Publications

PUBLICATIONS ARTICLES

Current H-index of 11 with 583 total citations (data from Google Scholar). 

  1. Moreno I., Cicinelli E., Garcia-Grau I., Gonzalez M., Baù D., Vilella F., De Ziegler D., Resta L., Valbuena D., Simon C., “The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology”, Am J Obstet Gynecol 2018 Feb 22
  1. Serra F*., Baù D*., Goodstadt M., Castillo D.,Filion G., Marti-Renom M.A., “Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors”, PLOS Computational Biology 13(7)
  2. *These authors contributed equally to this work.

  1. Trussart, M, Yus, E, Martinez, S., Baù, D., Tahara, Y., Pengo, T., Kretshmer, S., Swoger, J., Miyata, M., Marti-Renom, M.A., Lluch-Senar, M. and Serrano, L., “Defined chromosome structure in a minimal cell”, Nature Communication, (2017) 8 14665
  1. Belton, J-M., Lajoie, B.R., Audibert, S., Cantaloube, S., Lassadi, I., Goiffon, I., Baù, D., Marti-Renom, M.A., Bystricky, K. and Dekker, J., “The conformation of yeast chromosome III is mating type-dependent and controlled by the recombination enhancer”, Cell Reports (2015); 13, 1-13
  1. Serra, F., Di Stefano, M., Spill, Y. G., Cuartero, Y.,Goodstadt, M., Baù, D., and Marti-Renom, M.A., “Restraint based three-dimensional modeling of genomes and genomic domains”, FEBS Letters (2015), 589, (20), 2987-2995
  1. Trussart, M., Serra, F., Baù, D., Junier, I., Serrano, L. and Marti-Renom, M.A., “Assessing the limits of restraint-based 3D modeling of genomes and genomic domains”, Nucleic Acids Research (2015)
  1. Le Dily, F., Baù, D., Pohl, A., Vicent, G, Serra, F., Soronellas, D., Castellano, G., Wright, R.H.G, Ballare, C., Filion, F., Marti-Renom, M.A. and Beato, B. “Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation” Genes & Development (2014) 28, (19), 2151-62
  1. Baù, D. and Marti-Renom M.A. “Genome structure determination via 3C-based data integration by the Integrative Modeling Platform” Methods (2012) 58 300-306
  1. Umbarger, M.A., Toro, E., Wright, M.A., Porreca, G.J.,Baù, D., Hong, S-H., Fero, M.J., Zhu, J.,Marti-Renom, M.A., McAdams, J.H., Shapiro, L., Dekker, J. and Church, G.M. “The three-dimensional architecture of a bacterial genome” Molecular Cell, (2011) 44, Issue 2, 252-264

This article has been selected in a “Journal Club” for Nature Reviews Molecular Cell Biology (http://dx.doi.org/10.1038/nrm3247) in a “Research Highlight” for Nature Reviews Microbiology (http://dx.doi.org/10.1038/nrmicro2703) and in a “Review” for F1000 (http://f1000.com/10403956).

  1. Feuerriegel, I., Köser, C.,Baù, D., Rüsch-Gerdes, S., Summers, D., Archer, Marti-Renom, M.A. and Niemann, S “Impact of fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824″ Antimicrobial Agents and Chemotherapy (2011) 55 5718-5722
  1. Sanyal, D. Baù, M.A. Marti-Renom and J. Dekker “Chromatin globules: a common motif of higher-order chromosome structure?” Current Opinion in Cell Biology (2011) (2011) 23325–33
  1. Baù, M.A. Marti-Renom “Structure determination of genomic domains by satisfaction of spatial restraints” Chromosome Research (2011) 19 (1) 25
  1. Baù, A. Sanyal, B. R. Lajoie, E. Capriotti, J. Dekker, and M. A. Marti-Renom “The three-dimensional folding of the alpha-globin gene domain reveals formation of chromatin globules” Nature Structural and Molecular Biology (2011) 18 107-115

This article has been featured in a “Technology Feature” for Nature (http://dx.doi.org/10.1038/470289a).

  1. Walsh, D. Baù, A.J. M. Martin, C. Mooney, A. Vullo, G. Pollastri “Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks” BMC Structural Biology, 9:5, 2009
  1. J. M. Martin, D. Baù, A. Vullo, I. Walsh and G. Pollastri “Long-range information and physicality constraints improve predicted protein contact maps” Journal of Bioinformatics and Computational Biology, 6(5):1001-20, 2008
  1. Baù, A. J. M. Martin, C. Mooney, A. Vullo, I. Walsh, G. Pollastri “Distill: A suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins” BMC Bioinformatics, 7:402, 2006
  1. Heuser, D. Baù, P. Benkert, D. Schomburg “Refinement of unbound protein docking studies using biological knowledge” Proteins, 2005 Dec 1;61(4):1059-67
  1. Baù, G. Carta, L. Crociani, G. Paolucci, F. Raggiotto, G. Rossetto and P. Zanella “Non-cyclopentadienyl zirconium complexes as catalysts for 1-hexene polymerization” Inorganica Chimica Acta, 358 (2005) 36-40

 Book chapters

  1. Baù, I. Walsh, G. Pollastri, A. Vullo “Fast Modeling of Protein Structures Through Multi-level Contact Maps” Computational Biology: New Research, Alona S. Russe editor, Nova Publishers, 2008
  1. Baù, G. Pollastri, A. Vullo “DISTILL: A Machine Learning Approach to Ab Initio Protein Structure Prediction” Analysis of Biological Data: A Soft Computing Approach, edited by S. Bandyopadhyay, U. Maulik and J. T. L. Wang
  1. Co-author of the chapter “Estructura y organizacion del DNA” of the book “Bioinformática con Ñ”,  http://http://www.scribd.com/doc/231270078/Bioinformatica-con-N

 

INVITED TALKS

Peer-reviewed accepted conference talks

  1. Learning the genome: Artificial Neural Networks applied to genomic data, XXXIX Congreso de la Sociedad Española de Bioquímica y Biología Molecular (SEBBM), 05-08/09/2016, Salamanca, Spain
  1. Structure determination of genomes, EMBO Practical Course on Integrative modeling of biomolecular interactions, 04-09/07/2016, Barcelona, Spain
  1. Structural features of the 5-colors Drosophila chromatin types, ISMB 2015, 10/07/2015, Dublin, Ireland
  1. Structural features of the 5-colors Drosophila chromatin types, XII Jornadas de Bioinformática, 23/09/2014, Seville, Spain
  1. Determination of hormone induced structural changes in genomic topological domains, ISMB 2013, 27/07/2013, Berlin, Germany
  1. The Three-Dimensional architecture of a bacterial genome and its alteration by genetic perturbation, ISMB 2012, 17/07/2012, Long Beach, CA, USA
  1. The Three-Dimensional architecture of a bacterial genome and its alteration by genetic perturbation, The Biology and Physics of Bacterial Genome Organization, 18/06/2012, Lorentz Center, Leiden, Holland
  1. The three-dimensional folding of the alpha-globin gene domain reveals formation of chromatin globules, XI Jornadas de Bioinformática, 23/01/2012, Barcelona, Spain
  1. The Three-Dimensional Architecture of a Bacterial Genome, Chromatin and Systems Biology Spetses Summer School, 13/09/2011, Spetses, Greece

Conference posters

  1. trussart, D. Baù, M. A. Marti-Renom and L. Serrano “The three-dimensional genome conformation of Mycoplasma pneumoniae“, Chromatin and Systems Biology Spetses Summer School, Sep 13 2011, Spetses, Greece
  1. trussart, D. Baù, M. A. Marti-Renom and L. Serrano “The three-dimensional genome conformation of Mycoplasma pneumoniae“, ISMB, Jul 15 2012, Long Beach, CA, USA
  1. trussart, D. Baù, M. A. Marti-Renom and L. Serrano “The three-dimensional genome conformation of Mycoplasma pneumoniae” The Biology and Physics of Bacterial Genome Organization, Jun 18 2012, Lorentz Center, Leiden, Holland
  1. trussart, D. Baù, M. A. Marti-Renom and L. Serrano “The three-dimensional genome conformation of Mycoplasma pneumoniae” Chromosomes, Stem Cells and Diseases, Sep 20 2012, Center for Genomics Regulation (CRG), Barcelona
  1. Baù, M. Umbarger, E. Toro, M. A. Wright, G. J. Porreca, S-H. Hong, H. J. Fero, M. A. Marti-Renom, H. H. McAdams, L. Shapiro, J. Dekker and G. Church “The Three-Dimensional Architecture of a Bacterial Genome” EMBO Conference Series on Nuclear Structure and Dynamics, Sep 28-Oct 2 2011, L’Isle sur la Sorgue, France
  1. Baù, A. Sanyal, B. Lajoie, E. Capriotti, J. Dekker and M.A. Marti-Renom “From 5C to 3D: a hybrid method for determining the structure of genomes” Jornadas de Bioinformatica 2009, Nov 3-6, Lisbon, Portugal
  1. Baù, B. Lajoie, Y. Zhan, E. Capriotti, J. Dekker and M.A. Marti-Renom “From 5C to 3D: a hybrid method for determining the structure of genomes” EMBO Conference Series on Nuclear Structure and Dynamics, Sep 30-Oct 4 2009, L’Isle sur la Sorgue, France
  1. Baù, A. Sanyal, B. Lajoie, E. Capriotti, J. Dekker and M.A. Marti-Renom “From 5C to 3D: a hybrid method for determining the structure of genomes” UNIA Current Trends in Biomedicine Workshop 2009 on: Chromatin Domains and Insulators
  1. Baù, A. Vullo, G. Pollastri “A New Neural Network Ranker To Evaluate Protein Structure Predictions” 15th International Conference on Intelligent Systems for Molecular Biology (ISMB), July 21-25, 2007, Vienna, Austria
  1. Roche, D. Baù, A.J.M. Martin, C. Mooney, A. Vullo, I. Walsh, G. Pollastri “High-Throughput Comparative Modeling of Protein Structures by Machine Learning” Microsoft Research Summer School 2007
  1. Baù, A. J. M. Martin, C. Mooney, A. Vullo, I. Walsh, G. Pollastri “Modeling of Protein C-Traces Through Structural Constraints Predicted by Machine Learning” 7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, Asilomar Conference Center, Pacific Grove, CA, November 26-30, 2006
  1. Baù, A. Vullo, G. Pollastri “Ab Initio Modeling of Protein C-Traces Through Structural Predicted by Machine Learning” 14th. International Conference on Intelligent Systems for Molecular Biology (ISMB), August 6-10, 2006, Fortaleza, Caera, Brazil
  1. Baù, A. Vullo, G. Pollastri “Ab Initio Modeling of Protein C-Traces Through Structural Predicted by Machine Learning” MGMS International Meeting 2005, Biomolecular Simulation, Trinity College Dublin Sept 11-14 2005
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