A synergistic approach toward understanding receptor signaling in the cell at very high resolution

Publications

Peer reviewed articles (20)

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

Author(s): Herreros, D; Lederman, RR; Krieger, J; Jimenez-Moreno, A; Martinez, M; Myska, D; Strelak, D; Filipovic, J; Bahar, I; Carazo, JM; Sanchez, COS
Published in: IUCrJ, Volume 8| Part 6| November 2021| Pages 992-1005, 2021, ISSN 2052-2525
Publisher: IUCRJ
DOI: 10.1107/s2052252521008903

Structural analysis of receptors and actin polarity in platelet protrusions

Author(s): Sorrentino S, Conesa JJ, Cuervo A, Melero R, Martins B, Fernandez-Gimenez E, de Isidro-Gomez FP, de la Morena J, Studt JD, Sorzano COS, Eibauer M, Carazo JM, Medalia O.
Published in: PNAS Vol. 118 | No. 37, 2021, ISSN 1091-6490
Publisher: PNAS
DOI: 10.1073/pnas.2105004118

Differential cellular responses to adhesive interactions with galectin-8- and fibronectin-coated substrates

Author(s): Li W, Sancho A, Chung WL, Vinik Y, Groll J, Zick Y, Medalia O, Bershadsky AD, Geiger B.
Published in: Journal of Cell Science, 2021, ISSN 0021-9533
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/jcs.252221

FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation.

Author(s): Erney Ramírez-Aportela; David Maluenda; Yunior C. Fonseca; Pablo Conesa; Roberto Marabini; J. Bernard Heymann; José María Carazo; C.O.S. Sorzano
Published in: Nature Communications, 4, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20295-w

Proteomic investigation of Cbl and Cbl-b in neuroblastoma cell differentiation highlights roles for SHP-2 and CDK16

Author(s): Pedersen, A.K., Pfeiffer, A., Karemore, G., Akimov, V., Bekker-Jensen, D.B., Blagoev, B., Francavilla, C., and Olsen, J.V.
Published in: iScience, Volume 24, Issue 4,, 2021, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.isci.2021.102321

Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures

Author(s): Franciosa, G., Smits, J.G.A., Minuzzo, S., Martinez-Val, A., Indraccolo, S., and Olsen, J.V.
Published in: Nature communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22787-9

FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy

Author(s): David Střelák, Jiří Filipovič, Amaya Jiménez-Moreno, Jose Carazo, Carlos Sánchez Sorzano
Published in: Electronics, 9/6, 2020, Page(s) 1040, ISSN 2079-9292
Publisher: Electronics (MDPI)
DOI: 10.3390/electronics9061040

Principal component analysis is limited to low-resolution analysis in cryoEM

Author(s): Sorzano, COS; Carazo, JM
Published in: INT UNION CRYSTALLOGRAPHY - ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2021, ISSN 2059-7983
Publisher: INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/s2059798321002291

Unveiling the polarity of actin filaments by cryo-electron tomography

Author(s): Bruno Martins, Simona Sorrentino, Wen-Lu Chung, Meltem Tatli, Ohad Medalia, Matthias Eibauer
Published in: Structure, Volume 29, Issue 5, 6 May 2021, Pages 488-498.e4, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1016/j.str.2020.12.014

Measurement of local resolution in electron tomography

Author(s): J.L. Vilas, J. Oton, C. Messaoudi, R. Melero, P. Conesa, E. Ramirez-Aportela, J. Mota, M. Martinez, A. Jimenez, R. Marabini, J.M. Carazo, J. Vargas, C.O.S. Sorzano
Published in: Journal of Structural Biology: X, 4, 2020, Page(s) 100016, ISSN 2590-1524
Publisher: Journal of Structural Biology: X (Elsevier Inc)
DOI: 10.1016/j.yjsbx.2019.100016

Structures of neurokinin 1 receptor in complex with Gq and Gs proteins reveal substance P binding mode and unique activation features

Author(s): Christian Thom, Janosch Ehrenmann, Santiago Vacca, Yann Waltenspühl, Jendrik Schöppe, Ohad Medalia, Andreas Plückthun
Published in: S C I E N C E A D V A N C E S, 2021, ISSN 2375-2548
Publisher: American Association for the Advancement of Science’s
DOI: 10.1126/sciadv.abk2872

Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Author(s): Martinez-Val, A., Bekker-Jensen, D.B., Steigerwald, S., Koenig, C., Ostergaard, O., Mehta, A., Tran, T., Sikorski, K., Torres-Vega, E., Kwasniewicz, E., et al.
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27398-y

Measuring local-directional resolution and local anisotropy in cryo-EM maps

Author(s): Jose Luis Vilas, Hemant D. Tagare, Javier Vargas, Jose Maria Carazo, Carlos Oscar S. Sorzano
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-13742-w

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion

Author(s): Strelak, D; Jimenez-Moreno, A; Vilas, JL; Ramirez-Aportela, E; Sanchez-Garcia, R; Maluenda, D; Vargas, J; Herreros, D; Fernandez-Gimenez, E; de Isidro-Gomez, FP; Horacek, J; Myska, D; Horacek, M; Conesa, P; Fonseca-Reyna, YC; Jimenez, J; Martinez, M; Harastani, M; Jonic, S; Filipovic, J; Marabini, R; Carazo, JM; Sorzano, COS.
Published in: MOLECULES Special Issue Cryo-EM and Hybrid Methods Development: Current Progress and Future Perspectives), Volume 26 Issue 20, 2021, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26206224

Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods

Author(s): Sorzano, COS; Jimenez-Moreno, A; Maluenda, D; Ramirez-Aportela, E; Martinez, M; Cuervo, A; Melero, R; Conesa, JJ; Sanchez-Garcia, R; Strelak, D; Filipovic, J; Fernandez-Gimenez, E; de Isidro-Gomez, F; Herreros, D; Conesa, P; del Cano, L; Fonseca, Y; de la Morena, JJ; Macias, JR; Losana, P; Marabini, R; Carazo, JM
Published in: Structural Proteomics pp 257-289, 2021, ISSN 1064-3745
Publisher: Humana Press, Inc.
DOI: 10.1007/978-1-0716-1406-8_13

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

Author(s): Ruben Sanchez Garcia; Josué Gómez-Blanco; Ana Maria Cuervo; José María Carazo; Carlos Oscar S. Sorzano; Javier Vargas
Published in: Communications Biology, 2, 2021, ISSN 2399-3642
Publisher: SpringerNature
DOI: 10.1101/2020.06.12.148296

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

Author(s): Dorte B. Bekker-Jensen, Oliver M. Bernhardt, Alexander Hogrebe, Ana Martinez-Val, Lynn Verbeke, Tejas Gandhi, Christian D. Kelstrup, Lukas Reiter, Jesper V. Olsen
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-14609-1

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

Author(s): Roberto Melero, Carlos Oscar S. Sorzano, Brent Foster, José-Luis Vilas, Marta Martínez, Roberto Marabini, Erney Ramírez-Aportela, Ruben Sanchez-Garcia, David Herreros, Laura del Caño, Patricia Losana, Yunior C. Fonseca-Reyna, Pablo Conesa, Daniel Wrapp, Pablo Chacon, Jason S. McLellan, Hemant D. Tagare, Jose-Maria Carazo
Published in: IUCrJ, 7/6, 2020, ISSN 2052-2525
Publisher: International Union of Crystallography
DOI: 10.1107/s2052252520012725

Cryo-EM density maps adjustment for subtraction, consensus and sharpening.

Author(s): E. Fernández-Giménez; María Jesús Martínez; Rubén J. Sánchez-García; Roberto Marabini; Erney Ramírez-Aportela; Pablo Conesa; José María Carazo; Carlos Oscar S. Sorzano
Published in: Journal of Structural Biology, 5, 2021, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2021.107780

Cryo-EM and Single-Particle Analysis with Scipion

Author(s): Jimenez-Moreno, A; del Cano, L; Martinez, M; Ramirez-Aportela, E; Cuervo, A; Melero, R ; Sanchez-Garcia, R; Strelak, D; Fernandez-Gimenez, E; de Isidro-Gomez, FP; Herreros, D; Conesa, P; Fonseca, Y; Maluenda, D; de la Morena, JJ ; Macias, JR; Losana, P; Marabini, R; Carazo, JM; Sorzano, COS
Published in: Biochemistry, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62261