Search Results - "Harmanci, O"

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data by Serin Harmanci, Akdes, Harmanci, Arif O., Zhou, Xiaobo

“…RNA sequencing experiments generate large amounts of information about expression levels of genes. Although they are mainly used for quantifying expression…”
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TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences by Harmanci, Arif O, Sharma, Gaurav, Mathews, David H

“…The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function…”
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Integrated clinical genomic analysis reveals xenobiotic metabolic genes are downregulated in meningiomas of current smokers by Khan, A. Basit, Patel, Rajan, McDonald, Malcolm F., Goethe, Eric, English, Collin, Gadot, Ron, Shetty, Arya, Nouri, Shervin Hosseingholi, Harmanci, Arif O., Harmanci, Akdes S., Klisch, Tiemo J., Patel, Akash J.

“…Introduction Meningiomas are the most common primary intracranial tumor. Recently, various genetic classification systems for meningioma have been described…”
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Patient-Derived Orthotopic Xenograft (PDOX) Mouse Models of Primary and Recurrent Meningioma by Zhang, Huiyuan, Qi, Lin, Du, Yuchen, Huang, L. Frank, Braun, Frank K., Kogiso, Mari, Zhao, Yanling, Li, Can, Lindsay, Holly, Zhao, Sibo, Injac, Sarah G., Baxter, Patricia A., Su, Jack M., Stephan, Clifford, Keller, Charles, Heck, Kent A., Harmanci, Akdes, Harmanci, Arif O., Yang, Jianhua, Klisch, Tiemo J., Li, Xiao-Nan, Patel, Akash J.

“…Background. Meningiomas constitute one-third of all primary brain tumors. Although typically benign, about 20% of these tumors recur despite surgery and…”
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Comparative analysis of the transcriptome across distant species by Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A., Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak H., Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E., Boley, Nathan P., Booth, Benjamin W., Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A., Frankish, Adam, Gao, Guanjun, Good, Peter J., Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A., Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim J. P., Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C., Kitchen, Robert R., Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M., Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J., Pazin, Michael J., Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I., Schlesinger, Felix, Sethi, Anurag, Slack, Frank J., Spencer, William C., Stoiber, Marcus H., Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A., Wan, Kenneth H., Wang, Guilin, Wang, Huaien, Watkins, Kathie L., Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E., Graveley, Brenton R., Celniker, Susan E., Gingeras, Thomas R., Waterston, Robert

“…Uniform processing and detailed annotation of human, worm and fly RNA-sequencing data reveal ancient, conserved features of the transcriptome, shared…”
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HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models by Nguyen, Trang Thi Thu, Zhang, Yiru, Shang, Enyuan, Shu, Chang, Torrini, Consuelo, Zhao, Junfei, Bianchetti, Elena, Mela, Angeliki, Humala, Nelson, Mahajan, Aayushi, Harmanci, Arif O, Lei, Zhengdeng, Maienschein-Cline, Mark, Quinzii, Catarina M, Westhoff, Mike-Andrew, Karpel-Massler, Georg, Bruce, Jeffrey N, Canoll, Peter, Siegelin, Markus D

“…The Warburg effect is a tumor-related phenomenon that could potentially be targeted therapeutically. Here, we showed that glioblastoma (GBM) cultures and…”
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Peer Assisted Video Streaming With Supply-Demand-Based Cache Optimization by Kozat, U.C., Harmanci, O., Kanumuri, S., Demircin, M.U., Civanlar, M.R.

“…In this paper, we consider a hybrid P2P video on-demand architecture that utilizes both the server and the peer resources for efficient transmission of popular…”
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A Stochastic Framework for Rate-Distortion Optimized Video Coding Over Error-Prone Networks by Harmanci, O., Tekalp, A.M.

“…This paper proposes a complete stochastic framework for RD optimal encoder design for video over error-prone networks, which applies to any motion-compensated…”
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Aggressive human MenG C meningiomas have a molecular counterpart in canines by Harmanci, Akdes S., Boudreau, Beth, Lau, Sean, Hosseingholi Nouri, Shervin, Mandel, Jacob J., Lu, Hsiang-Chih, Harmanci, Arif O., Klisch, Tiemo J., Levine, Jonathan M., Patel, Akash J.

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Rate-Distortion Optimal Video Transport Over IP Allowing Packets With Bit Errors by Harmanci, O., Tekalp, A.M.

“…We propose new models and methods for rate-distortion (RD) optimal video delivery over IP, when packets with bit errors are also delivered. In particular, we…”
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Leveraging single-cell sequencing to classify and characterize tumor subgroups in bulk RNA-sequencing data by Shetty, Arya, Wang, Su, Khan, A. Basit, English, Collin W., Nouri, Shervin Hosseingholi, Magill, Stephen T., Raleigh, David R., Klisch, Tiemo J., Harmanci, Arif O., Patel, Akash J., Harmanci, Akdes Serin

“…Purpose Accurate classification of cancer subgroups is essential for precision medicine, tailoring treatments to individual patients based on their cancer…”
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Correction to: Leveraging single-cell sequencing to classify and characterize tumor subgroups in bulk RNA-sequencing data by Shetty, Arya, Wang, Su, Khan, A. Basit, English, Collin W., Nouri, Shervin Hosseingholi, Magill, Stephen T., Raleigh, David R., Klisch, Tiemo J., Harmanci, Arif O., Patel, Akash J., Harmanci, Akdes Serin

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Even heterozygous loss of CDKN2A/B greatly accelerates recurrence in aggressive meningioma by Khan, A. Basit, English, Collin W., Chen, William C., Athukuri, Prazwal, Bayley, James C., Brandt, Vicky L., Shetty, Arya, Hadley, Caroline C., Choudhury, Abrar, Lu, Hsiang-Chih, Harmanci, Arif O., Harmanci, Akdes S., Magill, Stephen T., Raleigh, David R., Klisch, Tiemo J., Patel, Akash J.

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Racial and Socioeconomic Disparities in Patients With Meningioma: A Retrospective Cohort Study by Jackson, Hudin N, Hadley, Caroline C, Khan, A Basit, Gadot, Ron, Bayley, 5th, James C, Shetty, Arya, Mandel, Jacob, Jalali, Ali, Gallagher, K Kelly, Sweeney, Alex D, Harmanci, Arif O, Harmanci, Akdes S, Klisch, Tiemo, Gopinath, Shankar P, Rao, Ganesh, Yoshor, Daniel, Patel, Akash J

“…Meningiomas are the most common intracranial neoplasms. Although genomic analysis has helped elucidate differences in survival, there is evidence that racial…”
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Content Adaptive Hash Lookups for Near-Duplicate Image Search by Full or Partial Image Queries by Harmanci, O, Haritaoglu, I

“…In this paper we present a scalable and high performance near-duplicate image search method. The proposed algorithm follows the common paradigm of computing…”
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Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies by Bayley, 5th, James C, Hadley, Caroline C, Harmanci, Arif O, Harmanci, Akdes S, Klisch, Tiemo J, Patel, Akash J

“…One-fifth of meningiomas classified as benign by World Health Organization (WHO) histopathological grading will behave malignantly. To better diagnose these…”
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Hospital-acquired pneumonia: challenges and options for diagnosis and treatment by Harmanci, A., Harmanci, Ö., Akova, M.

“…The management of hospital-acquired pneumonia (HAP) presents a major challenge for the clinician. The insensitivity of current diagnostic methods and the…”
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Autoimmune polyendocrine syndrome with atrial septal defect by Aksoy, D Y, Ağbaht, K, Harmanci, O, Karadağ, O, Aytemir, K, Sungur, A, Onat, A M, Apraş, S, Yildiz, B O, Bayraktar, M

“…Atrial septal defect is frequently reported with genetic syndromes. But, to the best of our knowledge, it has not been reported with autoimmune polyendocrine…”
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Identification of novel fusion transcripts in meningioma by Khan, A. Basit, Gadot, Ron, Shetty, Arya, Bayley, James C., Hadley, Caroline C., Cardenas, Maria F., Jalali, Ali, Harmanci, Akdes S., Harmanci, Arif O., Wheeler, David A., Klisch, Tiemo J., Patel, Akash J.

“…Introduction Meningiomas are the most common primary intracranial tumor. Recent next generation sequencing analyses have elaborated the molecular drivers of…”
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Optimization of H264 for low delay video communications over lossy channels by Harmanci, O., Tekalp, A.M.

“…In this paper, we study the data partitioning (DP) and its optimization for H264 video coding standard. H264 does not include DP in baseline profile, which is…”
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