Rhiju Das

Rhiju Das

Investigator

Biography

Dr. Das is a computational biochemist at Stanford University School of Medicine. His lab seeks a predictive understanding of how RNA molecules code for complex biological machines. The lab’s computer algorithms have consistently achieved leading predictions in world-wide structure prediction trials. Complementary to these computer methods, Dr. Das is developing high-throughput ‘multidimensional chemical mapping’ experiments to uncover three-dimensional structures and conformational changes of non-coding RNAs in their biological milieu, leading to discoveries of RNA regulons and influenza packaging signals that are critical for mammalian development and viral infection. Towards novel molecules of biomedical interest, Dr. Das leads the Eterna massive open laboratory, which couples a 100,000-player videogame to the lab’s massively parallel experimental tools and deep learning, the first such platform in citizen science. Dr. Das’s research has been recognized with the Burroughs-Wellcome Career Award at the Interface of Science, a W.M. Keck Medical Research Program award, and the OpenEye/American Chemical Society Outstanding Junior Faculty Award. Dr. Das mentors students from the biochemistry, biophysics, biomedical informatics, chemistry, and learning sciences Ph.D. programs.

Research interests

The Das Lab explores algorithms to predict the structures and energetics of RNAs and RNA/protein interfaces at high resolution, focusing initially on small building blocks. We test these ideas through community-wide blind trials and by solving molecule structures and structure ensembles with sparse chemical mapping, NMR, crystallographic, and cryoelectron microscopy data.

Complementary to this computational research, the lab is developing information-rich biochemical methods to model the myriad structures of non-coding RNAs that remain unknown. Current efforts focus on probing the extent of RNA structure and conformational change inside cells and viruses, in close collaboration with expert biologists at Stanford.

In addition to modeling RNAs, the Das Lab aims to design new ones for basic science, diagnostics, and therapeutics. The videogame project EteRNA seeks missing rules and novel molecules for medicine by giving citizen scientists access to high-throughput wet-lab experiments.

Distinctions and Awards

  • British Marshall Scholar, Marshall Aid Commemoration Commission (1998-2000)
  • Jane Coffin Childs Foundation Fellowship, Jane Coffin Childs Foundation (2006-2008)
  • Career Award at the Scientific Interface, Burroughs-Wellcome Foundation (2008-present)
  • Keck Medical Research Grant award, W. M. Keck Foundation (2012)
  • OpenEye Outstanding Junior Faculty Award, American Chemical Society (2015)

Recent publications

  • Kappel, K., Liu, S., Larsen, K. P., Skiniotis, G., Puglisi, E. V., Puglisi, J. D., Zhou, Z. H., Zhao, R., Das, R. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nature methods 2018

  • Watkins, A. M., Geniesse, C., Kladwang, W., Zakrevsky, P., Jaeger, L., Das, R. Blind prediction of noncanonical RNA structure at atomic accuracy. Science advances 2018; 4 (5): eaar5316

  • Tian, S., Kladwang, W., Das, R. Allosteric mechanism of the V-vulnificus adenine riboswitch resolved by four-dimensional chemical mapping eLife 2018; 7

  • Chou, F., Kladwang, W., Kappel, K., Das, R. Blind tests of RNA nearest-neighbor energy prediction PNAS 2016; 113 (30): 8430-8435

  • Tian, S., Das, R. RNA structure through multidimensional chemical mapping Quarterly Reviews of Biophysics 2016; 49

  • Anderson-Lee, J., Fisker, E., Kosaraju, V., Wu, M., Kong, J., Lee, J., Lee, M., Zada, M., Treuille, A., Das, R. Principles for Predicting RNA Secondary Structure Design Difficulty. Journal of molecular biology 2016; 428 (5): 748-757

  • Miao, Z., Adamiak, R. W., Blanchet, M., Boniecki, M., Bujnicki, J. M., Chen, S., Cheng, C., Chojnowski, G., Chou, F., Cordero, P., Cruz, J. A., Ferre-D’Amare, A. R., Das, R., Ding, F., Dokholyan, N. V., Dunin-Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M., Major, F., Mann, T. H., Masquida, B., Matelska, D., Meyer, M., Peselis, A., Popenda, M., Purzycka, K. J., Serganov, A., Stasiewicz, J., Szachniuk, M., Tandon, A., Tian, S., Wang, J., Xia, Y., Xu, X., Zhang, J., Zha, P., Zok, T., Westhof, E.All Authors RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures RNA 2015; 21 (6): 1066-1084

  • Cheng, C. Y., Chou, F., Kladwang, W., Tian, S., Cordero, P., Das, R. Consistent global structures of complex RNA states through multidimensional chemical mapping. eLife 2015; 4

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