• Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models 

  Zhang, J.; Petersen, S.; Radivojevic, T.; Ramirez, A.; Pérez, A.; Abeliuk, E.; Sánchez, B.; Costello, Z.; Chen, Y.; Fero, M.; Garcia Martin, H.; Nielsen, J.; Keasling, J.; Jensen, M. (2019)

  In combination with advanced mechanistic modeling and the generation of high-quality multi-dimensional data sets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show ...

• Chemoinformatic-guided engineering of polyketide synthases 

  Zargar, A.; Lal, R.; Valencia, L.; Wang, J.; Backman, T.; Cruz-Morales, P.; Kothari, A.; Werts, M.; Wong, A.; Bailey, C.; Loubat, A.; Liu, Y.; Benites, V.; Chang, S.; Hernández, A.; Barajas, J.; Thompson, M.; Barcelos, C.; Anayah, R.; Garcia Martin, H.; Mukhopadhyay, A.; Baidoo, E.; Katz, L.; Keasling, J. (2019)

  Polyketide synthase (PKS) engineering is an attractive method to generate new molecules such as commodity, fine and specialty chemicals. A central challenge in PKS design is replacing a partially reductive module with a ...

• ART: A machine learning Automated Recommendation Tool for synthetic biology 

  Radivojević, T.; Costello, Z.; Workman, K.; Garcia Martin, H. (2019)

  Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable ...

• Mathematical models for glioma growth and migration inside the brain 

  Conte, M. (2021-01)

  Gliomas are the most prevalent, aggressive, and invasive subtype of primary brain tumors, characterized by rapid cell proliferation and great infiltration capacity. De- spite the advances of clinical research, these tumors ...

• Inflection, Canards and Folded Singularities in Excitable Systems: Application to a 3D FitzHugh–Nagumo Model 

  Uria-Albizuri, J.; Desroches, M.; Krupa, M.; Rodrigues, S. (2020-09-07)

  Specific kinds of physical and biological systems exhibit complex Mixed-Mode Oscillations mediated by folded-singularity canards in the context of slow-fast models. The present manuscript revisits these systems, specifically ...

• Why we should use topological data analysis in ageing: Towards defining the “topological shape of ageing” 

  Fülöp, T.; Desroches, M.; Cohen, A.; Santos, F.A.N.; Rodrigues, S. (2020-10-27)

  Living systems are subject to the arrow of time; from birth, they undergo complex transformations (self-organization) in a constant battle for survival, but inevitably ageing and disease trap them to death. Can ageing be ...

• Targeting Infectious Agents as a Therapeutic Strategy in Alzheimer’s Disease 

  Fülöp, T.; Munawara, U.; Larbi, A.; Desroches, M.; Rodrigues, S.; Catanzaro, M.; Guidolin, A.; Khalil, A.; Bernier, F.; Barron, A.E.; Hirokawa, K.; Beauregard, P.B.; Dumoulin, D.; Bellenger, J.-P.; Witkowski, J.M.; Frost, E. (2020-05-26)

  Alzheimer’s disease (AD) is the most prevalent dementia in the world. Its cause(s) are presently largely unknown. The most common explanation for AD, now, is the amyloid cascade hypothesis, which states that the cause of ...

• The Impact of Serotype Cross-Protection on Vaccine Trials: DENVax as a Case Study 

  Aguiar, M.; Stollenwerk, N. (2020-11)

  There is a growing public health need for effective preventive interventions against dengue, and a safe, effective and affordable dengue vaccine against the four serotypes would be a significant achievement for disease ...

• Modeling COVID-19: Challenges and results 

  Aguiar, M. (2020-10)

  Weird times we are living in. While lots of technological, medical and scientific advances are generated in a short period of time, we are now fighting a pandemic, trying to stop the spread of a new virus that has not only ...

• SHAR and effective SIR models: from dengue fever toy models to a COVID-19 fully parametrized SHARUCD framework 

  Aguiar, M.; Stollenwerk, N. (2020)

  We review basic models of severe/hospitalized and mild/asymptomatic infection spreading (with classes of susceptibles S, hopsitalized H, asymptomatic A and recovered R, hence SHAR-models) and develop the notion of comparing ...

• Reproduction ratio and growth rates: Measures for an unfolding pandemic 

  Aguiar, M.; Bidaurrazaga Van-Dierdonck, J.; Stollenwerk, N. (2020-05)

  The initial exponential growth rate of an epidemic is an important measure that follows directly from data at hand, commonly used to infer the basic reproduction number. As the growth rates λ(t) of tested positive COVID-19 ...

• Condition-specific mortality risk can explain differences in COVID-19 case fatality ratios around the globe 

  Aguiar, M.; Stollenwerk, N. (2020-09)

  Objectives With COVID-19 infections resulting in death according to a hierarchy of risks, with age and pre-existing health conditions enhancing disease severity, the objective of this study is to estimate the condition-specific ...

• Ethics of a partially effective dengue vaccine: Lessons from the Philippines 

  Halstead, B.S.; Katzelnick, L.C.; Russell, P.K.; Markoff, L.; Aguiar, M.; Dans, L.R.; Dans A , L. (2020-07)

  Dengvaxia, a chimeric yellow fever tetravalent dengue vaccine developed by SanofiPasteur is widely licensed in dengue-endemic countries. In a large cohort study Dengvaxia was found to partially protect children who had ...

•  Modelling COVID 19 in the Basque Country from introduction to control measure response 

  Aguiar, M.; Ortuondo, E.M.; Bidaurrazaga Van-Dierdonck, J.; Mar J; Stollenwerk, N. (2020-10)

  In March 2020, a multidisciplinary task force (so‐called Basque Modelling Task Force, BMTF) was created to assist the Basque health managers and Government during the COVID‐19 responses. BMTF is a modelling team, working ...

• Modeling latent infection transmissions through biosocial stochastic dynamics 

  Melnik, R.; Tadic, B. (2020-08)

  The events of the recent SARS-CoV-2 epidemics have shown the importance of social factors, especially given the large number of asymptomatic cases that effectively spread the virus, which can cause a medical emergency to ...

• Coupled Electro-mechanical Behavior of Microtubules 

  Singh, S.; Melnik, R. (2019)

  n this contribution, the coupled electro-mechanical behavior of the microtubules has been systematically investigated utilizing a continuum-based finite element framework. A three-dimensional computational model of a mi- ...

• Thermal ablation of biological tissues in disease treatment: A review of computational models and future directions 

  Singha, S.; Melnik, R. (2020-03)

  Percutaneous thermal ablation has proved to be an effective modality for treating both benign and malignant tumors in various tissues. Among these modalities, radiofrequency ablation (RFA) is the most promising and widely ...

• Atomistic to continuum model for studying mechanical properties of RNA nanotubes 

  Badua, S.; Prabhakara, S.; Melnik, R.; Singha, S. (2020-06)

  With rapid advancements in the emerging field of RNA nanotechnology, its current and potential applications, new important problems arise in our quest to better understand properties of RNA nanocomplexes. In this paper, ...

• Common principles and best practices for engineering microbiomes 

  Lawson, C.E.; Harcombe, W.R.; Hatzenpichler, R.; Noguera, D.R.; McMahon, K.D.; Lindemann, S.R.; Loffler, F.E.; O'Malley, M.A.; Garcia-Martin, H.; Pfleger, B.F.; Raskin, L.; Venturelli, O.S.; Weissbrodt, D.G. (2019)

  Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue hat structuring research ...

• Kinetic Parameter Estimation from Spectroscopic Data for a Multi-Stage Solid-Liquid Pharmaceutical Process 

  Schenk, C.; Biegler, L.T.; Han, L.; Mustakis, J. (2020-08-07)

  Laboratory and process measurements from spectroscopic instruments are ubiquitous in pharma processes, and directly using the data can pose a number of challenges for kinetic model building. Moreover, scaling up from ...

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