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

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TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences by Harmanci, Arif O, Sharma, Gaurav, Mathews, David H

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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.

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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.

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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

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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

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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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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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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

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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

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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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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.

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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.

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A Stochastic Framework for Rate-Distortion Optimized Video Coding Over Error-Prone Networks by Harmanci, O., Tekalp, A.M.

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Hospital-acquired pneumonia: challenges and options for diagnosis and treatment by Harmanci, A., Harmanci, Ö., Akova, M.

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Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion by Desai, Poonam N, Wang, Bofei, Fonseca, Andre, Borges, Pamella, Jelloul, Fatima Zahra, Reville, Patrick K, Lee, Eric, Ly, Christopher, Basi, Akshay, Root, Jessica, Baran, Natalia, Post, Sean M, Deng, Qing, Sun, Hanxiao, Harmanci, Arif O, Burks, Jared K, Gomez, Javier A, DiNardo, Courtney D, Daver, Naval G, Alatrash, Gheath, Konopleva, Marina, Green, Michael R, Antunes, Dinler A, Futreal, Andrew, Hao, Dapeng, Abbas, Hussein A

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

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Autoimmune Polyendocrine Syndrome With Atrial Septal Defect by Aksoy, D.Y., Ağbaht, K., Harmanci, Ö., Karadağ, Ö., Onat, A.M., Apraş, Ş., Aytemir, K., Sungur, A., Yildiz, B.O., Bayraktar, M.

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Content Adaptive Hash Lookups for Near-Duplicate Image Search by Full or Partial Image Queries by Harmanci, O, Haritaoglu, I

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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes by Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A., Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M., Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E., Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M. C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad

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