PUBLICATIONS

"All models are wrong,

but some are useful"

 
 
 
Journal Publications

39. Rodriguez Susana, da Rosa Gabriela, Radío Santiago, Barraco-Vega Mariana, Benko-Iseppon Ana María, Dans Pablo D., Smircich Pablo and Cecchetto Gianna. Antimicrobial peptides in the seedling transcriptome of the tree legume Peltophorum dubium. Biochimie, DOI: 10.1016/j.biochi.2020.11.005 (2020PDF

38. Ruifang Zheng, da Rosa Gabriela, Dans Pablo D., and Peluffo R. Daniel. Molecular Determinants for Nitric Oxide Regulation of the Murine Cationic Amino Acid Transporter CAT-2A. Biochemisty, DOI: 10.1021/acs.biochem.0c00729 (2020PDF

37. Battistini Federica, Dans Pablo D., Terrazas Montserrat, Castellazzi Chiara L., Portella Guillem, Labrador Mireia, Villegas Núria, Brun-Heath Isabelle, Gómez-Pinto Irene, González  Carlos and Orozco Modesto. The physical origins of the hydroxy-methyl-cytosine epigenetic signature. BioRxiv (2020PDF

36. Buitrago Diana, Labrador Mireia, ArcoN Juan Pablo, Rafael Lema, Flores Oscar, Esteve-Codina Anna, Blanc Jule, Villegas Nuria, Bellido David, Gut Marta, Dans Pablo D., Heath Simon, Gut Ivo, Brun Heath Isabelle, and Orozco Modesto. Impact of DNA methylation on 3D genome structure. Research square archive (2020PDF

35. Walther Jürgen, Dans Pablo D., Balaceanu Alexandra, Adam Hospital, Genís Bayarri, and Orozco Modesto. A Multi-Modal Coarse-Grain Model of DNA Flexibility Mappable to the Atomistic Level, Nucleic Acids Research, DOI: 10.1093/nar/gkaa015 (2020) PDF

*** Article of the month by the Biophysical Society of Spain K

34. Dans Pablo D., Balaceanu Alexandra, Pasi Marco, Patelli Alessandro S. P,  Petkevičiūtė Daiva, Walther Jürgen, Hospital Adam, Lavery Richard, Maddocks John, and Orozco Modesto. The Static and Dynamic Structural Heterogeneities of B-DNA: Extending Calladine-Dickerson rulesNucleic Acids Research, DOI: 10.1093/nar/gkz905 (2019PDF

*** Article of the month by the Biophysical Society of Spain K

33. Janin Maxime, Ortiz-Barahona Vanessa, ..., Dans Pablo D., Orozco Modesto, Thomas George, Blanco Sandra, Seoane Joan, Preiss Thomas, Pandolfi Pier Paolo, Esteller Manel. Epigenetic Loss of RNA Methyltransferase NSUN5 in Glioma Targets Ribosomes to Drive a Stress Adaptive Translational Program Associated with Long-Term Survival. Acta Neuropathologica, DOI: 10.1007/s00401-019-02062-4 (2019PDF

32. Rodriguez Susana, Dans Pablo D., Borba María Alejandra, Benko-Iseppon Ana María, and Cecchetto Gianna. Gene Isolation of a New Legume Defensin with a Broad Spectrum of Antimicrobial Activity. Planta Journal, DOI: 10.1007/s00425-019-03260-w (2019PDF

 

31. Battistini Federica, Hospital Adam, Buitrago Diana, Dans Pablo D., Gelpi Josep Lluis, and Orozco Modesto. How B-DNA Dynamics Decipher Sequence-selective Protein Recognition. Journal of Molecular Biology, DOI: 10.1016/j.jmb.2019.07.021 (2019PDF

30. Gallego Diego, Darré Leonardo, Dans Pablo D., and Orozco Modesto. VeriNA3d: An R Package for the Data Mining of Nucleic Acids. Bioinformatics – Application Notes, DOI: 10.1093/bioinformatics/btz553 (2019PDF

29. Balaceanu Alexandra, Buitrago Diana, Walther Jurgen, Dans Pablo D., and Orozco Modesto. Modulation of the Helical Properties of DNA: Next-To-Nearest Neighbour Effects and Beyond. Nucleic Acids Research, DOI: 10.1093/nar/gkz255, (2019PDF

*** Article of the month by the Biophysical Society of Spain K

28. Kuzmanic Antonia, Dans Pablo D., and Orozco Modesto. An in-depth look at DNA crystals through the prism of molecular dynamics simulations. CHEM, Cell press, DOI: 10.1016/j.chempr.2018.12.007, (2019PDF

27. Dans Pablo D., Gallego Diego, Balaceanu Alexandra, Darré Leonardo, Gómez Hansel, and Orozco Modesto. Modeling, Simulations, and Bioinformatics at the Service of RNA Structure. CHEM, Cell press, DOI: 10.1016/j.chempr.2018.09.015, (2018PDF

26. Elizabeth Sweeny, Anuradha Singh, Ritu Chakravarti, Osiris Martinez-Guzman, Arushi Saini, Mohammad Haque, Greer Garee, Dans Pablo D., Luciana Hannibal, Amit Reddi, and Dennis Stuehr. Glyceraldehyde 3-phosphate dehydrogenase is a chaperone that allocates labile heme in cells. Journal of Biological Chemistry. DOI: 10.1074/jbc.RA118.004169, (2018PDF

*** JBC editors’ pick highlight K

*** Pointed out as highly relevant by F1000 K

25. Balaceanu Alexandra, Pérez Alberto, Dans Pablo D., and Orozco Modesto. Allosterism and Signal Transfer in DNA. Nucleic Acids Research, DOI: 10.1093/nar/gky549, (2018PDF

*** Article of the month by the Biophysical Society of Spain K

*** Chosen as a successful case in the Barcelona Supercomputing Center annual report K

24. Rodríguez-Decuadro Susana, Barraco-Vega Mariana, Dans Pablo D., Pandolfi Valesca, Benko-Iseppon Ana Maria, and Cecchetto Gianna. Antimicrobial and structural insights of a new snakin-like peptide isolated from Peltophorum dubium (Fabaceae). Amino Acids, DOI: 10.1007/s00726-018-2598-3, (2018PDF

23. Dans Pablo D., Ivani Ivan, Hospital Adam, Portella Guillem, González Carlos, and Orozco Modesto. How accurate are accurate force-fields for B-DNA? Nucleic Acids Research, Volume 45, Issue 7, 4217-4230, (2017PDF

*** Article of the month by the Biophysical Society of Spain K

*** Pointed out as a highly relevant article in IRB Barcelona's annual report K

22. Balaceanu Alexandra, Pasi Marco, Dans Pablo D., Hospital Adam, Lavery Richard, and Orozco Modesto. The role of unconventional hydrogen bonds in determining BII propensities in B-DNA. Journal of Physical Chemistry Letters, Volume 8, Issue 1, 21-28, (2016PDF

21. Darre Leonardo, Ivani Ivan, Dans Pablo D., Gómez Hansel, Hospital Adam, Orozco Modesto. Small Details Matter: the Importance of the 2’Hydroxyl in RNA. Journal of American Chemical Society, Volume 138, Issue 50, 4217-4230 (2016PDF

20. Dans Pablo D., Danilāne L., Ivani Ivan, Dršata Tomáš, Lankaš Filip, Hospital Adam, Walther Jürgen, Illa Pujagut Ricard, Battistini Federica, Gelpí Josep Lluis, Lavery Ricard and Orozco Modesto. Long-timescale dynamics of the Drew-Dickerson dodecamer. Nucleic Acids Research, Volume 44, Issue 9, 4052-4066, (2016PDF

*** Article of the month by the Biophysical Society of Spain K

19. Saint-Léger Adélaïde, Bello-Cabrera Carla, Dans Pablo D., Torres Adrian Gabriel, Novoa Eva Maria, Camacho Noelia, Orozco Modesto, Kondrashov Fyodor A and Ribas de Pouplana Lluís. Saturation of recognition elements blocks evolution of new tRNA identities. Science advances, Volume 2, Issue 4, e1501860, (2016PDF

18. Hospital Adam, Andrio Pau, Cugnasco Cesare, Codó Laia, Becerra Yolanda, Dans Pablo D., Battistini Federica, Torres Jordi, Goni Ramon, Orozco Modesto, et al. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acid Research, Volume 44, Issue D1, D272-8, (2016PDF

17. Dans Pablo D., Walther Jurgen, Gómez Hansel, and Orozco Modesto. Multiscale simulation of DNA. Current Opinion in Structural Biology - Theory and simulation - Macromolecular machines, Volume 37, 29 - 45, (2016PDF

16. Ivani Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. Parmbsc1: a refined force field for DNA simulations. Nature Methods, Volume 13, Issue 1, 55-8, (2016PDF

*** Article of the month by the Biophysical Society of Spain K

*** Pointed out as highly relevant by F1000 K

*** +300 citations

15. Signorelli Santiago, Dans Pablo D., Coitiño Elena Laura, Borsani Omar, and Monza Jorge. Connecting proline and γ-aminobutyric acid in stressed plants through non-enzymatic reactions. PLoS One, Volume 10, Issue 3, e0115349, (2015PDF

*** In the top 10% of most cited articles of 2015 PLoS One publications

14. Rossetti Giulia, Dans Pablo D., Gómez-Pinto Irene, Ivani Ivan, González Carlos, and Orozco Modesto. The structural impact of DNA mismatches. Nucleic Acid Research, Volume 43, Issue 8, 4309-21, (2015PDF

13. Cuervo Ana, Dans Pablo D., Carrascosa José L., Orozco Modesto, Gomila Gabriel, and Fumagalli Laura. Direct measurement of the dielectric polarization properties of DNA. Proc. Natl. Acad. Sci. USA, Volume 111, Issue 35, E3624-30, (2014PDF

*** +100 citations 

12. Dans Pablo D., Faustino Ignacio, Battistini Federica, Zakrzewska Krystyna, Lavery Richard, and Orozco Modesto. Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA. Nucleic Acid Research, Volume 42, Issue 19, 11304-20, (2014PDF

11. Pasi Marco, Maddocks John H., Beveridge David, Bishop Thomas C., Case David A., Cheatham Thomas, Dans Pablo D., Jayaram B, Lankaš Filip, Laughton Charles, et al. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acid Research, Volume 42, Issue 19, 12272-83, (2014PDF

*** +100 citations 

10. Zeida Ari, Machado Matías Rodrigo, Dans Pablo D., and Pantano Sergio. Breathing, bubbling, and bending: DNA flexibility from multi microsecond simulations. Physical Review E, Volume 86, Number 2, 021903, (2012PDF

9. Dans Pablo D., Pérez Alberto, Faustino Ignacio, Lavery Richard, and Orozco Modesto. Exploring polymorphisms in B-DNA helical conformations. Nucleic Acid Research, Volume 40, Issue 21, 10668-78, (2012PDF

*** Pointed out as highly relevant by F1000 K

8. Machado Matías Rodrigo, Dans Pablo D., and Pantano Sergio. A hybrid all-atom/coarse grain model for multiscale simulations of DNA. Physical Chemistry Chemical Physics, Volume 13, Number 40, 18134–18144, (2011PDF

7. Perez Daniel I., Palomo Valle, Pérez Concepción, Gil Carmen, Dans Pablo D., Francisco Luque Javier, Conde Santiago, and Martínez Ana. Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds. Journal of medicinal chemistry, Volume 54, Number 12, 4042–4056, (2011PDF

6. Darré Leonardo, Machado Matias R., Dans Pablo D., Herrera Fernando E., and Pantano Sergio. Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? Journal of Chemical Theory and Computation, Volume 6, Number 12, 3793–3807, (2010PDF

5. Dans Pablo D., Zeida Ari, Machado Matías R., and Pantano Sergio. A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics. Journal of Chemical Theory and Computation, Volume 6, Number 5, 1711–1725, (2010PDF

*** +100 citations

4.  Machado Matias R., Dans Pablo D., and Pantano Sergio. Isoform-specific determinants in the HP1 binding to histone 3: insights from molecular simulations. Amino acids, Volume 38, Number 5, 1571–1581, (2010PDF

3. De Marco Alex, Dans Pablo D., Knezevich Anna, Maiuri Paolo, Pantano Sergio, and Marcello Alessandro. Subcellular localization of the interaction between the human immunodeficiency virus transactivator Tat and the nucleosome assembly protein 1. Amino acids, Volume 38, Number 5, 1583–1593, (2010PDF

2. Dans Pablo D., and E Coitiño Laura. Density functional theory characterization and descriptive analysis of cisplatin and related compounds. Journal of chemical information and modeling, Volume 49, Number 6, 1407–1419, (2009PDF

1. Dans Pablo D., Crespo Alejandro, Estrin Darío A., and E Coitiño Laura. Structural and Energetic Study of Cisplatin and Derivatives: Comparison of the Performance of Density Functional Theory Implementations. Journal of Chemical Theory and Computation, Volume 4, Number 5, 740–750, (2008PDF

2. Dans Pablo D., Degree in Biochemistry, Faculty of Science (UdelaR).TE1: Modelado Teórico Computacional de Procesos Reactivos de Interés Bioquímico (2000) PDF . TE2Modelado de la unión covalente entre fármacos para el tratamiento del cáncer de la familia del Cisplatino y el ADN : análisis de la viabilidad molecular de compuestos alternativos de Pd(II)  (2001PDF   

1. Dans Pablo D., PhD in Chemistry, Faculty of Chemistry (UdelaR). Modelado de las características estructurales y mecanismo de acción molecular de compuestos de Pd(II) y Pt(II) con potencial acción antineoplásica (2008PDF

Theses of Prof. Dans (spanish only)

2. Gómez Hansel, Walther Jürgen, Darré Leonardo, Ivani Ivan, Dans Pablo D. and Orozco Modesto. Molecular Modeling of Nucleic Acids in Computational Tools for Chemical Biology. Martín-Santamaría Sonsoles (Ed.). Royal Society of Chemistry (2017). ISBN-10: 1782627006. PDF

1. Dans Pablo D., Darré Leonardo, Machado Matias R., Zeida Ari, Brandner Astrid F., and Pantano Sergio. Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level. Advances in Bioinformatics and Computational Biology, 71–81, (2013). ISBN: 978-3-319-02623-7. PDF

Peer-reviewed book chapters
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