Now showing items 1-20 of 24

    • Automatic characterization of copy number polymorphism using high throughput sequencing 

      Alkan, Can (TÜBİTAK, 2020)
      Genome structural variation, broadly defined as alterations longer than 50 bp, are important sources for genetic variation among humans, including those that cause complex diseases such as autism, developmental delay, and ...
    • Building and improving reference genome assemblies 

      Steinberg, K. M.; Schneider, V. A.; Alkan, Can; Montague, M. J.; Warren, W. C.; Church, D. M.; Wilson, R. K. (IEEE, 2017-01)
      A genome sequence assembly provides the foundation for studies of genotypic and phenotypic variation, genome structure, and evolution of the target organism. In the past four decades, there has been a surge of new sequencing ...
    • Can you really anonymize the donors of genomic data in today’s digital world? 

      Alser, Mohammed; Almadhoun, Nour; Nouri, Azita; Alkan, Can; Ayday, Erman (Springer, 2016-09)
      The rapid progress in genome sequencing technologies leads to availability of high amounts of genomic data. Accelerating the pace of biomedical breakthroughs and discoveries necessitates not only collecting millions of ...
    • Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools 

      Demir, Gülfem; Alkan, Can (Scientific and Technical Research Council of Turkey, 2019)
      Microsatellite polymorphism has always been a challenge for genome assembly and sequence alignment due to sequencing errors, short read lengths, and high incidence of polymerase slippage in microsatellite regions. Despite ...
    • Copy number variation of individual cattle genomes using next-generation sequencing 

      Bickhart, D.M.; Hou, Y.; Schroeder, S.G.; Alkan C.; Cardone, M.F.; Matukumalli L.K.; Song J.; Schnabel, R.D.; Ventura M.; Taylor J.F.; Garcia J.F.; Van Tassell, C.P.; Sonstegard, T.S.; Eichler, E. E.; Liu G.E. (2012)
      Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we ...
    • Demographically-based evaluation of genomic regions under selection in domestic dogs 

      Freedman, A. H.; Schweizer, R. M.; Vecchyo, D. Ortega-Del; Han, E.; Davis, B. W.; Gronau, I.; Silva, P. M.; Galaverni, M.; Fan, Z.; Marx, P.; Lorente-Galdos, B.; Ramirez, O.; Hormozdiari, F.; Alkan C.; Vilà, C.; Squire K.; Geffen, E.; Kusak, J.; Boyko, A. R.; Parker, H. G.; Lee C.; Tadigotla, V.; Siepel, A.; Bustamante, C. D.; Harkins, T. T.; Nelson, S. F.; Marques Bonet, T.; Ostrander, E. A.; Wayne, R. K.; Novembre, J. (Public Library of Science, 2016)
      Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when ...
    • Fast and accurate mapping of complete genomics reads 

      Lee, D.; Hormozdiari, F.; Xin, H.; Hach, F.; Mutlu, O.; Alkan C. (Academic Press, 2015)
      Many recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of ...
    • GenASM: a high-performance, low-power approximate string matching acceleration framework for genome sequence analysis 

      Şenol-Çalı, D.; Kalsi, G. S.; Bingöl, Zülal; Fırtına, C.; Subramanian, L.; Kim, J. S.; Ausavarungnirun, R.; Alser, M.; Gomez-Luna, J.; Boroumand, A.; Norion, A.; Scibisz, A.; Subramoneyon, S.; Alkan, Can; Ghose, S.; Mutlu, Onur (IEEE Computer Society, 2020)
      Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. To perform genome sequencing, devices extract ...
    • Genetic education and the challenge of genomic medicine development of core competences to support preparation of health professionals in Europe 

      Skirton, H.; Lewis, C.; Kent, A.; Domenico, A. C.; Bloch-Zupan, A.; Cornel, M.; DeLozier, C.; Farndon, P.; Goetz, P.; Hongson, S.; Houge, G.; Hulten, M.; Kosztolanyi, G.; Kucinskas, V.; Ozcelik, T.; Serqueiros, J.; Soller, M.; Tranebjaerg, L. (Nature Publishing Group, 2010)
      The use of genetics and genomics within a wide range of health-care settings requires health professionals to develop expertise to practise appropriately. There is a need for a common minimum standard of competence in ...
    • Genome reconstruction attacks on genomic data-sharing beacons 

      Ayöz, Kerem (Bilkent University, 2021-07)
      Sharing genome data in a privacy-preserving way stands as a major bottleneck in front of the scientific progress promised by the big data era in genomics. A community-driven protocol named genomic data-sharing beacon ...
    • Genomic landscape of the Greater Middle East 

      Özçelik, T.; Onat, O. E. (Nature Publishing Group, 2016-09)
      Study of the Greater Middle East (GME), home to approximately 10% of the world's population, has made invaluable contributions to the characterization of rare genetic disease, especially recessive conditions arising from ...
    • A global reference for human genetic variation 

      Auton, A.; Abecasis, G. R.; Altshuler, D. M.; Durbin, R. M.; 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.; Boerwinkle, E.; Doddapaneni, H.; Han, Y.; Korchina, V.; Kovar, C.; Lee, S.; Muzny, D.; Reid, J. G.; Zhu, Y.; Chang, Y.; Feng, Q.; Fang, X.; Guo, X.; Jian, M.; Jiang, H.; Jin, X.; Lan, T.; Li, G.; Li, J.; Li, Y.; Liu, S.; Liu, X.; Lu, Y.; Ma, X.; Tang, M.; Wang, B.; Wang, G.; Wu, H.; Wu, R.; Xu, X.; Yin, Y.; Zhang, D.; Zhang, W.; Zhao, J.; Zhao, M.; Zheng, X.; Gupta, N.; Gharani, N.; Toji, L. H.; Gerry, N. P.; Resch, A. M.; Barker, J.; Clarke, L.; Gil, L.; Hunt, S. E.; Kelman, G.; Kulesha, E.; Leinonen, R.; McLaren, W. M.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Smith, R. E.; Streeter, I.; Thormann, A.; Toneva, I.; Vaughan, B.; 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, Marie-Laure; Fulton, L.; 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.; Phan, L.; Ponomarov, S.; Schneider, V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang, H.; Balasubramaniam, S.; Burton, J.; Danecek, P.; Keane, T. M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker, J.; Quail, M.; Davies, C. J.; Gollub, J.; Webster, T.; Wong, B.; Zhan, Y.; Campbell, C. L.; Kong, Y.; Marcketta, A.; Yu, F.; Antunes, L.; Bainbridge, M.; Sabo, A.; Huang, Z.; Coin, L. J. M.; Fang, L.; Li, Q.; Li, Z.; Lin, H.; Liu, B.; Luo, R.; Shao, H.; Xie, Y.; Ye, C.; Yu, C.; Zhang, F.; Zheng, H.; Zhu, H.; Alkan, C.; Dal, E.; Kahveci, F.; Garrison, E. P.; Kural, D.; Lee, W. P.; Leong, W. F.; Stromberg, M.; Ward, A. N.; Wu, J.; Zhang, M.; Daly, M. J.; DePristo, M. A.; Handsaker, R. E.; Banks, E.; Bhatia, G.; Del Angel, G.; Genovese, G.; Li, H.; Kashin, S.; McCarroll, S. A.; Nemesh, J. C.; Poplin, R. E.; Yoon, S. C.; Lihm, J.; Makarov, V.; Gottipati, S.; Keinan, A.; Rodriguez-Flores, J. L.; Rausch, T.; Fritz, M. H.; Stütz, A. M.; Beal, K.; Datta, A.; Herrero, J.; Ritchie, G. R. S.; Zerbino, D.; Sabeti, P. C.; Shlyakhter, I.; Schaffner, S. F.; Vitti, J.; Cooper, D. N.; Ball, E. V.; Stenson, P. D.; Barnes, B.; Bauer, M.; Cheetham, R. K.; Cox, A.; Eberle, M.; Kahn, S.; Murray, L.; Peden, J.; Shaw, R.; Kenny, E. E.; Batzer, M. A.; Konkel, M. K.; Walker, J. A.; MacArthur, D. G.; Lek, M.; Herwig, R.; Ding, L.; Koboldt, D. C.; Larson, D.; Ye, K.; Gravel, S.; Swaroop, A.; Chew, E.; Lappalainen, T.; Erlich, Y.; Gymrek, M.; Willems, T. F.; Simpson, J. T.; Shriver, M. D.; Rosenfeld, J. A.; Bustamante, C. D.; Montgomery, S. B.; De La Vega, F. M.; Byrnes, J. K.; Carroll, A. W.; DeGorter, M. K.; Lacroute, P.; Maples, B. K.; Martin, A. R.; Moreno-Estrada, A.; Shringarpure, S. S.; Zakharia, F.; Halperin, E.; Baran, Y.; Cerveira, E.; Hwang, J.; Malhotra, A.; Plewczynski, D.; Radew, K.; Romanovitch, M.; Zhang, C.; Hyland, F. C. L.; Craig, D. W.; Christoforides, A.; Homer, N.; Izatt, T.; Kurdoglu, A. A.; Sinari, S. A.; Squire, K.; Xiao, C.; Sebat, J.; Antaki, D.; Gujral, M.; Noor, A.; 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.; Devine, S. E.; Kang, H. M.; Kidd, J. M.; Blackwell, T.; Caron, S.; Chen, W.; Emery, S.; Fritsche, L.; Fuchsberger, C.; Jun, G.; Li, B.; Lyons, R.; Scheller, C.; Sidore, C.; Song, S.; Sliwerska, E.; Taliun, D.; Tan, A.; Welch, R.; Wing, M. K.; Zhan, X.; Awadalla, P.; Hodgkinson, A.; Li, Y.; Shi, X.; Quitadamo, A.; Lunter, G.; Marchini, J. L.; Myers, S.; Churchhouse, C.; Delaneau, O.; Gupta-Hinch, A.; Kretzschmar, W.; Iqbal, Z.; Mathieson, I.; Menelaou, A.; Rimmer, A.; Xifara, D. K.; Oleksyk, T. K.; Fu, Y.; Liu, X.; Xiong, M.; Jorde, L.; Witherspoon, D.; Xing, J.; Browning, B. L.; Browning, S. R.; Hormozdiari, F.; Sudmant, P. H.; Khurana, E.; Tyler-Smith, C.; Albers, C. A.; Ayub, Q.; Chen, Y.; Colonna, V.; Jostins, L.; Walter, K.; Xue, Y.; Gerstein, M. B.; Abyzov, A.; Balasubramanian, S.; Chen, J.; Clarke, D.; Fu, Y.; Harmanci, A. O.; Jin, M.; Lee, D.; Liu, J.; Mu, X. J.; Zhang, J.; Zhang, Y.; Hartl, C.; Shakir, K.; Degenhardt, J.; Meiers, S.; Raeder, B.; Casale, F. P.; Stegle, O.; Lameijer, E. W.; Hall, I.; Bafna, V.; Michaelson, J.; Gardner, E. J.; Mills, R. E.; Dayama, G.; Chen, K.; Fan, X.; Chong, Z.; Chen, T.; Chaisson, M. J.; Huddleston, J.; Malig, M.; Nelson, B. J.; Parrish, N. F.; Blackburne, B.; Lindsay, S. J.; Ning, Z.; Zhang, Y.; Lam, H.; Sisu, C.; Challis, D.; Evani, U. S.; Lu, J.; Nagaswamy, U.; Yu, J.; Li, W.; Habegger, L.; Yu, H.; Cunningham, F.; Dunham, I.; Lage, K.; Jespersen, J. B.; Horn, H.; Kim, D.; Desalle, R.; Narechania, A.; Sayres, M. A. W.; Mendez, F. L.; Poznik, G. D.; Underhill, P. A.; Mittelman, D.; Banerjee, R.; Cerezo, M.; Fitzgerald, T. W.; Louzada, S.; Massaia, A.; Yang, F.; Kalra, D.; Hale, W.; Dan, X.; Barnes, K. C.; Beiswanger, C.; Cai, H.; Cao, H.; Henn, B.; Jones, D.; Kaye, J. S.; Kent, A.; Kerasidou, A.; Mathias, R.; Ossorio, P. N.; Parker, M.; Rotimi, C. N.; Royal, C. D.; Sandoval, K.; Su, Y.; Tian, Z.; Tishkoff, S.; Via, M.; Wang, Y.; Yang, H.; Yang, L.; Zhu, J.; Bodmer, W.; Bedoya, G.; Cai, Z.; Gao, Y.; Chu, J.; Peltonen, L.; Garcia-Montero, A.; Orfao, A.; Dutil, J.; Martinez-Cruzado, J. C.; Mathias, R. A.; Hennis, A.; Watson, H.; McKenzie, C.; Qadri, F.; LaRocque, R.; Deng, X.; Asogun, D.; Folarin, O.; Happi, C.; Omoniwa, O.; Stremlau, M.; Tariyal, R.; Jallow, M.; Joof, F. S.; Corrah, T.; Rockett, K.; Kwiatkowski, D.; Kooner, J.; Hien, T. T.; Dunstan, S. J.; ThuyHang, N.; Fonnie, R.; Garry, R.; Kanneh, L.; Moses, L.; Schieffelin, J.; Grant, D. S.; Gallo, C.; Poletti, G.; Saleheen, D.; Rasheed, A.; Brooks, L. D.; Felsenfeld, A. L.; McEwen, J. E.; Vaydylevich, Y.; Duncanson, A.; Dunn, M.; Schloss, J. A. (Nature Publishing Group, 2015)
      The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report ...
    • 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.; 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.-L.; Fulton L.; Fulton, R.; Weinstock G.M.; Balasubramaniam, S.; Burton J.; Danecek P.; Keane, T.M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker J.; Quail, M.; Davies, C.J.; Gollub J.; Webster, T.; Wong, B.; Zhan, Y.; Auton, A.; Yu F.; Bainbridge, M.; Challis, D.; Evani, U.S.; Lu J.; Nagaswamy, U.; Sabo, A.; Wang Y.; Yu J.; Coin L.J.M.; Fang L.; Li Q.; 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.; Garrison, E.P.; Kural, D.; Lee W.-P.; Fung Leong W.; Ward, A.N.; Wu J.; Zhang, M.; Griffin L.; Hsieh, C.-H.; Mills, R.E.; Shi X.; Von Grotthuss, M.; Zhang, C.; Daly, M.J.; Depristo, M.A.; 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.; Yoon, S.C.; Lihm J.; Makarov V.; Jin H.; Kim W.; Cheol Kim, K.; Rausch, T.; Beal, K.; Cunningham F.; Herrero J.; McLaren W.M.; Ritchie G.R.S.; 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.; Barnes, B.; Bauer, M.; Keira Cheetham, R.; Cox, T.; Eberle, M.; Kahn, S.; Murray L.; Peden J.; Shaw, R.; Ye, K.; Batzer, M.A.; Konkel, M.K.; Walker J.A.; MacArthur, D.G.; Lek, M.; Herwig, R.; Shriver, M.D.; Bustamante, C.D.; Byrnes J.K.; De La Vega F.M.; Gravel, S.; Kenny, E.E.; Kidd J.M.; 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.; Xiao, C.; Sebat J.; Bafna V.; Ye, K.; Burchard, E.G.; Hernandez, R.D.; Gignoux, C.R.; Haussler, D.; Katzman, S.J.; James Kent W.; 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.; Min Kang H.; Anderson P.; Angius, A.; Bigham, A.; Blackwell, T.; Busonero F.; Cucca F.; Fuchsberger, C.; Jones, C.; Jun G.; Li Y.; Lyons, R.; Maschio, A.; Porcu, E.; Reinier F.; Sanna, S.; Schlessinger, D.; Sidore, C.; Tan, A.; Kate Trost, M.; Awadalla P.; Hodgkinson, A.; Lunter G.; 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.; Chen, K.; Chinwalla, A.; Ding L.; Dooling, D.; Koboldt, D.C.; McLellan, M.D.; Wallis J.W.; Wendl, M.C.; Zhang Q.; Tyler-Smith, C.; Albers, C.A.; Ayub Q.; Chen, Y.; Coffey, A.J.; Colonna V.; Huang, N.; Jostins L.; Li H.; Scally, A.; 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.; Jasmine Mu X.; Sisu, C.; Degenhardt J.; Stütz, A.M.; Keira Cheetham, R.; Church, D.; Michaelson J.J.; Blackburne, B.; Lindsay, S.J.; Ning, Z.; Frankish, A.; Harrow J.; Mu X.J.; Fowler G.; Hale W.; Kalra, D.; Barker J.; Kelman G.; Kulesha, E.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Streeter I.; Toneva I.; Vaughan, B.; 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.; O'Sullivan, C.; Ostapchuk, Y.; Phan L.; Ponomarov, S.; Schneider V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang H.; Barnes, K.C.; Beiswanger, C.; Cai H.; Cao H.; Gharani, N.; Henn, B.; Jones, D.; Kaye J.S.; Kent, A.; Kerasidou, A.; Mathias, R.; Ossorio P.N.; Parker, M.; Reich, D.; Rotimi, C.N.; Royal, C.D.; Sandoval, K.; Su, Y.; Tian, Z.; Tishkoff, S.; Toji L.H.; Via, M.; Wang Y.; Yang H.; Yang L.; Zhu J.; Bodmer W.; Bedoya G.; Ming, C.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. (Nature Publishing Group, 2012)
      By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes ...
    • Integrating biological pathways and genomic profiles with ChiBE 2 

      Babur, O.; Dogrusoz, U.; Çakır, M.; Aksoy, B. A.; Schultz, N.; Sander, C.; Demir, E. (BioMed Central Ltd., 2014)
      Background: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets.Results: ChiBE is a free, open-source software tool for visualizing, ...
    • Integrating biological pathways and genomic profiles with ChiBE 2 

      Çakır, Merve (Bilkent University, 2013)
      Biological pathways store information about spatial and temporal organization of interactions taking place in an organism. They hold valuable information that can assist scientific community in understanding the details ...
    • Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal 

      Gao J.; Aksoy, B. A.; Dogrusoz, U.; Dresdner, G.; Gross, B.; Sumer, S. O.; Sun, Y.; Jacobsen, A.; Sinha, R.; Larsson, E.; Cerami, E.; Sander, C.; Schultz, N. (American Association for the Advancement of Science (A A A S), 2013)
      The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer ...
    • On genomic repeats and reproducibility 

      Firtina, C.; Alkan C. (Oxford University Press, 2016)
      Results: Here, we present a comprehensive analysis on the reproducibility of computational characterization of genomic variants using high throughput sequencing data. We reanalyzed the same datasets twice, using the same ...
    • Privacy in the genomic era 

      Naveed, M.; Ayday, E.; Clayton, E.W.; Fellay J.; Gunter, C.A.; Hubaux J.-P.; Malin, B.A.; Wang, X. (Association for Computing Machinery, 2015)
      Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highlydetailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, ...
    • Privacy preserving and robust watermarking on sequential genome data using belief propagation and local differential privacy 

      Öksüz, Abdullah Çağlar (Bilkent University, 2020-08)
      Genome data is a subject of study for both biology and computer science since the start of Human Genome Project in 1990. Since then, genome sequencing for medical and social purposes becomes more and more available and ...
    • Privacy-preserving genomic testing in the clinic: a model using HIV treatment 

      Mclaren, P. J.; Raisaro, J. L.; Aouri, M.; Rotger, M.; Ayday, E.; Bartha, I.; Delgado, M. B.; Vallet, Y.; Günthard, H. F.; Cavassini, M.; Furrer, H.; Doco-Lecompte, T.; Marzolini, C.; Schmid, P.; Di Benedetto, C.; Decosterd, L. A.; Fellay, J.; Hubaux, Jean-Pierre; Telenti A. (Nature Publishing Group, 2016)
      Purpose:The implementation of genomic-based medicine is hindered by unresolved questions regarding data privacy and delivery of interpreted results to health-care practitioners. We used DNA-based prediction of HIV-related ...