Search Results - "Cicek, A."

Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy by Cakmakci, Doruk, Karakaslar, Emin Onur, Ruhland, Elisa, Chenard, Marie-Pierre, Proust, Francois, Piotto, Martial, Namer, Izzie Jacques, Cicek, A Ercument

“…Complete resection of the tumor is important for survival in glioma patients. Even if the gross total resection was achieved, left-over micro-scale tissue in…”
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Hercules: a profile HMM-based hybrid error correction algorithm for long reads by Firtina, Can, Bar-Joseph, Ziv, Alkan, Can, Cicek, A Ercument

“…Abstract Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several types of…”
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MatchMaker: A Deep Learning Framework for Drug Synergy Prediction by Kuru, Halil Ibrahim, Tastan, Oznur, Cicek, A. Ercument

“…Drug combination therapies have been a viable strategy for the treatment of complex diseases such as cancer due to increased efficacy and reduced side effects…”
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Re-identification of individuals in genomic data-sharing beacons via allele inference by von Thenen, Nora, Ayday, Erman, Cicek, A Ercument

“…Abstract Motivation Genomic data-sharing beacons aim to provide a secure, easy to implement and standardized interface for data-sharing by only allowing yes/no…”
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Metabolomic Profile of Aggressive Meningiomas by Using High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance by Bender, Laura, Somme, François, Ruhland, Elisa, Cicek, A. Ercüment, Bund, Caroline, Namer, Izzie Jacques

“…Meningiomas are in most cases benign brain tumors. The WHO 2016 classification defines three grades of meningiomas. This classification had a prognosis value…”
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A unifying network modeling approach for codon optimization by Karaşan, Oya, Şen, Alper, Tiryaki, Banu, Cicek, A Ercument

“…Abstract Motivation Synthesizing genes to be expressed in other organisms is an essential tool in biotechnology. While the many-to-one mapping from codons to…”
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The effect of kinship in re-identification attacks against genomic data sharing beacons by Ayoz, Kerem, Aysen, Miray, Ayday, Erman, Cicek, A Ercument

“…Abstract 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…”
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Uncovering complementary sets of variants for predicting quantitative phenotypes by Yilmaz, Serhan, Fakhouri, Mohamad, Koyutürk, Mehmet, Çiçek, A Ercüment, Tastan, Oznur

“…Abstract Motivation Genome-wide association studies show that variants in individual genomic loci alone are not sufficient to explain the heritability of…”
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Detailed modeling of positive selection improves detection of cancer driver genes by Zhao, Siming, Liu, Jun, Nanga, Pranav, Liu, Yuwen, Cicek, A. Ercument, Knoblauch, Nicholas, He, Chuan, Stephens, Matthew, He, Xin

“…Identifying driver genes from somatic mutations is a central problem in cancer biology. Existing methods, however, either lack explicit statistical models, or…”
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ST-Steiner: a spatio-temporal gene discovery algorithm by Norman, Utku, Cicek, A Ercument

“…Abstract Motivation Whole exome sequencing (WES) studies for autism spectrum disorder (ASD) could identify only around six dozen risk genes to date because the…”
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Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection by Caylak, Gizem, Tastan, Oznur, Cicek, A Ercument

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PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas by Kaynar, Gun, Cakmakci, Doruk, Bund, Caroline, Todeschi, Julien, Namer, Izzie Jacques, Cicek, A Ercument

“…Online assessment of tumor characteristics during surgery is important and has the potential to establish an intra-operative surgeon feedback mechanism. With…”
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A Tool for Detecting Complementary Single Nucleotide Polymorphism Pairs in Genome-Wide Association Studies for Epistasis Testing by Caylak, Gizem, Tastan, Oznur, Cicek, A Ercument

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SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS by Yilmaz, Serhan, Tastan, Oznur, Cicek, A. Ercument

“…Phenotypic heritability of complex traits and diseases is seldom explained by individual genetic variants identified in genome-wide association studies (GWAS)…”
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Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm by Firtina, Can, Kim, Jeremie S, Alser, Mohammed, Senol Cali, Damla, Cicek, A Ercument, Alkan, Can, Mutlu, Onur

“…Abstract Motivation Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to…”
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From cell lines to cancer patients: personalized drug synergy prediction by Kuru, Halil Ibrahim, Cicek, A Ercument, Tastan, Oznur

“…Abstract Motivation Combination drug therapies are effective treatments for cancer. However, the genetic heterogeneity of the patients and exponentially large…”
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ECOLE: Learning to call copy number variants on whole exome sequencing data by Mandiracioglu, Berk, Ozden, Furkan, Kaynar, Gun, Yilmaz, Mehmet Alper, Alkan, Can, Cicek, A. Ercument

“…Copy number variants (CNV) are shown to contribute to the etiology of several genetic disorders. Accurate detection of CNVs on whole exome sequencing (WES)…”
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Targeted metabolomics analyses for brain tumor margin assessment during surgery by Cakmakci, Doruk, Kaynar, Gun, Bund, Caroline, Piotto, Martial, Proust, Francois, Namer, Izzie Jacques, Cicek, A Ercument

“…Abstract Motivation Identification and removal of micro-scale residual tumor tissue during brain tumor surgery are key for survival in glioma patients. For…”
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Synaptic, transcriptional and chromatin genes disrupted in autism by De Rubeis, Silvia, He, Xin, Goldberg, Arthur P., Poultney, Christopher S., Samocha, Kaitlin, Ercument Cicek, A., Kou, Yan, Liu, Li, Fromer, Menachem, Walker, Susan, Singh, Tarjinder, Klei, Lambertus, Kosmicki, Jack, Fu, Shih-Chen, Aleksic, Branko, Biscaldi, Monica, Bolton, Patrick F., Brownfeld, Jessica M., Cai, Jinlu, Campbell, Nicholas G., Carracedo, Angel, Chahrour, Maria H., Chiocchetti, Andreas G., Coon, Hilary, Crawford, Emily L., Crooks, Lucy, Curran, Sarah R., Dawson, Geraldine, Duketis, Eftichia, Fernandez, Bridget A., Gallagher, Louise, Geller, Evan, Guter, Stephen J., Sean Hill, R., Ionita-Laza, Iuliana, Jimenez Gonzalez, Patricia, Kilpinen, Helena, Klauck, Sabine M., Kolevzon, Alexander, Lee, Irene, Lei, Jing, Lehtimäki, Terho, Lin, Chiao-Feng, Ma’ayan, Avi, Marshall, Christian R., McInnes, Alison L., Neale, Benjamin, Owen, Michael J., Ozaki, Norio, Parellada, Mara, Parr, Jeremy R., Purcell, Shaun, Puura, Kaija, Rajagopalan, Deepthi, Rehnström, Karola, Reichenberg, Abraham, Sabo, Aniko, Sachse, Michael, Sanders, Stephan J., Schafer, Chad, Schulte-Rüther, Martin, Skuse, David, Stevens, Christine, Szatmari, Peter, Tammimies, Kristiina, Valladares, Otto, Voran, Annette, Wang, Li-San, Weiss, Lauren A., Jeremy Willsey, A., Yu, Timothy W., Yuen, Ryan K. C., Cook, Edwin H., Freitag, Christine M., Gill, Michael, Hultman, Christina M., Lehner, Thomas, Palotie, Aarno, Schellenberg, Gerard D., Sklar, Pamela, State, Matthew W., Sutcliffe, James S., Walsh, Christopher A., Scherer, Stephen W., Zwick, Michael E., Barrett, Jeffrey C., Cutler, David J., Roeder, Kathryn, Devlin, Bernie, Daly, Mark J., Buxbaum, Joseph D.

“…The genetic architecture of autism spectrum disorder involves the interplay of common and rare variants and their impact on hundreds of genes. Using exome…”
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AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data by 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, Cicek, A Ercument, Ucar, Duygu

“…Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation…”
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