A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.

Current machine learning techniques enable robust association of biological signals with measured phenotypes, but these approaches are incapable of identifying causal relationships. Here, we develop an integrated "white-box" biochemical screening, network modeling, and machine learning approach for revealing causal mechanisms and apply this approach to understanding antibiotic efficacy. We counter-screen diverse metabolites against bactericidal antibiotics in Escherichia coli and simulate their corresponding metabolic states using a genome-scale metabolic network model. Regression of the measured screening data on model simulations reveals that purine biosynthesis participates in antibiotic lethality, which we validate experimentally. We show that antibiotic-induced adenine limitation increases ATP demand, which elevates central carbon metabolism activity and oxygen consumption, enhancing the killing effects of antibiotics. This work demonstrates how prospective network modeling can couple with machine learning to identify complex causal mechanisms underlying drug efficacy.

Bayesian network models identify cooperative GPCR:G protein interactions that contribute to G protein coupling.

Cooperative interactions in protein-protein interfaces demonstrate the interdependency or the linked network-like behavior and their effect on the coupling of proteins. Cooperative interactions also could cause ripple or allosteric effects at a distance in protein-protein interfaces. Although they are critically important in protein-protein interfaces, it is challenging to determine which amino acid pair interactions are cooperative. In this work, we have used Bayesian network modeling, an interpretable machine learning method, combined with molecular dynamics trajectories to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G protein-coupled receptor (GPCR) complexes with Gα subunits. Our results reveal six GPCR:Gα contacts that are common to the different Gα subtypes and show strong cooperativity in the formation of interface. Both the C terminus helix5 and the core of the G protein are codependent entities and play an important role in GPCR coupling. We show that a promiscuous GPCR coupling to different Gα subtypes, makes all the GPCR:Gα contacts that are specific to each Gα subtype (Gαs, Gαi, and Gαq). This work underscores the potential of data-driven Bayesian network modeling in elucidating the intricate dependencies and selectivity determinants in GPCR:G protein complexes, offering valuable insights into the dynamic nature of these essential cellular signaling components.

Variation in global network properties across risk factors for adolescent internalizing symptoms: evidence of cumulative effects on structure and connectivity.

BACKGROUND: Identifying adolescents at risk of internalizing problems is a key priority. However, studies have tended to consider such problems in simple ways using diagnoses, or item summaries. Network theory and methods instead allow for more complex interaction between symptoms. Two key hypotheses predict differences in global network properties for those at risk: altered structure and increased connectivity. METHODS: The current study evaluated these hypotheses for nine risk factors (e.g. income deprivation and low parent/carer support) individually and cumulatively in a large sample of 12-15 year-olds (N = 34 564). Recursive partitioning and bootstrapped networks were used to evaluate structural and connectivity differences. RESULTS: The pattern of network interactions was shown to be significantly different via recursive partitioning for all comparisons across risk-present/absent groups and levels of cumulative risk, except for income deprivation. However, the magnitude of differences appeared small. Most individual risk factors also showed relatively small effects for connectivity. Exceptions were noted for gender and sexual minority risk groups, as well as low parent/carer support, where larger effects were evident. A strong linear trend was observed between increasing cumulative risk exposure and connectivity. CONCLUSIONS: A robust approach to considering the effect of risk exposure on global network properties was demonstrated. Results are consistent with the ideas that pathological states are associated with higher connectivity, and that the number of risks, regardless of their nature, is important. Gender/sexual minority status and low parent/carer support had the biggest individual impacts on connectivity, suggesting these are particularly important for identification and prevention.

Mapping illegal trade routes of live cheetahs from the Horn of Africa to the Arabian Peninsula.

Less than 7000 cheetahs (Acinonyx jubatus) persist in Africa. Although human-wildlife conflict, habitat degradation, and loss of prey are major threats to cheetah populations, illegal trade in live cubs for pets may have the most significant impact on populations in the Horn of Africa. We developed a novel, stepwise decision support tool to predict probable trafficking routes by leveraging the power of distinct modeling approaches. First, we created a cheetah habitat suitability index (HSI) to determine where source cheetah populations may occur. We then created a trafficking network model linking known and predicted cheetah populations with documented destinations in the Arabian Peninsula. A significant area in Eastern Ethiopia and Northern Somalia was estimated to harbor undocumented cheetahs. When these predicted populations were used as a supply source, the trafficking network model showed multiple routes passing through Somaliland and across the Gulf of Aden to Yemen, supporting the notion that undocumented cheetahs may be supplying pet market demands. Though we demonstrate how our decision support tool can inform law enforcement, conservation strategies, and community engagement, we caution that our results are not fully validated due to limited accessibility, alternative trafficking routes, and the cryptic nature of illegal wildlife trade.

Mapeo de las rutas de tráfico ilegal de chitas vivas del Cuerno de África a la Península Arábiga Resumen En África hay menos de 7,000 chitas (Acinonyx jubatus). Aunque las principales amenazas para las poblaciones de chitas son el conflicto humano­fauna, la degradación del hábitat y la pérdida de presas, el mercado ilegal de cachorros como mascotas puede que tenga el impacto más significativo en las poblaciones del Cuerno de África. Desarrollamos una novedosa herramienta por pasos para la toma de decisiones para predecir las probables rutas de tráfico aprovechando el poder de las distintas estrategias de modelación. Primero creamos un índice de idoneidad del hábitat (IIH) de las chitas para determinar en dónde podrían encontrarse las poblaciones de origen de chitas. Después creamos un modelo de redes de tráfico que conecta las poblaciones conocidas y pronosticadas con los destinos documentados en la Península Arábiga. Estimamos que un área significativa en el este de Etiopía y en el norte de Somalia albergaba chitas de manera ilegal. Cuando usamos estas poblaciones pronosticadas como fuente de suministro, el modelo de redes de tráfico mostró varias rutas que atraviesan Somalilandia y el Golfo de Adén hacia Yemen, lo que apoya la noción de que las chitas ilegales podrían estar cumpliendo las demandas del mercado de mascotas. Aunque demostramos que nuestra herramienta de apoyo para las decisiones puede informar al orden público, también advertimos que nuestros resultados no están del todo validados debido a la accesibilidad restringida, rutas alternativas de tráfico y la naturaleza críptica del mercado ilegal de fauna.

Hydrologic Connectivity Regulates Riverine N2O Sources and Dynamics.

Indirect nitrous oxide (N2O) emissions from streams and rivers are a poorly constrained term in the global N2O budget. Current models of riverine N2O emissions place a strong focus on denitrification in groundwater and riverine environments as a dominant source of riverine N2O, but do not explicitly consider direct N2O input from terrestrial ecosystems. Here, we combine N2O isotope measurements and spatial stream network modeling to show that terrestrial-aquatic interactions, driven by changing hydrologic connectivity, control the sources and dynamics of riverine N2O in a mesoscale river network within the U.S. Corn Belt. We find that N2O produced from nitrification constituted a substantial fraction (i.e., >30%) of riverine N2O across the entire river network. The delivery of soil-produced N2O to streams was identified as a key mechanism for the high nitrification contribution and potentially accounted for more than 40% of the total riverine emission. This revealed large terrestrial N2O input implies an important climate-N2O feedback mechanism that may enhance riverine N2O emissions under a wetter and warmer climate. Inadequate representation of hydrologic connectivity in observations and modeling of riverine N2O emissions may result in significant underestimations.

Sensitivity to geometric shape regularity in humans and baboons: A putative signature of human singularity.

Among primates, humans are special in their ability to create and manipulate highly elaborate structures of language, mathematics, and music. Here we show that this sensitivity to abstract structure is already present in a much simpler domain: the visual perception of regular geometric shapes such as squares, rectangles, and parallelograms. We asked human subjects to detect an intruder shape among six quadrilaterals. Although the intruder was always defined by an identical amount of displacement of a single vertex, the results revealed a geometric regularity effect: detection was considerably easier when either the base shape or the intruder was a regular figure comprising right angles, parallelism, or symmetry rather than a more irregular shape. This effect was replicated in several tasks and in all human populations tested, including uneducated Himba adults and French kindergartners. Baboons, however, showed no such geometric regularity effect, even after extensive training. Baboon behavior was captured by convolutional neural networks (CNNs), but neither CNNs nor a variational autoencoder captured the human geometric regularity effect. However, a symbolic model, based on exact properties of Euclidean geometry, closely fitted human behavior. Our results indicate that the human propensity for symbolic abstraction permeates even elementary shape perception. They suggest a putative signature of human singularity and provide a challenge for nonsymbolic models of human shape perception.

Subgrouping with Chain Graphical VAR Models.

Recent years have seen the emergence of an "idio-thetic" class of methods to bridge the gap between nomothetic and idiographic inference. These methods describe nomothetic trends in idiographic processes by pooling intraindividual information across individuals to inform group-level inference or vice versa. The current work introduces a novel "idio-thetic" model: the subgrouped chain graphical vector autoregression (scGVAR). The scGVAR is unique in its ability to identify subgroups of individuals who share common dynamic network structures in both lag(1) and contemporaneous effects. Results from Monte Carlo simulations indicate that the scGVAR shows promise over similar approaches when clusters of individuals differ in their contemporaneous dynamics and in showing increased sensitivity in detecting nuanced group differences while keeping Type-I error rates low. In contrast, a competing approach-the Alternating Least Squares VAR (ALS VAR) performs well when groups were separated by larger distances. Further considerations are provided regarding applications of the ALS VAR and scGVAR on real data and the strengths and limitations of both methods.

Dynamic Individual Risk Networks: Personalized Network Modelling Based on Experience Sampling Data.

Following a network perspective, risk of sexual reoffending can be understood as a construct that emerges from the interactions between risk factors. If these interrelationships are validly mapped out, this leads to an increased understanding of the risk and thus may contribute to more effective and/or more efficient interventions. This paper reports on personalized network modeling mapping the interrelationships of dynamic risk factors for an individual convicted of sexual offenses, using experience sampling (ESM) based on Stable-2007 items. The longitudinal character of ESM enables both the assessment of interrelations between risk factors within a timeframe and the relationships between risk factors over time. Networks are calculated and compared to the clinical assessment of interrelationships between the risk factors.

Normalized L3-based link prediction in protein-protein interaction networks.

BACKGROUND: Protein-protein interaction (PPI) data is an important type of data used in functional genomics. However, high-throughput experiments are often insufficient to complete the PPI interactome of different organisms. Computational techniques are thus used to infer missing data, with link prediction being one such approach that uses the structure of the network of PPIs known so far to identify non-edges whose addition to the network would make it more sound, according to some underlying assumptions. Recently, a new idea called the L3 principle introduced biological motivation into PPI link predictions, yielding predictors that are superior to general-purpose link predictors for complex networks. Interestingly, the L3 principle can be interpreted in another way, so that other signatures of PPI networks can also be characterized for PPI predictions. This alternative interpretation uncovers candidate PPIs that the current L3-based link predictors may not be able to fully capture, underutilizing the L3 principle. RESULTS: In this article, we propose a formulation of link predictors that we call NormalizedL3 (L3N) which addresses certain missing elements within L3 predictors in the perspective of network modeling. Our computational validations show that the L3N predictors are able to find missing PPIs more accurately (in terms of true positives among the predicted PPIs) than the previously proposed methods on several datasets from the literature, including BioGRID, STRING, MINT, and HuRI, at the cost of using more computation time in some of the cases. In addition, we found that L3-based link predictors (including L3N) ranked a different pool of PPIs higher than the general-purpose link predictors did. This suggests that different types of PPIs can be predicted based on different topological assumptions, and that even better PPI link predictors may be obtained in the future by improved network modeling.

Surveying nonvisual arrestins reveals allosteric interactions between functional sites.

Arrestins are important scaffolding proteins that are expressed in all vertebrate animals. They regulate cell-signaling events upon binding to active G-protein coupled receptors (GPCR) and trigger endocytosis of active GPCRs. While many of the functional sites on arrestins have been characterized, the question of how these sites interact is unanswered. We used anisotropic network modeling (ANM) together with our covariance compliment techniques to survey all the available structures of the nonvisual arrestins to map how structural changes and protein-binding affect their structural dynamics. We found that activation and clathrin binding have a marked effect on arrestin dynamics, and that these dynamics changes are localized to a small number of distant functional sites. These sites include α-helix 1, the lariat loop, nuclear localization domain, and the C-domain ß-sheets on the C-loop side. Our techniques suggest that clathrin binding and/or GPCR activation of arrestin perturb the dynamics of these sites independent of structural changes.

Cross-attractor modeling of resting-state functional connectivity in psychiatric disorders.

Resting-state functional connectivity (RSFC) is altered across various psychiatric disorders. Brain network modeling (BNM) has the potential to reveal the neurobiological underpinnings of such abnormalities by dynamically modeling the structure-function relationship and examining biologically relevant parameters after fitting the models with real data. Although innovative BNM approaches have been developed, two main issues need to be further addressed. First, previous BNM approaches are primarily limited to simulating noise-driven dynamics near a chosen attractor (or a stable brain state). An alternative approach is to examine multi(or cross)-attractor dynamics, which can be used to better capture non-stationarity and switching between states in the resting brain. Second, previous BNM work is limited to characterizing one disorder at a time. Given the large degree of co-morbidity across psychiatric disorders, comparing BNMs across disorders might provide a novel avenue to generate insights regarding the dynamical features that are common across (vs. specific to) disorders. Here, we address these issues by (1) examining the layout of the attractor repertoire over the entire multi-attractor landscape using a recently developed cross-attractor BNM approach; and (2) characterizing and comparing multiple disorders (schizophrenia, bipolar, and ADHD) with healthy controls using an openly available and moderately large multimodal dataset from the UCLA Consortium for Neuropsychiatric Phenomics. Both global and local differences were observed across disorders. Specifically, the global coupling between regions was significantly decreased in schizophrenia patients relative to healthy controls. At the same time, the ratio between local excitation and inhibition was significantly higher in the schizophrenia group than the ADHD group. In line with these results, the schizophrenia group had the lowest switching costs (energy gaps) across groups for several networks including the default mode network. Paired comparison also showed that schizophrenia patients had significantly lower energy gaps than healthy controls for the somatomotor and visual networks. Overall, this study provides preliminary evidence supporting transdiagnostic multi-attractor BNM approaches to better understand psychiatric disorders' pathophysiology.

The triple psychological and neural bases underlying procrastination: Evidence based on a two-year longitudinal study.

The triple brain anatomical network model of procrastination theorized procrastination as the result of psychological and neural dysfunction implicated in self-control, emotion regulation and episodic prospection. However, no studies have provided empirical evidence for such model. To address this issue, we designed a two-wave longitudinal study where participants underwent the resting-state scanning and completed the questionnaires at two time-points that spanned 2-year apart (T1, n = 457; T2, n = 457). Using the cross-lagged panel network modeling (CLPN), we found that triple psychological components at T1, including self-control, emotion regulation (i.e., reappraisal) and episodic prospection, negatively predicted procrastination at T2 in the temporal network. Moreover, the CLPN modeling found that functional connectivity between networks accounting for episodic prospection (EP) and emotion regulation (ER) positively predicted future procrastination in the temporal network. The centrality analyzes further showed that procrastination was greatly affected by other nodes, whilst the psychological component (i.e., episodic prospection), and the functional network connectivity (FNC) of EP- ER exerted strongest impacts on other nodes in the networks, which indicated that treatments targeting episodic prospection might largely help reduce procrastination. Collectively, these findings firstly provide evidence for testifying the triple brain anatomical network model of procrastination, and highlights the contribution of triple psychological and neural components implicated in self-control, emotion regulation and episodic prospection to procrastination that enhances our understanding of causes of procrastination.

Network-based modeling of herb combinations in traditional Chinese medicine.

Traditional Chinese medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein-protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.

Network modeling of major depressive disorder symptoms in adult women.

BACKGROUND: Major depressive disorder (MDD) is one of the growing human mental health challenges facing the global health care system. In this study, the structural connectivity between symptoms of MDD is explored using two different network modeling approaches. METHODS: Data are from 'the Virginia Adult Twin Study of Psychiatric and Substance Use Disorders (VATSPSUD)'. A cohort of N = 2163 American Caucasian female-female twins was assessed as part of the VATSPSUD study. MDD symptoms were assessed using personal structured clinical interviews. Two network analyses were conducted. First, an undirected network model was estimated to explore the connectivity between the MDD symptoms. Then, using a Bayesian network, we computed a directed acyclic graph (DAG) to investigate possible directional relationships between symptoms. RESULTS: Based on the results of the undirected network, the depressed mood symptom had the highest centrality value, indicating its importance in the overall network of MDD symptoms. Bayesian network analysis indicated that depressed mood emerged as a plausible driving symptom for activating other symptoms. These results are consistent with DSM-5 guidelines for MDD. Also, somatic weight and appetite symptoms appeared as the strongest connections in both networks. CONCLUSIONS: We discuss how the findings of our study might help future research to detect clinically relevant symptoms and possible directional relationships between MDD symptoms defining major depression episodes, which would help identify potential tailored interventions. This is the first study to investigate the network structure of VATSPSUD data using both undirected and directed network models.

Gene Regulatory Networks in Coronary Artery Disease.

PURPOSE OF REVIEW: Coronary artery disease is a complex disorder and the leading cause of mortality worldwide. As technologies for the generation of high-throughput multiomics data have advanced, gene regulatory network modeling has become an increasingly powerful tool in understanding coronary artery disease. This review summarizes recent and novel gene regulatory network tools for bulk tissue and single cell data, existing databases for network construction, and applications of gene regulatory networks in coronary artery disease. RECENT FINDINGS: New gene regulatory network tools can integrate multiomics data to elucidate complex disease mechanisms at unprecedented cellular and spatial resolutions. At the same time, updates to coronary artery disease expression data in existing databases have enabled researchers to build gene regulatory networks to study novel disease mechanisms. Gene regulatory networks have proven extremely useful in understanding CAD heritability beyond what is explained by GWAS loci and in identifying mechanisms and key driver genes underlying disease onset and progression. Gene regulatory networks can holistically and comprehensively address the complex nature of coronary artery disease. In this review, we discuss key algorithmic approaches to construct gene regulatory networks and highlight state-of-the-art methods that model specific modes of gene regulation. We also explore recent applications of these tools in coronary artery disease patient data repositories to understand disease heritability and shared and distinct disease mechanisms and key driver genes across tissues, between sexes, and between species.

Inhibition of 3-phosphoinositide-dependent protein kinase 1 (PDK1) can revert cellular senescence in human dermal fibroblasts.

Cellular senescence is defined as a stable, persistent arrest of cell proliferation. Here, we examine whether senescent cells can lose senescence hallmarks and reenter a reversible state of cell-cycle arrest (quiescence). We constructed a molecular regulatory network of cellular senescence based on previous experimental evidence. To infer the regulatory logic of the network, we performed phosphoprotein array experiments with normal human dermal fibroblasts and used the data to optimize the regulatory relationships between molecules with an evolutionary algorithm. From ensemble analysis of network models, we identified 3-phosphoinositide-dependent protein kinase 1 (PDK1) as a promising target for inhibitors to convert the senescent state to the quiescent state. We showed that inhibition of PDK1 in senescent human dermal fibroblasts eradicates senescence hallmarks and restores entry into the cell cycle by suppressing both nuclear factor κB and mTOR signaling, resulting in restored skin regeneration capacity. Our findings provide insight into a potential therapeutic strategy to treat age-related diseases associated with the accumulation of senescent cells.

Evaluating Discrete Time Methods for Subgrouping Continuous Processes.

Rapid developments over the last several decades have brought increased focus and attention to the role of time scales and heterogeneity in the modeling of human processes. To address these emerging questions, subgrouping methods developed in the discrete-time framework-such as the vector autoregression (VAR)-have undergone widespread development to identify shared nomothetic trends from idiographic modeling results. Given the dependence of VAR-based parameters on the measurement intervals of the data, we sought to clarify the strengths and limitations of these methods in recovering subgroup dynamics under different measurement intervals. Building on the work of Molenaar and collaborators for subgrouping individual time-series by means of the subgrouped chain graphical VAR (scgVAR) and the subgrouping option in the group iterative multiple model estimation (S-GIMME), we present results from a Monte Carlo study aimed at addressing the implications of identifying subgroups using these discrete-time methods when applied to continuous-time data. Results indicate that discrete-time subgrouping methods perform well at recovering true subgroups when the measurement intervals are large enough to capture the full range of a system's dynamics, either via lagged or contemporaneous effects. Further implications and limitations are discussed therein.

Cell-Type-Specific Gene Regulatory Networks of Pro-Inflammatory and Pro-Resolving Lipid Mediator Biosynthesis in the Immune System.

Lipid mediators are important regulators in inflammatory responses, and their biosynthetic pathways are targeted by commonly used anti-inflammatory drugs. Switching from pro-inflammatory lipid mediators (PIMs) to specialized pro-resolving (SPMs) is a critical step toward acute inflammation resolution and preventing chronic inflammation. Although the biosynthetic pathways and enzymes for PIMs and SPMs have now been largely identified, the actual transcriptional profiles underlying the immune cell type-specific transcriptional profiles of these mediators are still unknown. Using the Atlas of Inflammation Resolution, we created a large network of gene regulatory interactions linked to the biosynthesis of SPMs and PIMs. By mapping single-cell sequencing data, we identified cell type-specific gene regulatory networks of the lipid mediator biosynthesis. Using machine learning approaches combined with network features, we identified cell clusters of similar transcriptional regulation and demonstrated how specific immune cell activation affects PIM and SPM profiles. We found substantial differences in regulatory networks in related cells, accounting for network-based preprocessing in functional single-cell analyses. Our results not only provide further insight into the gene regulation of lipid mediators in the immune response but also shed light on the contribution of selected cell types in their biosynthesis.

From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on "Allosteric Intersection" of Biochemical and Big Data Approaches.

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric regulation, the emerging structural biology technologies and AI approaches remains largely unexplored, calling for the development of AI-augmented integrative structural biology. In this review, we focus on the latest remarkable progress in deep high-throughput mining and comprehensive mapping of allosteric protein landscapes and allosteric regulatory mechanisms as well as on the new developments in AI methods for prediction and characterization of allosteric binding sites on the proteome level. We also discuss new AI-augmented structural biology approaches that expand our knowledge of the universe of protein dynamics and allostery. We conclude with an outlook and highlight the importance of developing an open science infrastructure for machine learning studies of allosteric regulation and validation of computational approaches using integrative studies of allosteric mechanisms. The development of community-accessible tools that uniquely leverage the existing experimental and simulation knowledgebase to enable interrogation of the allosteric functions can provide a much-needed boost to further innovation and integration of experimental and computational technologies empowered by booming AI field.

Health Care Logistics Network Design and Analysis on Pandemic Outbreaks: Insights From COVID-19.

Health care systems throughout the world are under pressure as a result of COVID-19. It is over two years since the first case was announced in China and health care providers are continuing to struggle with this fatal infectious disease in intensive care units and inpatient wards. Meanwhile, the burden of postponed routine medical procedures has become greater as the pandemic has progressed. We believe that establishing separate health care institutions for infected and non-infected patients would provide safer and better quality health care services. The aim of this study is to find the appropriate number and location of dedicated health care institutions which would only treat individuals infected by a pandemic during an outbreak. For this purpose, a decision-making framework including two multi-objective mixed-integer programming models is developed. At the strategic level, the locations of designated pandemic hospitals are optimized. At the tactical level, we determine the locations and operation durations of temporary isolation centers which treat mildly and moderately symptomatic patients. The developed framework provides assessments of the distance that infected patients travel, the routine medical services expected to be disrupted, two-way distances between new facilities (designated pandemic hospitals and isolation centers), and the infection risk in the population. To demonstrate the applicability of the suggested models, we perform a case study for the European side of Istanbul. In the base case, seven designated pandemic hospitals and four isolation centers are established. In sensitivity analyses, 23 cases are analyzed and compared to provide support to decision makers.