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Articles 1 - 5 of 5
Full-Text Articles in Engineering
Crowd Control: Regulating The Spatial Organization Of Biopolymers And Gene Expression By Macromolecular Crowding, Gaurav Chauhan
Crowd Control: Regulating The Spatial Organization Of Biopolymers And Gene Expression By Macromolecular Crowding, Gaurav Chauhan
Doctoral Dissertations
The intracellular environment is crowded with macromolecules that can occupy a significant fraction of the cellular volume. This can give rise to attractive depletion interactions that impact the conformations and interactions of biopolymers, as well as their interactions with confining surfaces. We used computer simulations to study the effects of crowding on biologically-inspired models of polymers. We showed that crowding can lead to attractive interactions between two flexible ring polymers, and we further characterized the adsorption of both flexible and semiflexible polymers onto confining surfaces. These results indicate that crowding-induced depletion interactions could play a role in the spatial organization …
A Comparison Of Computational Approaches For Intron Retention Detection, Jiantao Zheng, Cuixiang Lin, Zhenpeng Wu, Hong-Dong Li
A Comparison Of Computational Approaches For Intron Retention Detection, Jiantao Zheng, Cuixiang Lin, Zhenpeng Wu, Hong-Dong Li
Big Data Mining and Analytics
Intron Retention (IR) is an alternative splicing mode through which introns are retained in mature RNAs rather than being spliced in most cases. IR has been gaining increasing attention in recent years because of its recognized association with gene expression regulation and complex diseases. Continuous efforts have been dedicated to the development of IR detection methods. These methods differ in their metrics to quantify retention propensity, performance to detect IR events, functional enrichment of detected IRs, and computational speed. A systematic experimental comparison would be valuable to the selection and use of existing methods. In this work, we conduct an …
Subomiembed: Self-Supervised Representation Learning Of Multi-Omics Data For Cancer Type Classification, Sayed Hashim, Muhammad Ali, Karthik Nandakumar, Mohammad Yaqub
Subomiembed: Self-Supervised Representation Learning Of Multi-Omics Data For Cancer Type Classification, Sayed Hashim, Muhammad Ali, Karthik Nandakumar, Mohammad Yaqub
Computer Vision Faculty Publications
For personalized medicines, very crucial intrinsic information is present in high dimensional omics data which is difficult to capture due to the large number of molecular features and small number of available samples. Different types of omics data show various aspects of samples. Integration and analysis of multi-omics data give us a broad view of tumours, which can improve clinical decision making. Omics data, mainly DNA methylation and gene expression profiles are usually high dimensional data with a lot of molecular features. In recent years, variational autoencoders (VAE) [13] have been extensively used in embedding image and text data into …
The Role Of Son In Chromatin-Mediated Gene Expression, Melissa Jordan Ward
The Role Of Son In Chromatin-Mediated Gene Expression, Melissa Jordan Ward
Browse all Theses and Dissertations
Gene expression in mammalian cells requires complex nuclear choreography, and there is increasing evidence that spatiotemporal organization of chromatin and nuclear compartments plays an important role in gene expression. In this dissertation, I examined the function of SON, a splicing factor with a known role in nuclear organization, in chromatin-mediated gene expression. SON association with a transcriptionally inactive U2OS 2-6-3 reporter gene array provided a useful model to study SON’s chromatin dynamics. I demonstrated that SON associates with the inactive but not the activated array, and that SON’s RNA binding domains are not necessary for that association. Second, I discovered …
Assessment Of Scientific Payload Carrying Spirulina Onboard Blue Origin’S New Shepard Vehicle, Pedro J. Llanos, Morgan Shilling, Kristina Andrijauskaite, Kody Kidder, Vijay V. Duraisamy
Assessment Of Scientific Payload Carrying Spirulina Onboard Blue Origin’S New Shepard Vehicle, Pedro J. Llanos, Morgan Shilling, Kristina Andrijauskaite, Kody Kidder, Vijay V. Duraisamy
Publications
The research team at ERAU and UTHSCSA analyzed the effects of suborbital flight stressors and various light conditions (red, white, no light) on the Arthrospira platensis (Spirulina), onboard Blue Origin’s New Shepard vehicle. Commercially available cyanobacterium species were cultivated and closely monitored in mother colonies several months before the suborbital flight mission. The aim of this study was to estimate the biomass production and growth as a potential dietary alternative for prospective human spaceflight's life support system. Spirulina samples were flown in a NanoLab with adjacent avionics supporting the light conditions and sensors to monitor the temperature, relative humidity, and …