Directory

Juan B. Gutiérrez

Department Chair, Professor

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

FLN 4.01.10

Office Hours

N/A

Research Interests

Mathematical biology; Multiscale modeling; Bioinformatics; Machine Learning

A Word from the Chair

See what makes mathematics at UTSA special… (A Word from the Chair)

I am producing daily estimates for COVID-19 cases. Follow Twitter updates @biomathematicus with #ModelingSanAntonioCOVID19

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.Sc., Civil Engineering, Meritorious Thesis. National Prize of Excellence in B.Sc. Thesis, National University of Colombia.
Research Areas
  • Saeid Safaei, Vahid Safaei, Solmazi Safaei, Zerotti Woods, Hamid R Arabnia, Juan B Gutierrez. The SWAG Algorithm; a Mathematical Approach that Outperforms Traditional Deep Learning. Theory and Implementation. arXiv:1811.11813 [stat.ML]
  • Allahyari, Mehdi, Seyedamin Pouriyeh, Mehdi Assefi, Saied Safaei, Elizabeth D. Trippe, Juan B. Gutierrez, and Krys Kochut. "A brief survey of text mining: Classification, clustering and extraction techniques." arXiv preprint arXiv:1707.02919 (2017).
  • Allahyari, Mehdi, Seyedamin Pouriyeh, Mehdi Assefi, Saeid Safaei, Elizabeth D. Trippe, Juan B. Gutierrez, and Krys Kochut. "Text summarization techniques: a brief survey." arXiv preprint arXiv:1707.02268 (2017).
  • Pouriyeh, Seyedamin, Sara Vahid, Giovanna Sannino, Giuseppe De Pietro, Hamid Arabnia, and Juan Gutierrez. "A comprehensive investigation and comparison of Machine Learning Techniques in the domain of heart disease." In 2017 IEEE Symposium on Computers and Communications (ISCC), pp. 204-207. IEEE, 2017.
  • M. K. Hurdal, J. B. Gutierrez, C. Laing, A. D. Kline and D. A. Smith, "Geometric invariants for classification of cortical sulci," 2008 15th IEEE International Conference on Image Processing, San Diego, CA, 2008, pp. 1156-1159.
  • Shape analysis for automated sulcal classification and parcellation of MRI data. MK Hurdal, JB Gutierrez, C Laing, DA Smith. Journal of Combinatorial Optimization 15 (3), 257-275
Graduate Students
  • Zerotti Woods. Ph.D. Dissertation in Mathematics. A new regularization term for deep neural networks with applications to biological data. Committee Chair: Juan B Gutierrez. Committee Members: Juan B Gutierrez, Qing Zhang, Daniel Krashen, Caner Kazanci.
  • Tao Sheng. Ph.D. Dissertation in Bioinformatics. Integration of transcriptomic and high frequency telemetry data via machine learning m methods. Committee Chair: Juan B Gutierrez. Committee Members: Juan B Gutierrez, Liang Liu, Jessica Kissinger, Jonathan Arnold.
  • Gonzalez, K.J., Moncada-Giraldo, D.M. and Gutierrez, J.B., 2020. In silico identification of potential inhibitors against human 2'-5'-oligoadenylate synthetase (OAS) proteins. Computational Biology and Chemistry, 85, p.107211. DOI: 10.1016/j.compbiolchem.2020.107211
  • Houston MT, Juan B Gutierrez. The FRiND Model: A Mathematical Model for Representing Macrophage Plasticity in Muscular Dystrophy Pathogenesis. Bulletin of Mathematical Biology. DOI: 10.1007/s11538-019-00635-8.
  • Yi H. Yan, Diego M. Moncada, Elizabeth D. Trippe, Juan B Gutierrez. Correlates of severity of disease in Macaca mulatta infected with Plasmodium cynomolgi. arXiv:1706.08836 [q-bio.TO].
  • Derek Onken, Eric Marty, Roberto Palomares, Rui Xie, Leyao Zhang, Jonathan Arnold, Juan B Gutierrez. The lunar cycle’s influence on sex determination at conception in humans. arXiv:1706.08151 [q-bio.OT].
  • Yi H. Yan, Jacob B. Aguilar, Elizabeth D. Trippe, Juan B Gutierrez. Quantification of Healthy Red Blood Cell Removal and Preferential Invasion of Reticulocytes in Macaca mulatta during Plasmodium cynomolgi Infection. arXiv:1706.08139 [q-bio.CB].
  • Yi H. Yan, Elizabeth D. Trippe, Juan B Gutierrez. A Method for Massively Parallel Analysis of Time Series. arXiv:1612.08759 [q-bio.QM].
  • Yan, Y., Adam, B., Galinski, M., Kissinger, J.C., Moreno, A. and Gutierrez, J.B., 2015. Mathematical model of susceptibility, resistance, and resilience in the within-host dynamics between a Plasmodium parasite and the immune system. Mathematical biosciences, 270, pp.213-223.
  • Gutierrez, J.B., Harb, O.S., Zheng, J., Tisch, D.J., Charlebois, E.D., Stoeckert Jr, C.J. and Sullivan, S.A., 2015. A framework for global collaborative data management for malaria research. The American journal of tropical medicine and hygiene, 93(3_Suppl), pp.124-132.
Graduate Students:
  • Jessica A. Brady. Ph.D. Dissertation in Engineering. Mathematical modeling in health and disease. Committee Chair: Juan B Gutierrez, Karen Hallow. Committee Members: Juan B Gutierrez, Karen Hallow, Xianqiao Wang, Caner Kazanci, Jonathan Arnold.
  • Valerie N. Flint. Ph.D. Dissertation in Bioinformatics. Shield: SNV heuristic identification, exploration, and location detector . Committee Chair: Juan B Gutierrez. Committee Members: Juan B Gutierrez, Shaying Zhao, Liang Liu, Jonathan Arnold.
  • Matthew T. Houston. Ph.D. Dissertation in Mathematics. The FRiND model: a mathematical model for representing immunological interactions in muscular dystrophy pathogenesis . Committee Chair: Juan B Gutierrez. Committee Members: Juan B Gutierrez, Qing Zhang, Caner Kazanci, Jonathan Arnold
  • Yi H. Yan, Ph.D. Dissertation in Bioinformatics. Multi-Omic and multi-scale data integration for the characterization of malaria infection in non-human primates. Committee chair: Juan B Gutierrez. Committee Members: Juan B Gutierrez, Ying Xu, Julie Moore, Jonathan Arnold.
  • Elizabeth D. Trippe. Ph.D. Dissertation in Bioinformatics. Data Integration for Systems Biology. Committee Chair: Juan B Gutierrez. Committee Members: Juan B Gutierrez, Jonathan Arnold, Jessica Kissinger, David Peterson.
  • Juan B Gutierrez, Ming-Jun Lai, George Slavov. Bivariate Spline Solution of Time Dependent Nonlinear PDE for a Population Density over Irregular Domains. Mathematical Biosciences. Volume 270, Part B, December 2015, Pages 263–277. DOI: 10.1016/j.mbs.2015.08.013
  • JB Gutierrez, S Kouachi, RD Parshad. Global existence and asymptotic behavior of a model for biological control of invasive species via supermale introduction. Communications in Mathematical Sciences. 11(4):971-992. DOI: 10.4310/CMS.2013.v11.n4.a4
  • JL Teem, JB Gutierrez. Combining the Trojan Y Chromosome and Daughterless Carp Eradication Strategies. Biological Invasions, May 2013. DOI: 10.1007/s10530-013-0476-1.
  • JL Teem, JB Gutierrez, RD Parshad. A Comparison of the Trojan Y Chromosome and Daughterless Carp Eradication Strategies. Biological Invasions, May 2013. DOI: 10.1007/s10530-013-0475-2
  • JB Gutierrez, MK Hurdal, RD Parshad, JL Teem. Analysis of the Trojan Y Chromosome Model for Eradication of Invasive Species in a Riverine System. Journal of Mathematical Biology. Volume 64, Numbers 1-2 (2012), 319-340. DOI: 10.1007/s00285-011-0413-9.
  • John Teem and Juan B Gutierrez. A theoretical strategy for eradication of Asian carps using a Trojan Y chromosome to shift the sex ratio of the population. 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.
  • RD Parshad, JB Gutierrez. On the Well Posedness of the Trojan Y Chromosome Model. Boundary Value Problems, vol. 2010, Article ID 405816, Nov. 2010. DOI: 10.1155/2010/405816
  • RD Parshad, JB Gutierrez. On the Global Attractor of the Trojan Y Chromosome Model. Communications in Pure and Applied Analysis, 10(10):339-359, January 2010. DOI: 10.3934/cpaa.2011.10.339
  • Gutierrez, Juan B., and John L. Teem. "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." Journal of Theoretical Biology 241, no. 2 (2006): 333-341.
  • Karen Aguar, Hamid R. Arabnia, Juan B Gutierrez, Walter D. Potter, Thiab R. Taha. Towards Interest-based Adaptive Learning and Community Knowledge Sharing. The 13th International Conference on Frontiers in Education: Computer Science and Computer Engineering. FECS’17: July 17-20, 2017, Las Vegas, USA.
  • Aguar, K., Arabnia, H. R., Juan B Gutierrez, Potter, W. D., and Taha, T. R. Towards Interestbased Adaptive Learning and Community Knowledge Sharing. International Conference Frontiers in Education: CS and CE. FECS’17. CSREA Press, 2017, pp 58-61.
  • Aguar, Karen, Hamid R. Arabnia, Juan B Gutierrez, Walter D. Potter, and Thiab R. Taha. Making CS inclusive: An overview of efforts to expand and diversify cs education. In Computational Science and Computational Intelligence (CSCI), 2016 International Conference on, pp. 321-326. IEEE, 2016. DOI: 10.1109/CSCI.2016.0067
  • Juan B Gutierrezand Mark C Marino. Literatronica. Adaptive Digital Narrative. In ACM’s Hypertext’08. 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. DOI: 10.1145/1379153.1379156
  • 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, J¨orgen Sch¨afer, Eds. Transcript Verlag, 2010. Bielefeld, Germany.
  • 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.
  • 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.
  • 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.
  • JB Gutierrez, MC Marino. Entretenimientos de N-Capas: Literatura Electr´onica Como un Sistema de Informaci´on (N-Tier Entertainments: Electronic Literature as an Information System). Proceedings of the III Congreso ONLINE del Observatorio para la CiberSociedad. Barcelona, Spain, November 2006.
  • 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.
  • JB Gutierrez. Literatr´onica: Hipertexto Literario Adaptativo. (Literatronic: Adaptive Literary Hypertext.) in Proceedings of the 2o Congreso del Observatorio para la Cibersociedad. (2nd Congress of the Observatory for the Cibersociety.) Barcelona, Spain, November 2004.
  • JB Gutierrez. Literatr´onica: Sobre C´omo y Porqu´e Crear Ficci´on para medos digitales (Literatronic: About how and why create fiction for digital media.) in Proceedings of the 1er Congreso del Observatorio para la Cibersociedad (1st Congress of the Observatory for the Cibersociety.) Barcelona, Spain, September 2002.
  • 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.
  • 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.
Graduate Student:
  • Karen E. Aguar, Ph.D. in Computer Science. SAIL: A system for adaptive interest-based learning in STEM education. Committee Chairs: Juan B Gutierrez, Hamid R. Arabnia. Committee Members: Juan B Gutierrez, Hamid R. Arabnia, Thiab R. Taha, Walter D. Potter
  • El primer Vuelo de los Hermanos Wright (The first Flight of the Wright Brothers). Written with support from the National Grants of The Ministry of Culture of Colombia (COLCULTURA), 1996. Grant COLCULTURA-SECAB 014/1996. Bogota, Colombia. With contributions by Carlos E. Herrera P. (programmer). Version 2: 2006. Currently available at http://www.literatronica.com
  • Condiciones Extremas (Extreme Conditions). Version 1: Multimedia novel (book and CD-ROM). Written with support from the Repository of Artistic Projects of the Institute of Culture of Bogota. Grants 514/1997 and 410/1998, Bogota, Colombia. Published by Multimedia Lab, Repository of Artistic Proposals 1997, Institute of Culture of Bogota. Version 2: 2002. Version 3: 2005. Currently available at http://www.literatronica.com
  • 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
  • La Sagrada Geometría (The Sacred Geometry.) In Antolog´ıa Colombiana de Ciencia Ficci´on (Companion of Colombian Science Fiction). Pag. 93-96. Rene Rebetez (ed.) Espasa, 2000. Bogota, Colombia. ISBN: 958-614-804-1. Also in In (CREA: An Expedition through the Colombian Culture). Ministry of Culture of Colombia (formerly Colcultura), 1995.
  • 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
  • Siete Curiosas Formas de Morir. (Seven Curious Ways to Die). Unidad de Publicaciones. Facultad de Ingeniería. Universidad Nacional de Colombia (Publishing Unit. School of Engineering. National University of Colombia.) 1996.
  • Gonz´alez, Archivos y Documentos. (Gonzalez, Files and Documents.) In Sunday Readings of El Tiempo (Sunday Readings from The Times), newspaper. 475,000 copies (ISSN: 0121-9790). Also in Carta Universitaria, Journal of the National University, December 1996. Bogota, Colombia. ISSN: 0122- 2929. Winner of the International Story Award ‘Carlos Castro Saavedra’, 1996, Medellin, Colombia
  • Atyseikuiwandi´u, o los Avatares de la Cruel Sangre (Atyseikuiwandi´u, or the Fortune of the Cruel Blood). In Lecturas Dominicales de El Tiempo (Sunday Readings from The Times), newspaper. 01/15/1995. Bogota, Colombia. 475,000 copies (ISSN: 0121-9790). Also in Ko’ey´u, Journal of Cultural and Politic Analysis. Number 64, April-June 1994. Caracas, Venezuela. Winner of the International Story Award ‘Ko’ey´u Latinoamericano’, 1995, Caracas, Venezuela.
 

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.

Recently funded projects are:

(PI Gutierrez) ALICE (Adaptive Learning for Interdisciplinary Learning Environments, 2016-2018, $299K), NSF award #1645325: ALICE is a Web-based information system that generates individualized development plans, according to previous experiences and current challenges. Furthermore, ALICE is designed to connect lexias from multiple subject matters, thus bypassing disciplinary barriers that in many cases are artificial. The principles behind ALICE are generalizable, and hence it has the potential to be used in K-16, graduate, and continuing education.

(Co-PI Gutierrez, PI Galinski) Technologies for Host Resilience (2016-2019, $1.9M UGA out of $6.5M) – Host Acute Models of Malaria to study Experimental Resilience (THoR’s HAMMER), DARPA contract contract #W911NF-16-C-0008, 2016-2019: This project will explore the molecular mechanisms of resilience, susceptibility and resistance of non-human primate hosts when challenged with a malaria infection.

(Co-PI Gutierrez, PI Barbour) Collaborative Research: NSF INCLUDES: An Integrated Approach to Retain Underrepresented Minority Students in STEM Disciplines (2016-2018, $117K). NSF award 1649226: The University of Georgia, Florida International University, Savannah State University, Clark Atlanta University and Fort Valley State University will lead this Design and Development Launch Pilot to address enhancing recruitment, retention, productivity and satisfaction of historically underrepresented minority (URM) undergraduate students who enroll in STEM graduate programs at primarily white (PWI) and research intensive (RI) universities

(Co-I Gutierrez, PI Galinski) Malaria Host-Pathogen Interaction Center (2012-2017, $19M), MaHPIC, NIAID contract #HHSN272201200031C, 2012-2017. PI Mary Galinski: MaHPIC involves the multidisciplinary study of malaria infections, immunity and pathogenesis of P. falciparum, P. vivax and P. knowlesi in the context of host-pathogen interactions, in humans and nonhuman primates, using a systems biology approach. Three nonhuman primate malaria species will be studied: P. coatneyi to model P. falciparum, P. cynomolgi to model P. vivax, and P. knowlesi, a monkey malaria species that has been causing illness and cases of death in humans in Southeast Asia.

(Co-I Gutierrez, PI Herrera) International Centers of Excellence in Malaria Research (2011-2017, $5.5M) – Center for non-Amazonian regions of Latin America – CLAIM, NIAID cooperative agreement #U19AI089702-01, 2010-2017. PI Sócrates Herrera: CLAIM is divided into three projects: Project 1 is evaluating the diversity of the ecology and parasite populations related to the epidemiology and clinical findings to establish a scientific framework that supports the development of new intervention strategies for malaria elimination in non-Amazonian areas of Latin America. Project 2 is addressing major gaps in understanding of the ecology, behavior, vector potential, and control of Anopheles malaria vectors to guide the development and implementation of more effective integrated vector management (IVM) strategies of National Malaria Control Programs (NMCPs). Project 3 aims to determine the clinical outcomes and their association with parasite and host features of malaria-infected individuals living in non-Amazon regions of LA with different intensities of malaria transmission.

Publications