TITLE: "Genomics for precision public health in Colombia" Hosted by Juan De La Hoz.
https://socalsysbio.qcb.ucla.edu
Phylogenetics – the reconstruction of the evolutionary history of a the variety of species known to us, is among the most fundamental and traditional tasks in Biology. With the dramatic developments in molecuar biology and the exponential growth in annotated genetic sequences, novel directions and goals have been developed in this seemingly stagnant field. Phylogenetic […]
The workshop will mainly focus on teaching the fundamentals of bacterial genomics and basic bioinformatics analysis. As a sample data Vibrio cholerae genome will be used as the practice dataset, and workshop participants will try to reproduce the expected results. The workshop will start with detailed instructions on how to quality control the raw sequence […]
TITLE: "G-Flux: a metabolic flux and free energy analysis software for interpreting 13C, 2H, 18O, and 15N isotope tracing data." ABSTRACT: Metabolic fluxes offer insights into pathway utilization, kinetics, and thermodynamics. Stable isotope tracing and metabolic footprinting are widely used for inferring metabolic fluxes. However, quantitative flux measurement across broad metabolism remains challenging due to […]
TITLE: "PCA outperforms popular hidden variable inference methods for QTL mapping." ABSTRACT: Estimating and accounting for hidden variables is widely practiced as an important step in quantitative trait locus (QTL) analysis for improving the power of QTL identification. However, few benchmark studies have been performed to evaluate the efficacy of the various methods developed for […]
TITLE: "Stochastic Model and Optimization of SELEX." ABSTRACT: Systematic Evolution of Ligands by EXponential enrichment (SELEX) is a process to select the best aptamer sequence in a huge aptamer library that binds a specified target molecule with the highest affinity. There has been a deterministic model of SELEX, and we develop a fully discrete stochastic […]
TITLE: "Tensor Factorization for Interpreting the Mechanisms of MRSA Persistence." ABSTRACT: Methicillin-resistant Staphylococcus aureus (MRSA) bacteria is an increasingly common and life-threatening infection. While some antibiotics resolve MRSA infections in vitro, these same antibiotics often fail to clear an infection when used to treat patients, suggesting that MRSA persistence is a confluence of both host […]
TITLE: "Baseline MEthylation Patterns prior to flu vaccination." ABSTRACT: Influenza affects millions worldwide each year with responses varying from individual to individual. Influenza can be broken down into subtypes specifically H1N1, H3N2, Yamagata, and Victoria. One way to measure the immune response to influenza is to measure a person’s antibody response to influenza. To measure how […]
TITLE: "Universal annotation of the human genome through integration of over a thousand epigenomic datasets." ABSTRACT: Genome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states […]
