Martí-Renom, Marc A.: search on Z-Library

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1

Prediction of enzyme function by combining sequence similarity and protein interactions

Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X Avilés, Andrej Sali, Marc A Marti-Renom, Baldomero Oliva

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 958 KB

english, 2008

2

Software for predicting the 3D structure of RNA molecules

Dufour, David, Marti-Renom, Marc A.

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2015

Language:

english

File:

PDF, 182 KB

english, 2015

3

COMPARATIVE PROTEIN STRUCTURE MODELING OF GENES AND GENOMES

Martí-Renom, Marc A., Stuart, Ashley C., Fiser, András, Sánchez, Roberto, Melo, Francisco, Šali, Andrej

Journal:

Annual Review of Biophysics and Biomolecular Structure

Year:

2000

Language:

english

File:

PDF, 352 KB

english, 2000

4

Structure-based statistical analysis of transmembrane helices

Carlos Baeza-Delgado, Marc A. Marti-Renom, Ismael Mingarro

Journal:

European Biophysics Journal

Year:

2013

Language:

english

File:

PDF, 615 KB

english, 2013

5

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

Bogu, Gireesh K., Vizán, Pedro, Stanton, Lawrence W., Beato, Miguel, Di Croce, Luciano, Marti-Renom, Marc A.

Journal:

Molecular and Cellular Biology

Year:

2015

Language:

english

File:

PDF, 2.23 MB

english, 2015

6

Protein translocation into peroxisomes by ring-shaped import receptors

Will A. Stanley, Krisztian Fodor, Marc A. Marti-Renom, Wolfgang Schliebs, Matthias Wilmanns

Journal:

Year:

2007

Language:

english

File:

PDF, 614 KB

english, 2007

7

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

MartÃnez-JimÃ©nez, Francisco, Papadatos, George, Yang, Lun, Wallace, Iain M., Kumar, Vinod, Pieper, Ursula, Sali, Andrej, Brown, James R., Overington, John P., Marti-Renom, Marc A., MacKerell, Alexan

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 4.55 MB

english, 2013

8

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

Marti-Renom, Marc A., Mirny, Leonid A., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 630 KB

english, 2011

9

A Kernel for Open Source Drug Discovery in Tropical Diseases

Ortí, Leticia, Carbajo, Rodrigo J., Pieper, Ursula, Eswar, Narayanan, Maurer, Stephen M., Rai, Arti K., Taylor, Ginger, Todd, Matthew H., Pineda-Lucena, Antonio, Sali, Andrej, Marti-Renom, Marc A., Ge

Journal:

PLoS Neglected Tropical Diseases

Year:

2009

Language:

english

File:

PDF, 1.31 MB

english, 2009

10

Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells

Cuadrado, Ana, Giménez-Llorente, Daniel, Kojic, Aleksandar, Rodríguez-Corsino, Miriam, Cuartero, Yasmina, Martín-Serrano, Guillermo, Gómez-López, Gonzalo, Marti-Renom, Marc A., Losada, Ana

Journal:

Year:

2019

Language:

english

File:

PDF, 4.33 MB

english, 2019

11

Localization of binding sites in protein structures by optimization of a composite scoring function

Andrea Rossi, Marc A. Marti-Renom, Andrej Sali

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 747 KB

english, 2006

12

Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs

Alejandro Panjkovich, Francisco Melo, Marc A Marti-Renom

Journal:

Year:

2008

Language:

english

File:

PDF, 651 KB

english, 2008

13

Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions

Aragues, Ramon, Sali, Andrej, Bonet, Jaume, Marti-Renom, Marc A., Oliva, Baldo

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 459 KB

english, 2007

14

Challenges and guidelines toward 4D nucleome data and model standards

Marti-Renom, Marc A., Almouzni, Genevieve, Bickmore, Wendy A., Bystricky, Kerstin, Cavalli, Giacomo, Fraser, Peter, Gasser, Susan M., Giorgetti, Luca, Heard, Edith, Nicodemi, Mario, Nollmann, Marcelo,

Journal:

Nature Genetics

Year:

2018

Language:

english

File:

PDF, 1.09 MB

english, 2018

15

Membrane protein integration into the endoplasmic reticulum

Luis Martínez-Gil, Ana Saurí, Marc A. Marti-Renom, Ismael Mingarro

Journal:

Year:

2011

Language:

english

File:

PDF, 277 KB

english, 2011

16

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Mark A. Umbarger, Esteban Toro, Matthew A. Wright, Gregory J. Porreca, Davide Baù, Sun-Hae Hong, Michael J. Fero, Lihua J. Zhu, Marc A. Marti-Renom, Harley H. McAdams, Lucy Shapiro, Job Dekker, George

Journal:

Year:

2011

Language:

english

File:

PDF, 3.89 MB

english, 2011

17

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer

Belton, Jon-Matthew, Lajoie, Bryan R., Audibert, Sylvain, Cantaloube, Sylvain, Lassadi, Imen, Goiffon, Isabelle, Baù, Davide, Marti-Renom, Marc A., Bystricky, Kerstin, Dekker, Job

Journal:

Year:

2015

Language:

english

File:

PDF, 4.46 MB

english, 2015

18

3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?

Le Dily, François, Serra, François, Marti-Renom, Marc A.

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2017

Language:

english

File:

PDF, 829 KB

english, 2017

19

Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure

Florescu, Ana-Maria, Therizols, Pierre, Rosa, Angelo, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 2.90 MB

english, 2016

20

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

Doyle, Boryana, Fudenberg, Geoffrey, Imakaev, Maxim, Mirny, Leonid A., Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.07 MB

english, 2014

21

Structure determination of genomic domains by satisfaction of spatial restraints

Davide Baù, Marc A. Marti-Renom

Journal:

Chromosome Research

Year:

2011

Language:

english

File:

PDF, 417 KB

english, 2011

22

Vanilloid Receptor–Related Osmotically Activated Channel (VR-OAC), a Candidate Vertebrate Osmoreceptor

Wolfgang Liedtke, Yong Choe, Marc A. Martí-Renom, Andrea M. Bell, Charlotte S. Denis, AndrejŠali, A.J. Hudspeth, Jeffrey M. Friedman, Stefan Heller

Journal:

Year:

2000

Language:

english

File:

PDF, 1.77 MB

english, 2000

23

Partially Glycosylated Dendrimers Block MD-2 and Prevent TLR4-MD-2-LPS Complex Mediated Cytokine Responses

Barata, Teresa S., Teo, Ian, Brocchini, Steve, Zloh, Mire, Shaunak, Sunil, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.20 MB

english, 2011

24

Reply to Moult et al.

Andrej Sali, Marc A Marti-Renom, M.S Madhusudhan, András Fiser, Burkhard Rost

Journal:

Year:

2002

Language:

english

File:

PDF, 28 KB

english, 2002

25

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets

Francisco Melo, Marc A. Marti-Renom

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 205 KB

english, 2006

26

CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction

Galan, Silvia, Machnik, Nick, Kruse, Kai, DÃaz, Noelia, Marti-Renom, Marc A., Vaquerizas, Juan M.

Journal:

Nature Genetics

Year:

2020

File:

PDF, 11.00 MB

2020

27

Reliability of Assessment of Protein Structure Prediction Methods

Marc A Marti-Renom, M.S Madhusudhan, András Fiser, Burkhard Rost, Andrej Sali

Journal:

Year:

2002

Language:

english

File:

PDF, 335 KB

english, 2002

28

Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze

Martínez-Jiménez, Francisco, Marti-Renom, Marc A., Schlessinger, Avner

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.75 MB

english, 2015

29

Exploring chromatin hierarchical organization via Markov State Modelling

Tan, Zhen Wah, Guarnera, Enrico, Berezovsky, Igor N., Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 22.22 MB

english, 2018

30

N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon

Manuel Bañó-Polo, Francesca Baldin, Silvia Tamborero, Marc A. Marti-Renom, Ismael Mingarro

Journal:

Protein Science

Year:

2011

Language:

english

File:

PDF, 700 KB

english, 2011

31

The C-type lectin fold as an evolutionary solution for massive sequence variation

McMahon, Stephen A, Miller, Jason L, Lawton, Jeffrey A, Kerkow, Donald E, Hodes, Asher, Marti-Renom, Marc A, Doulatov, Sergei, Narayanan, Eswar, Sali, Andrej, Miller, Jeff F

Journal:

Nature Structural and Molecular Biology

Year:

2005

Language:

english

File:

PDF, 748 KB

english, 2005

32

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

Baù, Davide, Sanyal, Amartya, Lajoie, Bryan R, Capriotti, Emidio, Byron, Meg, Lawrence, Jeanne B, Dekker, Job, Marti-Renom, Marc A

Journal:

Nature Structural and Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.95 MB

english, 2010

33

A composite score for predicting errors in protein structure models

David Eramian, Min-yi Shen, Damien Devos, Francisco Melo, Andrej Sali, Marc A. Marti-Renom

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 603 KB

english, 2006

34

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

Serra, François, Baù, Davide, Goodstadt, Mike, Castillo, David, Filion, Guillaume J., Marti-Renom, Marc A., Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 13.88 MB

english, 2017

35

Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting

Maya Topf, Matthew L. Baker, Marc A. Marti-Renom, Wah Chiu, Andrej Sali

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 717 KB

english, 2006

36

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

Davide Baù, Marc A. Marti-Renom

Journal:

Year:

2012

Language:

english

File:

PDF, 991 KB

english, 2012

37

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints

Diament, Alon, Tuller, Tamir, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.04 MB

english, 2015

38

Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints

Marc A. Martí-Renom, Roland H. Stote, Enrique Querol, Francesc X. Aviles, Martin Karplus

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 174 KB

english, 2000

39

Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans

Emidio Capriotti, Leonardo Arbiza, Rita Casadio, Joaquín Dopazo, Hernán Dopazo, Marc A. Marti-Renom

Journal:

Year:

2008

Language:

english

File:

PDF, 238 KB

english, 2008

40

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2

Patrick Aloy, José M. Mas, Marc A. Martí-Renom, Enrique Querol, Francesc X. Avilés, Baldomero Oliva

Journal:

Journal of Computer-Aided Molecular Design

Year:

2000

Language:

english

File:

PDF, 178 KB

english, 2000

41

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells

Sasai, Masaki, Kawabata, Yudai, Makishi, Koh, Itoh, Kazuhito, Terada, Tomoki P., Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.93 MB

english, 2013

42

A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly

Burton, Brittany, Zimmermann, Michael T., Jernigan, Robert L., Wang, Yongmei, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.77 MB

english, 2012

43

Rational design of non-resistant targeted cancer therapies

Martínez-Jiménez, Francisco, Overington, John P., Al-Lazikani, Bissan, Marti-Renom, Marc A.

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 1.60 MB

english, 2017

44

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

Dekker, Job, Marti-Renom, Marc A., Mirny, Leonid A.

Journal:

Nature Reviews Genetics

Year:

2013

Language:

english

File:

PDF, 6.32 MB

english, 2013

45

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

Mas, Glòria, Blanco, Enrique, Ballaré, Cecilia, Sansó, Miriam, Spill, Yannick G., Hu, Deqing, Aoi, Yuki, Le Dily, François, Shilatifard, Ali, Marti-Renom, Marc A., Di Croce, Luciano

Journal:

Nature Genetics

Year:

2018

Language:

english

File:

PDF, 5.63 MB

english, 2018

46

Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology

Zhang, Nan, Mendieta-Esteban, Julen, Magli, Alessandro, Lilja, Karin C., Perlingeiro, Rita C. R., Marti-Renom, Marc A., Tsirigos, Aristotelis, Dynlacht, Brian David

Journal:

Nature Communications

Year:

2020

File:

PDF, 4.52 MB

2020

47

Challenges for visualizing three-dimensional data in genomic browsers

Goodstadt, Mike, Marti-Renom, Marc A.

Journal:

Year:

2017

Language:

english

File:

PDF, 432 KB

english, 2017

48

Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner

Warnecke, Tobias, Supek, Fran, Lehner, Ben, Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 625 KB

english, 2012

49

Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution

Spill, Yannick G., Castillo, David, Vidal, Enrique, Marti-Renom, Marc A.

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 966 KB

english, 2019

50

Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells

Cuadrado, Ana, Giménez-Llorente, Daniel, Kojic, Aleksandar, Rodríguez-Corsino, Miriam, Cuartero, Yasmina, Martín-Serrano, Guillermo, Gómez-López, Gonzalo, Marti-Renom, Marc A., Losada, Ana

Journal:

Year:

2019

File:

PDF, 4.33 MB

2019

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