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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

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

One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes

Author(s): Zilu Ye, Pierre Sabatier, Javier Martin-Gonzalez, Akihiro Eguchi, Maico Lechner, Ole Østergaard, Jingsheng Xie, Yuan Guo, Lesley Schultz, Rafaela Truffer, Dorte B. Bekker-Jensen, Nicolai Bache, Jesper V. Olsen
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-46777-9

A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions

Author(s): F.P. de Isidro-Gómez, J.L. Vilas, P. Losana, J.M. Carazo, C.O.S. Sorzano
Published in: Journal of Structural Biology, Issue 216, 2024, Page(s) 108056, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2023.108056

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

Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

Author(s): Ulises H. Guzman, Ana Martinez-Val, Zilu Ye, Eugen Damoc, Tabiwang N. Arrey, Anna Pashkova, Santosh Renuse, Eduard Denisov, Johannes Petzoldt, Amelia C. Peterson, Florian Harking, Ole Østergaard, Rasmus Rydbirk, Susana Aznar, Hamish Stewart, Yue Xuan, Daniel Hermanson, Stevan Horning, Christian Hock, Alexander Makarov, Vlad Zabrouskov, Jesper V. Olsen
Published in: Nature Biotechnology, Issue 42, 2024, Page(s) 1855-1866, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-02099-7

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

Real-time correction of chromatic aberration in optical fluorescence microscopy

Author(s): Ana Cayuela López, Pablo Conesa, Ana María Oña Blanco, José Antonio Gómez-Pedrero, Carlos Oscar S Sorzano
Published in: Methods and Applications in Fluorescence, Issue 11, 2023, Page(s) 045001, ISSN 2050-6120
Publisher: bioRxiv
DOI: 10.1088/2050-6120/ace153

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

Multi-layered proteomics identifies insulin-induced upregulation of the EphA2 receptor via the ERK pathway which is dependent on low IGF1R level

Author(s): Sarah Hyllekvist Jørgensen, Kristina Bennet Emdal, Anna-Kathrine Pedersen, Lene Nygaard Axelsen, Helene Faustrup Kildegaard, Damien Demozay, Thomas Åskov Pedersen, Mads Grønborg, Rita Slaaby, Peter Kresten Nielsen, Jesper Velgaard Olsen
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-77817-5

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

Deep Proteome Analysis of Cerebrospinal Fluid from Pediatric Patients with Central Nervous System Cancer

Author(s): Christian Mirian, Ole Østergaard, Maria Thastrup, Signe Modvig, Jon Foss-Skiftesvik, Jane Skjøth-Rasmussen, Marianne Berntsen, Josefine Britze, Alex Christian Yde Nielsen, René Mathiasen, Kjeld Schmiegelow, Jesper Velgaard Olsen
Published in: Journal of Proteome Research, Issue 23, 2024, Page(s) 5048-5063, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.4c00471

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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