PLoS Computational Biology

Publishing science
  • Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies
    [Apr 2015]

    by Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields

    Identifying effective therapeutic drug combinations that modulate complex signaling pathways in platelets is central to the advancement of effective anti-thrombotic therapies. However, there is no systems model of the platelet that predicts responses to different inhibitor combinations. We developed an approach which goes beyond current inhibitor-inhibitor combination screening to efficiently consider other signaling aspects that may give insights into the behaviour of the platelet as a system. We investigated combinations of platelet inhibitors and activators. We evaluated three distinct strands of information, namely: activator-inhibitor combination screens (testing a panel of inhibitors against a panel of activators); inhibitor-inhibitor synergy screens; and activator-activator synergy screens. We demonstrated how these analyses may be efficiently performed, both experimentally and computationally, to identify particular combinations of most interest. Robust tests of activator-activator synergy and of inhibitor-inhibitor synergy required combinations to show significant excesses over the double doses of each component. Modeling identified multiple effects of an inhibitor of the P2Y12 ADP receptor, and complementarity between inhibitor-inhibitor synergy effects and activator-inhibitor combination effects. This approach accelerates the mapping of combination effects of compounds to develop combinations that may be therapeutically beneficial. We integrated the three information sources into a unified model that predicted the benefits of a triple drug combination targeting ADP, thromboxane and thrombin signaling.
    Categories: Journal Articles
  • A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions
    [Apr 2015]

    by Pedro Saa, Lars K. Nielsen

    Kinetic models provide the means to understand and predict the dynamic behaviour of enzymes upon different perturbations. Despite their obvious advantages, classical parameterizations require large amounts of data to fit their parameters. Particularly, enzymes displaying complex reaction and regulatory (allosteric) mechanisms require a great number of parameters and are therefore often represented by approximate formulae, thereby facilitating the fitting but ignoring many real kinetic behaviours. Here, we show that full exploration of the plausible kinetic space for any enzyme can be achieved using sampling strategies provided a thermodynamically feasible parameterization is used. To this end, we developed a General Reaction Assembly and Sampling Platform (GRASP) capable of consistently parameterizing and sampling accurate kinetic models using minimal reference data. The former integrates the generalized MWC model and the elementary reaction formalism. By formulating the appropriate thermodynamic constraints, our framework enables parameterization of any oligomeric enzyme kinetics without sacrificing complexity or using simplifying assumptions. This thermodynamically safe parameterization relies on the definition of a reference state upon which feasible parameter sets can be efficiently sampled. Uniform sampling of the kinetics space enabled dissecting enzyme catalysis and revealing the impact of thermodynamics on reaction kinetics. Our analysis distinguished three reaction elasticity regions for common biochemical reactions: a steep linear region (0> ΔGr >-2 kJ/mol), a transition region (-2> ΔGr >-20 kJ/mol) and a constant elasticity region (ΔGr <-20 kJ/mol). We also applied this framework to model more complex kinetic behaviours such as the monomeric cooperativity of the mammalian glucokinase and the ultrasensitive response of the phosphoenolpyruvate carboxylase of Escherichia coli. In both cases, our approach described appropriately not only the kinetic behaviour of these enzymes, but it also provided insights about the particular features underpinning the observed kinetics. Overall, this framework will enable systematic parameterization and sampling of enzymatic reactions.
    Categories: Journal Articles
  • General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks
    [Apr 2015]

    by Joon-Young Moon, UnCheol Lee, Stefanie Blain-Moraes, George A. Mashour

    The balance of global integration and functional specialization is a critical feature of efficient brain networks, but the relationship of global topology, local node dynamics and information flow across networks has yet to be identified. One critical step in elucidating this relationship is the identification of governing principles underlying the directionality of interactions between nodes. Here, we demonstrate such principles through analytical solutions based on the phase lead/lag relationships of general oscillator models in networks. We confirm analytical results with computational simulations using general model networks and anatomical brain networks, as well as high-density electroencephalography collected from humans in the conscious and anesthetized states. Analytical, computational, and empirical results demonstrate that network nodes with more connections (i.e., higher degrees) have larger amplitudes and are directional targets (phase lag) rather than sources (phase lead). The relationship of node degree and directionality therefore appears to be a fundamental property of networks, with direct applicability to brain function. These results provide a foundation for a principled understanding of information transfer across networks and also demonstrate that changes in directionality patterns across states of human consciousness are driven by alterations of brain network topology.
    Categories: Journal Articles
  • Twisting Right to Left: A…A Mismatch in a CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation
    [Apr 2015]

    by Noorain Khan, Narendar Kolimi, Thenmalarchelvi Rathinavelan

    Conformational polymorphism of DNA is a major causative factor behind several incurable trinucleotide repeat expansion disorders that arise from overexpansion of trinucleotide repeats located in coding/non-coding regions of specific genes. Hairpin DNA structures that are formed due to overexpansion of CAG repeat lead to Huntington’s disorder and spinocerebellar ataxias. Nonetheless, DNA hairpin stem structure that generally embraces B-form with canonical base pairs is poorly understood in the context of periodic noncanonical A…A mismatch as found in CAG repeat overexpansion. Molecular dynamics simulations on DNA hairpin stems containing A…A mismatches in a CAG repeat overexpansion show that A…A dictates local Z-form irrespective of starting glycosyl conformation, in sharp contrast to canonical DNA duplex. Transition from B-to-Z is due to the mechanistic effect that originates from its pronounced nonisostericity with flanking canonical base pairs facilitated by base extrusion, backbone and/or base flipping. Based on these structural insights we envisage that such an unusual DNA structure of the CAG hairpin stem may have a role in disease pathogenesis. As this is the first study that delineates the influence of a single A…A mismatch in reversing DNA helicity, it would further have an impact on understanding DNA mismatch repair.
    Categories: Journal Articles
  • Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees
    [Apr 2015]

    by Ickwon Choi, Amy W. Chung, Todd J. Suscovich, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayaphan, Jaranit Kaewkungwal, Robert J. O'Connell, Donald Francis, Merlin L. Robb, Nelson L. Michael, Jerome H. Kim, Galit Alter, Margaret E. Ackerman, Chris Bailey-Kellogg

    The adaptive immune response to vaccination or infection can lead to the production of specific antibodies to neutralize the pathogen or recruit innate immune effector cells for help. The non-neutralizing role of antibodies in stimulating effector cell responses may have been a key mechanism of the protection observed in the RV144 HIV vaccine trial. In an extensive investigation of a rich set of data collected from RV144 vaccine recipients, we here employ machine learning methods to identify and model associations between antibody features (IgG subclass and antigen specificity) and effector function activities (antibody dependent cellular phagocytosis, cellular cytotoxicity, and cytokine release). We demonstrate via cross-validation that classification and regression approaches can effectively use the antibody features to robustly predict qualitative and quantitative functional outcomes. This integration of antibody feature and function data within a machine learning framework provides a new, objective approach to discovering and assessing multivariate immune correlates.
    Categories: Journal Articles
  • Optimising and Communicating Options for the Control of Invasive Plant Disease When There Is Epidemiological Uncertainty
    [Apr 2015]

    by Nik J. Cunniffe, Richard O. J. H. Stutt, R. Erik DeSimone, Tim R. Gottwald, Christopher A. Gilligan

    Although local eradication is routinely attempted following introduction of disease into a new region, failure is commonplace. Epidemiological principles governing the design of successful control are not well-understood. We analyse factors underlying the effectiveness of reactive eradication of localised outbreaks of invading plant disease, using citrus canker in Florida as a case study, although our results are largely generic, and apply to other plant pathogens (as we show via our second case study, citrus greening). We demonstrate how to optimise control via removal of hosts surrounding detected infection (i.e. localised culling) using a spatially-explicit, stochastic epidemiological model. We show how to define optimal culling strategies that take account of stochasticity in disease spread, and how the effectiveness of disease control depends on epidemiological parameters determining pathogen infectivity, symptom emergence and spread, the initial level of infection, and the logistics and implementation of detection and control. We also consider how optimal culling strategies are conditioned on the levels of risk acceptance/aversion of decision makers, and show how to extend the analyses to account for potential larger-scale impacts of a small-scale outbreak. Control of local outbreaks by culling can be very effective, particularly when started quickly, but the optimum strategy and its performance are strongly dependent on epidemiological parameters (particularly those controlling dispersal and the extent of any cryptic infection, i.e. infectious hosts prior to symptoms), the logistics of detection and control, and the level of local and global risk that is deemed to be acceptable. A version of the model we developed to illustrate our methodology and results to an audience of stakeholders, including policy makers, regulators and growers, is available online as an interactive, user-friendly interface at http://www.webidemics.com/. This version of our model allows the complex epidemiological principles that underlie our results to be communicated to a non-specialist audience.
    Categories: Journal Articles
  • Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks
    [Apr 2015]

    by Adam J. Kucharski, W. John Edmunds

    The transmission potential of a novel infection depends on both the inherent transmissibility of a pathogen, and the level of susceptibility in the host population. However, distinguishing between these pathogen- and population-specific properties typically requires detailed serological studies, which are rarely available in the early stages of an outbreak. Using a simple transmission model that incorporates age-stratified social mixing patterns, we present a novel method for characterizing the transmission potential of subcritical infections, which have effective reproduction number R<1, from readily available data on the size of outbreaks. We show that the model can identify the extent to which outbreaks are driven by inherent pathogen transmissibility and pre-existing population immunity, and can generate unbiased estimates of the effective reproduction number. Applying the method to real-life infections, we obtained accurate estimates for the degree of age-specific immunity against monkeypox, influenza A(H5N1) and A(H7N9), and refined existing estimates of the reproduction number. Our results also suggest minimal pre-existing immunity to MERS-CoV in humans. The approach we describe can therefore provide crucial information about novel infections before serological surveys and other detailed analyses are available. The methods would also be applicable to data stratified by factors such as profession or location, which would make it possible to measure the transmission potential of emerging infections in a wide range of settings.
    Categories: Journal Articles
  • Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae
    [Apr 2015]

    by Giulia Menconi, Andrea Bedini, Roberto Barale, Isabella Sbrana

    In this study we provide the first comprehensive map of DNA conformational flexibility in Saccharomyces cerevisiae complete genome. Flexibility plays a key role in DNA supercoiling and DNA/protein binding, regulating DNA transcription, replication or repair. Specific interest in flexibility analysis concerns its relationship with human genome instability. Enrichment in flexible sequences has been detected in unstable regions of human genome defined fragile sites, where genes map and carry frequent deletions and rearrangements in cancer. Flexible sequences have been suggested to be the determinants of fragile gene proneness to breakage; however, their actual role and properties remain elusive. Our in silico analysis carried out genome-wide via the StabFlex algorithm, shows the conserved presence of highly flexible regions in budding yeast genome as well as in genomes of other Saccharomyces sensu stricto species. Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3’UTR, a region affecting mRNA translation, localization and stability. (TA)n repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE) signals. ORFs with flexible peaks share common features. Transcripts are characterized by decreased half-life: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. Our findings support the functional importance of flexibility peaks, suggesting that the flexible sequence may be derived by an expansion of canonical TAYRTA polyadenylation efficiency element. The flexible (TA)n repeat amplification could be the outcome of an evolutionary neofunctionalization leading to a differential 3’-end processing and expression regulation in genes with peculiar function. Our study provides a new support to the functional role of flexibility in genomes and a strategy for its characterization inside human fragile sites.
    Categories: Journal Articles
  • What Is the Most Realistic Single-Compartment Model of Spike Initiation?
    [Apr 2015]

    by Romain Brette

    A large variety of neuron models are used in theoretical and computational neuroscience, and among these, single-compartment models are a popular kind. These models do not explicitly include the dendrites or the axon, and range from the Hodgkin-Huxley (HH) model to various flavors of integrate-and-fire (IF) models. The main classes of models differ in the way spikes are initiated. Which one is the most realistic? Starting with some general epistemological considerations, I show that the notion of realism comes in two dimensions: empirical content (the sort of predictions that a model can produce) and empirical accuracy (whether these predictions are correct). I then examine the realism of the main classes of single-compartment models along these two dimensions, in light of recent experimental evidence.
    Categories: Journal Articles
  • GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
    [Apr 2015]

    by Teresa K. Atwood, Erik Bongcam-Rudloff, Michelle E. Brazas, Manuel Corpas, Pascale Gaudet, Fran Lewitter, Nicola Mulder, Patricia M. Palagi, Maria Victoria Schneider, Celia W. G. van Gelder, GOBLET Consortium

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.
    Categories: Journal Articles
  • Quantification of Diabetes Comorbidity Risks across Life Using Nation-Wide Big Claims Data
    [Apr 2015]

    by Peter Klimek, Alexandra Kautzky-Willer, Anna Chmiel, Irmgard Schiller-Frühwirth, Stefan Thurner

    Despite substantial progress in the study of diabetes, important questions remain about its comorbidities and clinical heterogeneity. To explore these issues, we develop a framework allowing for the first time to quantify nation-wide risks and their age- and sex-dependence for each diabetic comorbidity, and whether the association may be consequential or causal, in a sample of almost two million patients. This study is equivalent to nearly 40,000 single clinical measurements. We confirm the highly controversial relation of increased risk for Parkinson’s disease in diabetics, using a 10 times larger cohort than previous studies on this relation. Detection of type 1 diabetes leads detection of depressions, whereas there is a strong comorbidity relation between type 2 diabetes and schizophrenia, suggesting similar pathogenic or medication-related mechanisms. We find significant sex differences in the progression of, for instance, sleep disorders and congestive heart failure in diabetic patients. Hypertension is a highly sex-sensitive comorbidity with females being at lower risk during fertile age, but at higher risk otherwise. These results may be useful to improve screening practices in the general population. Clinical management of diabetes must address age- and sex-dependence of multiple comorbid conditions.
    Categories: Journal Articles
  • A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
    [Apr 2015]

    by Susan Dina Ghiassian, Jörg Menche, Albert-László Barabási

    The observation that disease associated proteins often interact with each other has fueled the development of network-based approaches to elucidate the molecular mechanisms of human disease. Such approaches build on the assumption that protein interaction networks can be viewed as maps in which diseases can be identified with localized perturbation within a certain neighborhood. The identification of these neighborhoods, or disease modules, is therefore a prerequisite of a detailed investigation of a particular pathophenotype. While numerous heuristic methods exist that successfully pinpoint disease associated modules, the basic underlying connectivity patterns remain largely unexplored. In this work we aim to fill this gap by analyzing the network properties of a comprehensive corpus of 70 complex diseases. We find that disease associated proteins do not reside within locally dense communities and instead identify connectivity significance as the most predictive quantity. This quantity inspires the design of a novel Disease Module Detection (DIAMOnD) algorithm to identify the full disease module around a set of known disease proteins. We study the performance of the algorithm using well-controlled synthetic data and systematically validate the identified neighborhoods for a large corpus of diseases.
    Categories: Journal Articles
  • A Bayesian Model of Category-Specific Emotional Brain Responses
    [Apr 2015]

    by Tor D. Wager, Jian Kang, Timothy D. Johnson, Thomas E. Nichols, Ajay B. Satpute, Lisa Feldman Barrett

    Understanding emotion is critical for a science of healthy and disordered brain function, but the neurophysiological basis of emotional experience is still poorly understood. We analyzed human brain activity patterns from 148 studies of emotion categories (2159 total participants) using a novel hierarchical Bayesian model. The model allowed us to classify which of five categories—fear, anger, disgust, sadness, or happiness—is engaged by a study with 66% accuracy (43-86% across categories). Analyses of the activity patterns encoded in the model revealed that each emotion category is associated with unique, prototypical patterns of activity across multiple brain systems including the cortex, thalamus, amygdala, and other structures. The results indicate that emotion categories are not contained within any one region or system, but are represented as configurations across multiple brain networks. The model provides a precise summary of the prototypical patterns for each emotion category, and demonstrates that a sufficient characterization of emotion categories relies on (a) differential patterns of involvement in neocortical systems that differ between humans and other species, and (b) distinctive patterns of cortical-subcortical interactions. Thus, these findings are incompatible with several contemporary theories of emotion, including those that emphasize emotion-dedicated brain systems and those that propose emotion is localized primarily in subcortical activity. They are consistent with componential and constructionist views, which propose that emotions are differentiated by a combination of perceptual, mnemonic, prospective, and motivational elements. Such brain-based models of emotion provide a foundation for new translational and clinical approaches.
    Categories: Journal Articles
  • Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
    [Apr 2015]

    by Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška, Jaroslav Koča

    The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals.
    Categories: Journal Articles
  • Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models
    [Apr 2015]

    by Timo R. Maarleveld, Meike T. Wortel, Brett G. Olivier, Bas Teusink, Frank J. Bruggeman

    High-throughput data generation and genome-scale stoichiometric models have greatly facilitated the comprehensive study of metabolic networks. The computation of all feasible metabolic routes with these models, given stoichiometric, thermodynamic, and steady-state constraints, provides important insights into the metabolic capacities of a cell. How the feasible metabolic routes emerge from the interplay between flux constraints, optimality objectives, and the entire metabolic network of a cell is, however, only partially understood. We show how optimal metabolic routes, resulting from flux balance analysis computations, arise out of elementary flux modes, constraints, and optimization objectives. We illustrate our findings with a genome-scale stoichiometric model of Escherichia coli metabolism. In the case of one flux constraint, all feasible optimal flux routes can be derived from elementary flux modes alone. We found up to 120 million of such optimal elementary flux modes. We introduce a new computational method to compute the corner points of the optimal solution space fast and efficiently. Optimal flux routes no longer depend exclusively on elementary flux modes when we impose additional constraints; new optimal metabolic routes arise out of combinations of elementary flux modes. The solution space of feasible metabolic routes shrinks enormously when additional objectives---e.g. those related to pathway expression costs or pathway length---are introduced. In many cases, only a single metabolic route remains that is both feasible and optimal. This paper contributes to reaching a complete topological understanding of the metabolic capacity of organisms in terms of metabolic flux routes, one that is most natural to biochemists and biotechnologists studying and engineering metabolism.
    Categories: Journal Articles
  • Embodied Choice: How Action Influences Perceptual Decision Making
    [Apr 2015]

    by Nathan F. Lepora, Giovanni Pezzulo

    Embodied Choice considers action performance as a proper part of the decision making process rather than merely as a means to report the decision. The central statement of embodied choice is the existence of bidirectional influences between action and decisions. This implies that for a decision expressed by an action, the action dynamics and its constraints (e.g. current trajectory and kinematics) influence the decision making process. Here we use a perceptual decision making task to compare three types of model: a serial decision-then-action model, a parallel decision-and-action model, and an embodied choice model where the action feeds back into the decision making. The embodied model incorporates two key mechanisms that together are lacking in the other models: action preparation and commitment. First, action preparation strategies alleviate delays in enacting a choice but also modify decision termination. Second, action dynamics change the prospects and create a commitment effect to the initially preferred choice. Our results show that these two mechanisms make embodied choice models better suited to combine decision and action appropriately to achieve suitably fast and accurate responses, as usually required in ecologically valid situations. Moreover, embodied choice models with these mechanisms give a better account of trajectory tracking experiments during decision making. In conclusion, the embodied choice framework offers a combined theory of decision and action that gives a clear case that embodied phenomena such as the dynamics of actions can have a causal influence on central cognition.
    Categories: Journal Articles
  • Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency
    [Apr 2015]

    by Nancy K. Drew, Mackenzie A. Eagleson, Danny B. Baldo Jr., Kevin Kit Parker, Anna Grosberg

    In biology, organization at multiple scales potentiates biological function. Current advances in staining and imaging of biological tissues provide a wealth of data, but there are few metrics to quantitatively describe these findings. In particular there is a need for a metric that would characterize the correlation and consistency of orientation of different biological constructs within a tissue. We aimed to create such a metric and to demonstrate its use with images of cardiac tissues. The co-orientational order parameter (COOP) was based on the mathematical framework of a classical parameter, the orientational order parameter (OOP). Theorems were proven to illustrate the properties and boundaries of the COOP, which was then applied to both synthetic and experimental data. We showed the COOP to be useful for quantifying the correlation of orientation of constructs such as actin filaments and sarcomeric Z-lines. As expected, cardiac tissues showed perfect correlation between actin filaments and Z-lines. We also demonstrated the use of COOP to quantify the consistency of construct orientation within cells of the same shape. The COOP provides a quantitative tool to characterize tissues beyond co-localization or single construct orientation distribution. In the future, this new parameter could be used to represent the quantitative changes during maturation of cardiac tissue, pathological malformation, and other processes.
    Categories: Journal Articles
  • Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
    [Apr 2015]

    by Fabio Pardi, Celine Scornavacca

    Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms of the trees it displays, which represent all the possible histories of the characters carried by the organisms in the network. Interestingly, however, different networks may display exactly the same set of trees, an observation that poses a problem for network reconstruction: from the perspective of many inference methods such networks are “indistinguishable”. This is true for all methods that evaluate a phylogenetic network solely on the basis of how well the displayed trees fit the available data, including all methods based on input data consisting of clades, triples, quartets, or trees with any number of taxa, and also sequence-based approaches such as popular formalisations of maximum parsimony and maximum likelihood for networks. This identifiability problem is partially solved by accounting for branch lengths, although this merely reduces the frequency of the problem. Here we propose that network inference methods should only attempt to reconstruct what they can uniquely identify. To this end, we introduce a novel definition of what constitutes a uniquely reconstructible network. For any given set of indistinguishable networks, we define a canonical network that, under mild assumptions, is unique and thus representative of the entire set. Given data that underwent reticulate evolution, only the canonical form of the underlying phylogenetic network can be uniquely reconstructed. While on the methodological side this will imply a drastic reduction of the solution space in network inference, for the study of reticulate evolution this is a fundamental limitation that will require an important change of perspective when interpreting phylogenetic networks.
    Categories: Journal Articles
  • Cell Fate Reprogramming by Control of Intracellular Network Dynamics
    [Apr 2015]

    by Jorge G. T. Zañudo, Réka Albert

    Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell’s fate, such as disease therapeutics and stem cell reprogramming. Here we develop a novel network control framework that integrates the structural and functional information available for intracellular networks to predict control targets. Formulated in a logical dynamic scheme, our approach drives any initial state to the target state with 100% effectiveness and needs to be applied only transiently for the network to reach and stay in the desired state. We illustrate our method’s potential to find intervention targets for cancer treatment and cell differentiation by applying it to a leukemia signaling network and to the network controlling the differentiation of helper T cells. We find that the predicted control targets are effective in a broad dynamic framework. Moreover, several of the predicted interventions are supported by experiments.
    Categories: Journal Articles