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Reinaldo Molina Ruiz, Titular Professor (current position) of Organic- and Computational Chemistry at the Center for Bioactive Chemicals (CBQ), located at Central University ‘Las Villas’, Santa Clara, Cuba. Bachelor of Science in Chemistry (5 pts awarded with a plus 0.45 pts). PhD degree in Chemistry (2001) under the supervision of Prof. Dr. rer. Nat. habil. Klaus Peseke at Rostocker University, Germany. Thesis dissertation: 'Organic Synthesis to obtaining novel push pull functionalized monosaccharide derivatives' (Cum Laude evaluation). The work was developed under the financial support of DAAD (German Agency for Academical Exchange). From 2001, got an Auxiliary Researcher position at the Organic Chemistry Synthesis Group of CBQ, but also did a postdoc stay (2001-2005) granted by the DAAD in the University of Rostock. Later, visited this University in several times as Invited Researcher/Teacher. From 2006-2009, I was granted with a postdoc fellowship (SFRH/BPD/24512/2005) by Portugal Foundation for Sciences (FCT) in the topic "Theory and Application of Quantum Chemistry Methods" (DFT, Molecular Dynamic). Science Faculty, University of Porto. Since 2001, I began an intensive experience in Cheminformatics and Bioinformatics, including the development of computational tools for both fields. I have programming skills in Borland Delphi, Python, Django and in Web development tools (PHP, HTML, JavaScript). Manipulation of Big Data with tools such as KNIME, R, and PySpark. I have been the main programmer of computer software such as MARCH-INSIDE, TI2BioP, SVPhylA among others. These computational tools provide topological and topographical molecular descriptors for both small organic molecules and biomolecules (sequences) addressed to Quantitative Structure Activity Relationships (QSAR) studies in drug design/search, and to comparative analyses of DNA, RNA and protein sequences. I have contributed to the formation of several undergraduate and postgrad students (12 bachelor’s, 8 MSc’s and 2 PhD’s theses in several topics related to Bioinformatics and Cheminformatics fields. The results of my research work have been awarded by the Cuban National Academic of Sciences in several times. I belong to the National Council for Doctorate in Chemistry in Cuba and to the Scientific Research/Academic Council of the Master in Drugs Development at CBQ. I have accumulated > 45 publications, most of them in peer-reviewed (Q1) journals, have coauthored book chapters, two invention patents and several software. Currently, I am very interested to work under PySpark paradigm in order to analyze great volume of information in areas such as Genomics, Phylogenomics, Proteomics, and Environmental and Biomedical Biotechnology. The collaboration with international excellence centers/colleagues have also contributed to my professional and personal growth.
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Identification

Personal identification

Full name
Reinaldo Molina Ruiz

Citation names

  • Molina-Ruiz, Reinaldo

Author identifiers

Ciência ID
C11D-B8B3-3097
ORCID iD
0000-0001-5098-5432
Google Scholar ID
iIPZy7kAAAAJ
Scopus Author Id
6506258035

Knowledge fields

  • Exact Sciences - Chemical Sciences - Organic Chemistry
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Basic Medicine - Medicinal Chemistry
  • Exact Sciences - Computer and Information Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
Spanish; Castilian Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
German Intermediate (B1) Advanced (C1) Intermediate (B1) Intermediate (B1)
English Intermediate (B1) Advanced (C1) Intermediate (B1) Intermediate (B1)
Portuguese Beginner (A1) Advanced (C1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2006 - 2013
Concluded
 In silico Modeling and DFT study of reactions aza-Diels-Alder type (SFRH/BPD/24512/2005). (Pós-doutoramento)
Universidade do Porto, Portugal

Fundação para a Ciência e a Tecnologia, Portugal
2003 - 2004
Concluded
 Synthesis and Reactions of novel push pull compounds (Pós-doutoramento)
Universität Rostock, Germany
2001/07/03
Concluded
 2001 (Doktorgrad)
Universität Rostock, Germany
"Verscuhe zur Darstellung neuer push pull funktionalisierter Monosaccharidderivate (Experiments for obtaining novel push pull functionalized monosaccharide derivatives)" (THESIS/DISSERTATION)
 Cum Laude
1993/07/24
Concluded
 Diurno (Licence)
Universidad Central Marta Abreu de las Villas, Cuba
"Estudio y síntesis de derivados push pull a partir de la cianoacetamida" (THESIS/DISSERTATION)
 5.2 5.2 (escala de 2-5; bónus de 0.2 por mérito)
Affiliation

Science

Category
Host institution 		Employer
2012/11/02 - 2013/05/27 Researcher (Research) Universitat d'Alacant, Spain
1994/09/01 - 2012/04/01 Auxiliary Researcher (Research) Universidad Central Marta Abreu de las Villas, Cuba
2003 - 2004 Postdoc (Research) Universität Rostock, Germany
University of Rostock - Institut fuer Chemie, Germany

Others

Category
Host institution 		Employer
2014/04/10 - 2020/01/15 Docente, Profesor Titular Universidad Central Marta Abreu de las Villas, Cuba
2006/01/10 - 2009/12/31 FCT Bolseiro, SFRH/BPD/24512/2005 Universidade do Porto, Portugal
1996/10/01 - 2001/07/16 Bolseiro, Universität Rostock, Germany
Projects

Grant

Designation Funders
2010 - 2015 Red Biofarma. ALFA III
DCI-ALA/19.09.01/10/21526/245-297/ALFA III
Integration into Research Grant Fellow
European Commission
2010/01 - 2013/12 Creation of a Computational Chemistry Laboratory, with academic and scientific purposes, for the rational design of drugs in high social impact diseases
D/024153/09
Integration into Research Grant Fellow
Agencia Española de Cooperación Internacional para el Desarrollo
2006/01 - 2013/12 In silico Modeling and DFT study of reactions aza-Diels-Alder type
J632180
SFRH/BPD/24512/2005
Post-doc Fellow
Universidade do Porto Departamento de Química e Bioquímica, Portugal

Fundação para a Ciência e a Tecnologia, Portugal
Portuguese Fundação para a Ciência e a Tecnologia
Concluded
2003 - 2004 Synthesis and Reactions of novel push pull compounds
BAT-OSt-IIa
Post-doc Fellow
Universität Rostock, Germany
1997/04 - 2001/07 Experiments for obtaining novel push pull functionalized monosaccharide derivatives.
KZ: a/96/15752
 Deutscher Akademischer Austauschdienst
Outputs

Publications

Book chapter
  1. Aguero-Chapin, Guillermin; Molina-Ruiz, Reinaldo; Pérez-Machado, Gisselle; Vasconcelos, Vitor; Rodríguez-Negrin, Zenaida; Antunes, Agostinho. "TI2BioP — Topological Indices to BioPolymers. A Graphical– Numerical Approach for Bioinformatics". In Recent Advances in Biopolymers. InTech, 2016.
    10.5772/61887
Journal article
  1. Quero-Jiménez, Pedro César; Arias Felipe, Lester Alejandro; Prieto García, Julio Omar; Jorge Rodríguez, María Elisa; De la Torre López, Jorge Basilio; Montenegro, Osvaldo Norman; Molina Ruíz, Reinaldo; Tiscornia, Inés Silvia. "Local Cuban bentonite clay: composition, structure and textural characterization". Andean Geology 48 3 (2021): 546. http://dx.doi.org/10.5027/andgeov48n3-3362.
    10.5027/andgeov48n3-3362
  2. Casanova-Alvarez, Omar; Morales-Helguera, Aliuska; Cabrera-Pérez, Miguel Ángel; Molina-Ruiz, Reinaldo; Molina, Christophe. "A Novel Automated Framework for QSAR Modeling of Highly Imbalanced Leishmania High-Throughput Screening Data". Journal of Chemical Information and Modeling 61 7 (2021): 3213-3231. http://dx.doi.org/10.1021/acs.jcim.0c01439.
    10.1021/acs.jcim.0c01439
  3. Agüero-Chapin, Guillermin; Jiménez, Yuliana; Sánchez-Rodríguez, Aminael; Molina-Ruiz, Reinaldo; Vivanco, Oscar; Antunes, Agostinho. "DISTATIS: A Promising Framework to Integrate Distance Matrices in Molecular Phylogenetics.". Current Topics in Medicinal Chemistry 21 (2021): http://dx.doi.org/10.2174/1568026621666210113164605.
    10.2174/1568026621666210113164605
  4. Diana Rosa Lopes Oliveira; Anabela Borges; Reinaldo Molina-Ruiz; Zenaida Rodríguez Negrín; Simona Distinto; Borges Fernanda; Manuel Simões. "2-(2-Methyl-2-nitrovinyl)furan but Not Furvina Interfere with Staphylococcus aureus Agr Quorum-Sensing System and Potentiate the Action of Fusidic Acid against Biofilms". International Journal of Molecular Sciences (2021): https://www.mdpi.com/1422-0067/22/2/613.
    10.3390/ijms22020613
  5. PC, Quero-Jiménez; Maria Elisa Jorge Rodriguez; Molina-Ruiz, Reinaldo; Arias Felipe, Lester Alejandro; Julio Omar Prieto; Jorge de la Torre; Montenegro, Osvaldo Norman. "Development and validation of a GC-FID method for quantitative analysis of four major fatty acids extracted shark liver oil". J Pharm Pharmacogn Res 9 2 (2021): 208-221. https://jppres.com/jppres/pdf/vol9/jppres20.936_9.2.208.pdf.
    Published
  6. González Valle, Y; Galpert Cañizares, D.; Molina-Ruiz, Reinaldo; Agüero-Chapin, G.. "Ensemble K-means for semi-supervised learning in enzymatic activity classification of GH-70 enzymes". MDPI SciForum 6 1 (2020): 1-4. https://sciforum.net/paper/view/conference/6891.
    Open access
  7. González Valle, Y; Galpert Cañizares, D.; Molina-Ruiz, Reinaldo; Agüero-Chapin, G. "Integración de rasgos y aprendizaje semi-supervisado para la clasificación funcional de enzimas utilizando K-medias de Spark". Revista Cubana de Ciencias Informáticas 14 4 (2020): 134-161. https://rcci.uci.cu/?journal=rcci&page=article&op=view&path[]=2021&path[]=834.
    Open access • Published
  8. PC, Quero-Jiménez; Lester Alejandor Arias Felipe; Darlene Lugo Ramirez; Julio Omar Prieto; Maria Elisa Jorge Rodriguez; Jorge de la Torre; Osvaldo Norman Montene; et al. "Assessment of new conditions for oil extraction from shark liver pool". Open Access Jounal of Science 4 1 (2020): 17-22. http://dx.doi.org/10.1111/j.1745-4530.2011.00657.x.
    10.15406/oajs.2020.04.00145
  9. Quero-Jimenez, Pedro Cesar; Arias Felipe, Lester Alejandro; Ramirez, Darlene Lugo; Garcia, Julio Omar Prieto; Rodriguez, Maria Elisa Jorge; Torre, Jorge de la; Montenegro, Osvaldo Norman; et al. "Assessment of new conditions for oil extraction from shark liver pool". Open Access Journal of Science 4 1 (2020): http://dx.doi.org/10.15406/oajs.2020.04.00145.
    10.15406/oajs.2020.04.00145
  10. Agüero-Chapin, G.; Galpert, D.; Molina-Ruiz, R.; Ancede-Gallardo, E.; Pérez-Machado, G.; de la Riva, G.A.; Antunes, A.. "Graph theory-based sequence descriptors as remote homology predictors". Biomolecules 10 1 (2020): http://dx.doi.org/10.3390/biom10010026.
    10.3390/biom10010026
  11. Domínguez-Pérez, Dany; Durban, Jordi; Agüero-Chapin, Guillermin; López, Javier Torres; Molina-Ruiz, Reinaldo; Almeida, Daniela; Calvete, Juan J.; Vasconcelos, Vítor; Antunes, Agostinho. "The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba". Genomics 111 6 (2019): 1720-1727. http://dx.doi.org/10.1016/j.ygeno.2018.11.026.
    10.1016/j.ygeno.2018.11.026
  12. Huici Corrales, A; Morales-Helguera, A.; Ancede-Gallardo, E.; Molina-Ruiz, Reinaldo; Tejeira Bautista, M; Abreu Stincer, G; Martinez Albelo, E. "Predicción de afinidad de ligandos antagonistas por receptores de adenosina A2A usando árboles de desición". Biotecnologia Vegetal 19 2 (2019): 113-126. https://revista.ibp.co.cu/index.php/BV/article/view/623.
    Open access • Published
  13. Quintana-Zaez, Julio César; Molina-Ruiz, Reynaldo; Santiesteban-Toca, Cosme Ernesto. "Tree-based Secondary Structure Interactions Predictor Method for Protein Contact Maps". Computación y Sistemas 22 4 (2018): http://dx.doi.org/10.13053/cys-22-4-2827.
    10.13053/cys-22-4-2827
  14. Galpert, D.; Fernández, A.; Herrera, F.; Antunes, A.; Molina-Ruiz, R.; Agüero-Chapin, G.. "Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers". BMC Bioinformatics 19 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85046456370&partnerID=MN8TOARS.
    10.1186/s12859-018-2148-8
  15. Quintana-Zaez, J.C.; Molina-Ruiz, R.; Santiesteban-Toca, C.E.. "Tree-based secondary structure interactions predictor method for protein contact maps". Computacion y Sistemas 22 4 (2018): 1559-1571. http://www.scopus.com/inward/record.url?eid=2-s2.0-85069600866&partnerID=MN8TOARS.
    10.13053/CyS-22-4-2827
  16. Quintana-Zaez, J.C.; Molina-Ruiz, Reinaldo; Quintana-Bernabé, N.; Santiesteban-Toca, Cosme Ernesto. "Predictor de interacciones entre estructuras secundarias de proteínas". Revista Cubana de Ciencias Informáticas 6 3 (2017): https://rcci.uci.cu/?journal=rcci&page=article&op=view&path%5B%5D=1613.
  17. Ruiz, Reinaldo. "Exploring the Adenylation Domain Repertoire of Nonribosomal Peptide Synthetases Using an Ensemble of Sequence-Search Methods". PLoS ONE 8 7 (2013): e65926-e65926. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3712989{\&}tool=pmcentrez{\&}rendertype=abstract.
    10.1371/journal.pone.0065926
  18. Ruiz-Blanco, Yasser B.; Alves, Maria José Chão; Rodríguez-Borges, José E.; Molina, Reinaldo. "Study based on electronic descriptors of the diastereoselective aza-diels-alder cycloaddition of [(1r)-10-(n,n-diethylsulfamoyl)isobornyl] 2h-azirine-3-carboxylate to e,e-1,4-diacetoxy-1,3-butadiene". (2013): http://hdl.handle.net/1822/63863.
    10.4067/S0717-97072013000400074
  19. Ruiz-Blanco, Yasser B.; Alves, Maria José Chão; Rodríguez-Borges, José E.; Molina, Reinaldo. "Study based on electronic descriptors of the diastereoselective aza-diels-alder cycloaddition of [(1r)-10-(n,n-diethylsulfamoyl)isobornyl] 2h-azirine-3-carboxylate to e,e-1,4-diacetoxy-1,3-butadiene". (2013): http://hdl.handle.net/1822/63863.
    10.4067/S0717-97072013000400074
  20. Agüero-Chapin, G.; de la Riva, G.A.; Molina-Ruiz, R.; Sánchez-Rodríguez, A.; Pérez-Machado, G.; Vasconcelos, V.; Antunes, A.. "Non-linear models based on simple topological indices to identify RNase III protein members". Journal of Theoretical Biology 273 1 (2011): 167-178. http://www.scopus.com/inward/record.url?eid=2-s2.0-78651360965&partnerID=MN8TOARS.
    10.1016/j.jtbi.2010.12.019
  21. Agüero-Chapin, G.; Pérez-Machado, G.; Molina-Ruiz, R.; Pérez-Castillo, Y.; Morales-Helguera, A.; Vasconcelos, V.; Antunes, A.. "TI2BioP: Topological Indices to BioPolymers. Its practical use to unravel cryptic bacteriocin-like domains". Amino Acids 40 2 (2011): 431-442. http://www.scopus.com/inward/record.url?eid=2-s2.0-78751579274&partnerID=MN8TOARS.
    10.1007/s00726-010-0653-9
  22. Agüero-Chapin, G.; Sánchez-Rodríguez, A.; Hidalgo-Yanes, P.I.; Pérez-Castillo, Y.; Molina-Ruiz, R.; Marchal, K.; Vasconcelos, V.; Antunes, A.. "An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference". PLoS ONE 6 10 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80055061063&partnerID=MN8TOARS.
    10.1371/journal.pone.0026638
  23. Molina-Ruiz, R.; Saíz-Urra, L.; Rodríguez-Borges, J.E.; Pérez-Castillo, Y.; González, M.P.; García-Mera, X.; Cordeiro, M.N.D.S.. "A TOPological Sub-structural Molecular Design (TOPS-MODE)-QSAR approach for modeling the antiproliferative activity against murine leukemia tumor cell line (L1210)". Bioorganic and Medicinal Chemistry 17 2 (2009): 537-547. http://www.scopus.com/inward/record.url?eid=2-s2.0-58549101459&partnerID=MN8TOARS.
    10.1016/j.bmc.2008.11.084
  24. Cruz-Monteagudo, M.; Borges, F.; Cordeiro, M.N.D.S.; Cagide Fajin, J.L.; Morell, C.; Molina Ruiz, R.; Cañizares-Carmenate, Y.; Dominguez, E.R.. "Desirability-based methods of multiobjective optimization and ranking for global QSAR studies. Filtering safe and potent drug candidates from combinatorial libraries". Journal of Combinatorial Chemistry 10 6 (2008): 897-913. http://www.scopus.com/inward/record.url?eid=2-s2.0-57549088552&partnerID=MN8TOARS.
    10.1021/cc800115y
  25. Ruiz, Reinaldo. "Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments". Journal of computational chemistry (2007): https://doi.org/10.1002/jcc.20649.
    10.1002/jcc.20649
  26. Ruiz, Reinaldo. "2D-RNA-coupling numbers: a new computational chemistry approach to link secondary structure topology with biological function". Journal of computational chemistry (2007): https://doi.org/10.1002/jcc.20576.
    10.1002/jcc.20576
  27. Ruiz, Reinaldo. "A model for the recognition of protein kinases based on the entropy of 3D van der Waals interactions". Journal of proteome research (2007): https://doi.org/10.1021/pr060493s.
    10.1021/pr060493s
  28. Ruiz, Reinaldo. "Novel 2D maps and coupling numbers for protein sequences. The first QSAR study of polygalacturonases; isolation and prediction of a novel sequence from Psidium guajava L.". FEBS Letters 580 3 (2006): 723-730.
    10.1016/j.febslet.2005.12.072
  29. Ruiz, Reinaldo. "Markovian chemicals "in silico" design (MARCH-INSIDE), a promising approach for computer-aided molecular design III: 2.5D indices for the discovery of antibacterials". J Mol Model 11 2 (2005): 116-123. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}dopt=Citation{\&}list{\_}uids=15723208.
    10.1007/s00894-004-0228-3
  30. Ruiz, Reinaldo. "Recognition of stable protein mutants with 3D stochastic average electrostatic potentials". FEBS Letters 579 20 (2005): 4297-4301.
    10.1016/j.febslet.2005.06.065
  31. Ruiz, Reinaldo. "Stochastic-based descriptors studying biopolymers biological properties: Extended MARCH-INSIDE methodology describing antibacterial activity of lactoferricin derivatives". Biopolymers 77 5 (2005): 247-256.
    10.1002/bip.20202
  32. Ruiz, Reinaldo. "Predicting multiple drugs side effects with a general drug-target interaction thermodynamic Markov model". Bioorganic and Medicinal Chemistry 13 4 (2005): 1119-1129.
    10.1016/j.bmc.2004.11.030
  33. Ruiz, Reinaldo. "A topological substructural approach applied to the computational prediction of rodent carcinogenicity". Bioorganic and Medicinal Chemistry 13 7 (2005): 2477-2488.
    10.1016/j.bmc.2005.01.035
  34. Ruiz, Reinaldo. "2D RNA-QSAR: assigning ACC oxidase family membership with stochastic molecular descriptors; isolation and prediction of a sequence from Psidium guajava L". Bioorganic & medicinal chemistry letters (2005): https://doi.org/10.1016/j.bmcl.2005.03.017.
    10.1016/j.bmcl.2005.03.017
  35. Ruiz, Reinaldo. "Unified Markov thermodynamics based on stochastic forms to classify drugs considering molecular structure, partition system, and biological species: distribution of the antimicrobial G1 on rat tissues". Bioorganic & medicinal chemistry letters (2005): https://doi.org/10.1016/j.bmcl.2004.11.059.
    10.1016/j.bmcl.2004.11.059
  36. Ruiz, Reinaldo. "Markovian Backbone Negentropies: Molecular descriptors for protein research. I. Predicting protein stability in Arc repressor mutants". Proteins (2004): https://doi.org/10.1002/prot.20159.
    10.1002/prot.20159
  37. Ruiz, Reinaldo. "Synthesis of novel anellated pyranosides as precursors of C-nucleoside analogues using isopropyl 6-O-acetyl-3-deoxy-4-S-ethyl-4-thio-alpha-D-threo-hexopyranosid-2-ulose". JOURNAL OF CARBOHYDRATE CHEMISTRY 23 5 (2004): 337-351.
    10.1081/CAR-200035744
  38. Ruiz, Reinaldo. "A novel approach to predict a toxicological property of aromatic compounds in the Tetrahymena pyriformis". Bioorganic and Medicinal Chemistry 12 4 (2004): 735-744.
    10.1016/j.bmc.2003.11.028
  39. Ruiz, Reinaldo. "Markov entropy backbone electrostatic descriptors for predicting proteins biological activity". Bioorganic and Medicinal Chemistry Letters 14 18 (2004): 4691-4695.
    10.1016/j.bmcl.2004.06.100
  40. Ruiz, Reinaldo. "Stochastic-based descriptors studying peptides biological properties: modeling the bitter tasting threshold of dipeptides". Bioorganic & medicinal chemistry (2004): https://doi.org/10.1016/j.bmc.2004.07.017.
    10.1016/j.bmc.2004.07.017
  41. Ruiz, Reinaldo. "Synthesis of new pyrazole and pyrimidine steroidal derivatives". Molecules 8 5 (2003): 444-452.
    10.3390/80500444
  42. Ruiz, Reinaldo. "Vibrational Markovian Modelling of Footprints after the Interaction of Antibiotics with the Packaging Region of HIV Type 1". Bulletin of Mathematical Biology 65 6 (2003): 991-1002.
    10.1016/s0092-8240(03)00064-8
  43. Ruiz, Reinaldo. "Markovian negentropies in bioinformatics. 1. A picture of footprints after the interaction of the HIV-1 $¿$-RNA packaging region with drugs". Bioinformatics 19 16 (2003): 2079-2087.
    10.1093/bioinformatics/btg285
  44. Ruiz, Reinaldo. "TOPS-MODE Based QSARs Derived from Heterogeneous Series of Compounds. Applications to the Design of New Herbicides". Journal of Chemical Information and Computer Sciences 43 4 (2003): 1192-1199. http://dx.doi.org/10.1021/ci034039+.
    10.1021/ci034039+

Intellectual property

Patent
  1. Molina-Ruiz, Reinaldo. 2007. "Substituted acetophenonederivatives". Germany.
    Granted/Issued

Other

Other output
  1. Software: TI2BioP (Topological indices tobiopolymers) version 3.0 (latest). TI2BioP software allows mainly the calculation oftopological indices (spectral moments) derived from inferred and artificial 2Dstructures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Linux OS. https://sourceforge.net/projects/ti2biop/.. 2019. Molina-Ruiz, Reinaldo; Agüero-Chapin, G. https://sourceforge.net/projects/ti2biop/.
  2. Software: Sequence vectorization Phylogenetic Analysis (SVPhylA 2.0). SVPhylA is a python tool for the calculation of several alignment-free distances for phylogenetics analysis from the most popular alignment-free approaches. Such alignment-free distances are combined into a consensus/compromise matrix by using algorithms like DISTATIS based on Multidimensional Scaling (MSD), Lineal Principal Component Analysis (PCA) and PCA-Kernel (non-lineal).. 2019. Molina-Ruiz, Reinaldo; Agüero-Chapin, G. https://sourceforge.net/projects/svphyla/.
  3. Software: BigD_ProtDescriptors 2.0 (Big Data for Protein Descriptors Calculations). This sofware is written on the Big Data PySpark platform for the massive calculation of alignment-free protein descriptors. 2019. Molina-Ruiz, Reinaldo; Agüero-Chapin, G.
  4. Software: MARCH-INSIDE (Markov Chain Invariants for Network Selection & Design). MARCH-INSIDE methodology encodes several types of topological molecular descriptors inspired on the k-th power of the electron-transition stochastic matrix weighted with the Pauling’s electronegativities. This matrix summarized the molecular topology of both organic compounds and biomolecues as Markov chain’ states.. 2007. Molina-Ruiz, Reinaldo. Requested to the author.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019 BigDataProtDescriptors, pHCode: High Performance Computer and Spark paradigm in the efficient manipulation of biomolecules SIGESTIC’ 2019
BioCubaFarma (Varadero)
2016 Evaluación de esquemas de predicción de plegamiento de proteínas UCIENCIA 2016
Universidad de las Ciencias Informáticas (UCI) (La Habana, Cuba)
2015 Vitrofural®: Creative local innovation to stop the microbial contamination as guarantee an inclusive and sustainable development. GLOBELICS HAVANA 2015
(La Habana, Cuba)
2013 TI2BioP: Topological Indices to Biopolymers. Its practical use to unravel cryptic bacteriocin-like domains 2nd BioSyst. EU
Federation of European Biolo (Vienna, Austria)
2013 An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference ISCB Africa ASBCB Conference on Bioinformatics
African Society for Bioinformatics and Computational Biology (Casablanca, Morocco)
2013 A Computational Chemistry Approach for ITS2 Annotation and Phylogenetic Inference V Simposio Internacional de Química (SIQ 2013)
Sociedad Cubana de Química (Santa Clara, Cuba)
2011 Alignment-free Models supported on the TI2BioP methodology to Identify RNase III Protein Members SEADIM8
Universidad de La Habana (La Habana, Cuba)
2011 Simulation of diasteroselective aza-diels-alder cycloaddition of [(1R)-10-(N,N-diethylsulfamoyl)isobornyl] 2h-azirine-3-carboxylate to E,E-1,4-diacetoxy-1,3-butadiene SEADIM8
Universidad de La Habana (La Habana, Cuba)
2008 Topological sub-structural molecular design (TOPS-MODE) approach for modelling the antiproliferative activity against murine leukemia cells . MATH/CHEM/COMP
(Verbania, Italy)
2007 DFT Study of Enantioselective Synthesis of 3-Functionalized 2-Azabicylco [2.2.1] Heptane Derivatives via Asymmetric Aza-Diels-Alder Reaction XXXIII Congreso de Químicos Teóricos de Expresión Latina (QUITEL).
(La Habana)
2004 TOPS-MODE: a topological sub-structural approach applied to the computational prediction of rodent carcinogenicity Alternativas 2004
Universidad de Oriente - Santiago de Cuba (Santiago de Cuba, Cuba)
2000 Synthesis of anellated carbohydrates on the basis of push-pull derivates of ulose and (-)-quinic acid International Carbohydrate Symposium
(Hamburg)
1995/06 Ampliación de las Posibilidades Analíticas de Espectrofotómetro IR Dispersivo PU9512 XII Seminario Científico del Centro Nacional de Investigaciones Científicas
Cuban Higher Education Ministery (La Habana, Cuba)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2005 - Current Síntesis y Reacciones de la Nitrocetona Bromada (Msc).
Supervisor of Elio Soto Casaya
 Master in Chemistry (Master)
Universidad de la Habana Facultad de Quimica, Cuba
2005 - Current Modelación y Síntesis de compuestos tipo cristales líquidos (MSc).
Co-supervisor of Dinardo González
 Chemistry (Master)
Universidad de la Habana Facultad de Quimica, Cuba
2016 - 2019 Determinación de la susceptibilidad de Mycobacterium tuberculosis frente a drogas anti-tuberculosas en Villa Clara (MSc).
Co-supervisor
 Drug Development (Master)
Universidad Central de Las Villas - Centro de Bioactivos Químicos, Cuba
2016 - 2019 Desarrollo de multiclasificadores para la predicción de mutagenicidad de ingredientes farmacéuticos activos (MSc).
Co-supervisor
 Drug Develpment (Master)
Universidad Central de Las Villas - Centro de Bioactivos Químicos, Cuba
2015 - 2019 Predictor de Mapas de Contacto de Estructuras de Proteínas basado en las Estructura Secundaria y Arboles de Decisión (PhD).
Co-supervisor
 Ciencias Técnicas (PhD)
Universidad de Las Ciencias Informaticas, Cuba
2015 - 2018 Extracción y Caracterización de Aceite de Higado de Tiburón (MSc).
Co-supervisor of Pedro César Quero-Jiménez
 Drug Development (Master)
Universidad Central de Las Villas - Centro de Bioactivos Químicos, Cuba
2009 - 2013 A Graphical and Numerical Approach for Functional Annotation and Phylogenetic (PhD).
Co-supervisor
 PhD in Biology (PhD)
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2010 - 2011 Modelación computacional de nitrovinilfuranos (Lic.)
Supervisor
 Chemistry (Degree)
Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba
2009 - 2010 Modelación in silico de la reacción tipo aza-diels-alder entre (1s, 2r, 4r)-1 ((n. ndietilsulfamoil) metil)-7, 7 dimetilbiciclo [2.2. 1] heptan-2-il-2h-azirina-3-carboxilato y (1e, 3e)-buta-1, 3-dien-1, 4-diil diacetato (Lic.)
Supervisor of Yasser Ruiz Blanco
 Chemistry (Degree)
Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba
2006 - 2009 Application of the MARCH-INSIDE methodolgy to search more efficient cellulase complexes (MSc).
Co-supervisor
 General Biochemistry (Master)
2001 - 2004 La Metodología MARCH-INSIDE aplicada a la Modelación de Propiedades de Biomoléculas. Predicción de Propiedades de Aminoácidos, Péptidos y Proteínas (MSc).
Co-supervisor
 Master in General Biochemisty (Master)
Instituto Superior de Ciencias Médicas de Villa Clara Dr Serafín Ruíz Facultad de Estomatologia de Villa Clara, Cuba

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2020 - Current Ensemble K-means for semi-supervised learning in enzymatic activity classification of GH-70 enzymes
Other
 MDPI SciForum
1999 - Current Synthesis and Characterization of push-pull Compounds starting from L-Rhamnose (Poster).
Conference
 Conferencia Internacional de Química
Universidad de Oriente, Cuba
2019/06/23 - 2019/06/30 Desarrollo de multiclasificadores para la predicción de mutagenicidad de ingredientes farmacéuticos activos
Symposium
 VII Simposio Internacional de Ciencias Farmacéuticas
Universidad Central Marta Abreu de las Villas, Cuba

Sociedad Cubana de Química, Cuba
2019 - 2019 Development of a New Formulation for Onychomycosis Treatment Using Furvina® as an Active Pharmaceutical Ingredient.
Conference
 Proceedings of the 2nd International Conference on BioGeoSciences, https://doi.org/10.1007/978-3-030-04233-2_17
Springer International Publishing AG, Switzerland
2018 - 2018 Modelación molecular de la actividad antileishmanial de compuestos químicos
Congress
 33º Congreso Latinoamericano de Química (33-CLAQ) & X Congreso de Ciencias Químicas, Tecnología e Innovación (QUIMICUBA'2018)
Sociedad Cubana de Química, Cuba
2016/09/18 - 2016/09/23 Exploring the toxin expression in theHarderian gland’s transcriptome ofthree Cuban snakes (Colubroidea) (Poster)
Congress
 XII Congress of the Pan American Section of the International Society onToxinology
2016 - 2016 Surveying Alignment-free Features for Ortholog Detection in Related Yeast Proteomes by using Supervised BigData Classifiers (doi: 10.3390/mol2net-04-05468; Conference Paper).
Conference
 Proceedings of MOL2NET 2018, International Conference onMultidisciplinary Sciences, 4th edition
Multidisciplinary Digital Publishing Institute AG, Switzerland

Ikerbasque, Spain
2014/12/03 - 2014/12/05 Paquete de herramientas bioinformáticas para la modelación y diseño de fármacos (Poster)
Conference
 21th Chemistry Conference
Universidad de Oriente, Cuba

Sociedad Cubana de Química, Cuba
2014/12/03 - 2014/12/05 Exploring the Adenylation Domain Repertoire of non-Ribosomal Peptide Synthetases using four-color maps
Conference
 21th Chemistry Conference
Universidad de Oriente, Cuba

Sociedad Cubana de Química, Cuba
2013 - 2013 An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference
Conference
 International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO)
IEEE, United States

Universidad de Granada, Spain
2012/10/09 - 2012/10/12 Exploring a Drug-like data for provisional classification of solubility on BDS and BDDCS (Poster).
Congress
 8th International Congress on Chemistry, Chemical Engineering and Biochemistry
Sociedad Cubana de Química, Cuba
2012/10/09 - 2012/10/12 Estudio Fotodegradativo preliminary del UC-244 (Poster).
Congress
 8th International Congress on Chemistry, Chemical Engineering and Biochemistry
Sociedad Cubana de Química, Cuba
2010/06/12 - 2010/06/15 TI2BioP methodology as Alignment-free Models to Identify Rnase III Protein Members
Meeting
 2nd Iberic Meeting on Medicinal Chemistry
Universidade do Porto, Portugal

Fundação para a Ciência e a Tecnologia, Portugal
2010/06/01 - 2010/06/04 A QSFR-like model to detect proteinaceous bacteriocins. Its practical application to the discovery of new bacteriocin-like domains (Poster).
Symposium
 IV International Symposium on Chemistry
Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba
2008 - 2008 Theoretical Approach to the Formation of Prebiotic Molecules in the Solar System and Beyond (Poster).
Symposium
 IAU Symposium 251: Organic Matters in Space
International Astronomical Union, France
2006 - 2006 RDF descriptors based QSTR model. A novel alternative towards prediction of drugs idiosyncratic hepatotoxicity (Poster)
Meeting
 REQUIMTE - Rede de Química e Tecnologia
REQUIMTE LAQV Porto, Portugal
2003/11/01 - 2003/11/30 MARCH-INSIDE Methodology Describing Physico-Chemical Properties of Amino Acids (Poster).
Conference
 8th International Electronic Conference on Synthetic Organic Chemistry ECSOC-8
Multidisciplinary Digital Publishing Institute AG, Switzerland
2003 - 2003 Comportamiento reactivo de derivados de la Rhamnosa (Poster)
Conference
 II Conferencia Internacional de Química
Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba
2001 - 2001 Síntesis de nuevos monosacáridos Condensados. Síntesis y funcionalización por vía push-pull de monosacáridos CH-ácidos (Poster)
Conference
 Convención Internacional 'Universidad de Granma 2001'
Universidad de Granma, Cuba
1999 - 1999 Functionalization of CH-acidic monosaccharides (Poster).
Workshop
 Workshop on Iminium salts
1997 - 1997 Annual General Meeting of the German Chemical Society and Centenary of the Austrian Chemical Society (Poster).
Meeting
Johannes Kepler Universität Linz, Austria

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2018/07/06 Jury of Doctoral Dissertation: Multicomponent Reactions in the Synthesis of Antibacterial Protease Inhibitors and Glycoconjugate Vaccine
(Thesis) Arguer
 M.Sc.Yanira Méndez Gómez (PhD)
Universidad Agraria de la Habana, Cuba
2018/07/06 Jury o Dissertation: Síntesis y Caracterización de Mallas Electro-hiladas basadas en Policianoacrilato de n-butilo
Thesis Member
 M.Sc. Yaquelin Ramos Carriles (PhD)
2013 Computer Science Board. Bacterial FabH inhitors: From bits to the wet-lab
(Thesis) Arguer
 Yunierkis Pérez Castillo (PhD)
Universidad Central Marta Abreu de las Villas Facultad de Matemática Física y Computación, Cuba
2013 Pharmaceutical Science Program. Understanding DNA GyraseB ATPase inhibition in the light of structure and ligand-based modelling techniques
(Thesis) Arguer
 Liane Saíz Urra (PhD)
Katholieke Universiteit Leuven Faculteit Farmaceutische Wetenschappen, Belgium
2007 Pharmaceutical Science PhD Program. Nuevo enfoque para el diseño molecular asistido por ordenador
(Thesis) Arguer
 Juan Alberto Castillo Garit (PhD)
Universidad de la Habana, Cuba
2006 Pharmaceutical Science, PhD program. Evaluación Fitoquímica y Farmacológica del Extracto Acuoso de las Hojas de la Especie Boldoa purpurascens, Cav.
(Thesis) Main arguer
 Dulce Ma. Mosquera (PhD)
Universidad de la Habana, Cuba

Association member

Society Organization name Role
2008 - Current Sociedad Cubana de Química, Havana, Cuba Memeber

Committee member

Activity description
Role 		Institution / Organization
2015 - Current National Council for PhD program in Chemistry, Havana, CU
Member
 Universidad de la Habana Facultad de Quimica, Cuba
2011/09/03 - Current Magister on Drugs development : Maestría “Desarrollo de Medicamentos”
Member
 Universidad Central de Las Villas - Centro de Bioactivos Químicos, Cuba
2001/09/02 - Current Council of Scientific Research of Center for Bioactive Chemicals (CBQ), UCLV, Santa Clara, Cuba
Member
 Universidad Central Marta Abreu de las Villas, Cuba

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2003 - Current Computational Chemistry. Molecular Dynamics and Quantum Chemistry for Molecular Modeling (Bachelor) Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba
2015 - 2020 Advance Topics in Bioinformatics. Master Program 'Vegetal Biothecnology' (Master) Universidad Central de Las Villas - Instituto de Biotecnología de las Plantas, Cuba
2011 - 2020 Advanced Methods in Synthesis of Drugs. Master Program 'Drug Design and Development' (Master) Universidad Central de Las Villas - Centro de Bioactivos Químicos, Cuba
2016 - 2018 Pharmaceutical Organic Chemistry (Bachelor) Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba
2012 - 2012 Chemical Quantum Topics for Physics (Bachelor) Universidad Central Marta Abreu de las Villas Facultad de Matemática Física y Computación, Cuba
2010 - 2010 Introduction to Linux. Postgraduate course (Postgraduate Certificate) Universidad Central de Las Villas - Centro de Bioactivos Químicos, Cuba
2003 - 2008 Organic Chemistry (Bachelor) Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba
2002 - 2003 General Chemistry (Bachelor) Universität Rostock, Germany
2001 - 2002 Organic Chemistry (Bachelor) Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba
1994 - 1996 Bioorganic Chemistry (Licence) Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba

Other jury / evaluation

Activity description Institution / Organization
2017 - 2020 External Evaluator of Internal Projects in Ecuador: Universidad de Las Américas (UDLA) Universidad de Las Américas, Ecuador
2010 - 2020 Referee of internatinal journals: Molecular Diversity, Molecules, BMC Bioinformatics y Afinidad (Spain) National Journals: Revista Cubana de Química & Revista Centro Azúcar Springer International Publishing AG, Switzerland

Multidisciplinary Digital Publishing Institute AG, Switzerland

Springer Nature, Luxembourg

Universidad Central de Las Villas - Facultad de Química y Farmacia, Cuba

Universidad de la Habana, Cuba
Distinctions

Award

2018 Annual Regional Award (Coauthor). “Combinación de medidas de similitud para la detección escalable de genes ortólogos en especies de levaduras”
Ministerio de Ciencia Tecnologia y Medio Ambiente, Cuba
2018 Medal of Cuban Education
2018 Annual Regional Award (Coauthor) Estudio químico-farmacéutico de una tintura con furvina® para el tratamiento de la onicomicosis
2015 Annual Award of the Cuban Academy of Sciences (CoAuthor). "Métodos grafo- numéricos de relevancia para la bioinformática. Aplicaciones en la biotecnología vegetal y en el descubrimiento de fármácos"
Ministerio de Ciencia Tecnologia y Medio Ambiente, Cuba
2014 Regional Award of Villa Clara Science Academy
2013 Regional Award of Villa Clara Science Academy
2007 National Prize of the Cuban Science Academy

Other distinction

2009 Top-50 most cited articles 2005-2008 Award
2008 Top-50 most cited articles 2005-2008 Award
2007 Annual Award of the Cuban Academy of Sciences
2007 Most Cited paper 2003-2006 Award
2005 Anual Award of the Cuban Academy of Sciences (Collaborator). "From molecular structure biological activity: Applications and potentialities of novel computational design methods in QSAR, QSPR, QSPkR, QSTR studies, proteomic and bioinformatics"
Academia de Ciencias de Cuba, Cuba
2002 A prize of the Cuban Science Academy