Peer Reviewed

Systems Medicine       

of Infectious Diseases

Research and Consulting Group

Machine Learning for Multiscale Analysis of Biomedical Data


Peer Reviewed Articles


2019


68. N. Sharma-Chawla, S. Stegemann-Koniszewski, H. Christen, D.J. Boehme, O. Kershaw, J. Schreiber, C.A. Guzmán, D. Bruder, E.A. Hernandez-Vargas. In vivo neutralization of pro-inflammatory cytokines during secondary Streptococcus pneumoniae infection post influenza A virus infection. Frontiers in Immunology. 10: 1864, 2019 [Link]


67. G.D. Vega-Magdaleno,  A.Y. Alanis, E.A. Hernandez-Vargas. Learning neural impulsive MPC for tailoring therapies in viral infections. Applied Soft Computing. 85:1-17, 2019 [Link]


66. E.A. Hernandez-Vargas, A.Y. Alanis, J. Tetteh. A new view of multiscale stochastic impulsive systems for modeling and control of epidemics. Annual Reviews in Control. 2019 [Link] 


65. C.E. Torres-Cerna, J.A. Morales, A.Y. Alanis, E.A. Hernandez-Vargas. Modeling Quorum Sensing Dynamics and Interference on Escherichia coli. Frontiers in Microbiology. 10, p. 1835. 2019 [Link]


64. N. J. Tobias,  C. Parra‐Rojas, Y.i ShiY. ShiS. Simonyi, A.Thanwisai, A. VittaN.ChantratitaE. A. Hernandez‐VargasH. B. Bode. Cyclo(tetrahydroxybutyrate) production is sufficient to distinguish between Xenorhabdus and Photorhabdus isolates in Thailand. Enviromental Microbiology. 21(8):2921-2932, 2019 [Link]


63. G. Hernandez-Mejia, A.Y. Alanis, M. Hernandez-Gonzalez, Rolf Findeisen, E.A. Hernandez-Vargas. Passivity-based Inverse Optimal Impulsive Control for Influenza Treatment in the Host. IEEE Transactions on Control Systems Technology. 2019 [Link]


62. C. Parra-Rojas, V. von Messling, E.A. Hernandez-Vargas. Adjuvanted influenza vaccine dynamics. Scientific Reports. 9(73):1-15, 2019 [Link]


61. A.E.S. Almocera, C. Parra-Rojas, G. Hernandez-Mejia, E.A. Hernandez-Vargas. The trichotomy of pneumococcal infection outcomes in the host. Communications in Nonlinear Science and Numerical Simulation. 2019 [Link]


60. A.E.S. Almocera, E.A. Hernandez-Vargas. Coupling multiscale within-host dynamics and between-host transmission with recovery (SIR) dynamics. Mathematical Bioscience. 309:34-41, 2019 [Link]


59. M. Hernandez-Gonzalez, G. Hernandez-Mejia, A.Y. Alanis, E.A. Hernandez-Vargas. State Estimation for stochastic nonlinear systems with applications to viral infections. Proceedings in the European Control Conference, Naples, Italy. 2019


58. C.E. Torres-Cerna, E.A. Hernandez-Vargas. Mathematical Modeling of the Quorum Sensing in Vibrio harveyi. Revista Mexicana de Ingeniería Biomédica. 40(1):1-10, 2019 [Link]





2018


57. M. Hernandez-Gonzalez,  E.A. Hernandez-Vargas, M.V. Basin. Discrete-time high order neural network identifier trained with cubature Kalman filter. Neurocomputing. 2018  [Link] 


56. C. Parra-Rojas, V.K. Nguyen, G. Hernandez-Mejia, E.A. Hernandez-Vargas. Neuraminidase inhibitors in influenza treatment and prevention– Is it time to call it a day?. Viruses.  10(9): 1-13, 2018    - [Link]


55. G. Montaseri, A. Boianelli, E.A. Hernandez-Vargas, M. Meyer-Hermann. PK/PD-based adaptive tailoring of oseltamivir doses to treat within-host influenza viral infections. Progress in Biophysics and Molecular Biology. 2018 - [Link]


54. G. Hernandez-Mejia, A.Y. Alanis, E.A. Hernandez-Vargas. Neural inverse optimal control for discrete-time impulsive systems. Neurocomputing. 2018  [Link] 


53. V.K. Nguyen, Rafael Mikolajczyk, E.A. Hernandez-Vargas. High-Resolution epidemic simulation using within-host infection and contact data.  BMC Public Health. 2018 [Preprint]  [PDF]


52. V.K. Nguyen, C. Parra-Rojas, E.A. Hernandez-Vargas. The 2017 plague outbreak in Madagascar: data descriptions and epidemic modelling.  Epidemics. 2018  [Link] 


51. A.E.S. Almocera, V.K. Nguyen, E.A. Hernandez-Vargas.  Multiscale model within-host and between-host for viral infectious diseases. Journal of Mathematical Biology. 76 (404), 1-23,  2018 [Link]  [Preprint]


50. M. Samir, M. Hamed, F. Abdallah, V.K. Nguyen,  E.A. Hernandez-Vargas, F. Seehusen, W. Baumgartner, A. Hussein, A.A.  Ali,  F. Pessler.

An Egyptian HPAI H5N1 isolate from clade 2.2.1.2 is highly pathogenic in an experimentally infected domestic duck breed (Sudani duck). Transboundary and Emerging Diseases. 1-15, 2018 [PDF]


49. C. Villaseñor, J.D. Rios, N. Arana-Daniel, A.Y. Alanis, C. Lopez-Franco, E.A. Hernandez-Vargas. Germinal Center Optimization Algorithm. International Journal of Computational Intelligence Systems, 12: 13-27, 2018 [Link]


48. E.A. Hernandez-Vargas, J. Martinez-Picado, G. Hernandez-Mejia. Long-term impact of antiretroviral strategies for a functional HIV cure: A virtual clinical trial.  Proceedings in the 10th IFAC Symposium on Biological and Medical Systems, Sao Paulo, Brazil. 2018 


47. E.A. Hernandez-Vargas, A. Boianelli, G. Hernandez-Mejia. Bacterial pneumonia fate decisions. Proceedings in the 10th IFAC Symposium on Biological and Medical Systems, Sao Paulo, Brazil. 2018


46. G. Hernandez-Mejia, N. Arana-Daniel, A.Y. Alanis, E.A. Hernandez-Vargas. Recurrent high order neural networks identification for infectious diseases. Proceedings in the IEEE World Congress on Computational Intelligence, Rio de Janeiro, Brazil. 2018


45. A. Boianelli, E.A. Hernandez-Vargas. A stochastic Markov branching process framework to evaluate HIV eradication. Proceedings in the 2nd IFAC Conference on Modelling, Identification and Control of Nonlinear Systems, Guadalajara, Mexico. 2018 [Link]


44. G.D. Vega-Magdaleno, G. Hernandez-Mejia, A.Y. Alanis, E.A. Hernandez-Vargas. Impulsive MPC for influenza infection treatment at variable time. Proceedings in the 2nd IFAC Conference on Modelling, Identification and Control of Nonlinear Systems, Guadalajara, Mexico. 2018 [Link]


43. C.E. Torres-Cerna, J.A. Morales, A.Y. Alanis, E.A. Hernandez-Vargas. Discrete-time neural network identification of Quorum sensing Escherichia coli regulators. Proceedings in the 2nd IFAC Conference on Modelling, Identification and Control of Nonlinear Systems, Guadalajara, Mexico. 2018 [Link]


42. R. Covarrubias, A.Y. Alanis, E. Sanchez, E.A. Hernandez-Vargas.  Optimal impulsive control for a SIR epidemic model. Proceedings in the 15th International Conference on Electrical Engineering, Computing Science and Automatic Control, Mexico. 2018



2017


41. V.K. Nguyen, E.A. Hernandez-Vargas. Windows of opportunity for Ebola virus infection treatment and vaccination. Scientific Reports. 7(8975):1-10, 2017 [PDF] 


40. E.A. Hernandez-Vargas. Modeling Kick-Kill strategies towards HIV cure. Frontiers in Immunology. 2017 [PDF]


39. C. Villaseñor, J.D. Rios, N. Arana-Daniel, A.Y. Alanis, C. Lopez-Franco, E.A. Hernandez-Vargas. Germinal center optimization applied to neural inverse optimal control for an all-terrain tracked robot. Applied Sciences. 8(1):1-16, 2017 [PDF]


38. C.E. Torres-Cerna, A.Y. Alanis, I. Poblete-Castro,  E.A. Hernandez-Vargas. Batch cultivation model for biopolymer production. Chemical and Biochemical Engineering Quarterly Journal. 31(1):89-99, 2017 [PDF]


37. G. Hernandez-Mejia, A.Y. Alanis,  E.A. Hernandez-Vargas. Inverse optimal impulsive control based treatment of influenza Infection. Proceedings in the 20th IFAC World Congress, Toulouse, France. 2017  [PDF]


2016


36.  S. Duvigneau, N. Sharma-Chawla, A. Boianelli,   S. Stegemann-Koniszewski, V. K. Nguyen,  D. Bruder,   E.A. Hernandez-Vargas. Hierarchical effects of pro-inflammatory cytokines on the post-influenza susceptibility to pneumococcal coinfection. Scientific Reports. Vol. 6(37045):1-11,  2016   [PDF]


35.  A. Boianelli,  N. Sharma-Chawla,  D. Bruder,  E.A. Hernandez-Vargas. Oseltamivir PK/PD modeling and simulation to evaluate treatment strategies against influenza-pneumococcus coinfection. Frontiers in Cellular and Infection Microbioly. Vol.  6(60):1-11, 2016   [PDF]


34.  V. K. Nguyen, F. Klawonn, R. Mikolajczyk,  E. A. Hernandez-Vargas. Analysis of practical identifiability of a viral infection model. Plos One. Vol.  11(12): e0167568, 2016   [PDF]


33. C. E. Torres-Cerna, A. Y. Alanis, I. Poblete-Castro, M. Bermejo-Jambrina,  E. A. Hernandez-Vargas. A Comparative Study of Differential Evolution Algorithms for Parameter Fitting Procedures. Proceedings in IEEE World Congress on Computational Intelligence.  2016   [PDF]


2015


32. A. Boianelli, V. K. Nguyen, T. Ebensen, K. Schulze, E. Wilk, N. Sharma, S. Stegemann-Koniszewski, D. Bruder, F. Toapanta, C. A. Guzman, M. Meyer-Hermann,  E.A. Hernandez-Vargas. Modeling Influenza Virus Infection: A Roadmap for Influenza Research. Viruses. Vol.  7:5274-5304, 2015   [PDF]


31. V.K. Nguyen, S. C. Binder, A. Boianelli, M. Meyer-Hermann,  E.A. Hernandez-Vargas.  Ebola Virus Infection Modelling and Identifiability Problems.  Frontiers Microbiology. Vol. 6(257): 1-11,  2015  [PDF]


30. S. C. Binder, E.A. Hernandez-Vargas, M. Meyer-Hermann.  Reducing complexity: An iterative strategy for parameter determination in biological networks.  Computer Physics Communications,  Vol.190, 15-22,  2015 [PDF]


29. V. K. Nguyen,  E.A. Hernandez-Vargas. Identifiability Challenges in Mathematical Models of Viral Infectious Diseases. Proceedings in the 17th IFAC Symposium on System Identification, Beijing, China. 1–6, 2015 [PDF]   


2014


28.  S. Jaafoura,M. G. de Goër de Herve, E.A. Hernandez-Vargas, H. Hendel-Chavez, M. Abdoh, M.C. Mateo, R. Krzysiek,M. Merad, R. Seng, M. Tardieu, J. F. Delfraissy, C. Goujard,   Y. Taoufik.  Progressive contraction of the latent HIV reservoir around a core of less-differentiated ​CD4+ memory T Cells.  Nature Communications, Vol.5,  5407, 1-8, 2014 [PDF]


27. E.A. Hernandez-Vargas, E. Wilk, L. Canini, F. Toapanta, S. Binder, A. Uvarovskii, T. Ross, C.A. Guzman, A.S. Perelson,   M.  Meyer-Herman. Effects of aging on influenza virus infection dynamics. Journal of Virology, Vol.88 (8), 4123–4131, 2014 [PDF]

             

26 M. Haering, A. Hördt, M. Meyer-Hermann, E.A. Hernandez-Vargas. Computational study to determine when to initiate and alternate therapy in HIV infection. BioMed Research International, Vol. 2014, 2014 [PDF]


25. E.A. Hernandez-Vargas, P. Colaneri, R.H. Middleton. Switching Strategies to Mitigate HIV Mutation. IEEE Transactions on Control Systems Technology,  Vol. 22 (4), 1623-1628, 2014 [PDF]


2013


24. E.A. Hernandez-Vargas, P. Colaneri,  R. Middleton. Optimal therapy scheduling for a simplified HIV infection model. Automatica, Vol.49 (9), 2874–2880, 2013 [PDF]


23. E.A. Hernandez-Vargas, R. Middleton. Modeling the three stages in HIV infection. Journal of Theoretical Biology, Vol. 320, 33-40, 2013  [PDF]


22. A.Y. Alanis, M. Hernandez-Gonzalez,  E.A. Hernandez-Vargas. Observers for biological systems. Applied Soft Computing, Vol.24, 1175–1182, 2014 [PDF]


21. C. Schmeitz, E.A. Hernandez-Vargas, R. Flyer, A.H. Guse,  M. Meyer-Hermann. A mathematical model of T lymphocyte calcium dynamics derived from single transmembrane protein properties. Frontiers in immunology, Vol. 4, 2013 [PDF]


2012


20. M. Hernandez-Gonzalez, A. Alanis, E.A. Hernandez-Vargas, Decentralized Discrete-Time Neural Control for a Quanser 2-DOF Helicopter.  Applied Soft Computing, Vol. 12, 2462–2469,  2012 [PDF]


19. E.A. Hernandez-Vargas, P. Colaneri,  R. Middleton. Sub-optimal switching with dwell time constraints for control of viral mutation. IEEE Conference on Decision Control, Maui, Hawaii, 2012 [PDF]


18. E.A. Hernandez-Vargas,  M. Meyer-Hermann. Innate immune system dynamics to influenza virus. Proceedings in the IFAC Symposium on Biological and Medical Systems, Budapest, 2012 [PDF]


17. E.A. Hernandez, A.Y. Alanis,   E. N. Sanchez. Discrete-time neural observer for HIV infection dynamics. Proceedings in the Word Automation Congress, Puerto Vallarta, Mexico  2012  [PDF]


2011


16. J. Ferreira, E.A. Hernandez-Vargas, R. Middleton. Computer Simulation of Structured Treatment Interruption for HIV infection. Computers Methods and Programs in Biomedicine, Vol. 104 (2), 50-61 2011 [PDF]


15. E.A. Hernandez-Vargas, Dhagash Mehta,  R. Middleton. Towards modeling HIV long term behavior.  Proceedings in the IFAC World Congress, Milan, Italy, 2011 [PDF]


14. E.A. Hernandez-Vargas, R. Middleton,  P. Colaneri. Optimal and MPC switching strategies for mitigating viral mutation escape. Proceedings in the IFAC World Congress, Milan, Italy, 2011 [PDF]


13. S. Zhan, E.A. Hernandez-Vargas, R. Middleton. A mathematical study on immune activation and related dynamics in HIV infection.  Proceedings in the IEEE Conference on Decision Control, Orlando, 2011 [PDF]


2010


12. E.A. Hernandez-Vargas, P. Colaneri, R. Middleton,  F. Blanchini. Discrete-time control for switched positive systems with application to mitigating viral escape. International Journal of Robust and Nonlinear Control, Vol. 21 (10), 1093–1111, 2010 [PDF]


11. A. Alanis, E. N. Sanchez, A. Loukianov,  E.A. Hernandez-Vargas.  Discrete-time recurrent high order neural networks for nonlinear identification. Journal of the Franklin Institute, Vol. 347  (7), 1253-1265, 2010 [PDF]


10. E.A. Hernandez-Vargas, P. Colaneri, R. Middleton,  F. Blanchini. Dynamic optimization algorithms to mitigate HIV escape. Proceedings in the IEEE Conference on Decision Control, Atlanta, 2010 [PDF]


9. R. Middleton, P. Colaneri, E.A. Hernandez-Vargas,  F. Blanchini. Continuous-time optimal control for switched positive systems with application to mitigating viral escape.  Proceedings in the IFAC Symposium on Nonlinear Control Systems, Bologna, Italy, 2010 [PDF]


2009


8. E.A. Hernandez-Vargas, E. N. Sanchez, C. Cadet,  J. F. Beteau. Neural observer based hybrid intelligent scheme for activated sludge wastewater treatment. Chemical and Biochemical Engineering Quarterly Journal, Vol. 23 (4), 2009 [PDF]


7. E.A. Hernandez-Vargas, A. Alanis, E. N. Sanchez,  M. Hernandez-Gonzalez. Supervisor difuso funcional aplicado a una planta urbana de tratamiento de aguas residuales basado en un observador neuronal. Ingeniería Química, Vol. 36, 2009 [PDF]


2008


6. E.A. Hernandez, E.N. Sanchez, C. Cadet,  J.F. Beteau. Observer based hybrid intelligent control for activated sludge wastewater treatment. Proceedings in the Latin American Congress of Automatic Control, Merida, Venezuela,  2008 [PDF]


5. E. N. Sanchez, E.A. Hernandez, C. Cadet,  J. F. Beteau. Hybrid intelligent control for activated sludge wastewater treatment. Proceedings in the IEEE Multi-Conference on Systems and Control, San Antonio, Texas, 2008 [PDF]


4. E. N. Sanchez, E.A. Hernandez, C. Cadet,  J. F. Beteau. Discrete-time recurrent high order neural observer for activated sludge wastewater treatment. Proceedings in the IEEE World Congress on Computational Intelligence, Hong Kong, 2008 [PDF]


2007


3. J.G. Segovia-Hernandez, E.A. Hernandez–Vargas,  J.A. Marquez–Muñoz. Control Properties of Thermally Coupled Distillation Sequences for Different Operating Conditions. Computers and Chemical Engineering Journal, Vol. 31, 867-874, 2007 [PDF]


2006


2. E. A. Hernandez–Vargas, J.G. Segovia- Hernandez, S. Hernandez,  A. Jimenez. Dynamic analysis of distillation with thermal coupling for different operating conditions. Distillation and Absorption 2006, IChemeE Symp. No. 152, Edited by Eva Sorensen, UK, 728-736. ISBN:0-85295-505-7, 2006 [PDF]


2005


1. J.G. Segovia-Hernandez, E.A. Hernandez–Vargas, J.A. Marquez–Muñoz, S. Hernandez,  A. Jimenez. Control properties and thermodynamic analysis of two alternatives to thermally coupled distillation systems with side columns. Chemical and Biochemical Engineering Quarterly Journal, Vol.19 (4), 325-332, 2005 [PDF]