Author: Barry Farmer

Website: https://teetslab.com/Scholars@UK: https://scholars.uky.edu/en/persons/nicholas-teetsSlides from CCS/RCD Seminar on 3/19/2024: 20240319-Teets-Seminar.pdf Genomics and transcriptomics of extreme insects Insects are the most diverse and abundant animals on the planet, but Antarctica is the exception to that rule. Only a handful of species can survive Antarctica’s harsh terrestrial environments, and these insects have unique adaptations for coping with extreme abiotic conditions and long winters. Our lab is interested in the physiological and molecular mechanisms by which these insects survive (and thrive) at the bottom of the earth. Antarctic insects are difficult to collect and currently unamenable to laboratory rearing, so genomics provides a powerful tool for identifying mechanisms that underpin adaptation to extreme environments. We use a combination of transcriptomics, whole genome sequencing, and population genomics to characterize the molecular and evolutionary genetic processes…

Website: https://pharmacy.uky.edu/people/chang-guo-zhanScholars@UK: https://scholars.uky.edu/en/persons/chang-guo-zhanSlides from CCS/RCD Seminar on 3/19/2024: 20240319-Zhan-Seminar.pdf State-of-the-art computational drug design, discovery, and development: Challenges and opportunities Discovery and development of a novel drug to meet an unmet medical need is generally an extremely long and very costly process. This process may be accelerated by performing state-of-the-art computational design in all phases of drug discovery and development. Computational drug design has been evolving from ligand-based drug design to structure-based drug design and further to mechanism-based drug design. All these computational drug design methods are further powered by artificial intelligence and machine learning. Overall, the accuracy and efficiency of state-of-the-art drug design rely on development of both computing power and computational algorithms. In this seminar, I will first briefly discuss the general strategies of high-performance supercomputing used in the…

Website: https://pa.as.uky.edu/users/cbcraw2Scholars@UK: https://scholars.uky.edu/en/persons/christopher-crawford Slides from CCS/RCD Seminar on 2/13/2024: sls_conv_2024-02-13_ccs.pdf Fitting Digital Signals in Real-Time using the Magic of Convolutions David Mathews, University of KentuckyAPS DNP talk, April 2019 With the availability of cost-effective digitizers and powerful pipeline processors, modern spectroscopy can be performed completely in the digital domain with minimal front-end analog signal processing. These systems offer the flexibility and extensibility of digital signal processing algorithms to simultaneously extract multiple waveform parameters such as pulse height and start time. However, up until now, the computationally intensive task of pulse fitting has traditionally been performed offline on computing clusters to obtain the final spectra. This research proposes new algorithms to perform these least-squares fits to template waveforms in real time on Field Programmable Gate Arrays (FPGAs) and GPUs. They will…

Website: https://gluck.ca.uky.edu/directory/ted-kalbfleischScholars@UK: https://scholars.uky.edu/en/persons/theodore-kalbfleischMember of the UK Genetics and Genomics Research Group: https://gluck.ca.uky.edu/geneticsSlides from CCS/RCD Seminar on 2/13/2024: CCS_Kalbfleisch_2024_02_13.pdf The Challenges and Opportunities of Reference Free Genomic Data Analysis Since its inception, the cost of generating high quality genomic sequence has plummeted toward zero. Pipelines that perform primary analyses and genome assembly have scaled well with available computing power and have rarely been a rate limiting step for genomic analyses. Historically, a species has had a single reference genome which has been well annotated for gene structure and epigenetic marks. Sequence data for any animals from that or a closely related species are mapped to that reference for analysis in that curated genomic context. The advent of inexpensive long, and ultralong sequencing technologies have made the assembly of phased, nearly gapless…