Directory

Juan B. Gutiérrez

Department Chair, Professor

juan.gutierrez3@utsa.edu
(210) 458-5735

FLN 4.01.10

Research Interests

Mathematical Biology
Multiscale modeling; Bioinformatics; Machine Learning

Curriculum Vitae

CV, updated on November 13, 2022

A Word from the Chair
Education
  • 9/2010 – 7/2012. Postdoctoral Fellow, Mathematical Biosciences Institute, Ohio State University, Columbus, OH.
  • 9/2009 – 8/2010. Postdoctoral Associate, Institute for Theoretical and Mathematical Ecology, University of Miami, Coral Gables, FL.
  • 12/2009. Ph.D. in Mathematics. Dissertation: Mathematical Analysis of the Use of Trojan Y Chromosomes as Means of Eradication of Invasive Species. Advisor: Dr. Monica K. Hurdal. Department of Mathematics, Florida State University, Tallahassee, Florida.
  • 05/2005. M.Sc. in Biomedical Mathematics. Department of Mathematics, Florida State University, Tallahassee, Florida.
  • 05/1996. B.Eng, Civil Engineering, Meritorious Thesis. National Prize of Excellence in B.Eng. Thesis, National University of Colombia.
COVID-19
Research Areas
  • "MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques." Jeremy DeBarry, Mustafa Nural, Suman Pakala, Vishal Nayak, Susanne Warrenfeltz, Jay Humphrey, Stacey Lapp, Monica Cabrera-Mora, Cristiana Ferreira Alves de Brito, Jianlin Jiang, Celia Saney, Allison Hankus, Hannah Stealey, Megan DeBarry, Nicolas Lackman, Noah Legall, Kevin Lee, Yan Tang, Anuj Gupta, Elizabeth Trippe, Robert Bridger, Daniel Weatherly, Mariko Peterson, Xuntian Jiang, ViLinh Tran, Karan Uppal, Luis Fonseca, Chester Joyner, Ebru Karpuzoglu, Regina Joice Cordy, Esmeralda Meyer, Lance Wells, Daniel Ory, Frances Lee, Rabindra Tirouvanziam, Juan B. Gutiérrez, Chris Ibegbu, Tracey Lamb, Jan Pohl, Sarah Pruett, Dean Jones, Mark Styczynski, Eberhard Voit, Alberto Moreno, Mary Galinski, and Jessica Kissinger. Nature Scientific Data. Paper #SDATA-22-00561A. Accepted for publication on 10/7/2022.
  • "Practical Recommendations for Supporting a Systems Biology Cyberinfrastructure." DeBarry, J.D., Kissinger, J.C., Nural, M.V., Pakala, S.B., Humphrey, J.C., Meyer, E.V.S., Cordy, R.J., Cabrera-Mora, M., Trippe, E.D., Aguilar, J.B., Karpuzoglu, E., Yan, Y.H., Brady, J.A., Hankus, A.N., Lackman, N., Gingle, A.R., Nayak, V., Moreno, A., Joyner, C.J., Gutiérrez, J.B., Galinski, M.R. and Consortium, . the M., 2020. Data Science Journal, 19(1), p.24.  DOI: 10.5334/dsj-2020-024
  • "The SWAG Algorithm; a Mathematical Approach that Outperforms Traditional Deep Learning." Saeid Safaei, Vahid Safaei, Solmazi Safaei, Zerotti Woods, Hamid R Arabnia, Juan B Gutiérrez. Theory and Implementation. arXiv:1811.11813 [stat.ML]. DOI: 10.48550/arXiv.1811.11813
  • "A brief survey of text mining: Classification, clustering and extraction techniques." Allahyari, Mehdi, Seyedamin Pouriyeh, Mehdi Assefi, Saied Safaei, Elizabeth D. Trippe, Juan B. Gutiérrez, and Krys Kochut. arXiv:1707.02919 (2017). DOI: 10.48550/arXiv.1707.02919
  •  "Text summarization techniques: a brief survey." Allahyari, Mehdi, Seyedamin Pouriyeh, Mehdi Assefi, Saeid Safaei, Elizabeth D. Trippe, Juan B. Gutiérrez, and Krys Kochut.arXiv:1707.02268 (2017). DOI: 10.48550/arXiv.1707.02268
  • "A comprehensive investigation and comparison of Machine Learning Techniques in the domain of heart disease." Pouriyeh, Seyedamin, Sara Vahid, Giovanna Sannino, Giuseppe De Pietro, Hamid Arabnia, and Juan B. Gutiérrez. In 2017 IEEE Symposium on Computers and Communications (ISCC), pp. 204-207. IEEE, 2017. DOI: 10.1109/ISCC.2017.8024530
  • "A framework for global collaborative data management for malaria research." Gutiérrez, J.B., Harb, O.S., Zheng, J., Tisch, D.J., Charlebois, E.D., Stoeckert Jr, C.J. and Sullivan, S.A., 2015.  The American Journal of Tropical Medicine and Hygiene, 93(3_Suppl), pp.124-132. DOI:  10.4269/ajtmh.15-0003
  • "Geometric invariants for classification of cortical sulci."  M. K. Hurdal, J. B. Gutiérrez, C. Laing, A. D. Kline and D. A. Smith, 2008 15th IEEE International Conference on Image Processing, San Diego, CA, 2008, pp. 1156-1159. DOI: 10.1109/ICIP.2008.4711965
  • "Shape analysis for automated sulcal classification and parcellation of MRI data." MK Hurdal, JB Gutiérrez, C Laing, DA Smith. Journal of Combinatorial Optimization 15 (3), 257-275. DOI: 10.1007/s10878-007-9096-y
Graduate Students
  • "Plasmodium knowlesi cytoadhesion involves SICA variant proteins." Peterson MS, Joyner CJ, Lapp SA, Brady JA, Wood JS, Cabrera-Mora M, Saney CL, Fonseca LL, Cheng WT, Jiang J, Soderberg SR, Nural MV, Hankus A, Machiah D, Karpuzoglu E, DeBarry JD, MaHPIC-Consortium, Tirouvanziam R, Kissinger JC, Moreno A, Gumber S, Voit EO, Gutierrez JB, Cordy RJ and Galinski MR (2022) Front. Cell. Infect. Microbiol. 12:888496. DOI: 10.3389/fcimb.2022.888496
  • "Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi." Mariko S Peterson, Chester J Joyner, Jessica A Brady, Jennifer S Wood, Monica Cabrera-Mora, Celia L Saney, Luis L Fonseca, Wayne T Cheng, Jianlin Jiang, Stacey A Lapp, Stephanie R Soderberg, Mustafa V Nural, Jay C Humphrey, Allison Hankus, Deepa Machiah, Ebru Karpuzoglu, Jeremy D DeBarry, Rabindra Tirouvanziam, Jessica C Kissinger, Alberto Moreno, Sanjeev Gumber, Eberhard O Voit, Juan B Gutiérrez, Regina Joice Cordy, Mary R Galinski. Malaria Journal 20, 486 (2021). DOI: 10.1186/s12936-021-03925-6
  • "In silico identification of potential inhibitors against human 2'-5'-oligoadenylate synthetase (OAS) proteins." Gonzalez, K.J., Moncada-Giraldo, D.M. and Gutiérrez, J.B., 2020. Computational Biology and Chemistry, 85, p.107211. DOI: 10.1016/j.compbiolchem.2020.107211
  • "A Model Describing COVID-19 Community Transmission Taking into Account Asymptomatic Carriers and Risk Mitigation." Jacob B. Aguilar, Jeremy Samuel Faust, Lauren M. Westafer, Juan B. Gutiérrez. medRxiv (2020). DOI: 10.1101/2020.03.18.20037994
  • "An Epidemiological Model of Malaria Accounting for Asymptomatic Carriers." Aguilar J.B., Gutiérrez J.B. Bulletin of Mathematical Biology. 82, 42 (2020). DOI: 10.1007/s11538-020-00717-y
  • "The FRiND Model: A Mathematical Model for Representing Macrophage Plasticity in Muscular Dystrophy Pathogenesis." Houston MT, Juan B Gutiérrez. Bulletin of Mathematical Biology. 81, pages 3976–3997 (2019). DOI: 10.1007/s11538-019-00635-8.
  • "Multi-scale dynamics of infectious diseases." Garabed Rebecca B., Jolles Anna, Garira Winston, Lanzas Cristina, Gutiérrez Juan and Rempala Grzegorz. Interface Focus. 10:20190118 (2019). doi: 10.1098/rsfs.2019.0118
  • "Malaria epidemiology in low-endemicity areas of the northern coast of Ecuador: high prevalence of asymptomatic infections." Sáenz, Fabián E., Andrea Arévalo-Cortés, Gabriela Valenzuela, Andrés F. Vallejo, Angélica Castellanos, Andrea C. Poveda-Loayza, Juan B. Gutiérrez et al.  Malaria Journal 16, no. 1 (2017): 300. doi: 10.1186%2Fs12936-017-1947-0
  • "From within host dynamics to the epidemiology of infectious disease: scientific overview and challenges." Gutiérrez, Juan B., Mary R. Galinski, Stephen Cantrell, and Eberhard O. Voit.  Mathematical Biosciences. (2015): 143-155. doi: doi.org/10.1016/j.mbs.2015.10.002
  • "Clinical profile of Plasmodium falciparum and Plasmodium vivax infections in low and unstable malaria transmission settings of Colombia." Arévalo-Herrera, M., Lopez-Perez, M., Medina, L., Moreno, A., Gutiérrez, J. B., & Herrera, S. (2015).  Malaria Journal, 14(1), 154. doi: 10.1186/s12936-015-0678-3
  • "Malaria-related anemia in patients from unstable transmission areas in Colombia." Lopez-Perez, M., Alvarez, A., Gutiérrez, J.B., Moreno, A., Herrera, S. and Arévalo-Herrera, M.  The American Journal of Tropical Medicine and Hygiene, 92(2), pp.294-301 (2015). DOI:  10.4269/ajtmh.14-0345
  • "Correlates of severity of disease in Macaca mulatta infected with Plasmodium cynomolgi." Yi H. Yan, Diego M. Moncada, Elizabeth D. Trippe, Juan B Gutiérrez. arXiv:1706.08836 [q-bio.TO]. DOI: 10.48550/arXiv.1706.08836
  • "The lunar cycle’s influence on sex determination at conception in humans." Derek Onken, Eric Marty, Roberto Palomares, Rui Xie, Leyao Zhang, Jonathan Arnold, Juan B GutiérrezarXiv:1706.08151 [q-bio.OT]. DOI: 10.48550/arXiv.1706.08151
  • "Quantification of Healthy Red Blood Cell Removal and Preferential Invasion of Reticulocytes in Macaca mulatta during Plasmodium cynomolgi Infection." Yi H. Yan, Jacob B. Aguilar, Elizabeth D. Trippe, Juan B Gutiérrez. arXiv:1706.08139 [q-bio.CB]. DOI:  10.48550/arXiv.1706.08139
  • "A Method for Massively Parallel Analysis of Time Series." Yi H. Yan, Elizabeth D. Trippe, Juan B Gutiérrez. arXiv:1612.08759 [q-bio.QM]. DOI: 10.48550/arXiv.1612.08759
  • "Mathematical model of susceptibility, resistance, and resilience in the within-host dynamics between a Plasmodium parasite and the immune system." Yan, Y., Adam, B., Galinski, M., Kissinger, J.C., Moreno, A. and Gutiérrez, J.B.  Mathematical Biosciences, 270, pp.213-223. (2015) DOI: 10.1016/j.mbs.2015.10.003
  • "Bivariate Spline Solution of Time Dependent Nonlinear PDE for a Population Density over Irregular Domains." Juan B. Gutiérrez, Ming-Jun Lai, George Slavov. Mathematical Biosciences. Volume 270, Part B, December 2015, Pages 263–277. DOI: 10.1016/j.mbs.2015.08.013
  • "Knowledge, attitudes and practices of malaria in Colombia." Forero, D. A., Chaparro, P. E., Vallejo, A. F., Benavides, Y., Gutiérrez, J. B., Arévalo-Herrera, M., & Herrera, S. (2014).  Malaria Journal, 13(1), 165. DOI: 10.1186/1475-2875-13-165
  • "Global existence and asymptotic behavior of a model for biological control of invasive species via supermale introduction." JB Gutiérrez, S Kouachi, RD Parshad. Communications in Mathematical Sciences. 11(4):971-992  (2013). DOI: 10.4310/CMS.2013.v11.n4.a4
  • "Combining the Trojan Y Chromosome and Daughterless Carp Eradication Strategies." JL Teem, JB Gutiérrez. Biological Invasions, May 2013. DOI: 10.1007/s10530-013-0476-1.
  • "A Comparison of the Trojan Y Chromosome and Daughterless Carp Eradication Strategies." JL Teem, JB Gutiérrez, RD Parshad. Biological Invasions, May 2013. DOI: 10.1007/s10530-013-0475-2
  • "Analysis of the Trojan Y Chromosome Model for Eradication of Invasive Species in a Riverine System." JB Gutiérrez, MK Hurdal, RD Parshad, JL Teem. Journal of Mathematical Biology. Volume 64, Numbers 1-2 (2012), 319-340. DOI: 10.1007/s00285-011-0413-9.
  • "Prospects for malaria elimination in non-Amazonian regions of Latin America." Herrera, S., Quiñones, M.L., Quintero, J.P., Corredor, V., Fuller, D.O., Mateus, J.C., Calzada, J.E., Gutiérrez, J.B., Llanos, A., Soto, E. and Menendez, C., Acta Tropica, 121(3), pp.315-323 (2012). DOI: 10.1016/j.actatropica.2011.06.018
  • "A theoretical strategy for eradication of Asian carps using a Trojan Y chromosome to shift the sex ratio of the population." John Teem and Juan B Gutiérrez. In Duane C. Chapman, editor, Bigheaded Carps in North America. Published by the American Fisheries Society, AFS Symposium 74, Bethesda, MD, 2011. ISBN: 978-1-934874-23-3 (2011). DOI: 10.47886/9781934874233
  • "On the Well Posedness of the Trojan Y Chromosome Model." RD Parshad, JB Gutiérrez. Boundary Value Problems, vol. 2010, Article ID 405816, Nov. 2010. DOI: 10.1155/2010/405816
  • "On the Global Attractor of the Trojan Y Chromosome Model." RD Parshad, JB Gutiérrez. Communications in Pure and Applied Analysis, 10(10):339-359, January 2010. DOI: 10.3934/cpaa.2011.10.339 (broken DOI). Journal link.
  • "A model describing the effect of sex-reversed YY fish in an established wild population: the use of a Trojan Y chromosome to cause extinction of an introduced exotic species." Gutiérrez, Juan B., and John L. Teem.  Journal of Theoretical Biology 241, no. 2 (2006): 333-341. DOI: 10.1016/j.jtbi.2005.11.032
Graduate Students:
  • "Towards Interest-based Adaptive Learning and Community Knowledge Sharing." Aguar, K., Arabnia, H. R., Juan B Gutiérrez, Potter, W. D., and Taha, T. R. International Conference Frontiers in Education: CS and CE. FECS’17. CSREA Press, 2017, pp 58-61. NSF Reporting Site.
  • "Making CS inclusive: An overview of efforts to expand and diversify CS education." Aguar, Karen, Hamid R. Arabnia, Juan B Gutiérrez, Walter D. Potter, and Thiab R. Taha. International Conference on Computational Science and Computational Intelligence (CSCI), 2016 pp. 321-326. IEEE, 2016. DOI: 10.1109/CSCI.2016.0067
  • "Reviving Computer Science Education through Adaptive, Interest-Based Learning."  K. Aguar, S. Safaei, H. R. Arabnia, J. B. Gutiérrez, W. D. Potter and T. R. Taha, 2017 International Conference on Computational Science and Computational Intelligence (CSCI), 2017, pp. 1161-1166, DOI: 10.1109/CSCI.2017.202
  • "Considerations on Interdisciplinary Instruction and Design Influenced by Adaptive Learning. A Case Study Involving Biology, Computer Science, Mathematics, and Statistics." Karen Aguar, Charles C. Sanchez, Diego Boada Beltran, Saeid Safaei, Mehdi Asefi, Jonathan Arnold, Pedro Portes, Hamid R. Arabnia, Juan B. Gutiérrez. arXiv:1703.06010 [physics.ed-ph]. DOI: 10.48550/arXiv.1703.06010
Graduate Student:

Before mathematics, I had a career as a fiction writer. The following list of literary publications, peer-reviewed articles about electronic literature, and articles/theses/dissertations about my literary work is also available at https://mathresearch.utsa.edu/wp/?p=1360

Regarding this area, I am particularly interested in: (i) artificial intelligence applied to storytelling, (ii) digital narratology (or digital neo-structuralism), (iii) narrative bots, and (iv) natural language processing. I believe that storytelling is an essential state of human minds, and that it can be mediated by digital technologies.

Juan B. Gutiérrez’s work as an author

2006
Novel. El primer Vuelo de los Hermanos Wright (The first Flight of the Wright Brothers). Written with the support of Award #COLCULTURA-SECAB 014/1996 by the Instituto Colombiano de Cultura - Colcultura, now the Ministry of Culture of Colombia. 1996-1998
2005
Novel. Condiciones Extremas (Extreme Conditions). Written with the support of Award #IDCT-514/1997 by the Instituto Distrital de Cultura y Turismo de Bogota  (Institute of Culture and Tourism of the City of Bogota.)   1997-1998.  
2000
Story. Las Fricciones de San Sebastián. (The Frictions of St. Sebastian). Revista Avianca. Magazine of Avianca Airlines. Number 254. Bogota. Colombia. Mar, 2000. Pag. 66-69. Bogota, Colombia.
2000
Story. La Sagrada Geometría (The Sacred Geometry.) In Antología Colombiana de Ciencia Ficción (Companion of Colombian Science Fiction). Pag. 93-96. Rene Rebetez (ed.) Espasa, 2000. Bogota, Colombia. ISBN: 958-614-804-1
1998
Story. Las Exquisitas Disquisiciones de Fray Leonardo Baz. (The exquisite reasoning of Father Leonardo Baz.) Gaceta. Magazine of the Ministry of Culture of Colombia. Pag. 150-145. Num. 44-45. Bogota, Colombia. 1999. ISSN: 0121-7194
1996
Short Story Book. Siete Curiosas Formas de Morir. (Seven Curious Ways to Die). Unidad de Publicaciones. Facultad de Ingeniería. Universidad Nacional de Colombia. 1996. (Press of the School of Engineeering of the National University of Colombia.)
1996
Story. González, Archivos y Documentos. (Gonzalez, Files and Documents.) In Sunday Readings of El Tiempo (Sunday Readings from The Times), newspaper. ISSN: 0121-9790. Also in Carta Universitaria, Magazine of the National University, December 1996. Bogota, Colombia. ISSN: 0122-2929
1995
Story. La Sagrada Geometría (The Sacred Geometry.) In Crea, Una Expedición por la Cultura Colombiana (CREA: An Expedition through the Colombian Culture). Ministry of Culture of Colombia (formerly Colcultura). Page 17-22.
1995
Story . Atyseikuiwandiú, o los Avatares de la Cruel Sangre (Atyseikuiwandiú, or the Fortune of the Cruel Blood). In Lecturas Dominicales de El Tiempo (Sunday Readings from The Times), newspaper. 01/15/1995. Bogota, Colombia. Also in Ko'eyú, Journal of Cultural and Politic Analysis. Number 64, April-June 1994. Caracas, Venezuela.
2010
CHAPTER. L Borràs, JB Gutierrez. The Global Poetic System (GPS): A System of Poetic Positioning. Chapter 15, pp. 345-364. Beyond the Screen: Transformations of Literary Structures, Interfaces and Genre. Peter Gendolla, Jörgen Schäfer, Eds. Transcript Verlag, 2010. Bielefeld, Germany.
2009
JOURNAL. JB Gutierrez, Mark C. Marino, Pablo Gervás, Laura Borràs Castanyer Electronic Literature as an Information System. In Hyperrhiz: New Media Cultures. Issue 6, Summer 2009.
2008
PROCEEDINGS. JB Gutierrez and MC Marino. Literatronica. Adaptive Digital Narrative. In Creating '08: Proceedings of the hypertext 2008 workshop on Creating out of the machine: hypertext, hypermedia, and web artists explore the craft, pages 5-8, New York, NY, USA.
2007
CHAPTER.     JB Gutierrez. The Limits of Digital Narrative: A Functional Analysis. Chapter 5, pp. 85-103. Literatures in the Digital Era: Theory and Praxis. Amelia Sanz, Dolores Romero, Eds. Cambridge Scholars Press, 2007. UK/Spain.
2006
PROCEEDINGS. JB Gutierrez. Literatronic: The use of Hamiltonian cycles to produce adaptivity in literary hypertext. In The Bridges Conference 2006: Mathematical Connections in Art, Music, and Science, pages 215-224, London, UK, August 2006.
2004
JOURNAL. JB Gutierrez. Hipertexto Literario: Replantemianto de las premisas. (Literary Hypertext: Rethinking the premises.) Hojas Universitarias. Journal of the School of Humanities of the Universidad Central, (56):128-132. Bogota, Colombia, October 2004.
2000
JOURNAL. JB Gutierrez. Hipertexto en Contexto III. (Hypertext in context III.) In Signo y Pensamiento. Journal of the School of Communication of the Pontificia Universidad Javeriana, XIX(36):111-118. Bogota, Colombia, 2000.
1999
JOURNAL. JB Gutierrez. Hipertexto en Contexto (Hypertext in Context.) In Revista de Literatura Hispanoamericana. (Journal of Latin-American Literature). Journal of the School of Literature of the Zulia University (38):83-90, Jan-Jun 1999. Maracaibo, Venezuela, 1999. ISSN: 0252-9017
2021
Colombia. Dissertation. Julian Alberto Cubillos Ocampo Alfabetización mediática en r evolución digital y literatura electrónica. (Doctoral dissertation, UNIVERSIDAD DE LOS ANDES, COLOMBIA.
2017
USA. Article. Melissa Fitch Latin American Literature and NewTechnology. In Critical Insights - Contemporary Latin American Fiction, Ignacio López-Calvo Ed. Salem Press, Gey House Publishing.
2015
USA. Dissertation. Julio Alejandro Pérez Digital Storytelling in Spanish: Narrative Techniques and Approaches . (Doctoral dissertation, UNIVERSITY OF CALIFORNIA, SANTA BARBARA).
2015
Germany. Dissertation. Klöpper-Mauermann, S. Die spanischsprachige Hyperfiction und ihr Leser: narratologische Auslotungen einer schwierigen Beziehung. (Doctoral dissertation, UNIVERSITY OF HAMBURG).
2015
Iceland. MA Thesis. Nevena Novakovic El uso de la literatura digital en el aula de ELE . (MA Thesis, UNIVERSITY OF ICELAND).
2014
Spain. Article. Linares, J. M. G. (2014). Literatrónica: un análisis hipertextual de Condiciones extremas, de Juan B. Gutiérrez. Álabe: Revista de Investigación sobre Lectura y Escritura, (9)6, 2014.
2013
USA. Dissertation. Gainza, C. (2013). Escrituras Electrónicas en América Latina. Producción Literaria en el Capitalismo Informacional (Doctoral dissertation, UNIVERSITY OF PITTSBURGH).
2012
2010
USA. MA Thesis. Fordyce, T. (2010). Linked variations: authoring-system specific link construction and the analysis of hypertext literature (MA Thesis, GEORGETOWN UNIVERSITY).
2010
Agentina. Article. Cobo, R. M. D. (2013). Modelos para armar: hacia la digitalización de la narración literaria. CELEHIS: Revista del Centro de Letras Hispanoamericanas, 19(21), 47-72, 2008.
2009
USA. Dissertation. Cleger, O. (2009). El arte de narrar en la era de las blogoficciones: Una aproximacion interdisciplinaria a la literatura en los blogs (Doctoral dissertation, THE UNIVERSITY OF ARIZONA).
2008
USA. Dissertation. Acuna-Zumbado, E. (2008). Hacia la construccion del sujeto y sus procesos de lectura en la hipertextualidad latinoamericana (Doctoral dissertation, UNIVERSITY OF KANSAS).
2007
Colombia. Article. Henry, P. S. (2013). Metamorfosis literaria en la era digital: El primer vuelo de los hermanos Wright. Cuadernos de Literatura, 12(23):142-452, 2007.
2007
UK/USA/Spain. Chapter in book. Perla Sasson-Henry. From Hypertexts To Blogs: "El Primer Vuelo De Los Hermanos Wright" And "Más Respeto Que Soy Tu Madre." Chapter 20, pp. 319-328. Literatures in the Digital Era: Theory and Praxis. Amelia Sanz, Dolores Romero Eds. Cambridge Scholars Press, 2007. UK.
2002
Germany. Article. Jochen Mecke. Ästhetische Differenz in Print- und Hypertext (fiktion) (Aesthetic difference in print and Hypertext fiction). PhiN-Beiheft 2/2004: 141. Philologie im Netz. (Philology in Net). Journal of philology of the University of Berlin. Germany. ISSN: 1433-7177
2001
USA. Chapter in book. Susana Pajares Tosca. Condiciones Extremas. Digital Science Fiction from Colombia. Latin American Literature and Mass Media. Garland. Hispanic Issues Series. New York, 2001. ISBN: 081-533-894-5.

I am passionate about mathematics in general, and specifically about mathermatical biology in my own research. I envision research in quantitative biology as a constant exchange of ideas between experts in quantitative fields (i.e. computer science, engineering, mathematics, physics, statistics) and experts in biological sciences. This conversation enriches biology with the insight provided by quantitiative methods, and it enriches quantitiative fields with the demands of complex problems originated in biology. Joel Cohen put it succinctly and brilliantly: “mathematics is biology’s next microscope, only better; biology is mathematics’ next physics, only better“.

I have worked on recently on the following areas:

Machine learning: We use machine learning on a regular basis, but we are also developing new algorithms that improve the performance of artificial neural networks as compared to the state of the art. Also, I have been involved in applications of machine learning to analysis of cardiac signals, text summarization, and student success at the university level.

Data harmonization: We are able to represent heterogeneous and complex data sets of arbitrary size with a reduced set of data primitives (well-defined mathematical objects that are the building blocks to represent reality). Our analysis pipelines only consume data primitives, and only produce data primitives. The ultimate goal is to design and implement an agent capable of automated knowledge discovery.

Adaptive learning: The training of interdisciplinary scientists poses tremendous challenges. This is particularly true when teams are comprised of people with heterogeneous backgrounds. We have developed technology that minimizes the cognitive overhead to train individuals, and to integrate teams into a research project.

Multi-scale analysis of infectious disease: We study mechanisms that connect multiple scales, from milliseconds through evolutionary time, and from quantum interactions through continental dynamics of infection. This endeavor requires advances in multiple areas, as described below. We have been able to produce advances in every single aspect, and we are capable of integration of all these dimensions.

Epidemiology of asymptomatic carriers: We study the effect of asymptomatic hosts in the dynamics of malaria transmission. The results can be extrapolated to other diseases.

Dispersal of vectors: We study methods to model the dispersal of mosquitoes in a heterogeneous landscape dominated by species distribution, climate, and vegetation cover.

Physiology: We are able to identify when a host is infected before the onset of symptoms occurs. We accomplish this via high-frequency measures of accelerometers, blood pressure, ECG, and temperature.

Cellular models of immune interaction: We are using flow-cytometry data and cytokine information during a malaria infection to model cellular-level interactions between the adaptive and innate immune system, and healthy and infected red blood cells.

Multi-omic integration: We are able to analyze transcriptomic data, and integrate it with proteomics, metabolomics, immunomics, and other -omic technologies. Using this type of integration we have been able to determine factors that confer resilience against an infection.

Computational Drug Design: Given a gene regulatory network (that we can reconstruct from a time series of transcriptomic data), we can identify the most sensitive elements of the network, and target them with molecular docking studies against of databases of drug-like molecules.

Website
Publications