Publications

  1. Numata, A., Kwok, H.S., Zhou, Q.L., Li J., Tirado-Magallanes, R., Angarica, V.E., Hannah, R.L., Park, J., Wang, C.Q., Krishnan, V., Rajagopalan, D., Zhang, Y., Zhou, S., Welner, R., Osato, M., Jha, S., Bohlander, S.K., Göttgens, B., Yang, H., Benoukraf, T., Lough, J.W., Bararia, D., and Tenen, D.G. (2020). Lysine acetyltransferase Tip60 is required for hematopoietic stem cell maintenance. Blood. 136(15): 1735-47. [PUBMED] [PDF]

  2. González, A., Casado, J., Chueca, E., Salillas, S., Velázquez-Campoy, A., Angarica, V.E., Bénejat, L., Guignard, J., Giese, A., Sancho, J., Lehours, P., Lanas, A., (2019). Repurposing Dihydropyridines for Treatment of Helicobacter pylori Infection. Pharmaceutics. 11(12): 681. [PUBMED] [PDF]

  3. González, A., Salillas, S., Velázquez-Campoy, A., Angarica, V.E., Fillat, M.F., Sancho, J., Lanas, A. (2019). Identifying potential novel drugs against Helicobacter pylori by targeting the essential response regulator HsrA. Sci. Rep. 9(1): 11294. [PUBMED] [PDF]

  4. 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]

  5. 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 Res. 27(11): 1783–94. [PUBMED] [PDF]

  6. 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. Rep. 7(1):4660. [PUBMED] [PDF]

  7. 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]

  8. 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. BioEssays. 38(8): 758–68 [PUBMED] [PDF]

  9. 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 hypercholesterolemia. Hum. Mol. Gen. 25(6): 1233–46. [PUBMED] [PDF] [Cover]

  10. 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 Dis. [PUBMED] [PDF]

  11. 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]

  12. 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]

  13. 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 Res. 42(8): 4833–46. [PUBMED] [PDF]

  14. 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 Genomics. 15: 102. [PUBMED] [PDF] [PrionScan]

  15. 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]

  16. 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]

  17. Angarica, V.E. and Sancho, J. (2012). Protein dynamics governed by interfaces of high polarity and low packing density. (2012). PLoS ONE. 7(10): e48212. [PUBMED] [PDF]

  18. 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 proteins. J. Mol. Biol. 400(4): 922–34. [PUBMED] [PDF]

  19. Contreras-Moreira, B., Sancho, J. and Angarica, V.E. (2010). Comparison of DNA-binding across protein superfamilies. Proteins. 78(1): 52–62. [PUBMED] [PDF]

  20. 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 promoters. BMC Mol. Biol. 10: 92. [PUBMED] [PDF]

  21. 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 complexes. BMC Bioinformatics. 9: 436. [PUBMED] [PDF]

  22. 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 networks. J. Mol. Biol. 379(3): 627–43. [PUBMED] [PDF]

  23. 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-proteobacteria. BMC Genomics. 9: 128. [PUBMED] [PDF]

  24. 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 regulons. J. Mol. Biol.374(1): 267–81. [PUBMED] [PDF]

  25. 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 genomes. Nucleic Acids Res. 35: D132–6. [PUBMED] [PDF]

  26. 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 genomes. J. Mol. Biol. 354(1): 184–99. [PUBMED] [PDF]

  27. 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 approach. In Silico Biol. 5(2): 209–19. [PUBMED] [PDF]

  28. 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 genomes. Nucleic Acids Res. 33: D98–102. [PUBMED] [PDF]