E47

    Research output: Contribution to journalArticlepeer-review

    Open Access
    2 Scopus citations
  • 2020

    Meltos: Multi-sample tumor phylogeny reconstruction for structural variants

    Ricketts, C., Seidman, D., Popic, V., Hormozdiari, F., Batzoglou, S. & Hajirasouliha, I., Feb 15 2020, In: Bioinformatics. 36, 4, p. 1082-1090 9 p.

    Research output: Contribution to journalArticlepeer-review

    4 Scopus citations
  • The effects of common structural variants on 3D chromatin structure

    Shanta, O., Noor, A., Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., Fan, X., Wen, J., Handsaker, R. E., Fairley, S., Kronenberg, Z. N., Kong, X., Hormozdiari, F., Lee, D. & 77 others, Wenger, A. M., Hastie, A. R., Antaki, D., Anantharaman, T., Audano, P. A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C. S., Chong, Z., Chuang, N. T., Lambert, C. C., Church, D. M., Clarke, L., Farrell, A., Flores, J., Galeey, T., Gujral, M., Guryev, V., Heaton, W. H., Korlach, J., Kumar, S., Kwon, J. Y., Lam, E. T., Lee, J. E., Lee, J., Lee, W. P., Lee, S. P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K. M., Navarro, F. C. P., Nelson, B. J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A. W. C., Rosanio, G., Ryan, M., Stütz, A., Spierings, D. C. J., Ward, A., Welch, A. M. E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C. L., Flicek, P., Chen, K., Gerstein, M. B., Kwok, P. Y., Lansdorp, P. M., Marth, G. T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S. E., Talkowski, M. E., Mills, R. E., Marschall, T., Korbel, J. O., Eichler, E. E., Lee, C. & Sebat, J., Jan 30 2020, In: BMC Genomics. 21, 1, 95.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    6 Scopus citations
  • 2019

    Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

    Soylev, A., Le, T. M., Amini, H., Alkan, C., Hormozdiari, F. & Berger, B., Oct 15 2019, In: Bioinformatics. 35, 20, p. 3923-3930 8 p.

    Research output: Contribution to journalArticlepeer-review

    12 Scopus citations
  • Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders

    Chow, J., Jensen, M., Amini, H., Hormozdiari, F., Penn, O., Shifman, S., Girirajan, S. & Hormozdiari, F., Oct 25 2019, In: Genome Medicine. 11, 1, 65.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    10 Scopus citations
  • Functional disease architectures reveal unique biological role of transposable elements

    Hormozdiari, F., van de Geijn, B., Nasser, J., Weissbrod, O., Gazal, S., Ju, C. J. T., Connor, L. O., Hujoel, M. L. A., Engreitz, J., Hormozdiari, F. & Price, A. L., Dec 1 2019, In: Nature communications. 10, 1, 4054.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    4 Scopus citations
  • How bioinformatics and open data can boost basic science in countries and universities with limited resources

    Mangul, S., Martin, L. S., Langmead, B., Sanchez-Galan, J. E., Toma, I., Hormozdiari, F., Pevzner, P. & Eskin, E., Mar 1 2019, In: Nature Biotechnology. 37, 3, p. 324-326 3 p.

    Research output: Contribution to journalArticlepeer-review

    11 Scopus citations
  • Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants

    Standage, D. S., Brown, C. & Hormozdiari, F., Aug 30 2019, In: iScience. 18, p. 28-36 9 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    12 Scopus citations
  • Multi-platform discovery of haplotype-resolved structural variation in human genomes

    Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., Fan, X., Wen, J., Handsaker, R. E., Fairley, S., Kronenberg, Z. N., Kong, X., Hormozdiari, F., Lee, D., Wenger, A. M., Hastie, A. R. & 77 others, Antaki, D., Anantharaman, T., Audano, P. A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C. S., Chong, Z., Chuang, N. T., Lambert, C. C., Church, D. M., Clarke, L., Farrell, A., Flores, J., Galeev, T., Gorkin, D. U., Gujral, M., Guryev, V., Heaton, W. H., Korlach, J., Kumar, S., Kwon, J. Y., Lam, E. T., Lee, J. E., Lee, J., Lee, W. P., Lee, S. P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K. M., Navarro, F. C. P., Nelson, B. J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A. W. C., Qiu, Y., Rosanio, G., Ryan, M., Stütz, A., Spierings, D. C. J., Ward, A., Welch, A. M. E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C. L., Ren, B., Flicek, P., Chen, K., Gerstein, M. B., Kwok, P. Y., Lansdorp, P. M., Marth, G. T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S. E., Talkowski, M. E., Mills, R. E., Marschall, T., Korbel, J. O., Eichler, E. E. & Lee, C., Dec 1 2019, In: Nature communications. 10, 1, 1784.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    238 Scopus citations
  • Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity

    Coe, B. P., Stessman, H. A. F., Sulovari, A., Geisheker, M. R., Bakken, T. E., Lake, A. M., Dougherty, J. D., Lein, E. S., Hormozdiari, F., Bernier, R. A. & Eichler, E. E., Jan 1 2019, In: Nature Genetics. 51, 1, p. 106-116 11 p.

    Research output: Contribution to journalArticlepeer-review

    104 Scopus citations
  • Skewed X-inactivation is common in the general female population

    BIOS consortium & GoNL consortium, Mar 1 2019, In: European Journal of Human Genetics. 27, 3, p. 455-465 11 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    35 Scopus citations
  • TAD fusion score: Discovery and ranking the contribution of deletions to genome structure

    Huynh, L. & Hormozdiari, F., Mar 21 2019, In: Genome Biology. 20, 1, 60.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    10 Scopus citations
  • WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene

    The Genome of the Netherlands Consortium, Dec 1 2019, In: Scientific reports. 9, 1, 18758.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1 Scopus citations
  • 2018

    Combinatorial approach for complex disorder prediction: Case study of neurodevelopmental disorders

    Huynh, L. & Hormozdiari, F., Dec 1 2018, In: Genetics. 210, 4, p. 1483-1495 13 p.

    Research output: Contribution to journalArticlepeer-review

  • Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii

    Main, B. J., Everitt, A., Cornel, A. J., Hormozdiari, F. & Lanzaro, G. C., Apr 4 2018, In: Parasites and Vectors. 11, 1, 225.

    Research output: Contribution to journalArticlepeer-review

    13 Scopus citations
  • High-resolution comparative analysis of great ape genomes

    Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., Munson, K. M., Hastie, A. R., Diekhans, M., Hormozdiari, F., Lorusso, N., Hoekzema, K., Qiu, R., Clark, K., Raja, A., Welch, A. M. E. & 24 others, Sorensen, M., Baker, C., Fulton, R. S., Armstrong, J., Graves-Lindsay, T. A., Denli, A. M., Hoppe, E. R., Hsieh, P. H., Hill, C. M., Pang, A. W. C., Lee, J., Lam, E. T., Dutcher, S. K., Gage, F. H., Warren, W. C., Shendure, J., Haussler, D., Schneider, V. A., Cao, H., Ventura, M., Wilson, R. K., Paten, B., Pollen, A. & Eichler, E. E., Jun 8 2018, In: Science. 360, 6393, eaar6343.

    Research output: Contribution to journalArticlepeer-review

    138 Scopus citations
  • 2017

    Genomic Patterns of De Novo Mutation in Simplex Autism

    Turner, T. N., Coe, B. P., Dickel, D. E., Hoekzema, K., Nelson, B. J., Zody, M. C., Kronenberg, Z. N., Hormozdiari, F., Raja, A., Pennacchio, L. A., Darnell, R. B. & Eichler, E. E., Oct 19 2017, In: Cell. 171, 3, p. 710-722.e12

    Research output: Contribution to journalArticlepeer-review

    146 Scopus citations
  • Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases

    Stessman, H. A. F., Xiong, B., Coe, B. P., Wang, T., Hoekzema, K., Fenckova, M., Kvarnung, M., Gerdts, J., Trinh, S., Cosemans, N., Vives, L., Lin, J., Turner, T. N., Santen, G., Ruivenkamp, C., Kriek, M., Van Haeringen, A., Aten, E., Friend, K., Liebelt, J. & 33 others, Barnett, C., Haan, E., Shaw, M., Gecz, J., Anderlid, B. M., Nordgren, A., Lindstrand, A., Schwartz, C., Kooy, R. F., Vandeweyer, G., Helsmoortel, C., Romano, C., Alberti, A., Vinci, M., Avola, E., Giusto, S., Courchesne, E., Pramparo, T., Pierce, K., Nalabolu, S., Amaral, D. G., Scheffer, I. E., Delatycki, M. B., Lockhart, P. J., Hormozdiari, F., Harich, B., Castells-Nobau, A., Xia, K., Peeters, H., Nordenskjöld, M., Schenck, A., Bernier, R. A. & Eichler, E. E., Mar 30 2017, In: Nature Genetics. 49, 4, p. 515-526 12 p.

    Research output: Contribution to journalArticlepeer-review

    244 Scopus citations
  • Toolkit for automated and rapid discovery of structural variants

    Soylev, A., Kockan, C., Hormozdiari, F. & Alkan, C., Oct 1 2017, In: Methods. 129, p. 3-7 5 p.

    Research output: Contribution to journalArticlepeer-review

    12 Scopus citations
  • 2016

    A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

    Hehir-Kwa, J. Y., Marschall, T., Kloosterman, W. P., Francioli, L. C., Baaijens, J. A., Dijkstra, L. J., Abdellaoui, A., Koval, V., Thung, D. T., Wardenaar, R., Renkens, I., Coe, B. P., Deelen, P., De Ligt, J., Lameijer, E. W., Van Dijk, F., Hormozdiari, F., Uitterlinden, A. G., Van Duijn, C. M., Eichler, E. E. & 47 others, De Bakker, P. I. W., Swertz, M. A., Wijmenga, C., Van Ommen, G. J. B., Slagboom, P. E., Boomsma, D. I., Schönhuth, A., Ye, K., Guryev, V., Bovenberg, J. A., De Craen, A. J. M., Beekman, M., Hofman, A., Willemsen, G., Wolffenbuttel, B., Platteel, M., Du, Y., Chen, R., Cao, H., Cao, R., Sun, Y., Cao, J. S., Neerincx, P. B. T., Dijkstra, M., Byelas, G., Kanterakis, A., Bot, J., Vermaat, M., Laros, J. F. J., Den Dunnen, J. T., De Knijff, P., Karssen, L. C., Van Leeuwen, E. M., Amin, N., Rivadeneira, F., Estrada, K., Hottenga, J. J., Kattenberg, V. M., Van Enckevort, D., Mei, H., Santcroos, M., Van Schaik, B. D. C., Handsaker, R. E., McCarroll, S. A., Ko, A., Sudmant, P. & Nijman, I. J., Oct 6 2016, In: Nature Communications. 7, 12989.

    Research output: Contribution to journalArticlepeer-review

    52 Scopus citations
  • Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

    Turner, T. N., Hormozdiari, F., Duyzend, M. H., McClymont, S. A., Hook, P. W., Iossifov, I., Raja, A., Baker, C., Hoekzema, K., Stessman, H. A., Zody, M. C., Nelson, B. J., Huddleston, J., Sandstrom, R., Smith, J. D., Hanna, D., Swanson, J. M., Faustman, E. M., Bamshad, M. J., Stamatoyannopoulos, J. & 4 others, Nickerson, D. A., McCallion, A. S., Darnell, R. & Eichler, E. E., Jan 7 2016, In: American Journal of Human Genetics. 98, 1, p. 58-74 17 p.

    Research output: Contribution to journalArticlepeer-review

    157 Scopus citations
  • The time scale of recombination rate evolution in great apes

    Great Ape Genome Project, Apr 1 2016, In: Molecular biology and evolution. 33, 4, p. 928-945 18 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    44 Scopus citations
  • 2015

    An integrated map of structural variation in 2,504 human genomes

    Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Fritz, M. H. Y., Konkel, M. K., Malhotra, A., Stütz, A. M., Shi, X., Casale, F. P., Chen, J., Hormozdiari, F., Dayama, G., Chen, K., Malig, M. & 62 others, Chaisson, M. J. P., Walter, K., Meiers, S., Kashin, S., Garrison, E., Auton, A., Lam, H. Y. K., Mu, X. J., Alkan, C., Antaki, D., Bae, T., Cerveira, E., Chines, P., Chong, Z., Clarke, L., Dal, E., Ding, L., Emery, S., Fan, X., Gujral, M., Kahveci, F., Kidd, J. M., Kong, Y., Lameijer, E. W., McCarthy, S., Flicek, P., Gibbs, R. A., Marth, G., Mason, C. E., Menelaou, A., Muzny, D. M., Nelson, B. J., Noor, A., Parrish, N. F., Pendleton, M., Quitadamo, A., Raeder, B., Schadt, E. E., Romanovitch, M., Schlattl, A., Sebra, R., Shabalin, A. A., Untergasser, A., Walker, J. A., Wang, M., Yu, F., Zhang, C., Zhang, J., Zheng-Bradley, X., Zhou, W., Zichner, T., Sebat, J., Batzer, M. A., McCarroll, S. A., Mills, R. E., Gerstein, M. B., Bashir, A., Stegle, O., Devine, S. E., Lee, C., Eichler, E. E. & Korbel, J. O., Sep 30 2015, In: Nature. 526, 7571, p. 75-81 7 p.

    Research output: Contribution to journalArticlepeer-review

    1042 Scopus citations
  • Characteristics of de novo structural changes in the human genome

    Genome of the Netherlands Consortium, Jun 1 2015, In: Genome Research. 25, 6, p. 792-801 10 p.

    Research output: Contribution to journalArticlepeer-review

    71 Scopus citations
  • Extreme selective sweeps independently targeted the X chromosomes of the great apes

    Great Ape Genome Diversity Project, May 19 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 20, p. 6413-6418 6 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    46 Scopus citations
  • Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

    The Genome of the Netherlands Consortium, Mar 9 2015, In: Nature Communications. 6, 6065.

    Research output: Contribution to journalArticlepeer-review

    28 Scopus citations
  • Global diversity, population stratification, and selection of human copy-number variation

    Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., Jorde, L. B., Posukh, O. L., Sahakyan, H., Watkins, W. S., Yepiskoposyan, L., Abdullah, M. S., Bravi, C. M., Capelli, C., Hervig, T., Wee, J. T. S. & 31 others, Tyler-Smith, C., Van Driem, G., Romero, I. G., Jha, A. R., Karachanak-Yankova, S., Toncheva, D., Comas, D., Henn, B., Kivisild, T., Ruiz-Linares, A., Sajantila, A., Metspalu, E., Parik, J., Villems, R., Starikovskaya, E. B., Ayodo, G., Beall, C. M., Di Rienzo, A., Hammer, M. F., Khusainova, R., Khusnutdinova, E., Klitz, W., Winkler, C., Labuda, D., Metspalu, M., Tishkoff, S. A., Dryomov, S., Sukernik, R., Patterson, N., Reich, D. & Eichler, E. E., Sep 11 2015, In: Science. 349, 6253, aab3761.

    Research output: Contribution to journalArticlepeer-review

    192 Scopus citations
  • Resolving the complexity of the human genome using single-molecule sequencing

    Chaisson, M. J. P., Huddleston, J., Dennis, M., Sudmant, P. H., Malig, M., Hormozdiari, F., Antonacci, F., Surti, U., Sandstrom, R., Boitano, M., Landolin, J. M., Stamatoyannopoulos, J. A., Hunkapiller, M. W., Korlach, J. & Eichler, E. E., Jan 29 2015, In: Nature. 517, 7536, p. 608-611 4 p.

    Research output: Contribution to journalArticlepeer-review

    416 Scopus citations
  • The discovery of integrated gene networks for autism and related disorders

    Hormozdiari, F., Penn, O., Borenstein, E. & Eichler, E. E., Jan 1 2015, In: Genome Research. 25, 1, p. 142-154 13 p.

    Research output: Contribution to journalArticlepeer-review

    150 Scopus citations
  • 2014

    Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

    Colonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., Garrison, E., Xue, Y., Tyler-Smith, C., Abecasis, G. R., Auton, A., Brooks, L. D., Depristo, M. A., Durbin, R. M., Handsaker, R. E., Kang, H. M., Marth, G. T., McVean, G., Altshuler, D. M., Durbin, R. M. & 685 others, Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Donnelly, P., Eichler, E. E., Flicek, P., Gabriel, S. B., Gibbs, R. A., Green, E. D., Hurles, M. E., Knoppers, B. M., Korbel, J. O., Lander, E. S., Lee, C., Lehrach, H., Mardis, E. R., Marth, G. T., McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Gibbs, R. A., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Wang, J., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Li, Z., Liu, X., Lu, Y., Ma, X., Su, Z., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Zhou, Y., Lander, E. S., Altshuler, D. M., Gabriel, S. B., Gupta, N., Flicek, P., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Bentley, D. R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Lehrach, H., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Sherry, S. T., McVean, G. A., Mardis, E. R., Wilson, R. K., Fulton, L., Fulton, R., Weinstock, G. M., Durbin, R. M., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Schmidt, J. P., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Auton, A., Gibbs, R. A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Muzny, D., Nagaswamy, U., Reid, J., Sabo, A., Wang, Y., Yu, J., Wang, J., Coin, L. J., Fang, L., Guo, X., Jin, X., Li, G., Li, Q., Li, Y., Li, Z., Lin, H., Liu, B., Luo, R., Qin, N., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zhang, F., Zheng, H., Zhu, H., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., von Grotthuss, M., Zhang, C., Daly, M. J., Depristo, M. A., Altshuler, D. M., Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Gabriel, S. B., Genovese, G., Gupta, N., Handsaker, R. E., Hartl, C., Lander, E. S., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Kim, K. C., Korbel, J. O., Rausch, T., Flicek, P., Beal, K., Clarke, L., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R., Smith, R. E., Zheng-Bradley, X., Clark, A. G., Gottipati, S., Keinan, A., Rodriguez-Flores, J. L., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Cooper, D. N., Ball, E. V., Stenson, P. D., Bentley, D. R., Barnes, B., Bauer, M., Cheetham, R., Cox, T., Eberle, M., Humphray, S., Kahn, S., Murray, L., Peden, J., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., Macarthur, D. G., Lek, M., Sudbrak, R., Amstislavskiy, V. S., Herwig, R., Shriver, M. D., Bustamante, C. D., Byrnes, J. K., De La Vega, F. M., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Squire, K., Sherry, S. T., Xiao, C., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Anderson, P., Angius, A., Bigham, A., Blackwell, T., Busonero, F., Cucca, F., Fuchsberger, C., Jones, C., Li, Y., Lyons, R., Maschio, A., Porcu, E., Reinier, F., Sanna, S., Schlessinger, D., Sidore, C., Tan, A., Trost, M. K., Awadalla, P., Hodgkinson, A., Lunter, G., McVean, G. A., Marchini, J. L., Myers, S., Churchhouse, C., Delaneau, O., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Oleksyk, T. K., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Ko, A., Sudmant, P. H., Mardis, E. R., Chen, K., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Durbin, R. M., Hurles, M. E., Tyler-Smith, C., Albers, C. A., Ayub, Q., Balasubramaniam, S., Chen, Y., Coffey, A. J., Colonna, V., Danecek, P., Huang, N., Jostins, L., Keane, T. M., Li, H., McCarthy, S., Scally, A., Stalker, J., Walter, K., Xue, Y., Zhang, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Habegger, L., Harmanci, A. O., Jin, M., Khurana, E., Mu, X. J., Sisu, C., Li, Y., Luo, R., Zhu, H., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., von Grotthuss, M., Zhang, C., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Ward, A. N., Wu, J., Zhang, M., McCarroll, S. A., Altshuler, D. M., Banks, E., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., Nemesh, J. C., Shakir, K., Yoon, S. C., Lihm, J., Makarov, V., Degenhardt, J., Flicek, P., Clarke, L., Smith, R. E., Zheng-Bradley, X., Korbel, J. O., Rausch, T., Stütz, A. M., Bentley, D. R., Barnes, B., Cheetham, R., Eberle, M., Humphray, S., Kahn, S., Murray, L., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., Lacroute, P., Craig, D. W., Homer, N., Church, D., Xiao, C., Sebat, J., Bafna, V., Michaelson, J. J., Ye, K., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Lunter, G., McVean, G. A., Iqbal, Z., Witherspoon, D., Xing, J., Eichler, E. E., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Ko, A., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., McLellan, M. D., Wallis, J. W., Hurles, M. E., Blackburne, B., Li, H., Lindsay, S. J., Ning, Z., Scally, A., Walter, K., Zhang, Y., Gerstein, M. B., Abyzov, A., Chen, J., Clarke, D., Khurana, E., Mu, X. J., Sisu, C., Gibbs, R. A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Kovar, C., Lewis, L., Lu, J., Muzny, D., Nagaswamy, U., Reid, J., Sabo, A., Yu, J., Guo, X., Li, Y., Wu, R., Marth, G. T., Garrison, E. P., Leong, W. F., Ward, A. N., Del Angel, G., Depristo, M. A., Gabriel, S. B., Gupta, N., Hartl, C., Poplin, R. E., Clark, A. G., Rodriguez-Flores, J. L., Flicek, P., Clarke, L., Smith, R. E., Zheng-Bradley, X., Macarthur, D. G., Bustamante, C. D., Gravel, S., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Sherry, S. T., Xiao, C., Dermitzakis, E., Abecasis, G. R., Kang, H. M., McVean, G. A., Mardis, E. R., Dooling, D., Fulton, L., Fulton, R., Koboldt, D. C., Durbin, R. M., Balasubramaniam, S., Keane, T. M., McCarthy, S., Stalker, J., Gerstein, M. B., Balasubramanian, S., Habegger, L., Garrison, E. P., Gibbs, R. A., Bainbridge, M., Muzny, D., Yu, F., Yu, J., Del Angel, G., Handsaker, R. E., Makarov, V., Rodriguez-Flores, J. L., Jin, H., Kim, W., Kim, K. C., Flicek, P., Beal, K., Clarke, L., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R., Zheng-Bradley, X., Tabrizi, S., Macarthur, D. G., Lek, M., Bustamante, C. D., De La Vega, F. M., Craig, D. W., Kurdoglu, A. A., Lappalainen, T., Rosenfeld, J. A., Michelson, L. P., Awadalla, P., Hodgkinson, A., McVean, G. A., Chen, K., Tyler-Smith, C., Chen, Y., Colonna, V., Frankish, A., Harrow, J., Xue, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Harmanci, A. O., Jin, M., Khurana, E., Mu, X. J., Sisu, C., Gibbs, R. A., Kovar, C., Kalra, D., Hale, W., Fowler, G., Muzny, D., Reid, J., Wang, J., Guo, X., Li, G., Li, Y., Zheng, X., Altshuler, D. M., Flicek, P., Clarke, L., Barker, J., Kelman, G., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Roa, A., Smirnov, D., Smith, R. E., Streeter, I., Toneva, I., Vaughan, B., Zheng-Bradley, X., Bentley, D. R., Cox, T., Humphray, S., Kahn, S., Sudbrak, R., Albrecht, M. W., Lienhard, M., Craig, D. W., Izatt, T., Kurdoglu, A. A., Sherry, S. T., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Church, D., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., O'sullivan, C., Ostapchuk, Y., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Xiao, C., Zhang, H., Haussler, D., Abecasis, G. R., McVean, G. A., Alkan, C., Ko, A., Dooling, D., Durbin, R. M., Balasubramaniam, S., Keane, T. M., McCarthy, S., Stalker, J., Chakravarti, A., Abecasis, G. R., Barnes, K. C., Beiswanger, C., Burchard, E., Bustamante, C. D., Cai, H., Cao, H., Durbin, R. M., Gharani, N., Gibbs, R. A., Gignoux, C. R., Gravel, S., Henn, B., Jones, D., Jorde, L., Kaye, J. S., Keinan, A., Kent, A., Kerasidou, A., Li, Y., Mathias, R., McVean, G., Moreno-Estrada, A., Ossorio, P. N., Parker, M., Reich, D., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Sudbrak, R., Tian, Z., Timmermann, B., Tishkoff, S., Toji, L. H., Tyler-Smith, C., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Ruiz-Linares, A., Ming, C. Z., Yang, G., You, C. J., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Oleksyk, T. K., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Duncanson, A., Dunn, M., Green, E. D., Guyer, M. S. & Peterson, J. L., Jun 30 2014, In: Genome Biology. 15, 6, R88.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    46 Scopus citations
  • Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

    Delaneau, O., Marchini, J., McVeanh, G. A., Donnelly, P., Lunter, G., Marchini, J. L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Kerasidou, A., Churchhouse, C., Altshuler, D. M., Gabriel, S. B., Lander, E. S., Gupta, N., Daly, M. J., DePristo, M. A. & 363 others, Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Li, H., Reich, D., Durbin, R. M., Hurles, M. E., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Ayub, Q., Chen, Y., Coffey, A. J., Colonna, V., Huang, N., Jostins, L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S. J., Ning, Z., Frankish, A., Harrow, J., Chris, T. S., Abecasis, G. R., Kang, H. M., Anderson, P., Blackwell, T., Busonero, F., Fuchsberger, C., Jun, G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M. K., Bentley, D. R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., Murray, L., Shaw, R., Chakravarti, A., Clark, A. G., Keinan, A., Rodriguez-Flores, J. L., De LaVega, F. M., Degenhardt, J., Eichler, E. E., Flicek, P., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Beal, K., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R. S., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Gibbs, R. A., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Fowler, G., Hale, W., Kalra, D., Green, E. D., Knoppers, B. M., Korbel, J. O., Rausch, T., Sttz, A. M., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Von Grotthuss, M., Zhang, C., Shi, X., Lehrach, H., Sudbrak, R., Amstislavskiy, V. S., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Herwig, S. R., Mardis, E. R., Wilson, R. K., Fulton, L., Fulton, R., Weinstock, G. M., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Nickerson, D. A., Alkan, C., Hormozdiari, F., Ko, A., Sudmant, P. H., Schmidt, J. P., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Sherry, S. T., Xiao, C., Church, D., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Wang, J., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Liu, X., Lu, Y., Ma, X., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Lachlan, H., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zheng, H., Zhu, H., Cai, H., Cao, H., Su, Y., Tian, Z., Yang, H., Yang, L., Zhu, J., Cai, Z., Wang, J., Albrecht, M. W., Borodina, T. A., Auton, A., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Kim, K. C., Gottipati, S., Jones, D., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Kahn, S., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Shriver, M. D., Bustamante, C. D., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Henn, B., Sandoval, K., Byrnes, J. K., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Homer, N., Squire, K., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Angius, A., Cucca, F., Sanna, S., Bigham, A., Jones, C., Reinier, F., Li, Y., Lyons, R., Schlessinger, D., Awadalla, P., Hodgkinson, A., Oleksyk, T. K., Martinez-Cruzado, J. C., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Hajirasouliha, I., Chen, K., Albers, C. A., Gerstein, M. B., Abyzov, A., Chen, J., Fu, Y., Habegger, L., Harmanci, A. O., Mu, X. J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson, J. J., OSullivan, C., Barnes, K. C., Gharani, N., Toji, L. H., Gerry, N., Kaye, J. S., Kent, A., Mathias, R., Ossorio, P. N., Parker, M., Rotimi, C. N., Royal, C. D., Tishkoff, S., Via, M., Bodmer, W., Bedoya, G., Yang, G., You, C. J., Garcia-Montero, A., Orfao, A., Dutil, J., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Guyer, M. S., Peterson, J. L., Duncanson, A., Dunn, M. & Peltonen, L., Jun 13 2014, In: Nature Communications. 5, 3934.

    Research output: Contribution to journalArticlepeer-review

    215 Scopus citations
  • Whole-genome sequence variation, population structure and demographic history of the Dutch population

    Francioli, L. C., Menelaou, A., Pulit, S. L., Van Dijk, F., Palamara, P. F., Elbers, C. C., Neerincx, P. B. T., Ye, K., Guryev, V., Kloosterman, W. P., Deelen, P., Abdellaoui, A., Van Leeuwen, E. M., Van Oven, M., Vermaat, M., Li, M., Laros, J. F. J., Karssen, L. C., Kanterakis, A., Amin, N. & 64 others, Hottenga, J. J., Lameijer, E. W., Kattenberg, M., Dijkstra, M., Byelas, H., Van Setten, J., Van Schaik, B. D. C., Bot, J., Nijman, I. J., Renkens, I., Marschall, T., Schönhuth, A., Hehir-Kwa, J. Y., Handsaker, R. E., Polak, P., Sohail, M., Vuzman, D., Hormozdiari, F., Van Enckevort, D., Mei, H., Koval, V., Moed, M. H., Van Der Velde, KJ., Rivadeneira, F., Estrada, K., Medina-Gomez, C., Isaacs, A., McCarroll, S. A., Beekman, M., Mde Craen, A. J., Suchiman, H. E. D., Hofman, A., Oostra, B., Uitterlinden, A. G., Willemsen, G., Platteel, M., Veldink, J. H., Van Den Berg, L. H., Pitts, S. J., Potluri, S., Sundar, P., Cox, D. R., Sunyaev, S. R., Den Dunnen, J. T., Stoneking, M., De Knijff, P., Kayser, M., Li, Q., Li, Y., Du, Y., Chen, R., Cao, H., Li, N., Cao, S., Wang, J., Bovenberg, J. A., Pe'er, I., Slagboom, P. E., Van Duijn, C. M., Boomsma, D. I., Van Ommen, G. J. B., De Bakker, P. I. W., Swertz, M. A. & Wijmenga, C., Jan 1 2014, In: Nature Genetics. 46, 8, p. 818-825 8 p.

    Research output: Contribution to journalArticlepeer-review

    448 Scopus citations
  • Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma

    Campbell, C. D., Mohajeri, K., Malig, M., Hormozdiari, F., Nelson, B., Du, G., Patterson, K. M., Eng, C., Torgerson, D. G., Hu, D., Herman, C., Chong, J. X., Ko, A., O'Roak, B. J., Krumm, N., Vives, L., Lee, C., Roth, L. A., Rodriguez-Cintron, W., Rodriguez-Santana, J. & 13 others, Brigino-Buenaventura, E., Davis, A., Meade, K., LeNoir, M. A., Thyne, S., Jackson, D. J., Gern, J. E., Lemanske, R. F., Shendure, J., Abney, M., Burchard, E. G., Ober, C. & Eichler, E. E., Aug 12 2014, In: PLoS One. 9, 8, e104396.

    Research output: Contribution to journalArticlepeer-review

    22 Scopus citations
  • 2013

    Great ape genetic diversity and population history

    Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., Veeramah, K. R., Woerner, A. E., O'Connor, T. D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A. E., Malig, M., Hernandez-Rodriguez, J., Hernando-Herraez, I. & 55 others, Prüfer, K., Pybus, M., Johnstone, L., Lachmann, M., Alkan, C., Twigg, D., Petit, N., Baker, C., Hormozdiari, F., Fernandez-Callejo, M., Dabad, M., Wilson, M. L., Stevison, L., Camprub, C., Carvalho, T., Ruiz-Herrera, A., Vives, L., Mele, M., Abello, T., Kondova, I., Bontrop, R. E., Pusey, A., Lankester, F., Kiyang, J. A., Bergl, R. A., Lonsdorf, E., Myers, S., Ventura, M., Gagneux, P., Comas, D., Siegismund, H., Blanc, J., Agueda-Calpena, L., Gut, M., Fulton, L., Tishkoff, S. A., Mullikin, J. C., Wilson, R. K., Gut, I. G., Gonder, M. K., Ryder, O. A., Hahn, B. H., Navarro, A., Akey, J. M., Bertranpetit, J., Reich, D., Mailund, T., Schierup, M. H., Hvilsom, C., Andrés, A. M., Wall, J. D., Bustamante, C. D., Hammer, M. F., Eichler, E. E. & Marques-Bonet, T., Jul 5 2013, In: Nature. 499, 7459, p. 471-475 5 p.

    Research output: Contribution to journalArticlepeer-review

    474 Scopus citations
  • Integrative annotation of variants from 1092 humans: Application to cancer genomics

    1000 Genomes Project Consortium, Jan 1 2013, In: Science. 342, 6154, 1235587.

    Research output: Contribution to journalArticlepeer-review

    258 Scopus citations
  • Rates and patterns of great ape retrotransposition

    Hormozdiari, F., Konkel, M. K., Prado-Martinez, J., Chiatante, G., Herraez, I. H., Walker, J. A., Nelson, B., Alkan, C., Sudmant, P. H., Huddleston, J., Catacchio, C. R., Ko, A., Malig, M., Baker, C., Marques-Bonet, T., Ventura, M., Batzer, M. A. & Eichler, E. E., Aug 13 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 33, p. 13457-13462 6 p.

    Research output: Contribution to journalArticlepeer-review

    38 Scopus citations
  • The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild

    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., de la Calle-Mustienes, E., Casillas, S., Rubio-Acero, R., Melé, M., Engelken, J. & 11 others, Caceres, M., Gomez-Skarmeta, J. L., Gut, M., Bertranpetit, J., Gut, I. G., Abello, T., Eichler, E. E., Mingarro, I., Lalueza-Fox, C., Navarro, A. & Marques-Bonet, T., May 31 2013, In: BMC Genomics. 14, 1, 363.

    Research output: Contribution to journalArticlepeer-review

    31 Scopus citations
  • 2012

    An integrated map of genetic variation from 1,092 human genomes

    Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Donnelly, P., Eichler, E. E., Flicek, P., Gabriel, S. B., Gibbs, R. A., Green, E. D., Hurles, M. E., Knoppers, B. M., Korbel, J. O., Lander, E. S., Lee, C., Lehrach, H., Mardis, E. R., Marth, G. T. & 371 others, McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Li, Z., Liu, X., Lu, Y., Ma, X., Su, Z., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Zhou, Y., Gupta, N., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. 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Z., Yang, G., Jia You, C., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Duncanson, A., Dunn, M., Guyer, M. S., Peterson, J. L. & Lacroute, P., Nov 1 2012, In: Nature. 491, 7422, p. 56-65 10 p.

    Research output: Contribution to journalArticlepeer-review

    5373 Scopus citations
  • From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer

    Lapuk, A. V., Wu, C., Wyatt, A. W., McPherson, A., McConeghy, B. J., Brahmbhatt, S., Mo, F., Zoubeidi, A., Anderson, S., Bell, R. H., Haegert, A., Shukin, R., Wang, Y., Fazli, L., Hurtado-Coll, A., Jones, E. C., Hach, F., Hormozdiari, F., Hajirasouliha, I., Boutros, P. C. & 12 others, Bristow, R. G., Zhao, Y., Marra, M. A., Fanjul, A., Maher, C. A., Chinnaiyan, A. M., Rubin, M. A., Beltran, H., Cenk Sahinalp, S., Gleave, M. E., Volik, S. V. & Collins, C. C., Jan 1 2012, In: Journal of Pathology. 227, 3, p. 286-297 12 p.

    Research output: Contribution to journalArticlepeer-review

    140 Scopus citations
  • Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer

    Wu, C., Wyatt, A. W., Lapuk, A. V., McPherson, A., McConeghy, B. J., Bell, R. H., Anderson, S., Haegert, A., Brahmbhatt, S., Shukin, R., Mo, F., Li, E., Fazli, L., Hurtado-Coll, A., Jones, E. C., Butterfield, Y. S., Hach, F., Hormozdiari, F., Hajirasouliha, I., Boutros, P. C. & 10 others, Bristow, R. G., Jones, S. J. M., Hirst, M., Marra, M. A., Maher, C. A., Chinnaiyan, A. M., Sahinalp, S. C., Gleave, M. E., Volik, S. V. & Collins, C. C., Jan 1 2012, In: Journal of Pathology. 227, 1, p. 53-61 9 p.

    Research output: Contribution to journalArticlepeer-review

    54 Scopus citations
  • 2011

    Alu repeat discovery and characterization within human genomes

    Hormozdiari, F., Alkan, C., Ventura, M., Hajirasouliha, I., Malig, M., Hach, F., Yorukoglu, D., Dao, P., Bakhshi, M., Sahinalp, S. C. & Eichler, E. E., Jan 1 2011, In: Genome Research. 21, 6, p. 840-849 10 p.

    Research output: Contribution to journalArticlepeer-review

    79 Scopus citations
  • Comrad: Detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data

    McPherson, A., Wu, C., Hajirasouliha, I., Hormozdiari, F., Hach, F., Lapuk, A., Volik, S., Shah, S., Collins, C. & Sahinalp, S. C., Jan 1 2011, In: Bioinformatics. 27, 11, p. 1481-1488 8 p., btr184.

    Research output: Contribution to journalArticlepeer-review

    28 Scopus citations
  • Defuse: An algorithm for gene fusion discovery in tumor rna-seq data

    McPherson, A., Hormozdiari, F., Zayed, A., Giuliany, R., Ha, G., Sun, M. G. F., Griffith, M., Moussavi, A., Senz, J., Melnyk, N., Pacheco, M., Marra, M. A., Hirst, M., Nielsen, T. O., Sahinalp, S. C., Huntsman, D. & Shah, S. P., May 1 2011, In: PLoS Computational Biology. 7, 5, e1001138.

    Research output: Contribution to journalArticlepeer-review

    378 Scopus citations
  • Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

    Ventura, M., Catacchio, C. R., Alkan, C., Marques-Bonet, T., Sajjadian, S., Graves, T. A., Hormozdiari, F., Navarro, A., Malig, M., Baker, C., Lee, C., Turner, E. H., Chen, L., Kidd, J. M., Archidiacono, N., Shendure, J., Wilson, R. K. & Eichler, E. E., Oct 1 2011, In: Genome Research. 21, 10, p. 1640-1649 10 p.

    Research output: Contribution to journalArticlepeer-review

    53 Scopus citations
  • Mapping copy number variation by population-scale genome sequencing

    Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., Cheetham, R. K., Chinwalla, A., Conrad, D. F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L. M., Iqbal, Z., Kang, S., Kidd, J. M. & 38 others, Konkel, M. K., Korn, J., Khurana, E., Kural, D., Lam, H. Y. K., Leng, J., Li, R., Li, Y., Lin, C. Y., Luo, R., Mu, X. J., Nemesh, J., Peckham, H. E., Rausch, T., Scally, A., Shi, X., Stromberg, M. P., Sütz, A. M., Urban, A. E., Walker, J. A., Wu, J., Zhang, Y., Zhang, Z. D., Batzer, M. A., Ding, L., Marth, G. T., McVean, G., Sebat, J., Snyder, M., Wang, J., Ye, K., Eichler, E. E., Gerstein, M. B., Hurles, M. E., Lee, C., McCarroll, S. A., Korbel, J. O. & Collins, F. S., Feb 3 2011, In: Nature. 470, 7332, p. 59-65 7 p.

    Research output: Contribution to journalArticlepeer-review

    775 Scopus citations
  • Simultaneous structural variation discovery among multiple paired-end sequenced genomes

    Hormozdiari, F., Hajirasouliha, I., McPherson, A., Eichler, E. E. & Cenk Sahinalp, S., Jan 1 2011, In: Genome Research. 21, 12, p. 2203-2212 10 p.

    Research output: Contribution to journalArticlepeer-review

    52 Scopus citations
  • 2010

    A map of human genome variation from population-scale sequencing

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    Research output: Contribution to journalArticlepeer-review

    5670 Scopus citations
  • Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

    Hajirasouliha, I., Hormozdiari, F., Alkan, C., Kidd, J. M., Birol, I., Eichler, E. E. & Sahinalp, S. C., Apr 12 2010, In: Bioinformatics. 26, 10, p. 1277-1283 7 p., btq152.

    Research output: Contribution to journalArticlepeer-review

    78 Scopus citations
  • Diversity of human copy number variation and multicopy genes

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    Research output: Contribution to journalArticlepeer-review

    460 Scopus citations
  • Next-generation VariationHunter: Combinatorial algorithms for transposon insertion discovery

    Hormozdiari, F., Hajirasouliha, I., Dao, P., Hach, F., Yorukoglu, D., Alkan, C., Eichler, E. E. & Sahinalp, S. C., Jun 1 2010, In: Bioinformatics. 26, 12, btq216.

    Research output: Contribution to journalArticlepeer-review

    154 Scopus citations