Recent Submissions

  • Microarray data analysis and pathway activity inference in PATIKA 

    Babur, Özgün; Demir, Emek; Ayaz, Aslı; Doğrusöz, Uğur; Sakarya, Onur (ISCB Org, 2004)
    Pathway activity inference attempts to infer differential activity of cellular networks, given a qualitative state - transition model of the network and an expression profile of RNA molecules. We present an efficient ...
  • Pathway activity inference using microarray data 

    Babur, Özgün; Demir, Emek; Ayaz, Aslı; Doğrusöz, Uğur; Sakarya, Onur (Bilkent Center for Bioinformatics (BCBI), 2004)
    Motivation: Microarray technology provides cell-scale expression data; however, analyzing this data is notoriously difficult. It is becoming clear that system-oriented methods are needed in order to best interpret this ...
  • PATIKAweb: a Web service for querying, visualizing and analyzing a graph-based pathway database 

    Aksay, Çağrı; Arık, Fatma; Ataer, Esra; Ayaz, Aslı; Babur, Özgün; Belviranlı, Mehmet E.; Çetintaş, Ahmet; Çolak, Recep; Çözen, G.; Demir, Emek; Dilek, Alptuğ; Doğrusöz, Uğur; Giral, Erhan; Kaya, Engin; Küçük, Evren; Tekin, A. S.; Yıldırım, Hilmi; Erson, Zeynep (ISCB Org, 2005-06)
    PATIKAweb provides a Web service for retrieving and analyzing biological pathways in PATIKA database, which currently contains data integrated from popular public pathway databases like Reactome. It features a user-friendly ...
  • PATIKA: An informatics infrastructure for cellular networks 

    Aksay, Çağrı; Ayaz, Aslı; Babur, Özgün; Bilgin, C.; Çetintaş, Ahmet; Çivril, Ali; Çolak, Recep; Çözen, G.; Demir, Emek; Doğrusöz, Uğur; Erson, Zeynep; Gerdaneri, Ozan; Giral, Erhan; Güleşır, Gürcan; Nişancı, Gürkan; Sakarya, O.; Yıldırım, Hilmi (ISCB Org, 2004)
    The PATIKA Project aims for an informatics infrastructure to cope with the inherently complex cellular pathway data and provides software tools with sophisticated visualization technology around a central database using ...
  • 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)
  • Towards interactive data exploration 

    Binnig, C.; Basık, Fuat; Buratti, B.; Çetintemel, U.; Chung, Y.; Crotty, A.; Cousins, C.; Ebert, D.; Eichmann, P.; Galakatos, A.; Hattasch, B.; Ilkhechi, A.; Kraska, T.; Shang, Z.; Tromba, I.; Usta, Arif; Utama, P.; Upfal, E.; Wang, L.; Weir, N.; Zeleznik, R.; Zgraggen, E. (Springer, 2019)
    Enabling interactive visualization over new datasets at “human speed” is key to democratizing data science and maximizing human productivity. In this work, we first argue why existing analytics infrastructures do not support ...
  • Metabolomic profile of aggressive meningiomas by using high-resolution magic angle spinning nuclear magnetic resonance 

    Bender, L.; Somme, F.; Ruhland, E.; Çiçek, A. Ercüment; Bund, C.; Namer, J. (American Chemical Society, 2019)
    Meningiomas are in most cases benign brain tumors. The WHO 2016 classification defines three grades of meningiomas. This classification had a prognosis value because grade III meningiomas have a worse prognosis value ...
  • Discovery of tandem and interspersed segmental duplications using high-throughput sequencing 

    Söylev, Arda; Le, T. M.; Amini, H.; Alkan, Can; Hormozdiari, F. (Oxford University Press, 2019-04)
    Motivation: Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of ...
  • Shouji: a fast and efficient pre-alignment filter for sequence alignment 

    Alser, Mohammed; Hassan, H.; Kumar, A.; Mutlu, Onur; Alkan, Can (Oxford University Press, 2019-11-01)
    The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design ...
  • ST-Steiner: a spatio-temporal gene discovery algorithm 

    Norman, Utku; Çiçek, A. Ercüment (Oxford University Press, 2019-09-15)
    Motivation: Whole exome sequencing (WES) studies for autism spectrum disorder (ASD) could identify only around six dozen risk genes to date because the genetic architecture of the disorder is highly complex. To speed the ...
  • Understanding the knowledge gaps of software engineers: an empirical analysis based on SWEBOK 

    Garousi, V.; Giray, G.; Tüzün, Eray (Association for Computing Machinery, 2019)
    Context: Knowledge level and productivity of the software engineering (SE) workforce are the subject of regular discussions among practitioners, educators, and researchers. There have been many efforts to measure and improve ...
  • What does reduced FDG uptake mean in high-grade gliomas? 

    Bund, C.; Lhermitte, B.; Çiçek, A. Ercüment; Ruhland, E.; Proust, F.; Namer, I. J. (NLM (Medline), 2019-12)
    Purpose: As well as in many others cancers, FDG uptake is correlated with the degree of malignancy in gliomas, that is, commonly high FDG uptake in high-grade gliomas. However, in clinical practice, it is not uncommon to ...
  • Detailed modeling of positive selection improves detection of cancer driver genes 

    Zhao, S.; Liu, J.; Nanga, P.; Liu, Y.; Çiçek, A. Ercüment; Knoblauch, N.; He, C.; Stephens, M.; He, X. (Nature Publishing Group, 2019-07)
    Identifying driver genes from somatic mutations is a central problem in cancer biology. Existing methods, however, either lack explicit statistical models, or use models based on simplistic assumptions. Here, we present ...
  • A hypergraph partitioning model for profile minimization 

    Acer, Seher; Kayaaslan, E.; Aykanat, Cevdet (Society for Industrial and Applied Mathematics Publications, 2019)
    In this paper, the aim is to symmetrically permute the rows and columns of a given sparse symmetric matrix so that the profile of the permuted matrix is minimized. We formulate this permutation problem by first defining ...
  • Metabolomics of small intestine neuroendocrine tumors and related hepatic metastases 

    Çiçek, A. Ercüment; Imperiale, A.; Poncet, G.; Addeo, P.; Ruhland, E.; Roche, C.; Battini, S.; Chenard, M. P.; Hervieu, V.; Goichot, B.; Bachellier, P.; Walter, T.; Namer, I. J. (MDPI AG, 2019-12)
    To assess the metabolomic fingerprint of small intestine neuroendocrine tumors (SI-NETs) and related hepatic metastases, and to investigate the influence of the hepatic environment on SI-NETs metabolome. Ninety-four tissue ...
  • Auction-based serious game for bug tracking 

    Üsfekes, Ç.; Tüzün, Eray; Yılmaz, M.; Macit, Y.; Clarke, P. (The Institution of Engineering and Technology(IET ), 2019-10)
    Today, one of the challenges in software engineering is utilising application lifecycle management (ALM) tools effectively in software development. In particular, it is hard for software developers to engage with the work ...
  • An MPEG-7 compatible video retrieval system with integrated support for complex multimodal queries 

    Baştan, Muhammet; Çam, Hayati; Güdükbay, Uğur; Ulusoy, Özgür (IEEE Computer Society, 2019)
    We present BilVideo-7, an MPEG-7 compatible, video indexing and retrieval system that supports complex multimodal queries in a unified framework. An MPEG-7 profile is developed to represent the videos by decomposing them ...
  • Topic-based influence computation in social networks under resource constraints 

    Bingöl, Kaan; Eravcı, Bahaeddin; Etemoğlu, Ç. Ö.; Ferhatosmanoğlu, Hakan; Gedik, Buğra (Institute of Electrical and Electronics Engineers, 2019)
    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 ...
  • Spatiotemporal graph and hypergraph partitioning models for sparse matrix-vector multiplication on many-core architectures 

    Abubaker, Nabil; Akbudak, K.; Aykanat, Cevdet (IEEE Computer Society, 2019)
    There exist graph/hypergraph partitioning-based row/column reordering methods for encoding either spatial or temporal locality for sparse matrix-vector multiplication (SpMV) operations. Spatial and temporal hypergraph ...
  • An analysis of social networks based on tera-scale telecommunication datasets 

    Aksu, Hidayet; Körpeoğlu, İbrahim; Ulusoy, Özgür (IEEE Computer Society, 2019)
    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 are ...

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