Latest in q-bio.qm

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mGPfusion: Predicting protein stability changes with Gaussian process kernel learning and data fusionFeb 08 2018Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability are necessary ... More
Restate the reference for EEG microstate analysisFeb 08 2018Despite the decades of efforts, the choice of EEG reference is still a debated fundamental issue. Non-neutral reference can inevitably inject the uncontrolled temporal biases into all EEG recordings, which may influence the spatiotemporal analysis of ... More
Clustering Gene Expression Time Series with Coregionalization: Speed propagation of ALSFeb 08 2018Clustering of gene expression time series gives insight into which genes may be coregulated, allowing us to discern the activity of pathways in a given microarray experiment. Of particular interest is how a given group of genes varies with different model ... More
Unified Bayesian estimator of EEG reference at infinity: rRESTFeb 07 2018The choice of reference for electroencephalogram (EEG) is a long-lasting unsolved issue resulting in inconsistent usages and endless debates. Currently, both average reference (AR) and reference electrode standardization technique (REST) are two primary, ... More
Multilayer Network Modeling of Integrated Biological SystemsFeb 05 2018Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are ... More
Spatially-resolved Brillouin spectroscopy reveals biomechanical changes in early ectatic corneal disease and post-crosslinking in vivoFeb 04 2018Mounting evidence connects the biomechanical properties of tissues to the development of eye diseases such as keratoconus, a common disease in which the cornea thins and bulges into a conical shape. However, measuring biomechanical changes in vivo with ... More
Generalizing Gillespie's direct method to enable network-free simulationsJan 30 2018Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration of all reactions and all chemical species that may arise in the system. ... More
Methodological variations in lagged regression for detecting physiologic drug effects in EHR dataJan 26 2018We studied how lagged linear regression can be used to detect the physiologic effects of drugs from data in the electronic health record (EHR). We systematically examined the effect of methodological variations ((i) time series construction, (ii) temporal ... More
Pharmacokinetics Simulations for Studying Correlates of Prevention Efficacy of Passive HIV-1 Antibody Prophylaxis in the Antibody Mediated Prevention (AMP) StudyJan 25 2018A key objective in two phase 2b AMP clinical trials of VRC01 is to evaluate whether drug concentration over time, as estimated by non-linear mixed effects pharmacokinetics (PK) models, is associated with HIV infection rate. We conducted a simulation study ... More
Deep Learning in Pharmacogenomics: From Gene Regulation to Patient StratificationJan 25 2018This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: (1) identification of novel regulatory variants located in noncoding domains and their function as applied to pharmacoepigenomics; (2) ... More
Floating Forests: Quantitative Validation of Citizen Science Data Generated From Consensus ClassificationsJan 25 2018Large-scale research endeavors can be hindered by logistical constraints limiting the amount of available data. For example, global ecological questions require a global dataset, and traditional sampling protocols are often too inefficient for a small ... More
Convenient Interface to Inverse Ising (ConIII): A Python package for solving maximum entropy modelsJan 24 2018ConIII (pronounced CON-ee) is an open-source Python project providing a simple interface to solving maximum entropy models, with a focus on the Ising model. We describe the maximum entropy problem and give an overview of the algorithms that are implemented ... More
Centralized "big science" communities more likely generate non-replicable resultsJan 15 2018Growing concern that most published results, including those widely agreed upon, may be false are rarely examined against rapidly expanding research production. Replications have only occurred on small scales due to prohibitive expense and limited professional ... More
The Spectrum of Mechanism-oriented Models for Explanations of Biological PhenomenaJan 15 2018Within the diverse interdisciplinary life sciences domains, semantic, workflow, and methodological ambiguities can prevent the appreciation of explanations of phenomena, handicap the use of computational models, and hamper communication among scientists, ... More
Fast Methods for Solving the Cluster Containment Problem for Phylogenetic NetworksJan 14 2018Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has motivated ... More
Gene regulatory network inference: an introductory surveyJan 12 2018Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 90s, reconstructing the structure of such networks has been a central computational problem in ... More
Modeling sepsis progression using hidden Markov modelsJan 09 2018Characterizing a patient's progression through stages of sepsis is critical for enabling risk stratification and adaptive, personalized treatment. However, commonly used sepsis diagnostic criteria fail to account for significant underlying heterogeneity, ... More
High-throughput, high-resolution Generated Adversarial Network MicroscopyJan 07 2018We for the first time combine generated adversarial network (GAN) with wide-field light microscopy to achieve deep learning super-resolution under a large field of view (FOV). By appropriately adopting prior microscopy data in an adversarial training, ... More
Root Mean Square Minimum Distance: a Quality Metric for Localization Nanoscopy ImagingJan 06 2018A localization algorithm in optical localization nanoscopy plays an important role in obtaining a high-quality image. A universal and objective metric, which is crucial and necessary to evaluate qualities of nanoscopy images and performances of localization ... More
An Unsupervised Homogenization Pipeline for Clustering Similar Patients using Electronic Health Record DataDec 30 2017Electronic health records (EHR) contain a large variety of information on the clinical history of patients such as vital signs, demographics, diagnostic codes and imaging data. The enormous potential for discovery in this rich dataset is hampered by its ... More
Proteomics Analysis of FLT3-ITD Mutation in Acute Myeloid Leukemia Using Deep Learning Neural NetworkDec 29 2017Deep Learning can significantly benefit cancer proteomics and genomics. In this study, we attempt to determine a set of critical proteins that are associated with the FLT3-ITD mutation in newly-diagnosed acute myeloid leukemia patients. A Deep Learning ... More
Gene expression for simulation of biological tissueDec 23 2017BioDynaMo is a biological processes simulator developed by an international community of researchers and software engineers working closely with neuroscientists. The authors have taken part in the development of the physical engine, and they are currently ... More
Construction and Evaluation of Hierarchical Parcellation of the Brain using fMRI with PrewhiteningDec 21 2017Feb 07 2018Brain atlases are a ubiquitous tool used for analyzing and interpreting brain imaging datasets. Traditionally, brain atlases divided the brain into regions separated by anatomical landmarks. In the last decade, several attempts have been made to parcellate ... More
Searching for Biophysically Realistic Parameters for Dynamic Neuron Models by Genetic Algorithms from Calcium Imaging RecordingNov 04 2017Individual Neurons in the nervous systems exploit various dynamics. To capture these dynamics for single neurons, we tune the parameters of an electrophysiological model of nerve cells, to fit experimental data obtained by calcium imaging. A search for ... More
Spatially Adaptive Colocalization Analysis in Dual-Color Fluorescence MicroscopyOct 31 2017Colocalization analysis aims to study complex spatial associations between bio-molecules via optical imaging techniques. However, existing colocalization analysis workflows only assess an average degree of colocalization within a certain region of interest ... More
Designing RNA Secondary Structures is HardOct 31 2017An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can be represented ... More
Two-photon photoactivated voltage imaging in tissue with an Archaerhodopsin-derived reporterOct 27 2017Robust voltage imaging in tissue remains a technical challenge. Existing combinations of genetically encoded voltage indicators (GEVIs) and microscopy techniques cannot simultaneously achieve sufficiently high voltage sensitivity, background rejection, ... More
Nonparametric estimation of multivariate distribution function for truncated and censored lifetime dataOct 20 2017In this article we consider a number of models for the statistical data generation in different areas of insurance, including life, pension and non-life insurance. Insurance statistics are usually truncated and censored, and often are multidimensional. ... More
Automated and Robust Quantification of Colocalization in Dual-Color Fluorescence Microscopy: A Nonparametric Statistical ApproachOct 03 2017Colocalization is a powerful tool to study the interactions between fluorescently labeled molecules in biological fluorescence microscopy. However, existing techniques for colocalization analysis have not undergone continued development especially in ... More
Variational autoencoders for tissue heterogeneity exploration from (almost) no preprocessed mass spectrometry imaging dataAug 23 2017Aug 24 2017The paper presents the application of Variational Autoencoders (VAE) for data dimensionality reduction and explorative analysis of mass spectrometry imaging data (MSI). The results confirm that VAEs are capable of detecting the patterns associated with ... More
Automatic detection and decoding of honey bee waggle dancesAug 22 2017Dec 05 2017The waggle dance is one of the most popular examples of animal communication. Forager bees direct their nestmates to profitable resources via a complex motor display. Essentially, the dance encodes the polar coordinates to the resource in the field. Unemployed ... More
State space truncation with quantified errors for accurate solutions to discrete Chemical Master EquationJul 25 2017The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the ... More
Accurate Chemical Master Equation Solution Using Multi-Finite BuffersJul 25 2017The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable ... More
Machine Learning for Large-Scale Quality Control of 3D Shape Models in NeuroimagingJul 20 2017Aug 07 2017As very large studies of complex neuroimaging phenotypes become more common, human quality assessment of MRI-derived data remains one of the last major bottlenecks. Few attempts have so far been made to address this issue with machine learning. In this ... More
A regional model for estimating the aboveground carbon density of Borneo's tropical forests from airborne laser scanningMay 25 2017Borneo contains some of the world's most biodiverse and carbon dense tropical forest, but this 750,000-km2 island has lost 62% of its old-growth forests within the last 40 years. Efforts to protect and restore the remaining forests of Borneo hinge on ... More
Her2 Challenge Contest: A Detailed Assessment of Automated Her2 Scoring Algorithms in Whole Slide Images of Breast Cancer TissuesMay 23 2017Jul 24 2017Evaluating expression of the Human epidermal growth factor receptor 2 (Her2) by visual examination of immunohistochemistry (IHC) on invasive breast cancer (BCa) is a key part of the diagnostic assessment of BCa due to its recognised importance as a predictive ... More
Fast and Accurate Semi-Automatic Segmentation Tool for Brain Tumor MRIsMay 18 2017Segmentation, the process of delineating tumor apart from healthy tissue, is a vital part of both the clinical assessment and the quantitative analysis of brain cancers. Here, we provide an open-source algorithm (MITKats), built on the Medical Imaging ... More
Label-free three-dimensional (3D) structural imaging in live cells using intrinsic optical refractive indexApr 14 2017Here we report a method for visualization of volumetric structural information of live biological samples with no exogenous contrast agents. The process is made possible through a technique that involves generation, synthesis and analysis of three-dimensional ... More
Automated Diagnosis of Epilepsy Employing Multifractal Detrended Fluctuation Analysis Based FeaturesApr 05 2017This contribution reports an application of MultiFractal Detrended Fluctuation Analysis, MFDFA based novel feature extraction technique for automated detection of epilepsy. In fractal geometry, Multifractal Detrended Fluctuation Analysis MFDFA is a popular ... More
Quantitative Prediction of Linear B-Cell EpitopesMar 07 2017In scientific literature, there are many programs that predict linear B-cell epitopes from a protein sequence. Each program generates multiple B-cell epitopes that can be individually studied. This paper defines a function called <C> that combines results ... More
Absolute bacterial cell enumeration using flow cytometryMar 02 2017Jun 20 2017Aim: To evaluate a flow cytometry protocol that uses reference beads for the enumeration of live and dead bacteria present in a mixture. Methods and Results: Mixtures of live and dead Escherichia coli with live:dead concentration ratios varying from 0 ... More
Quantum magnetic resonance microscopyFeb 14 2017Magnetic resonance spectroscopy is universally regarded as one of the most important tools in chemical and bio-medical research. However, sensitivity limitations typically restrict imaging resolution to length scales greater than 10 \mu m. Here we bring ... More
Phenomenological forecasting of disease incidence using heteroskedastic Gaussian processes: a dengue case studyFeb 01 2017Aug 01 2017In 2015 the US federal government sponsored a dengue forecasting competition using historical case data from Iquitos, Peru and San Juan, Puerto Rico. Competitors were evaluated on several aspects of out-of-sample forecasts including the targets of peak ... More
DeadNet: Identifying Phototoxicity from Label-free Microscopy Images of Cells using Deep ConvNetsJan 22 2017Exposure to intense illumination light is an unavoidable consequence of fluorescence microscopy, and poses a risk to the health of the sample in every live-cell fluorescence microscopy experiment. Furthermore, the possible side-effects of phototoxicity ... More
Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancerDec 24 2016Apr 28 2017We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. Specifically, this framework is designed to enable detection of clusters of data in the presence of structural requirements ... More
Embedding of biological distribution networks with differing environmental constraintsDec 23 2016Distribution 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 ... More
RIDS: Robust Identification of Sparse Gene Regulatory Networks from Perturbation ExperimentsDec 20 2016Reconstructing 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. ... More
Advances in using Internet searches to track dengueDec 08 2016Dengue is a mosquito-borne disease that threatens more than half of the world's population. Despite being endemic to over 100 countries, government-led efforts and mechanisms to timely identify and track the emergence of new infections are still lacking ... More
A Multi-Pass Approach to Large-Scale ConnectomicsDec 07 2016The field of connectomics faces unprecedented "big data" challenges. To reconstruct neuronal connectivity, automated pixel-level segmentation is required for petabytes of streaming electron microscopy data. Existing algorithms provide relatively good ... More
Time-delayed model of RNA interferenceDec 05 2016RNA interference (RNAi) is a fundamental cellular process that inhibits gene expression through cleavage and destruction of target mRNA. It is responsible for a number of important intracellular functions, from being the first line of immune defence against ... More
Mathematical model of plant-virus interactions mediated by RNA interferenceDec 05 2016Cross-protection, which refers to a process whereby artificially inoculating a plant with a mild strain provides protection against a more aggressive isolate of the virus, is known to be an effective tool of disease control in plants. In this paper we ... More
Positive blood culture detection in time series data using a BiLSTM networkDec 03 2016The presence of bacteria or fungi in the bloodstream of patients is abnormal and can lead to life-threatening conditions. A computational model based on a bidirectional long short-term memory artificial neural network, is explored to assist doctors in ... More
Multi-stage Clustering of Breast Cancer for Precision MedicineDec 02 2016Cancer has become one of the most widespread diseases in the world. Specifically, breast cancer is diagnosed more often than any other type of cancer. However, breast cancer patients and their individual tumors are often unique. Identifying the underlying ... More
Survival Prediction with Limited Features: a Top Performing Approach from the DREAM ALS Stratification Prize4Life ChallengeDec 02 2016Survival prediction with small sets of features is a highly relevant topic for decision-making in clinical practice. I describe a method for predicting survival of amyotrophic lateral sclerosis (ALS) patients that was developed as a submission to the ... More
Probabilistic Broken-Stick Model: A Regression Algorithm for Irregularly Sampled Data with Application to eGFRNov 30 2016In order for clinicians to manage disease progression and make effective decisions about drug dosage, treatment regimens or scheduling follow up appointments, it is necessary to be able to identify both short and long-term trends in repeated biomedical ... More
Exploring Strategies for Classification of External Stimuli Using Statistical Features of the Plant Electrical ResponseNov 29 2016Plants sense their environment by producing electrical signals which in essence represent changes in underlying physiological processes. These electrical signals, when monitored, show both stochastic and deterministic dynamics. In this paper, we compute ... More
Time Dependent Saddle Node Bifurcation: Breaking Time and the Point of No Return in a Non-Autonomous Model of Critical TransitionsNov 29 2016We investigate a simple model of a non-autonomous system with a time dependent parameter $p(\tau)$ and its corresponding "dynamic" (time-dependent) saddle-node bifurcation. We show that the actual point of no return for a system undergoing a critical ... More
diagno-syst: a tool for accurate inventories in metabarcodingNov 28 2016Metabarcoding on amplicons is rapidly expanding as a method to produce molecular based inventories of microbial communities. Here, we work on freshwater diatoms, which are microalgae possibly inventoried both on a morphological and a molecular basis. ... More
Multiple Signal Classification Algorithm (MUSICAL) for super-resolution fluorescence microscopyNov 28 2016Super-resolution microscopy is providing unprecedented insights into biology by resolving details much below the diffraction limit. State-of-the-art Single Molecule Localization Microscopy (SMLM) techniques for super-resolution are restricted by long ... More
Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides: Understanding Randomness in Clinical Outcomes Following Stem Cell TransplantationNov 28 2016Alloreactivity following stem cell transplantation (SCT) is difficult to predict in patients undergoing transplantation from HLA matched donors. In this study we performed whole exome sequencing of SCT donor-recipient pairs (DRP). This allowed determination ... More
NMRProcFlow: A graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomicsNov 23 2016Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks, and so far the best way is to proceed interactively with a spectra viewer. NMRProcFlow is a graphical and interactive 1D NMR ... More
Universal proximity effect in target search kinetics in the few-encounter limitNov 23 2016When does a diffusing particle reach its target for the first time? This first-passage time (FPT) problem is central to the kinetics of molecular reactions in chemistry and molecular biology. Here we explain the behavior of smooth FPT densities, for which ... More
Specificity-determining DNA triplet code for positioning of human pre-initiation complexNov 23 2016The notion that transcription factors bind DNA only through specific, consensus binding sites has been recently questioned. In a pioneering study by Pugh and Venters no specific consensus motif for the positioning of the human pre-initiation complex (PIC) ... More
A statistical method for analyzing and comparing spatiotemporal cortical activation patternsNov 23 2016We present a new statistical method to analyze multichannel steady-state local field potentials (LFP) recorded within different sensory cortices of different rodent species. Our spatiotemporal multi-dimensional cluster statistics (MCS) method enables ... More
Solving multi-objective optimization problems in conservation with the reference point methodNov 23 2016Managing biodiversity extinction crisis requires wise decision-making processes able to account for the limited of resources available. In most decision problems in conservation biology, several conflicting objectives have to be taken into account. Most ... More
A Neural Network Model to Classify Liver Cancer Patients Using Data Expansion and CompressionNov 23 2016We develop a neural network model to classify liver cancer patients into high-risk and low-risk groups using genomic data. Our approach provides a novel technique to classify big data sets using neural network models. We preprocess the data before training ... More
A Neural Network Model to Classify Liver Cancer Patients Using Data Expansion and CompressionNov 23 2016Nov 25 2016We develop a neural network model to classify liver cancer patients into high-risk and low-risk groups using genomic data. Our approach provides a novel technique to classify big data sets using neural network models. We preprocess the data before training ... More
Analyzing Genome-wide Association Study Data with the R Package genMOSSNov 22 2016The R package (R Core Team (2016)) genMOSS is specifically designed for the Bayesian analysis of genome-wide association study data. The package implements the mode oriented stochastic search (MOSS) procedure as well as a simple moving window approach ... More
Potential landscape of high dimensional nonlinear stochastic dynamics and rare transitions with large noiseNov 22 2016Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including cell-fate decision in developmental processes as well as genesis and progression of cancers. While various attempts have been made to ... More
CMOS based image cytometry for detection of phytoplankton in ballast waterNov 21 2016We introduce an image cytometer (I-CYT) for the analysis of phytoplankton in fresh and marine water environments. A linear quantification of cell numbers was observed covering several orders of magnitude using cultures of Tetraselmis and Nannochloropsis ... More
Deep Learning for the Classification of Lung NodulesNov 21 2016Nov 26 2016Deep learning, as a promising new area of machine learning, has attracted a rapidly increasing attention in the field of medical imaging. Compared to the conventional machine learning methods, deep learning requires no hand-tuned feature extractor, and ... More
Deep Learning for the Classification of Lung NodulesNov 21 2016Deep learning, as a promising new area of machine learning, has attracted a rapidly increasing attention in the field of medical imaging. Compared to the conventional machine learning methods, deep learning requires no hand-tuned feature extractor, and ... More
3D Reconstruction of Heterogeneous Virus Particles with Statistical Geometric SymmetryNov 21 2016In 3-D reconstruction problems, the image data obtained from cryo electron microscopy is the projection of many heterogeneous instances of the object under study (e.g., a virus). When the object is heterogeneous but has an overall symmetry, it is natural ... More
Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesisNov 18 2016Burkholderia is an important genus encompassing a variety of species, including pathogenic strains as well as strains that promote plant growth. We have carried out a global strategy, which combined two complementary approaches. The first one is genome ... More
Controlling energy landscapes with correlations between minimaNov 17 2016Neural network models have been used to construct energy landscapes for modeling biological phenomena, in which the minima of the landscape correspond to memory patterns stored by the network. Here, we show that dynamic properties of those landscapes, ... More
RADAR: A Novel Fast-Screening Method for Reading Difficulties with Special Focus on DyslexiaNov 17 2016Nov 24 2016Dyslexia is a developmental learning disorder of single word reading accuracy and/or fluency, with compelling research directed towards understanding the contributions of the visual system. While dyslexia is not an oculomotor disease, readers with dyslexia ... More
RADAR: A Novel Fast-Screening Method for Reading Difficulties with Special Focus on DyslexiaNov 17 2016Nov 18 2016Dyslexia is a developmental learning disorder of single word reading accuracy and/or fluency, with compelling research directed towards understanding the contributions of the visual system. While dyslexia is not an oculomotor disease, readers with dyslexia ... More
RADAR: A Novel Fast-Screening Method for Reading Difficulties with Special Focus on DyslexiaNov 17 2016Dyslexia is a developmental learning disorder of single word reading accuracy and/or fluency, with compelling research directed towards understanding the contributions of the visual system. While dyslexia is not an oculomotor disease, readers with dyslexia ... More
Bridging the time scales of single-cell and population dynamicsNov 16 2016It is well known that population sizes increase exponentially during balanced growth. Concomitantly, at the single-cell level, the sizes of individual cells themselves increase exponentially; the single-cell exponential growth-rate also determines the ... More
Bridging the time scales of single-cell and population dynamicsNov 16 2016Nov 21 2016It is well known that population sizes increase exponentially during balanced growth. Concomitantly, at the single-cell level, the sizes of individual cells themselves increase exponentially; the single-cell exponential growth-rate also determines the ... More
Benchmarking inverse statistical approaches for protein structure and design with exactly solvable modelsNov 15 2016Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective ... More
Neural stochastic codes, encoding and decodingNov 15 2016Identifying informative aspects of brain activity has traditionally been thought to provide insight into how brains may perform optimal computations. However, here we show that this need not be the case when studying spike-time precision or response discrimination, ... More
DistributedFBA.jl: High-level, high-performance flux balance analysis in JuliaNov 15 2016Motivation: Flux balance analysis, and its variants, are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software ... More
EMDUnifrac: Exact Linear Time Computation of the Unifrac Metric and Identification of Differentially Abundant OrganismsNov 14 2016Both the weighted and unweighted Unifrac distances have been very successfully employed to assess if two communities differ, but do not give any information about how two communities differ. We take advantage of recent observations that the Unifrac metric ... More
Statistical mechanics of the inverse Ising problem and the optimal objective functionNov 14 2016The inverse Ising problem seeks to reconstruct the parameters of an Ising Hamiltonian on the basis of spin configurations sampled from the Boltzmann measure. Recently, strategies to solve the inverse Ising problem based on convex optimisation have proven ... More
Patterns of Selection of Human Movements III: Energy Efficiency, Mechanical Advantage, and Walking GaitNov 13 2016Human movements are physical processes combining the classical mechanics of the human body moving in space and the biomechanics of the muscles generating the forces acting on the body under sophisticated sensory-motor control. One way to characterize ... More
The Reasonable Effectiveness of Agent-Based Simulations in Evolutionary Game TheoryNov 13 2016This is a Reply to comments published in Physics of Life Reviews, on our article "Evolutionary game theory using agent-based methods" (Physics of Life Reviews, 2016, arXiv:1404.0994).
Mean-field models for non-Markovian epidemics on networks: from edge-based compartmental to pairwise modelsNov 12 2016This paper presents a novel extension of the edge-based compartmental model for epidemics with arbitrary distributions of transmission and recovery times. Using the message passing approach we also derive a new pairwise-like model for epidemics with Markovian ... More
Modelling correlated marker effects in genome-wide prediction via Gaussian concentration graph modelsNov 10 2016In genome-wide prediction, independence of marker allele substitution effects is typically assumed; however, since early stages of this technology it has been known that nature points to correlated effects. In statistics, graphical models have been identified ... More
Feature Selection with the R Package MXM: Discovering Statistically-Equivalent Feature SubsetsNov 10 2016The statistically equivalent signature (SES) algorithm is a method for feature selection inspired by the principles of constrained-based learning of Bayesian Networks. Most of the currently available feature-selection methods return only a single subset ... More
Therapeutic target discovery using Boolean network attractors: updates from kaliNov 10 2016In a previous article, an algorithm for discovering therapeutic targets in Boolean networks modeling disease mechanisms was introduced. In the present article, the updates made on this algorithm, named kali, are described. These updates are: i) the possibility ... More
Heter-LP: A heterogeneous label propagation algorithm and its application in drug repositioningNov 08 2016Drug repositioning offers an effective solution to drug discovery, saving both time and resources by finding new indications for existing drugs. Typically, a drug takes effect via its protein targets in the cell. As a result, it is necessary for drug ... More
Quantification of heparin in complex matrices (including urine) using a mix-and-read fluorescence assayNov 08 2016Heparin is an important anticoagulant drug, about one billion doses are produced annually. It is a polydisperse sulfated polysaccharide, and the inherent heterogeneity makes the analysis of heparin difficult. The global crisis resulting from adulterated ... More
A Theory of TaxonomyNov 04 2016A taxonomy is a standardized framework to classify and organize items into categories. Hierarchical taxonomies are ubiquitous, ranging from the classification of organisms to the file system on a computer. Characterizing the typical distribution of items ... More
Vortex arrays and ciliary tangles underlie the feeding-swimming tradeoff in starfish larvaeNov 03 2016Many marine invertebrates have larval stages covered in linear arrays of beating cilia, which propel the animal while simultaneously entraining planktonic prey. These bands are strongly conserved across taxa spanning four major superphyla, and they are ... More
Efficient causal inference with hidden confounders from genome-transcriptome variation dataNov 03 2016Natural genetic variation between individuals in a population leads to variations in gene expression that are informative for the inference of gene regulatory networks. Particularly, genome-wide genotype and transcriptome data from the same samples allow ... More
Efficient causal inference with hidden confounders from genome-transcriptome variation dataNov 03 2016Nov 06 2016Natural genetic variation between individuals in a population leads to variations in gene expression that are informative for the inference of gene regulatory networks. Particularly, genome-wide genotype and transcriptome data from the same samples allow ... More
Multitask Protein Function Prediction Through Task DissimilarityNov 03 2016Automated protein function prediction is a challenging problem with distinctive features, such as the hierarchical organization of protein functions and the scarcity of annotated proteins for most biological functions. We propose a multitask learning ... More
Analysis of Metagenome Composition by the Method of Random PrimersNov 02 2016Metagenome, a mixture of different genomes (as a rule, bacterial), represents a pattern, and the analysis of its composition is, currently, one of the challenging problems of bioinformatics. In the present study, the possibility of evaluating metagenome ... More
Geodesic curvature driven surface microdomain formationNov 01 2016Lipid bilayer membranes are not uniform and clusters of lipids in a more ordered state exist within the generally disorder lipid milieu of the membrane. These clusters of ordered lipids microdomains are now referred to as lipid rafts. Recent reports attribute ... More