Riccardo Marabini

Affiliations

Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.

Publications (27)

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

IUCrJ

Avec: 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

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

Journal of structural biology

Avec: E Fernández-Giménez , M Martínez , R Sánchez-García , R Marabini , E Ramírez-Aportela , P Conesa , J M Carazo , C O S Sorzano

Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening.

Journal of structural biology

Avec: J L Vilas , J Vargas , M Martinez , E Ramirez-Aportela , R Melero , A Jimenez-Moreno , E Garduño , P Conesa , R Marabini , D Maluenda , J M Carazo , C O S Sorzano

Integration of Cryo-EM Model Building Software in

Journal of chemical information and modeling

Avec: 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

The Microbial Diversity of Non-Korean Kimchi as Revealed by Viable Counting and Metataxonomic Sequencing.

Foods (Basel, Switzerland)

Avec: Antonietta Maoloni , Ilario Ferrocino , Vesna Milanović , Luca Cocolin , Maria Rita Corvaglia , Donatella Ottaviani , Chiara Bartolini , Giulia Talevi , Luca Belleggia , Federica Cardinali , Rico Marabini , Lucia Aquilanti , Andrea Osimani

ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation.

Journal of structural biology

Avec: 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 Sorzano , J M Carazo

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

Journal of structural biology

Avec: E Fernández-Giménez , M M Martínez , R Marabini , D Strelak , R Sánchez-García , J M Carazo , C O S Sorzano

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.

bioRxiv : the preprint server for biology

The PCNA interaction motifs revisited: thinking outside the PIP-box.

Cellular and molecular life sciences : CMLS

Avec: Andreas Prestel , Nanna Wichmann , Joao M Martins , Noah Kassem , Sebastian S Broendum , Marit Otterlei , Olaf Nielsen , Martin Willemoës , Michael Ploug , Wouter Boomsma , Birthe B Kragelund

Automatic local resolution-based sharpening of cryo-EM maps.

Bioinformatics (Oxford, England)

Avec: Erney Ramírez-Aportela , Jose Luis Vilas , Alisa Glukhova , Roberto Melero , Pablo Conesa , Marta Martínez , David Maluenda , Javier Mota , Amaya Jiménez , Javier Vargas , Roberto Marabini , Patrick M Sexton , Jose Maria Carazo , Carlos Oscar S Sorzano

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

Acta crystallographica. Section D, Structural biology

Avec: 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 Marabini , J M Carazo

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion.

Acta crystallographica. Section D, Structural biology

Avec: D Maluenda , T Majtner , P Horvath , J L Vilas , A Jiménez-Moreno , J Mota , E Ramírez-Aportela , R Sánchez-García , P Conesa , L Del Caño , Y Rancel , Y Fonseca , M Martínez , G Sharov , C A García , D Strelak , R Melero , R Marabini , J M Carazo , C O S Sorzano

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

Methods in molecular biology (Clifton, N.J.)

Avec: Carlos Oscar S Sorzano , Amaya Jiménez-Moreno , David Maluenda , Erney Ramírez-Aportela , Marta Martínez , Ana Cuervo , Robert Melero , Jose Javier Conesa , Ruben Sánchez-García , David Strelak , Jiri Filipovic , Estrella Fernández-Giménez , Federico de Isidro-Gómez , David Herreros , Pablo Conesa , Laura Del Caño , Yunior Fonseca , Jorge Jiménez de la Morena , Jose Ramon Macías , Patricia Losana , Roberto Marabini , Jose-Maria Carazo

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

Nature communications

Avec: Erney Ramírez-Aportela , David Maluenda , Yunior C Fonseca , Pablo Conesa , Roberto Marabini , J Bernard Heymann , Jose Maria Carazo , Carlos Oscar S Sorzano

Cryo-EM structure of enteric adenovirus HAdV-F41 highlights structural variations among human adenoviruses.

Science advances

Avec: Marta Pérez-Illana , Marta Martínez , Gabriela N Condezo , Mercedes Hernando-Pérez , Casandra Mangroo , Martha Brown , Roberto Marabini , Carmen San Martín

Cryo-EM and Single-Particle Analysis with Scipion.

Journal of visualized experiments : JoVE

Avec: A Jiménez-Moreno , L Del Caño , M Martínez , E Ramírez-Aportela , A Cuervo , R Melero , R Sánchez-García , D Strelak , E Fernández-Giménez , F P 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

Measurement of local resolution in electron tomography.

Journal of structural biology: X

Avec: 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

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors.

Protein science : a publication of the Protein Society

Avec: Peter S Millard , Katrine Bugge , Wouter Boomsma , Meike Burow , Birthe B Kragelund

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.

Acta crystallographica. Section F, Structural biology communications

Avec: C O S Sorzano , A Jiménez , J Mota , J L Vilas , D Maluenda , M Martínez , E Ramírez-Aportela , T Majtner , J Segura , R Sánchez-García , Y Rancel , L Del Caño , P Conesa , R Melero , S Jonic , J Vargas , F Cazals , Z Freyberg , J Krieger , I Bahar , R Marabini , J M Carazo

Validation of electron microscopy initial models via small angle X-ray scattering curves.

Bioinformatics (Oxford, England)

Avec: Amaya Jiménez , Slavica Jonic , Tomas Majtner , Joaquín Otón , Jose Luis Vilas , David Maluenda , Javier Mota , Erney Ramírez-Aportela , Marta Martínez , Yaiza Rancel , Joan Segura , Ruben Sánchez-García , Roberto Melero , Laura Del Cano , Pablo Conesa , Lars Skjaerven , Roberto Marabini , Jose M Carazo , Carlos Oscar S Sorzano

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

Molecules (Basel, Switzerland)

Avec: David Strelak , Amaya Jiménez-Moreno , José L Vilas , Erney Ramírez-Aportela , Ruben Sánchez-García , David Maluenda , Javier Vargas , David Herreros , Estrella Fernández-Giménez , Federico P de Isidro-Gómez , Jan Horacek , David Myska , Martin Horacek , Pablo Conesa , Yunior C Fonseca-Reyna , Jorge Jiménez , Marta Martínez , Mohamad Harastani , Slavica Jonić , Jiri Filipovic , Roberto Marabini , José M Carazo , Carlos O S Sorzano

Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins.

Science advances

Avec: Roberto Marabini , Gabriela N Condezo , Mart Krupovic , Rosa Menéndez-Conejero , Josué Gómez-Blanco , Carmen San Martín

Algorithmic robustness to preferred orientations in single particle analysis by CryoEM.

Journal of structural biology

Avec: C O S Sorzano , D Semchonok , S-C Lin , Y-C Lo , J L Vilas , A Jiménez-Moreno , M Gragera , S Vacca , D Maluenda , M Martínez , E Ramírez-Aportela , R Melero , A Cuervo , J J Conesa , P Conesa , P Losana , L Del Caño , J Jiménez de la Morena , Y C Fonseca , R Sánchez-García , D Strelak , E Fernández-Giménez , F de Isidro , D Herreros , P L Kastritis , R Marabini , B D Bruce , J M Carazo

Image processing tools for the validation of CryoEM maps.

Faraday discussions

Avec: C O S Sorzano , J L Vilas , E Ramírez-Aportela , J Krieger , D Del Hoyo , D Herreros , E Fernandez-Giménez , D Marchán , 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

Development of a Microgram Scale Video-Microscopic Method to Investigate Dissolution Behavior of Poorly Water-Soluble Drugs.

AAPS PharmSciTech

Avec: Malte Bøgh Senniksen , Juliane Fjelrad Christfort , Erik Spillum , Wayne Matthews , Luigi Da Vià , Jakob Plum , Thomas Rades , Anette Müllertz

Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology.

Biological imaging

Avec: Pablo Conesa , Yunior C Fonseca , Jorge Jiménez de la Morena , Grigory Sharov , Jose Miguel de la Rosa-Trevín , Ana Cuervo , Alberto García Mena , Borja Rodríguez de Francisco , Daniel Del Hoyo , David Herreros , Daniel Marchan , David Strelak , Estrella Fernández-Giménez , Erney Ramírez-Aportela , Federico Pedro de Isidro-Gómez , Irene Sánchez , James Krieger , José Luis Vilas , Laura Del Cano , Marcos Gragera , Mikel Iceta , Marta Martínez , Patricia Losana , Roberto Melero , Roberto Marabini , José María Carazo , Carlos Oscar Sánchez Sorzano

Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs.

Nucleic acids research

Avec: Johan G Olsen , Andreas Prestel , Noah Kassem , Sebastian S Broendum , Hossain Mohammad Shamim , Signe Simonsen , Martin Grysbæk , Josefine Mortensen , Louise Lund Rytkjær , Gitte W Haxholm , Christian Holmberg , Antony M Carr , Ramon Crehuet , Olaf Nielsen , Birthe B Kragelund

Réseau de co-auteurs

R Marabini 12 collaborations

J M Carazo 12 collaborations

C O S Sorzano 12 collaborations

P Conesa 11 collaborations

Roberto Marabini 10 collaborations

R Melero 9 collaborations

Marta Martínez 8 collaborations

Erney Ramírez-Aportela 8 collaborations

Pablo Conesa 8 collaborations

M Martínez 8 collaborations

R Sánchez-García 8 collaborations

E Ramírez-Aportela 8 collaborations

J L Vilas 8 collaborations

E Fernández-Giménez 7 collaborations

D Maluenda 7 collaborations

L Del Caño 7 collaborations

D Strelak 7 collaborations

Carlos Oscar S Sorzano 6 collaborations

Roberto Melero 5 collaborations

David Herreros 5 collaborations

A Jiménez-Moreno 5 collaborations

A Cuervo 5 collaborations

D Herreros 5 collaborations

David Maluenda 5 collaborations

Patricia Losana 4 collaborations

J Vargas 4 collaborations

Y C Fonseca 4 collaborations

P Losana 4 collaborations

Laura Del Caño 3 collaborations

Yunior C Fonseca-Reyna 3 collaborations

Jose-Maria Carazo 3 collaborations

J J Conesa 3 collaborations

J Jiménez de la Morena 3 collaborations

F P de Isidro-Gómez 3 collaborations

Birthe B Kragelund 3 collaborations

J Krieger 3 collaborations

J Mota 3 collaborations

Ruben Sánchez-García 3 collaborations

David Strelak 3 collaborations

Estrella Fernández-Giménez 3 collaborations

Brent Foster 2 collaborations

José-Luis Vilas 2 collaborations

Ruben Sanchez-Garcia 2 collaborations

Daniel Wrapp 2 collaborations

Pablo Chacon 2 collaborations

Jason S McLellan 2 collaborations

Hemant D Tagare 2 collaborations

M Martinez 2 collaborations

E Ramirez-Aportela 2 collaborations

F de Isidro 2 collaborations

S Jonic 2 collaborations

I Sánchez 2 collaborations

M Gragera 2 collaborations

G Sharov 2 collaborations

Andreas Prestel 2 collaborations

Noah Kassem 2 collaborations

Sebastian S Broendum 2 collaborations

Olaf Nielsen 2 collaborations

Wouter Boomsma 2 collaborations

Jose Luis Vilas 2 collaborations

Javier Mota 2 collaborations

Amaya Jiménez 2 collaborations

Javier Vargas 2 collaborations

Jose Maria Carazo 2 collaborations

T Majtner 2 collaborations

Y Rancel 2 collaborations

Y Fonseca 2 collaborations

Amaya Jiménez-Moreno 2 collaborations

Ana Cuervo 2 collaborations

Jiri Filipovic 2 collaborations

Jorge Jiménez de la Morena 2 collaborations

Yunior C Fonseca 2 collaborations

Gabriela N Condezo 2 collaborations

Carmen San Martín 2 collaborations

J R Macías 2 collaborations

Laura Del Cano 2 collaborations

A Jimenez-Moreno 1 collaboration

E Garduño 1 collaboration

Antonietta Maoloni 1 collaboration

Ilario Ferrocino 1 collaboration

Vesna Milanović 1 collaboration

Luca Cocolin 1 collaboration

Maria Rita Corvaglia 1 collaboration

Donatella Ottaviani 1 collaboration

Chiara Bartolini 1 collaboration

Giulia Talevi 1 collaboration

Luca Belleggia 1 collaboration

Federica Cardinali 1 collaboration

Rico Marabini 1 collaboration

Lucia Aquilanti 1 collaboration

Andrea Osimani 1 collaboration

E Moebel 1 collaboration

T O Buchholz 1 collaboration

F Jug 1 collaboration

A Martinez-Sanchez 1 collaboration

M Harastani 1 collaboration

M Iceta 1 collaboration

L Del Cano 1 collaboration

D Castaño-Díez 1 collaboration

A Koster 1 collaboration

J G Piccirillo 1 collaboration

J Otón 1 collaboration

M M Martínez 1 collaboration

Nanna Wichmann 1 collaboration

Joao M Martins 1 collaboration

Marit Otterlei 1 collaboration

Martin Willemoës 1 collaboration

Michael Ploug 1 collaboration

Alisa Glukhova 1 collaboration

Patrick M Sexton 1 collaboration

J Conesa 1 collaboration

J Filipovic 1 collaboration

J Jiménez-de la Morena 1 collaboration

P Horvath 1 collaboration

C A García 1 collaboration

Robert Melero 1 collaboration

Jose Javier Conesa 1 collaboration

Federico de Isidro-Gómez 1 collaboration

Yunior Fonseca 1 collaboration

Jose Ramon Macías 1 collaboration

J Bernard Heymann 1 collaboration

Marta Pérez-Illana 1 collaboration

Mercedes Hernando-Pérez 1 collaboration

Casandra Mangroo 1 collaboration

Martha Brown 1 collaboration

J Oton 1 collaboration

C Messaoudi 1 collaboration

A Jimenez 1 collaboration

Peter S Millard 1 collaboration

Katrine Bugge 1 collaboration

Meike Burow 1 collaboration

A Jiménez 1 collaboration

J Segura 1 collaboration

F Cazals 1 collaboration

Z Freyberg 1 collaboration

I Bahar 1 collaboration

Slavica Jonic 1 collaboration

Tomas Majtner 1 collaboration

Joaquín Otón 1 collaboration

Yaiza Rancel 1 collaboration

Joan Segura 1 collaboration

Lars Skjaerven 1 collaboration

Jose M Carazo 1 collaboration

José L Vilas 1 collaboration

Federico P de Isidro-Gómez 1 collaboration

Jan Horacek 1 collaboration

David Myska 1 collaboration

Martin Horacek 1 collaboration

Jorge Jiménez 1 collaboration

Mohamad Harastani 1 collaboration

Slavica Jonić 1 collaboration

José M Carazo 1 collaboration

Carlos O S Sorzano 1 collaboration

Mart Krupovic 1 collaboration

Rosa Menéndez-Conejero 1 collaboration

Josué Gómez-Blanco 1 collaboration

D Semchonok 1 collaboration

S-C Lin 1 collaboration

Y-C Lo 1 collaboration

S Vacca 1 collaboration

P L Kastritis 1 collaboration

B D Bruce 1 collaboration

D Del Hoyo 1 collaboration

E Fernandez-Giménez 1 collaboration

D Marchán 1 collaboration

Y Fonseca-Reyna 1 collaboration

A García-Mena 1 collaboration

J Burguet 1 collaboration

J García Condado 1 collaboration

J Méndez García 1 collaboration

A Muñoz-Barrutia 1 collaboration

Malte Bøgh Senniksen 1 collaboration

Juliane Fjelrad Christfort 1 collaboration

Erik Spillum 1 collaboration

Wayne Matthews 1 collaboration

Luigi Da Vià 1 collaboration

Jakob Plum 1 collaboration

Thomas Rades 1 collaboration

Anette Müllertz 1 collaboration

Grigory Sharov 1 collaboration

Jose Miguel de la Rosa-Trevín 1 collaboration

Alberto García Mena 1 collaboration

Borja Rodríguez de Francisco 1 collaboration

Daniel Del Hoyo 1 collaboration

Daniel Marchan 1 collaboration

Federico Pedro de Isidro-Gómez 1 collaboration

Irene Sánchez 1 collaboration

James Krieger 1 collaboration

José Luis Vilas 1 collaboration

Marcos Gragera 1 collaboration

Mikel Iceta 1 collaboration

José María Carazo 1 collaboration

Carlos Oscar Sánchez Sorzano 1 collaboration

Johan G Olsen 1 collaboration

Hossain Mohammad Shamim 1 collaboration

Signe Simonsen 1 collaboration

Martin Grysbæk 1 collaboration

Josefine Mortensen 1 collaboration

Louise Lund Rytkjær 1 collaboration

Gitte W Haxholm 1 collaboration

Christian Holmberg 1 collaboration

Antony M Carr 1 collaboration

Ramon Crehuet 1 collaboration