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Publications

Gold nanomaterials and their potential use as cryo-electron tomography labels

Author(s): Charlie Beales; Ohad Medalia
Published in: Crossref, Issue 8, 2022, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2022.107880

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, Issue Volume 8| Part 6| November 2021| Pages 992-1005, 2021, ISSN 2052-2525
Publisher: IUCRJ
DOI: 10.1107/s2052252521008903

A network of mixed actin polarity in the leading edge of spreading cells.

Author(s): Wen-Lu Chung, Matthias Eibauer, Wenhong Li, Rajaa Boujemaa-Paterski, Benjamin Geiger , Ohad Medalia
Published in: Communications Biology, 2022, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-022-04288-7

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

Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles

Author(s): Kverneland, AH, Østergaard O, Emdal KB, Svane IM, Olsen JV
Published in: Proteomics, 2022, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202200039

ScipionTomo: Towards Cryo-Electron Tomography Software Integration, Reproducibility, and Validation

Author(s): J. Jiménez de la Morena, P. Conesa, Y.C. Fonseca, F.P. de Isidro-Gómez, D. Herreros, E. Fernández-Giménez, D. Strelak, E. Moebel, T.O. Buchholz, F. Jug, A. Martinez-Sanchez, M. Harastani, S. Jonic, J.J. Conesa, A. Cuervo, P. Losana, I. Sánchez, M. Iceta, L. del Cano, M. Gragera, R. Melero, G. Sharov, D. Castaño-Díez, A. Koster, J.G. Piccirillo, J.L. Vilas, J. Otón, R. Marabini, C.O.S. Sorz
Published in: Journal of Structural Biology, 2022, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2022.107872

BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction

Author(s): R. Sanchez-Garcia, J.R. Macias, C.O.S. Sorzano, J.M. Carazo, J. Segura
Published in: Journal of Molecular Biology, 2022, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2022.167556

Local defocus estimation in single particle analysis in cryo-electron microscopy.

Author(s): Fernandez-Gimenez, E; Carazo, J M; Sorzano, C O S
Published in: Journal of Structural Biology, 2023, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2023.108030

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, Issue 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

Protein dynamics developments for the large scale and cryoEM: case study of <i>ProDy</i> 2.0

Author(s): Ivet Bahar; James Krieger; Carlos Oscar S. Sorzano; Jose Maria Carazo Garcia
Published in: Crossref, Issue 8, 2022, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1107/s2059798322001966

Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids

Author(s): Ana Martínez-Val, Kyle Fort, Claire Koenig, Leander Van der Hoeven, Giulia Franciosa, Thomas Moehring, Yasushi Ishihama, Yu-Ju Chen, Alexander Makarov, Yue Xuan, Jesper V Olsen
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-39347-y

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

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy

Author(s): C. O. S. Sorzano, A. Jiménez-Moreno, D. Maluenda, M. Martínez, E. Ramírez-Aportela, J. Krieger, R. Melero, A. Cuervo, J. Conesa, J. Filipovic, P. Conesa, L. del Caño, Y. C. Fonseca, J. Jiménez-de la Morena, P. Losana, R. Sánchez-García, D. Strelak,E. Fernández-Giménez, F. P. de Isidro-Gómez, D. Herreros, J. L. Vilas, R. Marabinid and J. M. Carazo
Published in: Acta Crystallographica Section D: Structural Biology, 2022, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1107/s2059798322001978

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, Issue 9/6, 2020, Page(s) 1040, ISSN 2079-9292
Publisher: Electronics (MDPI)
DOI: 10.3390/electronics9061040

Emerging Themes in CryoEM─Single Particle Analysis Image Processing

Author(s): Jose Luis Vilas; Jose Maria Carazo; Carlos Oscar S. Sorzano
Published in: Crossref, Issue 12, 2023, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1021/acs.chemrev.1c00850

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

Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography

Author(s): Chunyang Wang; Matthias Wojtynek; Ohad Medalia
Published in: Crossref, Issue 10, 2023, ISSN 0346-251X
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.jbior.2022.100923

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

Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM

Author(s): D. Herreros, J. M. Krieger, Y. Fonseca, P. Conesa, M. Harastani, R. Vuillemot, I. Hamitouche, R. Serrano Gutiérrez, M. Gragera, R. Melero, S. Jonic, J. M. Carazo and C. O. Sorzano
Published in: Acta Crystallographica Section D: Structural Biology, 2023, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1107/s2059798323004497

The Actin Network Interfacing Diverse Integrin-Mediated Adhesions

Author(s): Geiger B, Boujemaa-Paterski R, Winograd-Katz SE, Balan Venghateri J, Chung WL, Medalia O.
Published in: Biomolecules, 2023, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom13020294

ZART: a novel multiresolution reconstruction algorithm with motion-blur correction for single particle analysis

Author(s): D. Herreros, J. Kiska, E. Ramírez-Aportela, J. Filipovic, J.M. Carazo, C.O.S. Sorzano
Published in: Journal of Molecular Biology, 2023, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2023.168088

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, Issue 4, 2020, Page(s) 100016, ISSN 2590-1524
Publisher: Journal of Structural Biology: X (Elsevier Inc)
DOI: 10.1016/j.yjsbx.2019.100016

Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools

Author(s): Erney Ramírez-Aportela; Jose M. Carazo; Carlos Oscar S. Sorzano
Published in: Crossref, Issue 11, 2022, ISSN 2052-2525
Publisher: IUCrJ
DOI: 10.1107/s2052252522006959

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

Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.

Author(s): Krieger, JM; Sorzano, COS; Carazo, JM
Published in: International Journal of molecular Science, 2023, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms241814245

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, Issue 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), Issue Volume 26 Issue 20, 2021, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26206224

A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

Author(s): E. Fernández-Giménez, M.M. Martínez, R. Marabini, D. Strelak, R. Sánchez-García, J.M. Carazo, C.O.S. Sorzano
Published in: Journal of Structural Biology, 2023, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2023.108024

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, Issue 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, Issue 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, Issue 7/6, 2020, ISSN 2052-2525
Publisher: International Union of Crystallography
DOI: 10.1107/s2052252520012725

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

Author(s): D. Herreros, R. R. Lederman, J. M. Krieger, A. Jiménez-Moreno, M. Martínez, D. Myška, D. Strelak, J. Filipovic, C. O. S. Sorzano & J. M. Carazo
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-35791-y

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, Issue 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

Spatiotemporal Proteomics Deciphers Functional Selectivity of EGFR ligands

Author(s): Akihiro Eguchi,  Kristina B. Emdal, Zilu Ye,  Ulises H. Guzmán,  Jesper V. Olsen
Published in: Biorxiv.org, 2023, ISSN 2692-8205
Publisher: BioRxiv
DOI: 10.1101/2023.09.13.557663

Structural basis for the activation and ligand recognition of the human oxytocin receptor

Author(s): Yann Waltenspühl, Janosch Ehrenmann, Santiago Vacca, Christian Thom, Ohad Medalia, Andreas Plückthun
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31325-0

A Vaccinia-based system for directed evolution of GPCRs in mammalian cells

Author(s): Christoph Klenk, Maria Scrivens, Anina Niederer, Shuying Shi, Loretta Mueller, Elaine Gersz, Maurice Zauderer, Ernest S. Smith, Ralf Strohner & Andreas Plückthun
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-37191-8

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