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

COVID-19
Curriculum Vitae

CV, updated on January 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.
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.
  • DeBarry, Jeremy D., et al. "Practical Recommendations for Supporting a Systems Biology Cyberinfrastructure." Data Science Journal 19.1 (2020). DOI: 10.5334/dsj-2020-024
  • 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.
  • Aguar, K., Arabnia, H. R., Juan B Gutierrez, Potter, W. D., and Taha, T. R. Towards Interest-based 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

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.

Published Fiction
2006
Novel. El primer Vuelo de los Hermanos Wright (The first Flight of the Wright Brothers). Version 2. Currently available at http://www.literatronica.com
2005
Novel. Condiciones Extremas (Extreme Conditions). Version 3. Currently available at http://www.literatronica.com
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
1998
Novel. El primer Vuelo de los Hermanos Wright (The first Flight of the Wright Brothers). Version 1. Currently available at http://www.literatronica.com
1998
Novel. Condiciones Extremas (Extreme Conditions). Version 1. Multimedia novel (book and CD-ROM). Published by Laboratorio Multimedial, Banco de Propuestas Artísticas, Instituto Distrital de Cultura y Turismo, Bogotá (Multimedia Lab, Repository of Artistic Proposals 1997, Institute of Culture of Bogota). Bogota, Colombia. Currently available at http://www.literatronica.com
1996
Story Book. Siete Curiosas Formas de Morir. (Seven Curious Ways to Die). Unidad de Publicaciones. Facultad de Ingeniería. Universidad Nacional de Colombia. 1996. (Publishing Unit. School of Engineering. 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)
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.
Peer-Reviewed Chapters in Books
2010
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.
2007
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.
Peer-Reviewed Journal Papers
2009
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.
2004
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
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
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
Peer-Reviewed Papers in Proceedings
2008
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.
2006
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.
Publications About My Literary Work
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 Novaković El uso de la literatura digital en el aula de ELE . (MA Thesis, UNIVERSITY OF ICELAND).
2014
Spain. Paper. 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. Paper. 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. Paper. 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. Paper. 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.

See academic advice from back when I was a postdoc (2012). Most of it is still relevant today. Also available at: https://mathresearch.utsa.edu/wp/?p=1354

I am always available to talk to current and prospective students. If you need academic advice, you might want to check the following videos first. These videos were recorded in the 2012 SACNAS Conference, when I was a Postdoctoral Fellow at the Mathematical Biosciences Institute (2010-2012). They are part of the www.sciencecareerpath.org library. The following links will take you to specific videos in this page.


So, you think your can't overcome your circumstances...

I cannot advise you on how to carve your own path through life; however, I can assure that --no matter how hard you have had it-- many others have succeeded against all odds before (i.e. YOU CAN DO IT TOO!!!). Video recorded at the 2012 SACNAS Conference:


So, you are wondering whether post-graduate education is useful...

Why it is useful (at least how it was useful to me). Video recorded at the 2012 SACNAS Conference:


So, you are considering a career in science...

Part 1 (transition from undergraduate student to graduate student). Video recorded at the 2012 SACNAS Conference:

Part 2 (life as a graduate student). Video recorded at the 2012 SACNAS Conference:


Where to go next: Postdoctoral fellow? Postdoctoral associate? Research Scientist? What is the difference?

Video recorded at the 2012 SACNAS Conference:


So, you are wondering how to reach a balance between your personal life and your academic work...

Video recorded at the 2012 SACNAS Conference:


So, you are having trouble keeping up with academic work...

It is OK to fail, it is not OK to quit. You might want to jump to 1:49, or use this link. Video recorded at the 2012 SACNAS Conference:


So, you are wondering how to manage your time in academia...

Video recorded at the 2012 SACNAS Conference:


So, you are wondering what is mathematical biology...

Video recorded at the 2012 SACNAS Conference:


So, you are wondering why interdisciplinarity is important...

Video recorded at the 2012 SACNAS Conference:


So, you worry about how your ethnic background will impact your career...

I am deeply committed to contribute to have the face of success match the face of the nation; if the mismatch worries you, talk to me. Video recorded at the 2012 SACNAS Conference:

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