Shane Lofgren [Khatri Lab]

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====== Shane Lofgren ======
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====Research Interests====


I am working primarily on three collaborative projects in the lab.

1. Development of a robust diagnostic and prognostic mRNA signature of Systemic Sclerosis which can be used for patient monitoring and prediction of responsiveness to treatment.  This is in collaboration primarily with Dr. Hinchcliff at Northwestern.

2. Development of methods for finding new host targeted antiviral drugs.  This project has advanced to the point where we have found compounds with in vitro and in vivo efficacy and are now elucidating the mechanism of action in order to discover host pathways essential for viral proliferation.  This is in collaboration primarily with the Einav Lab at Stanford.

3. Development of Deep Learning methods for predicting the affinity between a T Cell Receptor and a given peptide-MHC for the purposes of determining the potential self-targets of a given TCR.  This is in collaboration with the Garcia and Davis Labs at Stanford.

Other general interests and projects generally revolve around the discovery of new targets and drugs in diseases, especially cancer, and the use of advanced machine learning methods.  
 
====Publications====

Scranton, Melissa A., Joseph T. Ostrand, D. Ryan Georgianna, Shane M. Lofgren, Daphne Li, Rosalie C. Ellis, David N. Carruthers, Andreas Dräger, David L. Masica, and Stephen P. Mayfield. "Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii." Algal Research 15 (2016): 135-142.

Reynoird, Nicolas, Pawel K. Mazur, Timo Stellfeld, Natasha M. Flores, Shane M. Lofgren, Scott M. Carlson, Elisabeth Brambilla et al. "Coordination of stress signals by the lysine methyltransferase SMYD2 promotes pancreatic cancer." Genes & Development 30, no. 7 (2016): 772-785.

Mazur, Pawel K., Alexander Herner, Stephano S. Mello, Matthias Wirth, Simone Hausmann, Francisco J. Sánchez-Rivera, Shane M. Lofgren et al. "Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma." Nature medicine (2015).

Lofgren, Shane and Farrel, Alvin. "Structure-Based Prediction of Transcription Factor Binding Sites." Tsinghua Science and Technology 19, no. 6 (2015): 568-577.