Recent Submissions

  • Author Correction: A robust benchmark for detection of germline large deletions and insertions 

    Zook, J. M.; Hansen, N. F.; Olson, N. D.; Chapman, L.; Mullikin, J. C.; Xiao, C.; Sherry, S.; Koren, S.; Phillippy, A. M.; Boutros, P. C.; Sahraeian, S. M. E.; Huang, V.; Rouette, A.; Alexander, N.; Mason, C. E.; Hajirasouliha, I.; Ricketts, C.; Lee, J.; Tearle, R.; Fiddes, I. T.; Barrio, A. M.; Wala, J.; Carroll, A.; Ghaffari, N.; Rodriguez, O. L.; Bashir, A.; Jackman, S.; Farrell, J. J.; Wenger, A. M.; Alkan, Can; Söylev, A.; Schatz, M. C.; Garg, S.; Church, G.; Marschall, T.; Chen, K.; Fan, X.; English, A. C.; Rosenfeld, J. A.; Zhou, W.; Mills, R. E.; Sage, J. M.; Davis, J. R.; Kaiser, M. D.; Oliver, J. S.; Catalano, A. P.; Chaisson, M. J. P.; Spies, N.; Sedlazeck, F. J.; Salit, M. (Nature Research, 2020)
    New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and ...
  • Abstract 207: the cBioPortal for cancer genomics 

    Gao, J.; Mazor, T.; de Bruijn, I.; Abeshouse, A.; Baiceanu, D.; Erkoç, Z.; Gross, B.; Higgins, D.; Jagannathan, P. K.; Kalletla, K.; Kumari, Priti; Kundra, R.; Li, X.; Lindsay, J.; Lisman, A.; Lukasse, P.; Madala, D.; Madupuri, R.; Ochoa, A.; Plantalech, O.; Quach, J.; Rodenburg, S.; Satravada, A.; Schaeffer, F.; Sheridan, R.; Sikina, L.; Sümer, S. O.; Sun, Y.; van Dijk, P.; van Nierop, P.; Wang, A.; Wilson, M.; Zhang, H.; Zhao, G.; van Hagen, S.; van Bochove, K.; Doğrusöz, Uğur; Heath, A.; Resnick, A.; Pugh, T. J.; Sander, C.; Cerami, E.; Schultz, N. (American Association for Cancer Research (AACR), 2021)
    The cBioPortal for Cancer Genomics is an open-source software platform that enables interactive, exploratory analysis of large-scale cancer genomics data sets with a user-friendly interface. It integrates genomic and ...
  • Multi-label sentiment analysis on 100 languages with dynamic weighting for label imbalance 

    Yılmaz, Selim Fırat; Kaynak, Ergün Batuhan; Koç, Aykut; Dibeklioğlu, Hamdi; Kozat, Süleyman Serdar (Institute of Electrical and Electronics Engineers, 2021-07-19)
    We investigate cross-lingual sentiment analysis, which has attracted significant attention due to its applications in various areas including market research, politics, and social sciences. In particular, we introduce a ...
  • Genetic circuits combined with machine learning provides fast responding living sensors 

    Saltepe, Behide; Bozkurt, Eray Ulaş; Güngen, Murat Alp; Çiçek, A. Ercüment; Şeker, Urartu Özgür Şafak (Elsevier BV, 2021-04-15)
    Whole cell biosensors (WCBs) have become prominent in many fields from environmental analysis to biomedical diagnostics thanks to advanced genetic circuit design principles. Despite increasing demand on cost effective and ...
  • Client-specific anomaly detection for face presentation attack detection 

    Fatemifar, S.; Arashloo, Shervin Rahimzadeh; Awais, M.; Kittler, J. (Elsevier BV, 2021-04)
    One-class anomaly detection approaches are particularly appealing for use in face presentation attack detection (PAD), especially in an unseen attack scenario, where the system is exposed to novel types of attacks. This ...
  • Correction to: NoRCE: non‑coding RNA sets cis enrichment tool 

    Olgun, Gülden; Nabi, Afshan; Tastan, Oznur (BioMed Central Ltd., 2021-08-04)
    While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional ...
  • Fast shared-memory streaming multilevel graph partitioning 

    Jafari, N.; Selvitopi, O.; Aykanat, Cevdet (Elsevier, 2020-09-12)
    A fast parallel graph partitioner can benefit many applications by reducing data transfers. The online methods for partitioning graphs have to be fast and they often rely on simple one-pass streaming algorithms, while the ...
  • A review of code reviewer recommendation studies: Challenges and future directions 

    Çetin, H. Alperen; Doğan, Emre; Tüzün, Eray (Elsevier, 2021-04-14)
    Code review is the process of inspecting code changes by a developer who is not involved in the development of the changeset. One of the initial and important steps of code review process is selecting code reviewer(s) for ...
  • Synthetic18K: Learning better representations for person re-ID and attribute recognition from 1.4 million synthetic images 

    Aslan, C.; Ercan, B.; Ates, T.; Celikcan, U.; Erdem, A.; Erdem, E.; Üner, Onur Can (Elsevier, 2021-05-26)
    Learning robust representations is critical for the success of person re-identification and attribute recognition systems. However, to achieve this, we must use a large dataset of diverse person images as well as annotations ...
  • Differentially private binary- and matrix-valued data query: an XOR mechanism 

    Ji, T.; Li, P.; Yilmaz, E.; Ayday, Erman; Ye, Y. F.; Sun, J. (Association for Computing Machinery, 2021-01)
    Differential privacy has been widely adopted to release continuous- and scalar-valued information on a database without compromising the privacy of individual data records in it. The problem of querying binary- and ...
  • DBTagger: multi-task learning for keyword mapping in NLIDBs using Bi-directional recurrent neural networks 

    Usta, Arif; Karakayali, Akifhan; Ulusoy, Özgür (Association for Computing Machinery, 2021-01)
    Translating Natural Language Queries (NLQs) to Structured Query Language (SQL) in interfaces deployed in relational databases is a challenging task, which has been widely studied in database community recently. Conventional ...
  • Causal interactions from proteomic profiles: Molecular data meet pathway knowledge 

    Babur, Ö.; Luna, A.; Korkut, A.; Durupınar, F.; Siper, M. C.; Doğrusöz, Uğur; Jacome, A. S. V.; Peckner, R.; Christiansen, K. E.; Jaffe, J.D; Spellman, P.T.; Aslan, J. E.; Sander, C.; Demir, E. (Cell Press, 2021-06)
    We present a computational method to infer causal mechanisms in cell biology by analyzing changes in high-throughput proteomic profiles on the background of prior knowledge captured in biochemical reaction knowledge bases. ...
  • PRER: a patient representation with pairwise relative expression of proteins on biological networks 

    Kuru, Halil İbrahim; Büyüközkan, Mustafa; Tastan, Öznur (Public Library of Science, 2021-05-26)
    Changes in protein and gene expression levels are often used as features in predictive modeling such as survival prediction. A common strategy to aggregate information contained in individual proteins is to integrate the ...
  • Weakly supervised instance attention for multisource fine-grained object recognition with an application to tree species classification 

    Aygüneş, Bulut; Cinbiş, R. G.; Aksoy, Selim (Elsevier BV, 2021-06)
    Multisource image analysis that leverages complementary spectral, spatial, and structural information benefits fine-grained object recognition that aims to classify an object into one of many similar subcategories. However, ...
  • Developing a scenario-based video game generation framework for computer and virtual reality environments: a comparative usability study 

    Surer, E.; Erkayaoğlu, M.; Öztürk, Zeynep Nur; Yücel, F.; Bıyık, E. A.; Altan, B.; Şenderin, B.; Oğuz, Zeliha; Gürer, S.; Düzgün, H. Ş. (Springer, 2021-12)
    Serious games—games that have additional purposes rather than only entertainment—aim to educate people, solve, and plan several real-life tasks and circumstances in an interactive, efficient, and user-friendly way. Emergency ...
  • Quantitative analysis of spoken discourse using memoirs of old-time moviegoers 

    Çalışkan, Sevil; Can, Fazlı; Akbulut, H.; Öztürk, S. R. (Routledge, 2021-02-24)
    We present the first quantitative analysis of spoken discourse for the Turkish language using memoirs of a group of old-time moviegoers of varying age groups whose birth year spreads over a period of four decades ranging ...
  • RSTrace+: Reviewer suggestion using software artifact traceability graphs 

    Sülün, Emre; Tüzün, Eray; Doğrusöz, Uğur (Elsevier BV, 2021-02)
    Context: Various types of artifacts (requirements, source code, test cases, documents, etc.) are produced throughout the lifecycle of a software. These artifacts are connected with each other via traceability links that ...
  • Multimodal assessment of apparent personality using feature attention and error consistency constraint 

    Aslan, Süleyman; Güdükbay, Uğur; Dibeklioğlu, Hamdi (Elsevier BV, 2021-06)
    Personality computing and affective computing, where the recognition of personality traits is essential, have gained increasing interest and attention in many research areas recently. We propose a novel approach to recognize ...
  • AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data 

    Thibodeau, Asa; Eroglu, Alper; McGinnis, Christopher S.; Lawlor, Nathan; Nehar-Belaid, Djamel; Kursawe, Romy; Marches, Radu; Conrad, Daniel N.; Kuchel, George A.; Gartner, Zev J.; Banchereau, Jacques; Stitzel, Michael L.; Çiçek, A. Ercüment; Ucar, Duygu (BioMed Central Ltd., 2021-12)
    Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned ...
  • Energy-efficient and fault-tolerant drone-BS placement in heterogeneous wireless sensor networks 

    Deniz, F.; Bagci, H.; Korpeoglu, Ibrahim; Yazıcı, A. (Springer, 2021-01)
    This paper introduces a distributed and energy-aware algorithm, called Minimum Drone Placement (MDP) algorithm, to determine the minimum number of base stations mounted on resource-rich Unmanned Aerial Vehicles (UAV-BS), ...

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