Résumé

My Résumé in PDF

General Info


  • Date and Place of Birth: November, 6th, 1978. Havana, Cuba
  • Marital Status: Married, no kids
  • Mailing Address: Cancer Science Institute, National University of Singapore (NUS). Center for Translational Medicine Building (MD6). 14 Medical Drive #12-01, 117599 Singapore.
  • Languages: Spanish (mother tongue), English (reads, writes, speaks, understands: excellent), French and Portuguese (reads, understands: well; speaks, writes: basic)

Education


  • 2009–2014: Ph.D. in Biochemistry at the Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Spain (summa cum laude[HTML[PDF]
  • 2007–2008: M.A.S. in Molecular and Cellular Biology at the University of Zaragoza, Spain (cum laude)
  • 2001–2002: Bioinformatics Specialists Training, coordinated by the Center for Genetic Engineering and Biotechnology (CIGB) at Havana
  • 1997–2002: B.Sc. in Biochemistry. Biology Faculty, University of Havana, Cuba (summa cum laude, Best Academic Results Award of the Biology Faculty, 2002)
  • 1996: Bachelor at the Exact Sciences Vocational Institute "Vladimir Ilich Lenin" of Havana, Cuba (summa cum laude)
  • 1996: Silver Medalist in the High School National Chemistry Competition. Integrant of the Cuban Team to the International Chemistry Olympiad
  • 1995: Gold Medalist in the High School National Chemistry Competition. Integrant of the Cuban Team to the Iberoamerican Chemistry Olympiad
  • 1994: Bronze Medalist in the High School National Chemistry Competition

Postgraduate Courses & Trainings


  • 2013: Postgraduate Course "Translational and Integrative Bioinformatics", organised by INBIOMEDvision in collaboration with Pompeu Fabra University (UPF), Bioinformatics Barcelona (BIB), Barcelona Supercomputing Center (BSC), Spanish Technological Platform for Innovative Medicines (PTEMI), and The Spanish Institute of Bioinformatics (INB), Barcelona, Spain
  • 2008: Workshop "Getting the most from biomolecular simulations", University of Barcelona/Institute for Research in Biomedicine/Barcelona Supercomputer Center, Barcelona, Spain
  • 2007: Trends in Transient Interactions between Biological Molecules, Institute of Plant Biochemistry and Photosynthesis, University of Sevilla, Sevilla, Spain
  • 2007: IInd Meeting of the Spanish Group of Protein Structure and Folding, University Miguel Hernández, San Juan de Alicante, Spain
  • 2003: International course New Frontiers of Bioinformatics in Latin America, University of "Los Andes", Mérida, Venezuela
  • 2002: Introduction to Logics, coordinated by the Mathematics Faculty from the University of Havana
  • 2002: French-Cuban Doctoral School (on the subject of Data Mining), coordinated by the Mathematics Faculty from the University of Havana and the Paris-VI University
  • 2002: Post-graduate Course on Bioinformatics, coordinated by the Mathematics Faculty from the University of Havana and the Udine University
  • 2001: Post-graduate course on Introduction to Protein Computational Modeling coordinated by the Physics Faculty from the University of Havana
  • 2001: IIIrd International Workshop on Nucleic Acids and Proteins sequence analysis, coordinated by the Center for Genetic Engineering and Biotechnology (CIGB) at Havana
  • 2001: Post-Congress course Interaction of Peptides and Proteins with Mimetic Membrane Systems, Ist International Symposium on Biochemistry and Molecular Biology, Havana, Cuba

Peer-Reviewed Publications


  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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. Gen25(6): 1233–46. [PUBMED[PDF] [Cover] 
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. Angarica, V.E., Ventura, S. and Sancho, J. (2013). Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domainsBMC Genomics14: 316. [PUBMED] [PDF]
  13. 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 pyloriFEBS J279(23): 4306–17. [PUBMED] [PDF]
  14. 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]
  15. 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]
  16. Contreras-Moreira, B., Sancho, J. and Angarica, V.E. (2010). Comparison of DNA-binding across protein superfamiliesProteins78(1): 52–62. [PUBMED] [PDF]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]

Research Meetings Talks & Posters


  • Angarica, V.E., Ventura, S. and Sancho, J. (2011). Prediction of prion proteins in complete proteomes using probabilistic representations of prionogenic domainsXXXIVth Congress of the Spanish Society for Biochemistry and Molecular Biology, Barcelona, Spain (Poster Presentation) [PDF]
  • Angarica, V.E., and Sancho, J. (2011). Protein buried interfaces in protein stability and dynamicsXIst Congress of the Spanish Biophysical Society, Murcia, Spain (Oral Presentation) [PDF]
  • Angarica, V.E., and Sancho, J. (2010). A computational study of protein intrafaces: prediction of unstructured regions in protein folding intermediates. XXXIIIrd Congress of the Spanish Society for Biochemistry and Molecular Biology, Córdoba, Spain (Oral Presentation) [PDF]
  • Angarica, V.E., and Sancho, J. (2010). A computational study of protein intrafaces and their implication in protein folding. IVth Spanish-Portuguese Biophysical Congress, Zaragoza, Spain (Poster Presentation) [PDF]
  • Angarica, V.E., and Sancho, J. (2010). Intrafaces and cavities in protein structures: implications in protein folding and dynamics. VIth Meeting of the Spanish Protein Structure and Function Network, Madrid, Spain (Oral Presentation) [PDF]
  • Angarica, V.E., Cuesta-Lopez, S., and Sancho, J. (2009). Exploring the mutational space of the LDL-r module using molecular dynamics: connecting SNPs to abnormal phenotypes in a conformational disease. XXXIInd Congress of the Spanish Society for Biochemistry and Molecular Biology, Oviedo, Spain (Poster Presentation) [PDF]
  • Contreras-Moreira, B., Angarica, V.E. (2009). Comparison of DNA-binding across protein superfamilies. Congress BIFI 2009, Zaragoza, Spain (Oral Presentation) [PDF]
  • Angarica, V.E., Cuesta-Lopez, S., Estrada, J. and Sancho, J. (2009). Using Molecular Dynamics to study the conformational changes of the LDL-r LA5 module upon mutation. Congress BIFI 2009, Zaragoza, Spain (Oral Presentation) [PDF]
  • Contreras-Moreira, B., Angarica, V.E. (2009). 3D-footprint: structural analysis of protein-DNA complexes. International Workshop Angel Ramirez Ortiz in memoriam, Madrid, Spain (Oral Presentation) [PDF]
  • Angarica, V.E., Cuesta-Lopez, S., Estrada, J. and Sancho, J. (2009). A computational study of the mutational space of the LDL-r LA5 module: in silico prediction of disease-like phenotypes in a conformational disease. International Workshop Angel Ramirez Ortiz in memoriam, Madrid, Spain (Poster Presentation)
  • Angarica, V.E., Cuesta-Lopez, S., Estrada, J. and Sancho, J. (2008). Conformational Changes of the LDL-r LA5 Module Upon Mutation: a Computational Approach. XXXIst Congress of the Spanish Society for Biochemistry and Molecular Biology, Bilbao, Spain (Poster Presentation) [PDF]
  • Contreras-Moreira, B., Lozada-Chavez, I. and Angarica, V.E. (2008). Structural (and sequence-based) analysis of transcriptional regulation. VIIIth Spanish Symposium on Bioinformatics and Computational Biology, Valencia, Spain (Oral Presentation) [PDF]
  • Angarica, V.E., Perez, A.G., Vasconcelos, A.T.R, Collado-Vides, J., Contreras-Moreira, B. (2007). Prediction of Transcription Factor Binding Sites using Structural Information. XXXth Congress of the Spanish Society for Biochemistry and Molecular Biology, Málaga, Spain (Poster Presentation) [PDF]
  • Espinosa, V., Gonzalez, A.D., Vasconcelos, A.T., Huerta, A.M and Collado-Vides, J. (2005). TRACTOR_DB as a source for comparative studies of transcriptional regulation mechanisms in gamma-proteobacterial genomes. Ist International Conference of the Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil (Poster Presentation - Honorary Mention Poster Award) [PDF]
  • Gonzalez A., Espinosa V., Vasconcelos A.T., Perez-Rueda E., Collado-Vides J. (2004). Predicting New Members of Regulons in Gamma-proteobacterial genomes: a Step Towards the Construction of a Multi-Genomic Database on Prokaryotic Transcriptional Regulation, Tractor_DB. International Conference on Bioinformatics and Computational Biology-ICOBICOBI, Angra dos Reis, Brazil (Poster Presentation)
  • Espinosa, V., Gonzalez, A.D., Vasconcelos, A.T., Collado-Vides, J. (2004). Site position study in a group of gamma-proteobacterial genomes. Co-ocurrence of binding sites for pairs of TFs and its implication in regulation of transcription. IInd International Symposium on Biochemistry and Molecular Biology, Havana, Cuba (Poster Presentation) [PDF]
  • Gonzalez, A., dos Santos. M.T., Espinosa. V., Vasconcelos. A.T., Collado-Vides, J. (2004). A novel database of computationally predicted new gamma-proteobacterial regulon members. Ist Bioinformatics Congress, Havana, Cuba (Oral presentation)
  • Gonzalez, A., dos Santos, M.T., Espinosa, V., Vasconcelos, A.T., Collado-Vides, J. (2003). New Members of over Seventy Regulons in Eight Gamma-Proteobacterial Genomes. Biotecnología Habana, Havana, Cuba (Poster presentation)
  • Espinosa, V., Bringas, R., Miranda, J.M. (2003). Prediction of Transcription Factors probably involved in the differential expression of genes in human Glioblastomes. Informatics 2003, Havana, Cuba (Poster Presentation)
  • Gonzalez, A., dos Santos, M.T., Espinosa, V., Vasconcelos, A.T., Collado-Vides, J. (2003). Predicting New Members of Regulons in eight Gamma-Proteobacterial Genomes. Congress of Medical Informatics, Havana, Cuba (Oral presentation)
  • Espinosa, V., Bringas, R., Miranda, J. (2003). Use of bioinformatics strategies for the prediction of Transcription Factors probably involved in the differential expression of groups of genes in human Glioblastomes. French-Cuban Bioinformatics Workshop, Havana, Cuba (Poster presentation)

Lecturing


  • 2002–2006: Seminars and Lectures of Molecular Genetics at the Biology Faculty, University of Havana, Cuba
  • 2004: Lectures of Relational Databases in the Graduate Course on Computational Biology and New Technologies, Biology Faculty, University of Havana, Cuba
  • 2004: Introduction to LINUX. University of Computer Sciences, Havana, Cuba
  • 2003: Introduction to Parallel Computing. Biology Faculty, University of Havana, Cuba

Grants


  • 2012: Grant from the "Consejo Superior de Investigaciones Científicas" (CSIC) for a 3-month research stay at the Molecular Recognition & Bioinformatics Group, Institute for Research in Biomedicine (IRB), Barcelona, Spain
  • 2009–2013: Ph.D. grant from the "Consejo Superior de Investigaciones Científicas" (CSIC), JAE Program
  • 2007–2009: M.A.S. Grant from the Banco Santander Central Hispano, Fundación Carolina and Universidad de Zaragoza
  • 2006: Grant from the Iberoamerican Bioinformatics Network (Red Iberoamericana de Bioinformática, RIBIOrt-VII.L CYTED) for a 6-month research stay at the Center for Genomic Sciences (CCG), Cuernavaca, Mexico
  • 2005: Travel Award from the Iberoamerican Bioinformatics Network (Red Iberoamericana de Bioinformática, RIBIO VII.L CYTED) to assist to a 3-month research stay at the National Laboratory for Scientific Computing (LNCC), Petrópolis, Brazil

Academic Awards


  • Nine first places in advanced competition exams
    1. Physics –Electromagnetism–, awarded by the Department of Applied Physics from the Physics Faculty, University of Havana
    2. Physics –Optics and Nuclear Physics–, awarded by the Department of Applied Physics from the Physics Faculty, University of Havana
    3. Philosophy II, awarded by the Department of Philosophy from the Philosophy and History Faculty, University of Havana
    4. Organic Chemistry II, awarded by the Department of Organic Chemistry from the Chemistry Faculty, University of Havana
    5. Enzymology, awarded by the Department of Biochemistry from the Biology Faculty, University of Havana
    6. Plant Morphology, awarded by the Department of Plant Biology from the Biology Faculty, University of Havana
    7. Microbiology, awarded by the Department of Microbiology from the Biology Faculty, University of Havana
    8. French V, awarded by the Department of French from the Foreign Languages Faculty, University of Havana
    9. French IV, awarded by the Department of French from the Foreign Languages Faculty, University of Havana
  • Four third places in advanced competition exams
    1. Animal Morphology, awarded by the Department of Human and Animal Biology from the Biology Faculty, University of Havana
    2. Biometrics and Experimental Design, awarded by the Department of Plant Biology from the Biology Faculty, University of Havana
    3. Plant Physiology, awarded by the Department of Plant Biology from the Biology Faculty, University of Havana
    4. Molecular Genetics, awarded by the Department of Biochemistry from the Biology Faculty, University of Havana
  • Final Grade Point Average (GPA): 5.64/5.00. Graduated with honors, Best Academic Results Award of the Biology Faculty, 2002

Journal Referee


  • Review Editor for:
    1. Molecular Bacterial PathogenesisFrontiers in Cellular and Infection Microbiology
  • Peer Reviewer for:
    1. Nucleic Acids Research
    2. BMC Genomics
    3. BMC Bioinformatics
    4. Microbiology

Skills


  • Operating Systems: Linux (RedHat 7.2, 8.0, 9.0; SuSE 8.0, 9.0; Debian); Windows (95, 98, NT, 2000, XP); Mac OS X (Tiger, Leopard). Advanced user and administrator skills
  • Programming Languages: PERL; Python; TCL; BASH; C; C++
  • Parallel Computing: Advanced user of Linux Beowulf Computer Clusters. Parallel programming skills (MPI)
  • Statistics: R
  • Databases: SQL; CGI. Advanced user and database administrator skills
  • Web design: HTML; CSS