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A collaborative paper I worked on with the Sage lab, Transcriptional networks underlying tumour plasticity in small-cell lung cancer is officially preprinted! Take a look for more info about the second generation of BooleaBayes, BoBa-T, which uses single cell ATAC-seq and RNA-seq to build, simulate, and perturb transcription factor networks.
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Our paper, YAP1 defines an emergent, plastic population of relapsed small cell lung cancer, is officially online.
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My paper with the Janes lab, “Cell-specific Cahn-Hilliard models predict condensed fates of the chromosomal passenger complex,” was accepted at PLOS Computational Biology!
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I just started as an Assistant Professor in the School of Data Science at UVA! I’m excited to teach DS2003 and DS5030 in the Fall.
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I presented a poster, “Cell-specific Cahn-Hilliard models predict condensed fates of the chromosomal passenger complex,” at the Annual SASCO Symposium, on physics-based modeling of the chromosomal passenger complex with Catalina Alvarez, Min-Jhe Liu, Montserrat Gerardo, John Lowengrub, Todd Stukenberg, and Kevin Janes.
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I gave a talk, “Transitions and Dynamics of a Mitotic Condensate,” at SBHD in Boston.
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My paper, “Integration of Social and Ethical AI Topics into a Computational Biomedical Engineering Course Increases Engagement Without Loss of Technical Learning,” was accepted to the ASEE (American Society for Engineering Education) Annual Conference.
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My video on system biology is now on youtube! Check it out here.
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I started as a postdoc in the Janes lab at UVA. I will be working on Project 1 of the U54 Center for Systems Analysis of Stress-adapted Organelles (SASCO). My goal will be to build a computational, physics-based model of the chromosome passenger complex (CPC) that controls chromosome segregation during mitosis. In cancer, it is unknown how the CPC is affected by dysregulated mitotic transcription factors. Using a reaction-diffusion model built in VCell, we will investigate the phase separation behavior of the CPC during mitosis in cancer systems.
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I published a paper in Molecular Cancer with a group of collaborators at Vanderbilt. I did a WGCNA analysis of melanoma RNA-seq data that provided supporting evidence for the importance of key transcription factors, such as Tfcp2l1, that regulate phenotype after loss of Cxcr2. The Richmond lab and other collaborators did a great job with this work, and I am grateful I was asked to help with the computational analysis for the project!
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I was selected as the Education Scholar for the SASCO Outreach Core at UVA. This means I will be making a 25 minute video to educate clinicians on systems biology.
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My first author manuscript was published in Cancers, which showed the relationship between an EMT spectrum and the continuum of transcription factor-driven subtypes in Small Cell Lung Cancer.
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I packaged my network analysis tools as a PYPI package, BooleaBayes. Check out my Projects page to see all of the code I have developed. This package was written by David Wooten and me, and refactored for packaging by Monica Del Valle.
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I was awarded an NIH Postdoctoral Training Grant (T32) to continue my research at the intersection of cancer systems biology and data science. I am working under Drs. Vito Quaranta and Scott Hiebert at Vanderbilt University.
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Today I officially defended my thesis title “Network Control of Cell Identity and Plasticity in Small Cell Lung Cancer.” You can view my Dissertation here.