1. Han, S., Okawa, S., Wilkinson, G.A., Ghazale, H., Adnani, L., Dixit, R., Tavares, L., Faisal, I., Brooks, M.J., Cortay, V., Zinyk, D., Sivitilli, A., Li, S., Malik, F., Ilnytskyy, Y., Angarica, V.E., Gao, J., Chinchalongporn, V., Oproescu, A.M., Vasan, L., Touahri, Y., David, L.A., Raharjo, E., Kim, J.W., Wu, W., Rahmani, W., Chan, J.A., Kovalchuk, I., Attisano, L., Kurrasch, D., Dehay, C., Swaroop, A., Castro, D.S., Biernaskie, J., Del Sol, A., Schuurmans, C. (2021). Proneural genes define ground-state rules to regulate neurogenic patterning and cortical folding. Neuron. 109(18): 2847-63. [PUBMED] [PDF]

  2. Trinh, B.Q., Ummarino, S., Zhang, Y., Ebralidze, A.K., Bassal, M.A., Nguyen, T.M., Heller, G., Coffey, R., Tenen, D.E., van der Kouwe, E., Fabiani, E., Gurnari, C., Wu, C.S., Angarica, V.E., Yang, H., Chen, S., Zhang, H., Thurm, A.R., Marchi, F., Levantini, E., Staber, P.B., Zhang, P., Voso, M.T., Pandolfi, P.P., Kobayashi, S.S., Chai, L., Di Ruscio, A., Tenen, D.G. (2021). Myeloid lncRNA LOUP mediates opposing regulatory effects of RUNX1 and RUNX1-ETO in t(8;21) AML. Blood. 138(15): 1735-47. [PUBMED] [PDF]

  3. 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]

  4. 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]

  5. 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]

  6. 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]

  7. 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]

  8. 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]

  9. 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]

  10. 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]

  11. 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]

  12. 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]

  13. 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]

  14. 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]

  15. 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]

  16. 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]

  17. 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]

  18. 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]

  19. 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]

  20. 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]

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

  22. 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]

  23. 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]

  24. 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]

  25. 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]

  26. 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]

  27. 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]

  28. 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]

  29. 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]

  30. 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]