Dr Ruben Sanchez-Garcia

Postdoctoral Researcher

About Me

I am a computational biologist developing methods for structural biology, primarily cryo-EM for drug discovery.

I hold a BSc degree in Biotechnology, another one in Computer Science and an MSc in Biophysics. I did my PhD at the Spanish National Center of Biotechnology (CSIC) and the Autonomous University of Madrid (UAM), under the supervision of Professor Jose Maria Carazo and Dr Joan Segura. During that time, I developed machine learning algorithms for structural biology, including BIPSPI and DeepEMhancer.

I joined the Department of Statistics in 2020 where, in collaboration with XChem, I worked on AI algorithms for fragment-based drug discovery for almost two years. Currently, I am trying to improve cryo-EM algorithms to facilitate drug discovery.

Research Interests

  • Machine Learning / Deep Learning 
  • Structural biology  
  • Cryo-EM 
  • Drug discovery 

Publications

Sanchez-Garcia, R., Saur, M., Vargas, J., Poelking, C. and Deane, C. (2023) “CESPED: a new benchmark for supervised particle pose estimation in Cryo-EM.”
Wills, S., Sanchez-Garcia, R., Dudgeon, T., Roughley, S., Merritt, A., Hubbard, R., Davidson, J., von Delft, F. and Deane, C. (2023) “Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search.”, Journal of chemical information and modeling, 63(11), pp. 3423–3437.
Sanchez-Garcia, R., Havasi, D., Takács, G., Robinson, M., Lee, A., von Delft, F. and Deane, C. (2022) “CoPriNet: Graph Neural Networks provide accurate and rapid compound price prediction for molecule prioritisation.”, ChemRxiv.
Sanchez-Garcia, R., Macias, J., Sorzano, C., Carazo, J. and Segura, J. (2022) “BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction.”, Journal of molecular biology, 434(11), p. 167556.
Wills, S., Sanchez-Garcia, R., Roughley, S., Merritt, A., Hubbard, R., Dudgeon, T., Davidson, J., von Delft, F. and Deane, C. (2022) “The use of a graph database is a complementary approach to a classical similarity search for identifying commercially available fragment merges”, bioRxiv.
Sanchez-Garcia, R., Gaullier, G., Gaullier, G., Cuadra-Troncoso, J. and Vargas, J. (2022) “Cryo-EM map anisotropy can be attenuated by map post-processing and a new method for its estimation”, bioRxiv.
Macias, J., Sanchez-Garcia, R., Conesa, P., Ramirez-Aportela, E., Martinez Gonzalez, M., Wert-Carvajal, C., Parra-Perez, A., Segura Mora, J., Horrell, S., Thorn, A., Sorzano, C. and Carazo, J. (2021) “3DBionotes COVID-19 edition.”, Bioinformatics (Oxford, England), 37(22), pp. 4258–4260.
Sanchez-Garcia, R., Gomez-Blanco, J., Cuervo, A., Carazo, J., Sorzano, C. and Vargas, J. (2021) “DeepEMhancer: a deep learning solution for cryo-EM volume post-processing.”, Communications biology, 4(1), p. 874.
Kaur, S., Gomez-Blanco, J., Khalifa, A., Adinarayanan, S., Sanchez-Garcia, R., Wrapp, D., McLellan, J., Bui, K. and Vargas, J. (2021) “Local computational methods to improve the interpretability and analysis of cryo-EM maps.”, Nature communications, 12(1), p. 1240.
Kaur, S., Gomez-Blanco, J., Khalifa, A., Adinarayanan, S., Sanchez-Garcia, R., Wrapp, D., McLellan, J., Bui, K. and Vargas, J. (2021) “Local methods to improve cryo-electron microcopy maps”, in Optics InfoBase Conference Papers.

Contact Details

Email: ruben.sanchez-garcia@stats.ox.ac.uk 

Office: 2.04

Research Groups

Computational Biology and Bioinformatics

Research Students

Stephanie Wills