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Hidden markov

Claire Guerrier, David Holcman
Binding of molecules, ions or proteins to small target sites is a generic step of cell activation. This process relies on rare stochastic events where a particle located in a large bulk has to find small and often hidden targets. We present here a hybrid discrete-continuum model that takes into account a stochastic regime governed by rare events and a continuous regime in the bulk. The rare discrete binding events are modeled by a Markov chain for the encounter of small targets by few Brownian particles, for which the arrival time is Poissonian...
October 18, 2016: Scientific Reports
Duncan K Ralph, Frederick A Matsen
The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member...
October 2016: PLoS Computational Biology
Amanda A Koepke, Ira M Longini, M Elizabeth Halloran, Jon Wakefield, Vladimir N Minin
Despite seasonal cholera outbreaks in Bangladesh, little is known about the relationship between environmental conditions and cholera cases. We seek to develop a predictive model for cholera outbreaks in Bangladesh based on environmental predictors. To do this, we estimate the contribution of environmental variables, such as water depth and water temperature, to cholera outbreaks in the context of a disease transmission model. We implement a method which simultaneously accounts for disease dynamics and environmental variables in a Susceptible-Infected-Recovered-Susceptible (SIRS) model...
June 2016: Annals of Applied Statistics
Mahsa Akhbari, Mohammad B Shamsollahi, Omid Sayadi, Antonis A Armoundas, Christian Jutten
In this paper, we propose a novel method for extracting fiducial points (FPs) of electrocardiogram (ECG) signals. We propose the use of multi hidden Markov model (MultiHMM) as opposed to the traditional use of Classic HMM. In the MultiHMM method, each segment of an ECG beat is represented by a separate ergodic continuous density HMM. Each HMM has different state number and is trained separately. In the test step, the log-likelihood of two consecutive HMMs is compared and a path is estimated, which shows the correspondence of each part of the ECG signal to the HMM with the maximum log-likelihood...
September 28, 2016: Computers in Biology and Medicine
Colin Kern, Li Liao
Protein-protein interactions play a central role in the biological processes of cells. Accurate prediction of the interacting residues in protein-protein interactions enhances understanding of the interaction mechanisms and enables in silico mutagenesis, which can help facilitate drug design and deepen our understanding of the inner workings of cells. Correlations have been found among interacting residues as a result of selection pressure to retain the interaction during evolution. In previous work, incorporation of such correlations in the interaction profile hidden Markov models with a special decoding algorithm (ETB-Viterbi) has led to improvement in prediction accuracy...
September 29, 2016: Computational Biology and Chemistry
Pritha Ghosh, Oommen K Mathew, Ramanathan Sowdhamini
BACKGROUND: RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information...
October 7, 2016: BMC Bioinformatics
Dylan Molenaar, Daniel Oberski, Jeroen Vermunt, Paul De Boeck
Current approaches to model responses and response times to psychometric tests solely focus on between-subject differences in speed and ability. Within subjects, speed and ability are assumed to be constants. Violations of this assumption are generally absorbed in the residual of the model. As a result, within-subject departures from the between-subject speed and ability level remain undetected. These departures may be of interest to the researcher as they reflect differences in the response processes adopted on the items of a test...
August 11, 2016: Multivariate Behavioral Research
Dan Valsky, Odeya Marmor-Levin, Marc Deffains, Renana Eitan, Kim T Blackwell, Hagai Bergman, Zvi Israel
BACKGROUND: Microelectrode recordings along preplanned trajectories are often used for accurate definition of the subthalamic nucleus (STN) borders during deep brain stimulation (DBS) surgery for Parkinson's disease. Usually, the demarcation of the STN borders is performed manually by a neurophysiologist. The exact detection of the borders is difficult, especially detecting the transition between the STN and the substantia nigra pars reticulata. Consequently, demarcation may be inaccurate, leading to suboptimal location of the DBS lead and inadequate clinical outcomes...
October 6, 2016: Movement Disorders: Official Journal of the Movement Disorder Society
Kathryn M Hart, Chris M W Ho, Supratik Dutta, Michael L Gross, Gregory R Bowman
TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM's specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity...
October 6, 2016: Nature Communications
Wonbae Lee, John P Gillies, Davis Jose, Brett A Israels, Peter H von Hippel, Andrew H Marcus
Gene 32 protein (gp32) is the single-stranded (ss) DNA binding protein of the bacteriophage T4. It binds transiently and cooperatively to ssDNA sequences exposed during the DNA replication process and regulates the interactions of the other sub-assemblies of the replication complex during the replication cycle. We here use single-molecule FRET techniques to build on previous thermodynamic studies of gp32 binding to initiate studies of the dynamics of the isolated and cooperative binding of gp32 molecules within the replication complex...
September 30, 2016: Nucleic Acids Research
Marwa Al Arab, Christian Höner Zu Siederdissen, Kifah Tout, Abdullah H Sahyoun, Peter F Stadler, Matthias Bernt
Mitochondrial genome sequences are available in large number and new sequences become published nowadays with increasing pace. Fast, automatic, consistent, and high quality annotations are a prerequisite for downstream analyses. Therefore, we present an automated pipeline for fast de novo annotation of mitochondrial protein-coding genes. The annotation is based on enhanced phylogeny-aware hidden Markov models (HMMs). The pipeline builds taxon-specific enhanced multiple sequence alignments (MSA) of already annotated sequences and corresponding HMMs using an approximation of the phylogeny...
September 28, 2016: Molecular Phylogenetics and Evolution
A Seara Vieira, L Borrajo, E L Iglesias
In text classification problems, the representation of a document has a strong impact on the performance of learning systems. The high dimensionality of the classical structured representations can lead to burdensome computations due to the great size of real-world data. Consequently, there is a need for reducing the quantity of handled information to improve the classification process. In this paper, we propose a method to reduce the dimensionality of a classical text representation based on a clustering technique to group documents, and a previously developed Hidden Markov Model to represent them...
November 2016: Computer Methods and Programs in Biomedicine
Elad Yom-Tov, Barbara Marino, Jennifer Pai, Dawn Harris, Michael Wolf
The Internet continues to be an important supplemental health information resource for an increasing number of U.S. adults, especially for those with a new or existing chronic condition. Here we examine how people use the Internet to learn about Type 2 diabetes and how health literacy (HL) influences this information-seeking behavior. We analyzed the searches of approximately 2 million people who queried for diabetes-related information on Microsoft's Bing search engine. The HL of searchers was imputed through a community-based HL score...
October 2016: Journal of Health Communication
Shi-Yuan Wang, Qi Zhang, Xiang Zhang, Pei-Quan Zhao
AIM: To make a comprehensive analysis of the potential pathogenic genes related with Leber congenital amaurosis (LCA) in Chinese. METHODS: LCA subjects and their families were retrospectively collected from 2013 to 2015. Firstly, whole-exome sequencing was performed in patients who had underwent gene mutation screening with nothing found, and then homozygous sites was selected, candidate sites were annotated, and pathogenic analysis was conducted using softwares including Sorting Tolerant from Intolerant (SIFT), Polyphen-2, Mutation assessor, Condel, and Functional Analysis through Hidden Markov Models (FATHMM)...
2016: International Journal of Ophthalmology
Michael Czerwinski, Anirudh Natarajan, Lindsey Barske, Loren L Looger, Blanche Capel
Temperature dependent sex determination (TSD) is the process by which the environmental temperature experienced during embryogenesis influences the sex of an organism, as in the red-eared slider turtle Trachemys scripta elegans. In accord with current paradigms of vertebrate sex determination, temperature is believed to exert its effects on sexual development in T. scripta entirely within the middle third of development, when the gonad is forming. However, whether temperature regulates the transcriptome in T...
September 23, 2016: Developmental Biology
Yuanyang Zhang, Tie Bo Wu, Bernie J Daigle, Mitchell Cohen, Linda Petzold
BACKGROUND: Trauma is the leading cause of death between the ages of 1 to 44 in the United States. Blood loss is the primary cause of these deaths. The discrimination of states through which patients transition would be helpful in understanding the disease process, and in identification of critical states and appropriate interventions. Even though these states are strongly associated with patients' blood composition data, there has not been a way to directly identify them. Statistical tools such as hidden Markov models can be used to infer the discrete latent states from the blood composition data...
2016: BMC Medical Informatics and Decision Making
Robin Dowell, Aaron Odell, Phillip Richmond, Daniel Malmer, Eitan Halper-Stromberg, Beth Bennett, Colin Larson, Sonia Leach, Richard A Radcliffe
The Inbred Long- and Short-Sleep (ILS, ISS) mouse lines were selected for differences in acute ethanol sensitivity using the loss of righting response (LORR) as the selection trait. The lines show an over tenfold difference in LORR and, along with a recombinant inbred panel derived from them (the LXS), have been widely used to dissect the genetic underpinnings of acute ethanol sensitivity. Here we have sequenced the genomes of the ILS and ISS to investigate the DNA variants that contribute to their sensitivity difference...
September 20, 2016: Mammalian Genome: Official Journal of the International Mammalian Genome Society
Kiyoshi Ezawa
BACKGROUND: Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. Recently, indel probabilistic models are mostly based on either hidden Markov models (HMMs) or transducer theories, both of which give the indel component of the probability of a given sequence alignment as a product of either probabilities of column-to-column transitions or block-wise contributions along the alignment...
2016: BMC Bioinformatics
Jorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt
: MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets...
September 16, 2016: Bioinformatics
Haitao Guo, Hongwei Huo, Qiang Yu
The discovery of cis-regulatory modules (CRMs) is a challenging problem in computational biology. Limited by the difficulty of using an HMM to model dependent features in transcriptional regulatory sequences (TRSs), the probabilistic modeling methods based on HMMs cannot accurately represent the distance between regulatory elements in TRSs and are cumbersome to model the prevailing dependencies between motifs within CRMs. We propose a probabilistic modeling algorithm called SMCis, which builds a more powerful CRM discovery model based on a hidden semi-Markov model...
2016: PloS One
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