Browsing by Author "Li, X."

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Open Access
Abstract 207: the cBioPortal for cancer genomics
(American Association for Cancer Research (AACR), 2021) Gao, J.; Mazor, T.; de Bruijn, I.; Abeshouse, A.; Baiceanu, D.; Erkoç, Z.; Gross, B.; Higgins, D.; Jagannathan, P. K.; Kalletla, K.; Kumari, Priti; Kundra, R.; Li, X.; Lindsay, J.; Lisman, A.; Lukasse, P.; Madala, D.; Madupuri, R.; Ochoa, A.; Plantalech, O.; Quach, J.; Rodenburg, S.; Satravada, A.; Schaeffer, F.; Sheridan, R.; Sikina, L.; Sümer, S. O.; Sun, Y.; van Dijk, P.; van Nierop, P.; Wang, A.; Wilson, M.; Zhang, H.; Zhao, G.; van Hagen, S.; van Bochove, K.; Doğrusöz, Uğur; Heath, A.; Resnick, A.; Pugh, T. J.; Sander, C.; Cerami, E.; Schultz, N.
The cBioPortal for Cancer Genomics is an open-source software platform that enables interactive, exploratory analysis of large-scale cancer genomics data sets with a user-friendly interface. It integrates genomic and clinical data, and provides a suite of visualization and analysis options, including OncoPrint, mutation diagram, variant interpretation, survival analysis, expression correlation analysis, alteration enrichment analysis, cohort and patient-level visualization, among others.The public site (https://www.cbioportal.org) hosts data from almost 300 studies spanning individual labs and large consortia. Data is also available in the cBioPortal Datahub (https://github.com/cBioPortal/datahub/). In 2020 we added data from 21 studies, totaling almost 30,000 samples. In addition, we added data to existing TCGA PanCancer Atlas studies, including MSI status, mRNA-seq z-scores relative to normal tissue, microbiome data, and RPPA-based protein expression. The cBioPortal also supports AACR Project GENIE with a dedicated instance hosting the GENIE cohort of 112,000 clinically sequenced samples from 19 institutions worldwide (https://genie.cbioportal.org).The site is accessed by over 30,000 unique visitors per month. To support these users, we hosted a five-part instructional webinar series. Recordings of these webinars are available on our website and have already been viewed thousands of times.In addition, more than 50 instances are installed at academic institutions and pharmaceutical/biotechnology companies. In support of these local instances, we continue to simplify the installation process: we now provide a docker compose solution which includes all microservices to run the web app as well as data validation, import and migration.We continue to enhance and expand the functionality of cBioPortal. This year we significantly enhanced the group comparison feature; it is now integrated into gene-specific queries and supports comparison of more data types including DNA methylation, microbiome, and any outcome measure. We also expanded support of longitudinal data: the existing patient timeline has been refactored and now supports a wider range of data and visualizations; a new “Genomic Evolution” tab highlights changes in mutation allele frequencies across multiple samples from a patient; and samples can now be selected based on pre- or post-treatment status. Other features released this year include: allowing users to add gene-level plots for continuous molecular profiles in study view, enabling users to select the desired transcript on the Mutations tab, and integration of PathwayMapper.The cBioPortal is fully open source (https://github.com/cBioPortal/) under a GNU Affero GPL license. Development is a collaborative effort among groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children's Hospital of Philadelphia, Princess Margaret Cancer Centre, Bilkent University and The Hyve.
Open Access
Activatable photosensitizers: agents for selective photodynamic therapy
(Wiley-VCH Verlag, 2017) Li, X.; Kolemen, S.; Yoon, J.; Akkaya, E. U.
Recent developments in the design of bifunctional and activatable photosensitizers rejuvenate the aging field of photodynamic sensitization and photodynamic therapy. While systematic studies have uncovered new dyes that can serve as potential photosensitizers, the most promising results have come from studies aimed at gaining precise control over the location and rate of cytotoxic singlet oxygen generation. As a consequence, higher selectivities and efficiencies in photodynamic treatment protocols are now within reach. This feature article highlights the variety of approaches that have been pursued to improve photodynamic therapy and to transform simple photosensitizers into smarter theranostic agents.
Open Access
Analysis and visualization of longitudinal genomic and clinical data from the AACR project GENIE biopharma collaborative in cBioPortal
(American Association for Cancer Research, 2023-12-01) de Bruijn, I.; Kundra, R.; Mastrogiacomo, B.; Tran, T. N.; Sikina, L.; Mazor, T.; Li, X.; Ochoa, A.; Zhao, G.; Lai, B.; Abeshouse, A.; Baiceanu, D.; Çiftçi, E.; Doğrusöz, Uğur; Dufilie, A.; Erkoç, Z.; Garcia Lara, E.; Fu, Z.; Gross, B.; Haynes, C.; Heath, A.; Higgins, D.; Jagannathan, P.; Kalletla, K.; Kumari, P.; Lindsay, J.; Lisman, A.; Leenknegt, B.; Lukasse, P.; Madela, D.; Madupuri, R.; van Nierop, P.; Plantalech, O.; Quach, J.; Resnick, A. C.; Rodenburg, S. Y. A.; Satravada, B. A.; Schaeffer, F.; Sheridan, R.; Singh, J.; Sirohi, R.; Sümer, S. O.; van Hagen, S.; Wang, A.; Wilson, M.; Zhang, H.; Zhu, K.; Rusk, N.; Brown, S.; Lavery, J. A.; Panageas, K. S.; Rudolph, J. E.; LeNoue-Newton, M. L.; Warner, J. L.; Guo, X.; Hunter-Zinck, H.; Yu, T. V.; Pilai, S.; Nichols, C.; Gardos, S. M.; Philip, J.; Kehl, K. L.; Riely, G. J.; Schrag, D.; Lee, J.; Fiandalo, M. V.; Sweeney, S. M.; Pugh, T. J.; Sander, C.; Cerami, E.; Gao, J.; Schultz, N.
International cancer registries make real-world genomic and clinical data available, but their joint analysis remains a challenge. AACR Project GENIE, an international cancer registry collecting data from 19 cancer centers, makes data from >130,000 patients publicly available through the cBioPortal for Cancer Genomics (https://genie.cbioportal.org). For 25,000 patients, additional real-world longitudinal clinical data, including treatment and outcome data, are being collected by the AACR Project GENIE Biopharma Collaborative using the PRISSMM data curation model. Several thousand of these cases are now also available in cBioPortal. We have significantly enhanced the functionalities of cBioPortal to support the visualization and analysis of this rich clinico-genomic linked dataset, as well as datasets generated by other centers and consortia. Examples of these enhancements include (i) visualization of the longitudinal clinical and genomic data at the patient level, including timelines for diagnoses, treatments, and outcomes; (ii) the ability to select samples based on treatment status, facilitating a comparison of molecular and clinical attributes between samples before and after a specific treatment; and (iii) survival analysis estimates based on individual treatment regimens received. Together, these features provide cBioPortal users with a toolkit to interactively investigate complex clinico-genomic data to generate hypotheses and make discoveries about the impact of specific genomic variants on prognosis and therapeutic sensitivities in cancer.
Open Access
Electrochemical properties of single-crystalline Mn3O4 nanostructures and their capacitive performance in basic electrolyte
(Electrochemical Science Group, 2016) Shah, H. U.; Wang, F.; Toufiq, A. M.; Khattak, A. M.; Iqbal, A.; Ghazi, Z. A.; Ali, S.; Li, X.; Wang, Z.
Single-crystalline Mn3O4 square-shaped nanostructures have been successfully synthesized by hydrothermal method without using any surfactant. The as-prepared products were characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), Transmission electron microscopy (TEM) and High Resolution transmission electron microscopy (HRTEM). To assess the potential properties of nanostructures, galvanostatic charging-discharging and cyclic voltammetry measurements were performed for their use in supercapacitors. The Mn3O4 nanoarchitectures used as supercapacitor electrode in 1mol L-1 KOH electrolyte have a specific capacitance value of 355.5 F g-1 at a low current density of 0.35 A.g-1. The device still retain 85.08% of its initial capacitance afterwards 2000 cycles at a current density of 5 A.g-1. The as-synthesized Mn3O4 nanostructures exhibited a good rate capability and stability for electrochemical properties. These results indicate their potential application as electrode material for high performance supercapacitor in basic medium.
Open Access
Light generation in lead halide perovskite nanocrystals: LEDs, color converters, lasers, and other applications
(WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim, 2019) Yan, F.; Tan, S.; Li, X.; Demir, Hilmi Volkan
Facile solution processing lead halide perovskite nanocrystals (LHP‐NCs) exhibit superior properties in light generation, including a wide color gamut, a high flexibility for tuning emissive wavelengths, a great defect tolerance and resulting high quantum yield; and intriguing electric feature of ambipolar transport with moderate and comparable mobility. As a result, LHP‐NCs have accomplished great achievements in various light generation applications, including color converters for lighting and display, light‐emitting diodes, low threshold lasing, X‐ray scintillators, and single photon emitters. Herein, the considerable progress that has been made thus far is reviewed along with the current challenges and future prospects in the light generation applications of LHP‐NCs.
Open Access
State of the art and prospects for Halide Perovskite nanocrystals
(American Chemical Society, 2021-06-17) Dey, A.; Ye, J.; De, A.; Debroye, E.; Ha, S. K.; Bladt, E.; Kshirsagar, A. S.; Wang, Z.; Yin, J.; Wang, Y.; Quan, L. N.; Yan, F.; Gao, M.; Li, X.; Shamsi, J.; Debnath, T.; Cao, M.; Scheel, M. A.; Kumar, S.; Steele, J. A.; Gerhard, M.; Chouhan, L.; Xu, K.; Wu, X-g; Li, Y.; Zhang, Y.; Han, C.; Dutta, A.; Vincon, I.; Rogach, A. L.; Nag, A.; Samanta, A.; Korgel, B. A.; Shih, C.-J.; Gamelin, D. R.; Son, D. H.; Zeng, H.; Zhong, H.; Sun, H.; Demir, Hilmi Volkan; Scheblykin, I. G.; Mora-Seró, I.; Stolarczyk, J. K.; Zhang, J. Z.; Feldmann, J.; Hofkens, J.; Luther, J. M.; Pérez-Prieto, J.; Li, L.; Manna, L.; Bodnarchuk, M. I.; Kovalenko, M. V.; Roeffaers, M. B. J.; Pradhan, N.; Mohammed, O. F.; Bakr, O. M.; Yang, P.; Müller-Buschbaum, P.; Kamat, P. V.; Bao, Q.; Zhang, Q.; Krahne, R.; Galian, R. E.; Stranks, S. D.; Bals, S.; Biju, V.; Tisdale, W. A.; Yan, Y.; Hoye, R. L. Z.; Polavarapu, L.
Metal-halide perovskites have rapidly emerged as one of the most promising materials of the 21st century, with many exciting properties and great potential for a broad range of applications, from photovoltaics to optoelectronics and photocatalysis. The ease with which metal-halide perovskites can be synthesized in the form of brightly luminescent colloidal nanocrystals, as well as their tunable and intriguing optical and electronic properties, has attracted researchers from different disciplines of science and technology. In the last few years, there has been a significant progress in the shape-controlled synthesis of perovskite nanocrystals and understanding of their properties and applications. In this comprehensive review, researchers having expertise in different fields (chemistry, physics, and device engineering) of metal-halide perovskite nanocrystals have joined together to provide a state of the art overview and future prospects of metal-halide perovskite nanocrystal research.