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

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Publications

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