Browsing by Author "Li, D."
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Item Open Access The cBioPortal for cancer genomics and its application in precision oncology(American Association for Cancer Research, 2016) Gao, J.; Lindsay, J.; Watt, S.; Doğrusöz, Uğur; Lukasse, P.; Abeshouse, A.; Chen, H.; Bruijn, I.; Gross, B.; Li, D.; Kundra, R.; Heins, Z.; Reis-Filho, J.; Sumer, O.; Sun, Y.; Wang, J.; Wang, Q.; Zhang, H.; Kumari, P.; Şahin, Mehmet Furkan; Ridder, S.; Schaeffer, F.; Bochove, K.; Pugh, T.; Sander, C.; Cerami, E.; Schultz, N.; Bahçeci, İstemiAbstract The cBioPortal for Cancer Genomics provides intuitive visualization and analysis of complex cancer genomics data. The public site (http://cbioportal.org/) is accessed by more than 1,500 researchers per day, and there are now dozens of local instances of the software that host private data sets at cancer centers around the globe. We have recently released the software under an open source license, making it free to use and modify by anybody. The software and detailed documentation are available at https://github.com/cBioPortal/cbioportal. We are now establishing a multi-institutional software development network, which will coordinate and drive the future development of the software and associated data pipelines. This group will focus on four main areas: 1. New analysis and visualization features, including: a. Improved support for cross-cancer queries and cohort comparisons. b. Enhanced clinical decision support for precision oncology, including an improved patient view with knowledge base integration, patient timelines and improved tools for visualizing tumor evolution. 2. New data pipelines, including support for new genomic data types and streamlined pipelines for TCGA and the International Cancer Genome Consortium (ICGC). 3. Software architecture and performance improvements. 4. Community engagement: Documentation, user support, and training. This coordinated effort will help to further establish the cBioPortal as the software of choice in cancer genomics research, both in academia and the pharmaceutical industry. Furthermore, as the sequencing of tumor samples has entered clinical practice, we are expanding the features of the software so that it can be used for precision medicine at cancer centers. In particular, clean, web-accessible, interactive clinical reports integrating multiple sources of genome variation and clinical annotation over time has potential to improve clinical action beyond current text-based molecular reports. By making complex genomic data easily interpretable and linking it to information about drugs and clinical trials, the cBioPortal software has the potential to facilitate the use of genomic data in clinical decision making. Citation Format: Jianjiong Gao, James Lindsay, Stuart Watt, Istemi Bahceci, Pieter Lukasse, Adam Abeshouse, Hsiao-Wei Chen, Ino de Bruijn, Benjamin Gross, Dong Li, Ritika Kundra, Zachary Heins, Jorge Reis-Filho, Onur Sumer, Yichao Sun, Jiaojiao Wang, Qingguo Wang, Hongxin Zhang, Priti Kumari, M. Furkan Sahin, Sander de Ridder, Fedde Schaeffer, Kees van Bochove, Ugur Dogrusoz, Trevor Pugh, Chris Sander, Ethan Cerami, Nikolaus Schultz. The cBioPortal for cancer genomics and its application in precision oncology. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5277.Item Open Access Dielectrophoresis in microfluidics technology(2011) Çetin B.; Li, D.Dielectrophoresis (DEP) is the movement of a particle in a non-uniform electric field due to the interaction of the particle's dipole and spatial gradient of the electric field. DEP is a subtle solution to manipulate particles and cells at microscale due to its favorable scaling for the reduced size of the system. DEP has been utilized for many applications in microfluidic systems. In this review, a detailed analysis of the modeling of DEP-based manipulation of the particles is provided, and the recent applications regarding the particle manipulation in microfluidic systems (mainly the published works between 2007 and 2010) are presented. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.Item Open Access Magnetic pumps(Springer, 2015) Çetin, Barbaros; Zeinali, Soheila; Li, D.; Li, D.Micropumps can be classified into two general categories: mechanical and nonmechanical micropumps (an excellent review on micropumps can be found elsewhere [1]). In a typical mechanical pump, a membrane is used to produce the pumping action. Nonmechanical micropumps on the other hand generally have no moving parts. Common mechanical micropumps fall into three categories based on the mechanical action used: check valve, peristaltic, and rotary pumps. They can also be categorized according to their actuation method: pneumatic, piezoelectric, external electric motor, or magnetic field. Among these actuation techniques, magnetic field actuation has shown promise for research purposes at micro- and nanoscales because of creating smooth fluid flow. Magnetic pumps can be found in both categories, mechanical, and nonmechanical in the literature.Item Open Access Magnetic resonance imaging–guided coronary interventions(John Wiley & Sons, 2004) Tsekos, N. V.; Ergin, A.; Li, D.; Omary, R. A.; Serfaty, J.-M.; Woodard, P. K.Magnetic resonance imaging (MRI) guidance for coronary interventions offers potential advantages over conventional x‐ray angiography. Advantages include the use of nonionizing radiation, combined assessment of anatomy and function, and three‐dimensional assessment of the coronary arteries leading to the myocardium. These advantages have prompted a series of recent studies in this field. Real‐time coronary MR angiography, with low‐dose catheter‐directed intraarterial (IA) infusion of contrast media, has achieved in‐plane spatial resolution as low as 0.8 × 0.8 mm2 and temporal resolution as short as 130 msec per image. Catheter‐based IA injection of contrast agent has proven useful in the collection of multislice and three‐dimensional images, not only for coronary intervention guidance, but also in the assessment of regional myocardial perfusion fed by the affected vessel. Actively visible guidewires and guiding catheters, based on the loopless antenna concept, have been effectively used to negotiate tortuous coronary vessels during catheterization, permitting placement of coronary angioplasty balloon catheters. Passive tracking approaches have been used to image contrast agent–filled coronary catheters and to place susceptibility‐based endovascular stents. Although the field is in its infancy, these early results demonstrate the feasibility for performing MRI‐guided coronary interventions. Although further methodological and technical developments are required before these methods become clinically applicable, we anticipate that MRI someday will be included in the armamentarium of techniques used to diagnose and treat coronary artery disease.Item Open Access Microfluidic optical devices(Springer, 2015) Çetin, Barbaros; Zeinali, Soheila; Li, D.; Li, D.Microfluidic optical devices (MOD) are the emerging technology that combines today’s microfluidics technology with the optics. However, MOD can be classified as the integration of these two technologies rather than combination of them. This integration provides a new approach for using microfluidics for control and manipulation of samples and optics for sensing. In this entry we propose a comprehensive review of emerging applications for microfluidic optical devices.Item Open Access Microfluidic rotary pump(Springer, 2015) Li, D.; Çetin, Barbaros; Salemmilani, Reza; Li, D.Rotary micropump is a type of micropump which consists of a rotary element used for moving fluids. Based on different design concepts, rotary micropumps make use of either viscous forces or pressure forces to carry out the pumping action.Item Open Access Operational research: methods and applications(Taylor and Francis Ltd., 2023-12-27) Petropoulos, F.; Laporte, G.; Aktas, E.; Alumur, S.; Archetti, C.; Ayhan, H.; Battarra, M.; Bennell, J.; Bourjolly, J.; Boylan, J. E.; Breton, M.; Canca, D.; Charlin, L.; Chen, B.; Cicek, C.; Cox, L.; Currie, C. S.M.; Demeulemeester, E.; Ding, L.; Disney, S. M.; Ehrgott, M.; Eppler, M. J.; Erdoğan, G.; Fortz, B.; Franco, L. A.; Frische, J.; Greco, S.; Gregory, A. J.; Hämäläinen, R. P.; Herroelen, W.; Hewitt, M.; Holmström, J.; Hooker, J. N.; Işık, T.; Johnes, J.; Kara, B. Y.; Karsu, Özlem; Kent, K.; Köhler, C.; Kunc, M.; Kuo, Y.; Letchford, A. N.; Leung, J.; Li, D.; Li, H.; Lienert, J.; Ljubić, I.; Lodi, A.; Lozano, S.; Lurkin, V.; Martello, S.; McHale, I. G.; Midgley, G.; Morecroft, J. D.W.; Mutha, A.; Oğuz, C.; Petrovic, S.; Pferschy, U.; Psaraftis, H. N.; Rose, S.Throughout its history, Operational Research has evolved to include methods, models and algorithms that have been applied to a wide range of contexts. This encyclopedic article consists of two main sections: methods and applications. The first summarises the up-to-date knowledge and provides an overview of the state-of-the-art methods and key developments in the various subdomains of the field. The second offers a wide-ranging list of areas where Operational Research has been applied. The article is meant to be read in a nonlinear fashion and used as a point of reference by a diverse pool of readers: academics, researchers, students, and practitioners. The entries within the methods and applications sections are presented in alphabetical order. The authors dedicate this paper to the 2023 Turkey/Syria earthquake victims. We sincerely hope that advances in OR will play a role towards minimising the pain and suffering caused by this and future catastrophes.Item Open Access Pressure measurements, methods(Springer, 2015) Çetin, Barbaros; Taze, Serdar; Li, D.; Li, D.Experimentation and novel measurement techniques are crucial for the further development of microfluidic devices. Pressure is one basic parameter involved in microfluidic experiments. However, it is not realistic to apply the conventional pressure measurement techniques to microsystems, since the characteristic dimension of these measurement instruments is already comparable with the size of the microdevices. Therefore, novel pressure measurement methods are needed for pressure measurement at the microscale.Item Open Access Quantum dots on vertically aligned gold nanorod monolayer: plasmon enhanced fluorescence(Royal Society of Chemistry, 2014) Peng, B.; Li, Z.; Mutlugun, E.; Martinez, P. L. H.; Li, D.; Zhang, Q.; Gao, Y.; Demir, Hilmi Volkan; Xiong, Q.CTAB-coated Au nanorods were directly self-assembled into a vertically aligned monolayer with highly uniform hot spots through a simple but robust approach. By coupling with CdSe/ZnS quantum dots, a maximum enhancement of 10.4 is achieved due to: increased excitation transition rate, radiative rate, and coupling efficiency of emission to the far field.Item Open Access Temperature gradient generation and control(Springer, 2015) Çetin, Barbaros; Li, D.; Li, D.In today’s microfluidic technology, electrokinetic transport is used to perform many chemical and biological analyses in lab-on-a-chip devices, such as clinical diagnoses, DNA scanning, cell manipulation, cell patterning, and molecular detection. Due to the presence of an electrical potential gradient in electrokinetic transport, Joule heating is a ubiquitous phenomenon which may lead to an increase in the overall temperature and to temperature gradients in the transverse and longitudinal directions inside the channels. These generated temperature gradients and their control are crucial for the performance of the devices.Item Open Access Ultrasonic pumps(Springer, 2015) Çetin, Barbaros; Salemmilani, Reza; Li, D.; Li, D.Item Open Access Vertically aligned gold nanorod monolayer on arbitrary substrates: self-assembly and femtomolar detection of food contaminants(American Chemical Society, 2013) Peng, B.; Li, G.; Li, D.; Dodson, S.; Zhang, Q.; Zhang, J.; Lee, Y. H.; Demir, Hilmi Volkan; Ling, X. Y.; Xiong, Q.Public attention to the food scandals raises an urgent need to develop effective and reliable methods to detect food contaminants. The current prevailing detections are primarily based upon liquid chromatography, mass spectroscopy, or colorimetric methods, which usually require sophisticated and time-consuming steps or sample preparation. Herein, we develop a facile strategy to assemble the vertically aligned monolayer of Au nanorods with a nominal 0.8 nm gap distance and demonstrate their applications in the rapid detection of plasticizers and melamine contamination at femtomolar level by surface-enhanced Raman scattering spectroscopy (SERS). The SERS signals of plasticizers are sensitive down to 0.9 fM concentrations in orange juices. It is the lowest detection limit reported to date, which is 7 orders of magnitude lower than the standard of United States (6 ppb). The highly organized vertical arrays generate the reproducible "SERS-active sites" and can be achieved on arbitrary substrates, ranging from silicon, gallium nitride, glass to flexible poly(ethylene naphthalate) substrates.