Now showing items 1-15 of 15

    • Apollo: A sequencing-technology-independent, scalable and accurate assembly polishing algorithm 

      Fırtına, C.; Kim, J. S.; Alser, M.; Şenol Cali, D.; Çiçek, A. Ercüment; Alkan, Can; Mutlu, Onur (Oxford University Press, 2020-03)
      Motivation: Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to construct an assembly (i.e. the subject’s genome), which is further ...
    • 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 ...
    • The effect of kinship in re-identification attacks against genomic data sharing beacons 

      Ayoz, Kerem; Ayşen, Miray; Ayday, Erman; Çiçek, A. Ercüment (NLM (Medline), 2020-12)
      Motivation: Big data era in genomics promises a breakthrough in medicine, but sharing data in a private manner limit the pace of field. Widely accepted ‘genomic data sharing beacon’ protocol provides a standardized and ...
    • An integrated genomic and metabolomic approach for defining survival time in adult oligodendrogliomas patients 

      Bund, C.; Guergova‑Kuras, M.; Çiçek, A. Ercüment; Moussallieh, F.-M.; Dali‑Youcef, N.; Piotto, M.; Schneider, P.; Heller, R.; Entz‑Werle, N.; Lhermitte, B.; Chenard, M.-P.; Schott, R.; Proust, F.; Noel, G.; Namer, I. J. (Springer, 2019)
      Introduction The identification of frequent acquired mutations shows that patients with oligodendrogliomas have divergent biology with differing prognoses regardless of histological classification. A better understanding ...
    • k-Shell decomposition reveals structural properties of the gene coexpression network for neurodevelopment 

      Çiçek, A. Ercüment (TÜBİTAK, 2017)
      Neurodevelopment is a dynamic and complex process, which involves interactions of thousands of genes. Understanding the mechanisms of brain development is important for uncovering the genetic architectures of neurodevelopmental ...
    • Matrix Metalloproteinase-11 promotes early mouse mammary gland tumor growth through metabolic reprogramming and increased IGF1/AKT/FoxO1 signaling pathway, enhanced ER stress and alteration in mitochondrial UPR 

      Tan, B.; Jaulin, A.; Bund, C.; Outilaft, H.; Wendling, C.; Chenard, M.-P.; Alpy, F.; Çiçek, A. Ercüment; Namer, I. J.; Tomasetto, C.; Dali-Youcef, N. (MDPI AG, 2020-08)
      Matrix metalloproteinase 11 (MMP11) is an extracellular proteolytic enzyme belonging to the matrix metalloproteinase (MMP11) family. These proteases are involved in extracellular matrix (ECM) remodeling and activation of ...
    • Metabolomic profiling highlights the metabolic bases of acute-on-chronic and post-hepatectomy liver failure 

      Faitot, F.; Ruhland, E.; Oncioiu, C.; Besch, C.; Addeo, P.; Çiçek, A. Ercüment; Bachellier, P.; Namer, I. -J. (Elsevier, 2019)
      Background Posthepatectomy liver failure (PHLF) is the main limitation to extending liver resection but its pathophysiology is not yet fully understood. The aim of the study was to describe the metabolic adaptations that ...
    • 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 ...
    • Potpourri: an epistasis test prioritization algorithm via diverse SNP selection 

      Çaylak, Gizem; Çiçek, A. Ercüment (Springer, 2020)
      Genome-wide association studies explain a fraction of the underlying heritability of genetic diseases. Investigating epistatic interactions between two or more loci help closing this gap. Unfortunately, sheer number of ...
    • Predicting carbon spectrum in Heteronuclear Single Quantum Coherence Spectroscopy for online feedback during surgery 

      Karakaşlar, E. Onur; Coşkun, B.; Outilaft, H.; Namer, I. J.; Çiçek, A. Ercüment (IEEE, 2020)
      1H High-Resolution Magic Angle Spinning (HRMAS) Nuclear Magnetic Resonance (NMR) is a reliable technology used for detecting metabolites in solid tissues. Fast response time enables guiding surgeons in real time, for ...
    • Revisiting the complex architecture of ALS in Turkey: expanding genotypes, shared phenotypes, molecular networks, and a public variant database 

      Tunca, C.; Şeker, T.; Akçimen, F.; Coşkun, C.; Bayraktar, E.; Palvadeau, R.; Zor, S.; Koçoğlu, C.; Kartal, E.; Şen, N. E.; Hamzeiy, H.; Özoğuz-Erimiş, A.; Norman, Utku; Karakahya, Oğuzhan; Olgun, Gülden; Akgün, T.; Durmuş, H.; Şahin, E.; Çakar, A.; Başar-Gürsoy, E.; Babacan-Yıldız, G.; İşak, B.; Uluç, K.; Hanağası, H.; Bilgiç, B.; Turgut, N.; Aysal, F.; Ertaş, M.; Boz, C.; Kotan, D.; İdrisoğlu, H.; Soysal, A.; Uzun-Adatepe, N.; Akalın, M. A.; Koç, F.; Tan, E.; Oflazer, P.; Deymeer, F.; Taştan, Ö.; Çiçek, A. Ercüment; Kavak, E.; Parman, Y.; Başak, A. N. (John Wiley and Sons, 2020)
      The last decade has proven that amyotrophic lateral sclerosis (ALS) is clinically and genetically heterogeneous, and that the genetic component in sporadic cases might be stronger than expected. This study investigates ...
    • ST-Steiner: a spatio-temporal gene discovery algorithm 

      Norman, Utku; Çiçek, A. Ercüment (Oxford University Press, 2019)
      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 ...
    • A statistical framework for mapping risk genes from de novo mutations in whole-genome-sequencing studies 

      Liu, Y.; Liang, Y.; Çiçek, A. Ercüment; Li, Z.; Li, J.; Muhle, R. A.; Krenzer, M.; Mei, Y.; Wang Y.; Knoblauch, N.; Morrison, J.; Zhao, S.; Jiang, Y.; Geller, E.; Ionita-Laza, I.; Wu, J.; Xia, K.; Noonan, J. P.; Sun, Z. S.; He, X. (Cell Press, 2018)
      Analysis of de novo mutations (DNMs) from sequencing data of nuclear families has identified risk genes for many complex diseases, including multiple neurodevelopmental and psychiatric disorders. Most of these efforts have ...
    • 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)
      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 ...
    • Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex 

      Werling, D. M.; Pochareddy, S.; Choi, J.; An, J.-Y.; Sheppard, B.; Peng, M.; Li, Z.; Dastmalchi, C.; Santpere, G.; Sousa, A. M. M.; Tebbenkamp, A. T. N.; Kaur, N.; Gulden, F. O.; Breen, M. S.; Liang, L.; Gilson, M. C.; Zhao, X.; Dong, S.; Klei, L.; Çiçek, A. Ercüment; Buxbaum, J. D.; Adle-Biassette, H.; Thomas, J.-L.; Aldinger, K. A.; O’Day, D. R.; Glass, I. A.; Zaitlen, N. A.; Talkowski, M. E.; Roeder, K.; State, M. W.; Devlin, B.; Sanders, S. J.; Sestan, N. (Elsevier, 2020-04)
      Gene expression levels vary across developmental stage, cell type, and region in the brain. Genomic variants also contribute to the variation in expression, and some neuropsychiatric disorder loci may exert their effects ...