Recent Submissions

  • MAGNET: understanding and improving the accuracy of genome pre-alignment filtering 

    Alser, M.; Mutlu, O.; Alkan, C. (I P S I, 2017)
    In the era of high throughput DNA sequencing (HTS) technologies, calculating the edit distance (i.e.,the minimum number of substitutions, insertions, and deletionsbetween a pair of sequences) forbillions of ...
  • A utility maximizing and privacy preserving approach for protecting kinship in genomic databases 

    Kale, G.; Ayday, E.; Tastan, O. (Oxford University Press, 2018-01-15)
    Rapid and low cost sequencing of genomes enabled widespread use of genomic data in research studies and personalized customer applications, where genomic data is shared in public databases. Although the identities of the ...
  • Spatio-temporal linkage over location-enhanced services 

    Basık, F.; Gedik, B.; Etemoğlu, Ç.; Ferhatosmanoğlu, H. (Institute of Electrical and Electronics Engineers, 2018)
    We are witnessing an enormous growth in the volume of data generated by various online services. An important portion of this data contains geographic references, since many of these services are location-enhanced and thus ...
  • Approximation algorithms for visibility computation and testing over a terrain 

    Alipour, S.; Ghodsi, M.; Güdükbay, U.; Golkari, M. (Springer, 2017)
    Given a 2.5D terrain and a query point p on or above it, we want to find the triangles of terrain that are visible from p. We present an approximation algorithm to solve this problem. We implement the algorithm and test ...
  • Characterization of the transcriptional and metabolic responses of pediatric high grade gliomas to mTOR-HIF-1a... 

    Nguyen, A.; Moussallieh, F. M.; Mackay, A.; Cicek, A. E.; Coca, A.; Chenard, M. P.; Weingertner, N.; Lhermitte, B.; Letouzé, E.; Guérin, E.; Pencreach, E.; Jannier, S.; Guenot, D.; Namer, I. J.; Jones, C.; Entz-Werlé, N. (Impact Journals LLC, 2017-03-23)
    Pediatric high grade glioma (pHGGs), including sus-tentorial and diffuse intrinsic pontine gliomas, are known to have a very dismal prognosis. For instance, even an increased knowledge on molecular biology driving this ...
  • Burn all your textbooks 

    Akman, V. (Australasian Association for Logic, 2017)
    The standard propositional exposition of necessary and su cient conditions, as available in introductory logic texts, leads to a contradiction. It should be abolished.
  • GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping 

    Alser, M.; Hassan, H.; Xin, H.; Ergin, O.; Mutlu, O.; Alkan, C. (Oxford University Press, 2017-11-01)
    High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of ...
  • Quantifying interdependent risks in genomic privacy 

    Humbert, M.; Ayday, E.; Hubaux, Jean-Pierre; Telenti, A. (Association for Computing Machinery, 2017-02)
    The rapid progress in human-genome sequencing is leading to a high availability of genomic data. These data is notoriously very sensitive and stable in time, and highly correlated among relatives. In this article, we study ...
  • Viva Europa, a land of excellence in research and innovation for health and wellbeing 

    Auffray, C.; Sagner, M.; Abdelhak, S; Adcock, I.; Antonarakis, S.; Arena, R.; Argoul, F.; Balling, R.; Barabasi, Albert-Laszlo; Beckmann, J.; Bjartell, A.; Bourgeon, T.; Boutron, B.; Brahmachari, S.; Brechot, C.; Brightling, C.; Cascante, M.; Cesario, A.; Charron, D.; Chen, Sai-Juan; Chen, Z.; Chung, F.; Clement, K.; Conesa, A.; Cozzone, A.; de Jong, M.; Deleuze, Jean-François; Demotes, J.; di Meglio, A.; Djukanovic, R.; Dogrusoz, U.; Epel, E.; Fischer, A.; Gelemanovic, A.; Goble, C.; Gojobori, T.; Goldman, M.; Goossens, H.; Gros, F.; Hainaut, P.; Guo, Yi-Ke; Harrison, D.; Hoffmann, H.; Hood, L.; Hunter, P.; Jacob, Y.; Kitano, H.; Klingmuller, U.; Knoppers, B.; Kolch, W.; Koopmans, M.; Lancet, D.; Laville, M.; Lehn, Jean-Marie; Lévi, F.; Lisistsa, A.; Lotteau, V.; Mayosi, B.; Metspalu, A.; Moreau, Y.; N'Dow, J.; Nicod, L.; Noble, D.; Nogueira, Maria-Manuela; Norrby-Teglund, A.; Openshaw, P.; Ozturk, M.; Palkonen, S.; Parodi, S.; Pellet, J.; Polasek, O.; Price, N.; Pristipino, C.; Radstake, T.; Raes, M.; Roca, J.; Rozman, D.; Sabatier, P.; Sasson, S.; Schmeck, B.; Serageldin, I.; Simonds, A.; Soares, B.; Sterk, P.; Superti-Furga, G.; Supple, D.; Tegner, J.; Uhlen, M.; van der Werf, S.; Villoslada, P.; Vinciguerra, M.; Volpert, V.; Webb, S.; Wouters, E.; Sanz, F.; Nobrega, F. (Wolters Kluwer Health, 2017-06-07)
  • Partitioning models for scaling parallel sparse matrix-matrix multiplication 

    Akbudak, K.; Selvitopi, O.; Aykanat, C. (Association for Computing Machinery, 2018-04)
    We investigate outer-product--parallel, inner-product--parallel, and row-by-row-product--parallel formulations of sparse matrix-matrix multiplication (SpGEMM) on distributed memory architectures. For each of these three ...
  • Metabolomic characterization of human hippocampus from drug-resistant epilepsy with mesial temporal seizure 

    Detour, J.; Bund, C.; Behr, C.; Cebula, H.; Cicek, E. A.; Valenti-Hirsch, Maria-Paola; Lannes, B.; Lhermitte, B.; Nehlig, A.; Kehrli, P.; Proust, F.; Hirsch, E.; Namer, Izzie-Jacques (Wiley-Blackwell Publishing, 2018-03)
    Within a complex systems biology perspective, we wished to assess whether hippocampi with established neuropathological features have distinct metabolome. Apparently normal hippocampi with no signs of sclerosis (noHS), ...
  • An inference attack on genomic data using kinship, complex correlations, and phenotype information 

    Deznabi, I.; Mobayen, M.; Jafari, N.; Tastan, O.; Ayday, E. (Association for Computing Machinery, 2018)
    Abstract—Individuals (and their family members) share (partial) genomic data on public platforms. However, using special characteristics of genomic data, background knowledge that can be obtained from the Web, and family ...
  • GOOWE: geometrically optimum and online-weighted ensemble classifier for evolving data streams 

    Bonab, H. R.; Can, F. (Association for Computing Machinery, 2018-01-25)
    Designing adaptive classifiers for an evolving data stream is a challenging task due to the data size and its dynamically changing nature. Combining individual classifiers in an online setting, the ensemble approach, is a ...
  • An analysis of social networks based on tera-scale telecommunication datasets 

    Aksu, H.; Korpeoglu, I.; Ulusoy, Ö. (Institute of Electrical and Electronics Engineers, 2016)
    With the popularization of mobile phone usage, telecommunication networks have turned into a socially binding medium. Considering the traces of human communication held inside these networks, telecommunication networks ...
  • Fine-grained object recognition and zero-shot learning in remote sensing imagery 

    Sumbul, G.; Cinbis, R. G.; Aksoy, S. (Institute of Electrical and Electronics Engineers, 2018-02)
    Fine-grained object recognition that aims to identify the type of an object among a large number of subcategories is an emerging application with the increasing resolution that exposes new details in image data. Traditional ...
  • Privacy-preserving aggregate queries for optimal location selection 

    Yilmaz, E.; Ferhatosmanoglu, H.; Ayday, E.; Aksoy, R. C. (IEEE, 2017-04-12)
    Today, vast amounts of location data are collected by various service providers. These location data owners have a good idea of where their users are most of the time. Other businesses also want to use this information for ...
  • Characterizing, predicting, and handling web search queries that match very few or no results 

    Sarigil, E.; Altingovde, I. S.; Blanco, R.; Cambazoglu, B. B.; Ozcan, R.; Ulusoy, Ö. (John Wiley & Sons, 2018)
    A non‐negligible fraction of user queries end up with very few or even no matching results in leading commercial web search engines. In this work, we provide a detailed characterization of such queries and show that search ...
  • Computational pan-genomics: status, promises and challenges 

    The Computational Pan-Genomics Consortium; Alkan, C. (Oxford University Press, 2018-01-01)
    Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of ...
  • Topic-based influence computation in social networks under resource constraints 

    Bingöl, K.; Eravcı, B.; Etemoğlu, Ç. Ö.; Ferhatosmanoğlu, H.; Gedik, B. (Institute of Electrical and Electronics Engineers, 2016-10-21)
    As social networks are constantly changing and evolving, methods to analyze dynamic social networks are becoming more important in understanding social trends. However, due to the restrictions imposed by the social network ...
  • Language runtime and optimizations in IBM streams 

    Schneider, S.; Gedik, B.; Hirzel, M. (IEEE, 2016)
    Stream processing is important for continuously transforming and analyzing the deluge of data that has revolutionized our world. Given the diversity of application domains, streaming applications must be both easy to ...

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