Publications

 My Articles in PUBMED
http://www.ncbi.nlm.nih.gov/pubmed/?term=Espinosa%2C+Vladimir%5BAuth%5D+or+Angarica%2C+Vladimir+Espinosa%5BAuth%5D+or+Espinosa+Angarica%2C+Vladimir%5BAuth%5D+or+Angarica%2C+Vladimir+E%5BAuth%5D+or+Angarica+VE%5BAuth%5D
 My Citations in Google Scholar


  1. Ebralidze A.K, Angarica V.E., Liu Y., Kappei D., Tenen D., Monteleone E., Coffey R., Magallanes R.T., Ummarino S., Wanet A., Bassal M., Trinh B., Sheen M.R., Benoukraf T., Crane-Robinson C., Di Ruscio A., and Tenen D.G. (2017). Formation of an active epigenetic mark is mediated by S-Phase Early RNAs - SPEARs. submitted
  2. Lynch, C., Bernad, R., Calvo, I., Nobrega-Pereira, S., Ruiz, R., Ibarz, N., Martinez del Val, A, Graña, O., Gomez, G., Andres-Leon, E., Angarica, V.E., del Sol, A., Rojo, E., Fernandez-Capetillo, O., Muñoz, J., Serrano, M. (2017). The RNA Polymerase II factor RPAP1 is critical for Mediator-driven transcription and cell identity. Cell Rep. 22: 396–410. [PUBMED] [PDF]
  3. Wang, J., Jenjaroenpun, P., Bhinge, A., Angarica, V.E., del Sol, A., Kuznetsov, V. A., Stanton, L. W. (2017). Single cell gene expression analysis reveals regulators of subpopulation-specific trajectories among developing human neurons. Genome Res27(11): 1783–94. [PUBMED] [PDF]
  4. Jung, S., Angarica, V.E.,  Andrade-Navarro, M.A., Buckley, N., del Sol, A. (2017). Prediction of chromatin accessibility in gene-regulatory regions from transcriptomics data. Sci. Rep7(1):4660. [PUBMED] [PDF]
  5. Angarica, V.E., and del Sol, A. (2017). Bioinformatics tools for Genome Wide Epigenetic Research. In Delgado Morales, R. (Ed.), Neuroepigenomics in Aging and Disease. Adv. Exp. Med. Biol. (Springer). Vol: 978, ISBN: 978-3-319-53888-4[PUBMED] [Full Book]
  6. Angarica, V.E., and del Sol, A. (2016). Modeling Heterogeneity in the Pluripotent State: a promising strategy for improving the efficiency and fidelity of stem cell differentiation. BioEssays38(8): 758–68. [PUBMED] [PDF]
  7. Angarica, V.E., Orozco, M. and Sancho, J. (2016). Exploring the complete mutational space of the LDLr LA5 domain using molecular dynamics: linking SNPs with abnormal phenotypes in Familial hypercholesterolemiaHum. Mol. Genet25(6): 1233–46. [PUBMED[PDF] [Cover]
  8. Zickenrott, S., Angarica, V.E., Upadhyahya, B.B., and del Sol, A. (2016). Prediction of disease-gene-drug relationships following a differential network analysis. Cell Death Dis7: e2040.  [PUBMED] [PDF]
  9. Okawa, S., Angarica, V.E., Lemischka, I., Moore, K., and del Sol, A. (2015). A differential network analysis approach for lineage specifier prediction in stem cell subpopulations. NPJ Syst. Biol. Appl. 1: 15012. [PUBMED[PDF]
  10. Martinez-Olivan, J., Rozado Aguirre, Z., Arias-Moreno, X., Angarica, V.E., Velazquez-Campoy, A., and Sancho, J. (2014). LDL receptor is a calcium/magnesium sensor: Role of LR4 and LR5 ion interaction kinetics in LDL release in the endosome. FEBS J. 281(11): 2638–58. [PUBMED[PDF]
  11. González, A., Angarica, V.E., Sancho, J., and Fillat, M.F. (2014). The FurA regulon in Anabaena sp. PCC 7120: in silico prediction and experimental validation of novel target genes. Nucleic Acids Res42(8): 4833–46. [PUBMED] [PDF]
  12. Angarica, V.E., Angulo, A., Giner, A., Losilla, G., Ventura, S., and Sancho, J. (2014). PrionScan: an online database of predicted prion domains in complete proteomes. BMC Genomics15: 102. [PUBMED] [PDF] [PrionScan]
  13. Angarica, V.E., Ventura, S. and Sancho, J. (2013). Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains. BMC Genomics. 14: 316. [PUBMED] [PDF]
  14. Martinez-Julvez, M., Rojas, A., Olekhnovich, I., Angarica, V.E., Hoffman, P.S., and Sancho, J. (2012). Structure of RdxA: an oxygen insensitive nitroreductase essential for metronidazole activation in Helicobacter pylori. FEBS J. 279(23): 4306–17. [PUBMED] [PDF]
  15. Angarica, V.E. and Sancho, J. (2012). Protein dynamics governed by interfaces of high polarity and low packing density. (2012). PLoS ONE7(10): e48212. [PUBMED] [PDF]
  16. Ayuso-Tejedor, S., Angarica, V.E., Bueno, M., Campos, L.A., Abian, O., Bernado, P., Sancho, J., Jimenez, M.A. (2010). Design and structure of a protein folding intermediate. A hint into dynamical regions of proteinsJ. Mol. Biol400(4): 922–34. [PUBMED] [PDF]
  17. Contreras-Moreira, B., Sancho, J. and Angarica, V.E. (2010). Comparison of DNA-binding across protein superfamiliesProteins78(1): 52–62. [PUBMED] [PDF]
  18. Perez, A.G., Angarica, V.E., Collado-Vides, J., Vasconcelos, A.T. (2009). From sequence to dynamics: The effects of transcription factor and polymerase concentration changes on activated and repressed promotersBMC Mol. Biol10: 92. [PUBMED] [PDF]
  19. Angarica, V.E., Perez, A.G., Vasconcelos, A.T., Collado-Vides, J., Contreras-Moreira, B. (2008). Prediction of TF target sites based on atomistic models of protein-DNA complexesBMC Bioinformatics9: 436. [PUBMED] [PDF]
  20. Lozada-Chavez, I., Angarica, V.E., Collado-Vides, J., Contreras-Moreira, B. (2008). The role of DNA-binding specificity in the evolution of bacterial regulatory networksJ. Mol. Biol379(3): 627–43. [PUBMED] [PDF]
  21. Gonzalez Perez, A.D., Gonzalez Gonzalez, E., Espinosa Angarica, V., Vasconcelos, A.T., Collado-Vides, J. (2008). Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteriaBMC Genomics9: 128. [PUBMED] [PDF]
  22. Lopez-Gomollon, S., Hernandez, J.A., Pellicer, S., Angarica, V.E., Peleato, M.L. and Fillat, M.F. (2007). Cross-talk between iron and nitrogen regulatory networks in Anabaena (Nostoc) sp. PCC 7120: Identification of overlapping genes from/in FurA and NtcA regulonsJ. Mol. Biol.374(1): 267–81. [PUBMED] [PDF]
  23. Perez, A.G., Angarica, V.E., Vasconcelos, A.T., Collado-Vides, J. (2007). Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomesNucleic Acids Res35: D132–6. [PUBMED] [PDF]
  24. Espinosa, V., Gonzalez, A.D., Vasconcelos, A.T., Huerta, A.M and Collado-Vides, J. (2005). Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomesJ. Mol. Biol354(1): 184–99. [PUBMED] [PDF]
  25. Guia, M.H., Perez, A.G., Angarica, V.E., Vasconcelos, A.T., Collado-Vides, J. (2005). Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approachIn Silico Biol5(2): 209–19. [PUBMED] [PDF]
  26. Gonzalez, A.D., Espinosa, V., Vasconcelos, A.T., Perez-Rueda, E., Collado-Vides, J. (2005). TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomesNucleic Acids Res33: D98–102. [PUBMED] [PDF]