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Creators/Authors contains: "Gupta, Ananya Sen"

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  1. Viral subtyping can facilitate visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Understanding the virus's evolution spatiotemporally can help forensic strategies. We have identified mutation variation within SARS-CoV-2 sequences via an entropy measure followed by frequency analysis. These signatures, Informative Subtype Markers (ISMs), define a compact set of nucleotide sites that characterize the most variable (and thus most informative) positions in the viral genomes sequenced from different individuals. Using these ISMs, we show that we can use them for a variety of downstream analyses, such as comparing countries' subtype compositions. We present association graphs as a visualization tool to connect different ISMs based on their co-occurrence across different individuals. In particular, we investigate dominant ISMs for different locations, across different factors such as gender and age.
  2. In this work, we present peak-cognizant quantification of environmental weathering of crude oil from the from the Deepwater Horizon oil spill. The key idea is to autonomously extract peak information from raw gas chromatography-mass spectrometry (GC-MS) signals from crude oil samples, and represent the relative weathering of different peaks in a graph-based quantitative computational framework. We also present results from pre-processing the raw signals with baseline correction and signal normalization. Retention time alignment is performed by first aligning the source oil by determining the retention time drift between prominent peaks within the signals and applying the calculated drift to the weathered oil samples. Peak finding, validation, and grouping of the five weathered oil samples to a source oil sample allows compound associations to be discovered. We present preliminary results as graphical visualizations allowing for rapid and precise interpretation of weathering compounds within polycyclic aromatic hydrocarbons (PAH). Results presented were generated with oil samples showing different degrees of weathering collected from the Deepwater Horizon spill.