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Federico P. de Isidro Gómez

Postdoctoral researcher

I am Fede, a scientist dedicated to applying engineering solutions to the fields of biology and health. My particular interests lie in image processing, data analysis, and tackling challenging problems in general. My expertise is focused on structural biology, where I have extensive experience in algorithm development for cryo-electron microscopy, culminating in a PhD in cryo-electron tomography from the Spanish National Center for Biotechnology (CNB-CSIC). Currently, I am a postdoctoral researcher based in Cambridge at Astex Pharmaceuticals, where I am pushing the detectability limits of cryo-electron microscopy.

I am eager to apply my knowledge to new problems in structural biology and explore other techniques that can benefit from improved data processing. I am passionate about collaborating with other scientists from any field to address interesting problems for the community.

Experience

Astex Pharmaceuticals

National Center for Biotechnology (CNB-CSIC)

Universidad CEU San Pablo

Academics

Masters in Biophysics | Universidad Autónoma de Madrid
Madrid | Sep. 2019 – Jun. 2020
Master Thesis: “Algorithm Automatization for Tilt-Series Alignment and Tomogram Reconstruction in Cryo-Electron Tomography”

Bachelor in Bioengineering | Universidad CEU San Pablo
Madrid | Sep. 2013 – Jun. 2019
Intern: National Center for Biotechnology
Bachelor Thesis: “Image Processing Algorithms for the Determination of Optical Aberrations of an Electron Microscope”

Bachelor in Electrical engineering | Universidad CEU San Pablo
Madrid | Sep. 2013 – Feb. 2019
Intern: Hospitales de Madrid (HM)
Bachelor Thesis: “Automatic speech recognition using Hidden Markov Models”

Bachelor in Bioengineering | University of California San Diego (UCSD)
Madrid | Sep. 2016 – Jun. 2017
Academic exchange

Bachelor in Computer science | University of California San Diego (UCSD)
Madrid | Sep. 2016 – Jun. 2017
Academic exchange

Publications in International Journals

  1. C.O.S. Sorzano, F. de Isidro-Gómez, E. Fernández-Giménez, D. Herreros, S. Marco, J.M. Carazo, C. Messaoudi, Improvements on marker-free images alignment for electron tomography, Journal of Structural Biology: X, vol. 4, p. 100037, 2020.
  2. M. Martínez, A. Jiménez-Moreno, D. Maluenda, E. Ramírez-Aportela, R. Melero, A. Cuervo, P. Conesa, L. Del Caño, Y.C. Fonseca, R. Sánchez-García, D. Strelak, J.J. Conesa, E. Fernández-Giménez, F. de Isidro, C.O.S. Sorzano, J.M. Carazo, R. Marabini, Integration of cryo-em model building software in scipion, Journal of Chemical Information and Modeling, vol. 60, no. 5, pp. 2533–2540, 2020.
  3. A. I. Gómez de Castro, M. Rheinstädter, P. Clancy, M. Castilla, F. de Isidro, J. I. Larruquert, T. de Lis-Sánchez, J. Britten, M. Cabero Piris, F.P. de Isidro-Gómez. Graphite to diamond transition induced by photoelectric absorption of ultraviolet photons, Scientific Reports, vol. 11, no. 1, p. 2492, 2021.
  4. C.O.S. Sorzano, D. Semchonok, S.C. Lin, J.L. Vilas, A. Jimenez-Moreno, M. Gragera, D. Maluenda, M. Martinez, E. Ramirez-Aportela, R. Melero, A. Cuervo, P. Conesa, L. del Caño, Y.C. Fonseca, R. Sánchez-García, D. Strelak, E. Fernández-Giménez, F. de Isidro, P. Kastritis, R. Marabini, B. Bruce, J.M. Carazo, Algorithmic robustness to preferred orientations in single particle analysis by cryoem, Journal of Structural Biology, vol. 213, no. 1, p. 107695, 2021.
  5. A. Jiménez-Moreno, L. del Caño, M. Martínez, E. Ramírez-Aportela, A. Cuervo, R. Melero, R. Sánchez-García, D. Strelak, E. Fernández-Giménez, F. de Isidro-Gómez, D. Herreros, P. Conesa, Y. Fonseca, D. Maluenda, J. Jiménez de la Morena, J.R. Macías, P. Losana, R. Marabini, J.M. Carazo, C.O.S. Sorzano, Cryo-em and single-particle analysis with scipion, JoVE (Journal of Visualized Experiments), no. 171, p. e62261, 2021.
  6. S. Sorrentino, J. Conesa, A. Cuervo, R. Melero, B. Martins, M.E. Fernández-Giménez, F. de Isidro, J. Jiménez, J.D. Studt, C.O.S. Sorzano, M. Eibauer, J.M. Carazo, O. Medalia. Structural analysis of receptors and actin polarity in platelet protrusions, Proceedings of the National Academy of Sciences, vol. 118, no. 37, p. e2105004118, 2021.
  7. D. Strelak, A. Jiménez-Moreno, J.L. Vilas, E. Ramírez-Aportela, R. Sánchez-García, D. Maluenda, J. Vargas, D. Herreros, E. Fernández-Giménez, F. de Isidro-Gómez, J. Horacek, D. Myska, M. Horacek, P. Conesa, Y.C. Fonseca-Reyna, J. Jiménez, M. Martínez, M. Harastani, S. Jonic, J. Filipovic, R. Marabini, J.M. Carazo, C.O.S. Sorzano, Advances in xmipp for cryo–electron microscopy: From xmipp to scipion, Molecules, vol. 26, no. 20, 2021.
  8. C.O.S. Sorzano, A. Jimenez-Moreno, D. Maluenda, M. Martinez, E. Ramirez-Aportela, R. Melero, A. Cuervo, J. Conesa, J. Filipovic, P.Conesa, L. del Caño, Y.C. Fonseca, J. Jiménez-de la Morena, P. Losana, R. Sáchez-García, D. Strelak, E. Fernandez-Gimenez, F. de Isidro, D.Herreros, J.L. Vilas, R. Marabini, J.M. Carazo, On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy, Acta Crystallographica Section D, vol. 78, pp. 410–423, Apr 2022.
  9. C.O.S. Sorzano, J.L. Vilas, E. Ramírez-Aportela, D. del Hoyo, D. Herreros, E. Fernandez-Giménez, D. Marchán, F. de Isidro-Gómez, J.R. Macías, I. Sánchez, L. del Caño, Y. Fonseca-Reyna, P. Conesa, A. García-Mena, J. Burguet, J. García Condado, J. Méndez García, M. Martínez, A. Muñoz Barrutia, R. Marabini, J. Vargas, J.M. Carazo, Image processing tools for the validation of cryoem maps, Faraday Discussions, vol. 240, pp. 210–227, 2022.
  10. J. Jimenez de la Morena, P. Conesa, Y. Fonseca, F. de Isidro-Gómez, D. Herreros, E. Fernandez-Gimenez, D. Strelak, E. Moebel, T. Buchholz, F. Jug, A. Martinez-Sanchez, M. Harastani, S. Jonic, J. Conesa, A. Cuervo, P. Losana, I. Sanchez, M. Iceta, L. del Cano, M. Gragera, R. Melero, G. Sharov, D. Casta˜no-Diez, A. Koster, J. Piccirillo, J. Vilas, J. Oton, R. Marabini, C. Sorzano, and J. Carazo, Scipiontomo: Towards cryo-electron tomography software integration, reproducibility, and validation, Journal of Structural Biology, vol. 214, no. 3, p. 107872, 2022.
  11. P. Conesa, Y. C. Fonseca, J. J. de la Morena, G. Sharov, J. M. de la Rosa-Trevin, A. Cuervo, A. G. Mena, B. R. de Francisco, D. Del Hoyo, D. Herreros, D. Marchan, D. Strelak, E. Fernández-Giménez, E. Ramírez-Aportela, F. P. de Isidro-Gómez, G. Sharov, I. Sánchez, J. Krieger, J. Jiménez de la Morena, J.L. Vilas, J.M. de la Rosa-Trevín, L. del Caño, M. Gragera, M. Iceta, M. Martínez, P. Losana, R. Melero, Y.C. Fonseca, R. Marabini, J.M. Carazo, C.O.S. Sorzano, Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology, Biological Imaging, vol. 3, p. e13, 2023.
  12. F. P. de Isidro-Gómez, J.L. Vilas, P. Losana, J.M. Carazo, and C.O.S. Sorzano, A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions, Journal of Structural Biology, vol. 216, no. 1, p. 108056, 2024.
  13. F. P. de Isidro-Gómez, J.L. Vilas, J.M. Carazo, and C.O.S. Sorzano, Automatic detection of alignment errors in cryo-electron tomography, Journal of Structural Biology, vol. 217, no. 1, p. 108153, 2025.

Publications in Books

  1. C.O.S. Sorzano, A. Jiménez-Moreno, D. Maluenda, E. Ramírez-Aportela, M. Martínez, A. Cuervo, R. Melero, P. Conesa, R. Sánchez-García, D. Strelak, J. Filipovic, E. Fernández-Giménez, F. P. de Isidro-Gómez, D. Herreros, P. Conesa, L. del Caño, Y. Fonseca, J. Jiménez de la Morena, J.R. Macías, P. Losada, R. Marabini, J.M. Carazo, Image processing in cryo-electron microscopy of single particles: the power of combining methods, in Structural Proteomics: High-Throughput Methods, pp. 257–289, Springer, 2021. ISBN:978-1-0716-1406-8.
  2. F.P. de Isidro-Gómez, J. L. Vilas, E. Fernández-Giménez, O.L. Zarrabeitia, D. Marchán, M. Iceta, D. Herreros, P. Conesa, Y.C. Fonseca, J. Jiménez de la Morena, A. Cuervo, B. Rodríguez-de-Francisco, P. Losana, J.M. Carazo, C.O.S. Sorzano, Validation methods in cryo-electron tomography. Book chapter from: Hanein, D. and Volkmann, N. Cryo-electron tomography: A Journey from Sample Preparation to Data Mining. Elsevier, 2025. ISBN: 9780443188299.

Conference Contributions

  1. J. Jiménez, F. de Isidro, E. Fernández-Giménez, D. Herreros, Y. Fonseca, P. Conesa, A. Cuervo, J. Conesa, R. Melero, J.M. Carazo, C.O.S. Sorzano. Electron Tomography Workflows using Scipion. Microscopy and microanalysis (2021).
  2. C.O.S. Sorzano, A. Jiménez-Moreno, E. Ramírez-Aportela, J. Krieger, J. Filipovic, P. Conesa, Y.C. Fonseca, J. Jiménez-de la Morena, D. Strelak, E. Fernández-Giménez, F. de Isidro, D. Herreros, D. Marchán, J.L. Vilas, R. Marabini, J.M. Carazo. Why is a single execution of a single algorithm not enough in CryoEM? Microscopy at the Frontiers of Science (2021).
  3. J. Jiménez de la Morena, P. Conesa, Y.C. Fonseca, F.P. de Isidro-Gómez, D. Herreros, E. Fernández-Giménez, A. Cuervo, P. Losana, J.M. Carazo, C.O.S. Sorzano, J.L. Vilas. ScipionTomo: a standard framework for cryoelectron tomography image processing. 9th Electron Tomography Congress (2022).
  4. F.P. de Isidro-Gómez, J.L. Vilas, J.M. Carazo, and C.O.S. Sorzano. Automatic detection of alignment errors in cryo-electron tomographic reconstructions. MFS2023, at International Iberian Nanotechnology Laboratory (2023).

Teaching

  1. Instructor of the course “Cryo-electron Tomography Image Processing”. Instruct Image Processing Center from National Center for Biotechnology (CNB-CSIC) (2021).
  2. Instructor of the course “IMpaCT Cryo-electron Tomography”. Weizmann Institute of Science, Israel (2022).
  3. Lecturer of the course “Digital Systems” (6 ECTS). Computer Science. Universidad CEU San Pablo (2022).
  4. Instructor of the course “Cryo-electron Tomography Image Processing”. Instruct Image Processing Center from National Center for Biotechnology (CNB-CSIC) (2022).
  5. Lecturer of the course “Programming I” (6 ECTS). Computer Science. Universidad CEU San Pablo (2022).
  6. Instructor of the course “Fronteras en el estudio de las Biomoléculas”. Master en Biomoléculas y Dinámica Celular, Universidad Autónoma de Madrid (UAM) (2023).
  7. Lecturer of the course “Digital Systems” (6 ECTS). Computer Science. Universidad CEU San Pablo (2023).
  8. Instructor of the course “Cryo-electron Tomography Image Processing”. Instruct Image Processing Center from National Center for Biotechnology (CNB-CSIC) (2023).
  9. Lecturer of the course “Programming I” (6 ECTS). Computer Science. Universidad CEU San Pablo (2023).

Supervised works

  1. Daniel Marchán Torres “Deep Learning model to estimate the defocus in Cryogenic Electron Microscopy” Master Thesis, University of Navarra (2021).