Now showing items 1-9 of 9

    • 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 ...
    • Determining the origin of synchronous multifocal bladder cancer by exome sequencing 

      Acar, Ö.; Özkurt, E.; Demir, G.; Saraç, H.; Alkan C.; Esen, T.; Somel, M.; Lack, N. A. (BioMed Central Ltd., 2015)
      Background: Synchronous multifocal tumours are commonly observed in urothelial carcinomas of the bladder. The origin of these physically independent tumours has been proposed to occur by either intraluminal migration ...
    • Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair 

      Dal, G. M.; Ergüner, B.; Saǧıroǧlu, M. S.; Yüksel, B.; Onat, O. E.; Alkan C.; Özçelik, T. (B M J Group, 2014)
      Background: Human de novo single-nucleotide variation (SNV) rate is estimated to range between 0.82-1.70×10-8 mutations per base per generation. However, contribution of early postzygotic mutations to the overall human de ...
    • A high-coverage genome sequence from an archaic Denisovan individual 

      Meyer, M.; Kircher, M.; Gansauge, Marie-Theres; Li, H.; Racimo, F.; Mallick, S.; Schraiber, J. G.; Jay, F.; Prüfer, K.; Filippo, Cesare de; Sudmant, P. H.; Alkan C.; Fu, Q.; Do, R.; Rohland, N.; Tandon, A.; Siebauer, M.; Green, R. E.; Bryc, K.; Briggs, A. W.; Stenzel, U.; Dabney, J.; Shendure, J.; Kitzman, J.; Hammer, M. F.; Shunkov, M. V.; Derevianko, A. P.; Patterson, N.; Andrés, A. M.; Eichler, E. E.; Slatkin, M.; Reich, D.; Kelso, J.; Pääbo, S. (American Association for the Advancement of Science (A A A S), 2012-10-12)
      We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30x) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation ...
    • Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci 

      Sanders, S. J.; He, X.; Willsey, A. J.; Ercan-Sencicek, A. G.; Samocha, K. E.; Cicek, A. E.; Murtha, M. T.; Bal, V. H.; Bishop, S. L.; Dong, S.; Goldberg, A. P.; Jinlu, C.; Keaney, J. F.; Keaney III, J. F.; Mandell, J. D.; Moreno-De-Luca, D.; Poultney, C. S.; Robinson, E. B.; Smith L.; Solli-Nowlan, T.; Su, M. Y.; Teran, N. A.; Walker, M. F.; Werling, D. M.; Beaudet, A. L.; Cantor, R. M.; Fombonne, E.; Geschwind, D. H.; Grice, D. E.; Lord, C.; Lowe, J. K.; Mane, S. M.; Martin, D.M.; Morrow, E. M.; Talkowski, M. E.; Sutcliffe, J. S.; Walsh, C. A.; Yu, T. W.; Ledbetter, D. H.; Martin, C. L.; Cook, E. H.; Buxbaum, J. D.; Daly, M. J.; Devlin, B.; Roeder, K.; State, M. W. (Cell Press, 2015)
      Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci (1q21.1, ...
    • PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways 

      Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Nişancı, Gürkan; Çetin Atalay, Rengül; Öztürk, Mehmet (Oxford University Press, 2002-06)
      Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about ...
    • PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways 

      Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Nişancı, Gürkan; Çetin Atalay, Rengül; Öztürk, Mehmet (American Society for Biochemistry and Molecular Biology(ASBMB), 2002-09)
    • A privacy-preserving solution for compressed storage and selective retrieval of genomic data 

      Huang Z.; Ayday, E.; Lin, H.; Aiyar, R. S.; Molyneaux, A.; Xu, Z.; Fellay, J.; Steinmetz, L. M.; Hubaux, Jean-Pierre (Cold Spring Harbor Laboratory Press, 2016)
      In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference ...
    • Skewed X inactivation in an X linked nystagmus family resulted from a novel, p.R229G, missense mutation in the FRMD7 gene 

      Kaplan, Y.; Vargel, I.; Kansu, T.; Akin, B.; Rohmann, E.; Kamaci, S.; Uz, E.; Ozcelik, T.; Wollnik, B.; Akarsu, N. A. (BMJ Group, 2008)
      Aims: This study aimed to identify the underlying genetic defect of a large Turkish X linked nystagmus (NYS) family. Methods: Both Xp11 and Xq26 loci were tested by linkage analysis. The 12 exons and intron-exon junctions ...