Quantitative Biology - Quantitative Methods Publications (50)

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Quantitative Biology - Quantitative Methods Publications

Quantum annealing is a promising technique which leverages quantum mechanics to solve hard optimization problems. Considerable progress has been made in the development of a physical quantum annealer, motivating the study of methods to enhance the efficiency of such a solver. In this work, we present a quantum annealing approach to measure similarity among molecular structures. Read More


The study of synchronization in populations of coupled biological oscillators is fundamental to many areas of biology to include neuroscience, cardiac dynamics and circadian rhythms. Studying these systems may involve tracking the concentration of hundreds of variables in thousands of individual cells resulting in an extremely high-dimensional description of the system. However, for many of these systems the behaviors of interest occur on a collective or macroscopic scale. Read More


This paper surveys various distance measures for networks and graphs that were introduced in persistent homology. The scope of the paper is limited to network distances that were actually used in brain networks but the methods can be easily adapted to any weighted graph in other fields. The network version of Gromov-Hausdorff, bottleneck, kernel distances are introduced. Read More


Fire propagation is a major concern in the world in general and in Argentinian northwestern Patagonia in particular where every year hundreds of hectares are affected by both natural and anthropogenic forest fires. We developed an efficient cellular automata model in Graphic Processing Units (GPUs) to simulate fire propagation. The graphical advantages of GPUs were exploded by overlapping wind direction maps, as well as vegetation, slope and aspect maps, taking into account relevant landscape characteristics for fire propagation. Read More


Trapping nanoscopic objects to observe their dynamic behaviour for extended periods of time is an ongoing quest. Particularly, sub-100nm transparent objects are hard to catch and most techniques rely on immobilisation or transient diffusion through a confocal laser focus. We present an Anti-Brownian ELectrokinetic trap (pioneered by A. Read More


The fiber g-ratio is the ratio of the inner to the outer diameter of the myelin sheath of a myelinated axon. It has a limited dynamic range in healthy white matter, as it is optimized for speed of signal conduction, cellular energetics, and spatial constraints. In vivo imaging of the g-ratio in health and disease would greatly increase our knowledge of the nervous system and our ability to diagnose, monitor, and treat disease. Read More


Dynamical compensation (DC) has been recently defined as the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. This concept is purported to describe a design principle that provides robustness to physiological circuits. Here we note the similitude between DC and Structural Identifiability (SI), and we argue that the former can be explained in terms of (lack of) the latter. Read More


The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The general purpose is to define positions of all proteins inside it. Read More


Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of patterns and motifs in mutual structural fragments. With the exponential increase of structural proteomics data, the methods that scale with the rate of increase of data lose efficiency. Hence, new methods that reduce the computational expense of this problem should be developed. Read More


Scientific legacy code in MATLAB/Octave not compatible with modernization of research workflows is vastly abundant throughout academic community. Performance of non-vectorized code written in MATLAB/Octave represents a major burden. A new programming language for technical computing Julia, promises to address these issues. Read More


The control of brain dynamics provides great promise for the enhancement of cognitive function in humans, and by extension the betterment of their quality of life. Yet, successfully controlling dynamics in neural systems is particularly challenging, not least due to the immense complexity of the brain and the large set of interactions that can affect any single change. While we have gained some understanding of the control of single neurons, the control of large-scale neural systems---networks of multiply interacting components---remains poorly understood. Read More


The evolutionary success of ants and other social insects is considered to be intrinsically linked to division of labor and emergent collective intelligence. The role of the brains of individual ants in generating these processes, however, is poorly understood. One genus of ant of special interest is Pheidole, which includes more than a thousand species, most of which are dimorphic, i. Read More


Assessing the performance and the characteristics (e.g. yield, quality, disease resistance, abiotic stress tolerance) of new varieties is a key component of crop performance improvement. Read More


How can tissues generate large numbers of cells, yet keep the divisional load (the number of divisions along cell lineages) low in order to curtail the accumulation of somatic mutations and reduce the risk of cancer? To answer the question we consider a general model of hierarchically organized self-renewing tissues and show that the lifetime divisional load of such a tissue is independent of the details of the cell differentiation processes, and depends only on two structural and two dynamical parameters. Our results demonstrate that a strict analytical relationship exists between two seemingly disparate characteristics of self-renewing tissues: divisional load and tissue organization. Most remarkably, we find that a sufficient number of progressively slower dividing cell types can be almost as efficient in minimizing the divisional load, as non-renewing tissues. Read More


This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the polypeptide chain using the tertiary structure of a molecule. Unknown amino acids are determined according to the principle of energy minimization. Read More


Many biological processes are governed by protein-ligand interactions. Of such is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Read More


Graph theoretical analysis of the community structure of networks attempts to identify the communities (or modules) to which each node affiliates. However, this is in most cases an ill-posed problem, as the affiliation of a node to a single community is often ambiguous. Previous solutions have attempted to identify all of the communities to which each node affiliates. Read More


Since the introduction of Direct Electron Detectors (DEDs), the resolution and range of macromolecules amenable to this technique has significantly widened, generating a broad interest that explains the well over a dozen reviews in top journal in the last two years. Similarly, the number of job offers to lead EM groups and/or coordinate EM facilities has exploded, and FEI (the main microscope manufacturer for Life Sciences) has received more than 100 orders of high-end electron microscopes by summer 2016. Strategic corporate movements are also happening, with very big players entering the market through key acquisitions (Thermo Fisher has recently bought FEI for \$4. Read More


Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, or migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. Read More


Local climate conditions play a major role in the development of the mosquito population responsible for transmitting Dengue Fever. Since the {\em Aedes Aegypti} mosquito is also a primary vector for the recent Zika and Chikungunya epidemics across the Americas, a detailed monitoring of periods with favorable climate conditions for mosquito profusion may improve the timing of vector-control efforts and other urgent public health strategies. We apply dimensionality reduction techniques and machine-learning algorithms to climate time series data and analyze their connection to the occurrence of Dengue outbreaks for seven major cities in Brazil. Read More


Functions of brain areas in complex animals are believed to rely on the dynamics of networks of neurons rather than on single neurons. On the other hand, the network dynamics reflect and arise from the integration and coordination of the activity of populations of single neurons. Understanding how single-neurons and neural-circuits dynamics complement each other to produce brain functions is thus of paramount importance. Read More


The Human Phenotype Ontology (HPO) is a structured repository of concepts (HPO Terms) that are associated to one or more diseases. The process of association is referred to as annotation. The relevance and the specificity of both HPO terms and annotations are evaluated by a measure defined as Information Content (IC). Read More


In the stochastic formulation of chemical kinetics, the stationary moments of the population count of species can be described via a set of linear equations. However, except for some specific cases such as systems with linear reaction propensities, the moment equations are underdetermined as a lower order moment might depend upon a higher order moment. Here, we propose a method to find lower, and upper bounds on stationary moments of molecular counts in a chemical reaction system. Read More


The Gene Ontology (GO) is a major bioinformatics ontology that provides structured controlled vocabularies to classify gene and proteins function and role. The GO and its annotations to gene products are now an integral part of functional analysis. Recently, the evaluation of similarity among gene products starting from their annotations (also referred to as semantic similarities) has become an increasing area in bioinformatics. Read More


A key challenge in drug delivery systems is the real time monitoring of delivered drug and subsequent response. Recent advancement in nanotechnology has enabled the design and preclinical implementation of novel drug delivery systems (DDS) with theranostic abilities. Herein, fluorescent cerium fluoride (CeF3) nanoparticles (nps) were synthesized and their surface modified with a coat of polyethylenimine (PEI). Read More


Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters. In this contribution we analyze the phylogenetic information content from a combinatorial point of view by considering the binary relation on the set of taxa defined by the existence of single event separating two taxa. We show that the graph-representation of this relation must be a tree. Read More


Quantification of system-wide perturbations from time series -omic data (i.e. a large number of variables with multiple measures in time) provides the basis for many downstream hypothesis generating tools. Read More


We introduce a tensor-based algebraic clustering method to extract sparse, low-dimensional structure from multidimensional arrays of experimental data. Our methodology is applicable to high dimensional data structures that arise across the sciences. Specifically we introduce a new way to cluster data subject to multi-indexed structural constraints via integer programming. Read More


Distribution networks -- from vasculature to urban transportation systems -- are prevalent in both the natural and consumer worlds. These systems are intrinsically physical in composition and are embedded into real space, properties that lead to constraints on their topological organization. In this study, we compare and contrast two types of biological distribution networks: mycelial fungi and the vasculature system on the surface of rodent brains. Read More


The computational properties of neural systems are often thought to be implemented in terms of their network dynamics. Hence, recovering the system dynamics from experimentally observed neuronal time series, like multiple single-unit (MSU) recordings or neuroimaging data, is an important step toward understanding its computations. Ideally, one would not only seek a state space representation of the dynamics, but would wish to have access to its governing equations for in-depth analysis. Read More


Brain development during adolescence is marked by substantial changes in brain structure and function, leading to a stable network topology in adulthood. However, most prior work has examined the data through the lens of brain areas connected to one another in large-scale functional networks. Here, we apply a recently-developed hypergraph approach that treats network connections (edges) rather than brain regions as the unit of interest, allowing us to describe functional network topology from a fundamentally different perspective. Read More


We obtain a closed form of generating functions of RNA substructure using hermitian matrix model with the Chebyshev polynomial of the second kind, which turns out to be the hypergeometric function. To match the experimental findings of the statistical behavior, we regard the substructure as a grand canonical ensemble and find its fugacity value. We also suggest a hierarchical picture based on the planar structure so that the non-planar structure such as pseudoknot are included. Read More


1. Electronic telemetry is frequently used to document animal movement through time. Methods that can identify underlying behaviors driving specific movement patterns can help us understand how and why animals use available space, thereby aiding conservation and management efforts. Read More


Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. Read More


Reconstructing the causal network in a complex dynamical system plays a crucial role in many applications, from sub-cellular biology to economic systems. Here we focus on inferring gene regulation networks (GRNs) from perturbation or gene deletion experiments. Despite their scientific merit, such perturbation experiments are not often used for such inference due to their costly experimental procedure, requiring significant resources to complete the measurement of every single experiment. Read More


We introduce the boundary length and point spectrum, as a joint generalization of the boundary length spectrum and boundary point spectrum in arXiv:1307.0967. We establish by cut-and-join methods that the number of partial chord diagrams filtered by the boundary length and point spectrum satisfies a recursion relation, which combined with an initial condition determines these numbers uniquely. Read More


We develop efficient ways to consider and correct for the effects of hidden units for the paradigmatic case of the inverse kinetic Ising model with fully asymmetric couplings. We identify two sources of error in reconstructing the connectivity among the observed units while ignoring part of the network. One leads to a systematic bias in the inferred parameters, whereas the other involves correlations between the visible and hidden populations and has a magnitude that depends on the coupling strength. Read More


In the context of bacteria and models of their evolution under genome rearrangement, we explore a novel application of group representation theory to the inference of evolutionary history. Our contribution is to show, in a very general maximum likelihood setting, how to use elementary matrix algebra to sidestep intractable combinatorial computations and convert the problem into one of eigenvalue estimation amenable to standard numerical approximation techniques. Read More


Diffusion MRI (dMRI) can reconstruct neuronal fibers in the brain, in vivo, by measuring water diffusion along angular gradient directions in q-space. High angular resolution diffusion imaging (HARDI) can produce better estimates of fiber orientation than the popularly used diffusion tensor imaging, but the high number of samples needed to estimate diffusivity requires lengthy patient scan times. To accelerate dMRI, compressed sensing (CS) has been utilized by exploiting a sparse representation of the data, discovered through sparse coding. Read More


In this article, the enumeration of partial chord diagrams is discussed via matrix model techniques. In addition to the basic data such as the number of backbones and chords, we also consider the Euler characteristic, the backbone spectrum, the boundary point spectrum, and the boundary length spectrum. Furthermore, we consider the boundary length and point spectrum that unifies the last two types of spectra. Read More


In this paper we consider the enumeration of orientable and non-orientable chord diagrams. We show that this enumeration is encoded in appropriate expectation values of the $\beta$-deformed Gaussian and RNA matrix models. We evaluate these expectation values by means of the $\beta$-deformed topological recursion, and - independently - using properties of quantum curves. Read More


Background. Wearable accelerometry devices allow collection of high-density activity data in large epidemiological studies both in-the-lab as well as in-the-wild (free-living). Such data can be used to detect and identify periods of sustained harmonic walking. Read More


Across a far-reaching diversity of scientific and industrial applications, a general key problem involves relating the structure of time-series data to a meaningful outcome, such as detecting anomalous events from sensor recordings, or diagnosing patients from physiological time-series measurements like heart rate or brain activity. Currently, researchers must devote considerable effort manually devising, or searching for, properties of their time series that are suitable for the particular analysis problem at hand. Addressing this non-systematic and time-consuming procedure, here we introduce a new tool, hctsa, that selects interpretable and useful properties of time series automatically, by comparing implementations over 7700 time-series features drawn from diverse scientific literatures. Read More


Several statistical models used in genome-wide prediction assume independence of marker allele substitution effects, but it is known that these effects might be correlated. In statistics, graphical models have been identified as a useful tool for covariance estimation in high dimensional problems and it is an area that has recently experienced a great expansion. In Gaussian covariance graph models (GCovGM), the joint distribution of a set of random variables is assumed to be Gaussian and the pattern of zeros of the covariance matrix is encoded in terms of an undirected graph G. Read More


The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules -- called inhibitors -- on the progression of enzymatic reactions, but "non-classical effects" and "anomalies" which seem to fall beyond its scope have forced practitioners and others to repeatedly patch and mend it ad-hoc. For example, depending on concentrations, some molecules can either inhibit, or facilitate, the progression of an enzymatic reaction. This duality gives rise to non-monotonic dose response curves which seriously complicate high throughput inhibitor screens and drug development, but it is widely believed that the three canonical modes of inhibition -- competitive, uncompetitive, and mixed -- cannot account for it. Read More


Non-parametric detrending or noise reduction methods are often employed to separate trends from noisy time series when no satisfactory models exist to fit the data. However, conventional detrending methods depend on subjective choices of detrending parameters. Here, we present a simple multivariate detrending method based on available nonlinear forecasting techniques. Read More


Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Read More


The accurate diagnosis and assessment of neurodegenerative disease and traumatic brain injuries (TBI) remain open challenges. Both cause cognitive and functional deficits due to focal axonal swellings (FAS), but it is difficult to deliver a prognosis due to our limited ability to assess damaged neurons at a cellular level in vivo. We simulate the effects of neurodegenerative disease and TBI using convolutional neural networks (CNNs) as our model of cognition. Read More