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Computational biology

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https://www.readbyqxmd.com/read/29031098/stepwise-construction-of-a-metabolic-network-in-event-b-the-heat-shock-response
#1
Usman Sanwal, Luigia Petre, Ion Petre
There is a high interest in constructing large, detailed computational models for biological processes. This is often done by putting together existing submodels and adding to them extra details/knowledge. The result of such approaches is usually a model that can only answer questions on a very specific level of detail, and thus, ultimately, is of limited use. We focus instead on an approach to systematically add details to a model, with formal verification of its consistency at each step. In this way, one obtains a set of reusable models, at different levels of abstraction, to be used for different purposes depending on the question to address...
September 30, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29029338/to-include-or-not-to-include-the-impact-of-gene-filtering-on-species-tree-estimation-methods
#2
Erin K Molloy, Tandy Warnow
With the increasing availability of whole genome data, many species trees are being constructed from hundreds to thousands of loci. Although concatenation analysis using maximum likelihood is a standard approach for estimating species trees, it does not account for gene tree heterogeneity, which can occur due to many biological processes, such as incomplete lineage sorting. Coalescent species tree estimation methods, many of which are statistically consistent in the presence of incomplete lineage sorting, include Bayesian methods that co-estimate the gene trees and the species tree, summary methods that compute the species tree by combining estimated gene trees, and site-based methods that infer the species tree from site patterns in the alignments of different loci...
September 15, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029321/rapid-novel-facile-biosynthesized-silver-nanoparticles-from-bacterial-release-induce-biogenicity-and-concentration-dependent-in-vivo-cytotoxicity-with-embryonic-zebrafish-a-mechanistic-insight
#3
Suresh K Verma, Ealisha Jha, Pritam Kumar Panda, Anurag Mishra, Arun Thirumurugan, Biswadeep Das, S K S Parashar, Mrutyunjay Suar
In this study, rapid one step facile synthesis of silver nanoparticles (AgNP) was done using culture supernatant of two Gram positive (B.thuringiensis, S.aureus) and Gram negative (E.coli, S.typhimurium) bacterial strains and were termed as "BTAgNP", "SAAgNP", "ECAgNP" and "STAgNP" respectively. Synthesized AgNPs were well characterized with the help of different standard techniques like FESEM, DLS, UV-Vis spectroscopy and FTIR. Mechanism of AgNPs synthesis was elucidated using in silico approach. In vivo cytotoxicity of synthesized AgNPs was assessed in embryonic Zebrafish model with the help of uptake, oxidative stress and apoptosis induction experimental assays and the mechanism was investigated through in silico approach at the molecular level...
September 28, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29029158/genetic-interaction-network-as-an-important-determinant-of-gene-order-in-genome-evolution
#4
Yu-Fei Yang, Wenqing Cao, Shaohuan Wu, Wenfeng Qian
Although it is generally accepted that eukaryotic gene order is not random, the basic principles of gene arrangement on a chromosome remain poorly understood. Here, we extended existing population genetics theories that were based on two-locus models and proposed a hypothesis that genetic interaction networks drive the evolution of eukaryotic gene order. We predicted that genes with positive epistasis would move toward each other in evolution, during which a negative correlation between epistasis and gene distance formed...
October 3, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029026/long-segment-pulmonary-artery-resection-to-avoid-pneumonectomy-long-term-results-after-prosthetic-replacement
#5
Antonio D'Andrilli, Giulio Maurizi, Anna Maria Ciccone, Claudio Andreetti, Mohsen Ibrahim, Cecilia Menna, Camilla Vanni, Federico Venuta, Erino A Rendina
OBJECTIVES: Resection of a long pulmonary artery (PA) segment infiltrated by tumour and reconstruction by conduit interposition or wide patch is a challenging but feasible option to avoid pneumonectomy. Our goal was to report the long-term results of our experience with this type of operation using various techniques and materials. METHODS: Between 1991 and 2015, 24 patients underwent sleeve resection of a long PA segment or extended resection (>2.5 cm) of 1 aspect of the circumference of the PA associated with lobectomy for centrally located lung cancer...
September 28, 2017: European Journal of Cardio-thoracic Surgery
https://www.readbyqxmd.com/read/29029016/an-r-package-to-compute-diffusion-based-scores-on-biological-networks-diffustats
#6
Sergio Picart-Armada, Wesley K Thompson, Alfonso Buil, Alexandre Perera-Lluna
Summary: Label propagation and diffusion over biological networks are a common mathematical formalism in computational biology for giving context to molecular entities and prioritising novel candidates in the area of study. There are several choices in conceiving the diffusion process -involving the graph kernel, the score definitions and the presence of a posterior statistical normalisation- which have an impact on the results. This manuscript describes diffuStats, an R package that provides a collection of graph kernels and diffusion scores, as well as a parallel permutation analysis for the normalised scores, that eases the computation of the scores and their benchmarking for an optimal choice...
October 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028987/in-silico-structural-modelling-of-multiple-epigenetic-marks-on-dna
#7
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M Deane, Peter Minary
Summary: There are four known epigenetic cytosine modifications in mammals: 5mC, 5hmC, 5fC and 5caC. The biological effects of 5mC are well understood but the roles of the remaining modifications remain elusive. Experimental and computational studies suggest that a single epigenetic mark has little structural effect but six of them can radically change the structure of DNA to a new form, F-DNA. Investigating the collective effect of multiple epigenetic marks requires the ability to interrogate all possible combinations of epigenetic states (e...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028926/structure-based-prediction-of-protein-peptide-binding-regions-using-random-forest
#8
Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
Motivation: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processes, functional mechanisms, and drug discovery. Protein-peptide interactions can be analyzed by studying the structures of protein-peptide complexes. However, only a small portion has known complex structures and experimental determination of protein-peptide interaction is costly and inefficient...
September 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028902/graphkernels-r-and-python-packages-for-graph-comparison
#9
Mahito Sugiyama, M Elisabetta Ghisu, Felipe Llinares-López, Karsten Borgwardt
Summary: Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based kernels, and the state-of-the-art Weisfeiler-Lehman graph kernel...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028896/pydream-high-dimensional-parameter-inference-for-biological-models-in-python
#10
Erin M Shockley, Jasper A Vrugt, Carlos F Lopez
Summary: Biological models contain many parameters whose values are difficult to measure directly via experimentation and therefore require calibration against experimental data. Markov chain Monte Carlo (MCMC) methods are suitable to estimate multivariate posterior model parameter distributions, but these methods may exhibit slow or premature convergence in high-dimensional search spaces. Here, we present PyDREAM, a Python implementation of the (Multiple-Try) Differential Evolution Adaptive Metropolis (DREAM(ZS)) algorithm developed by Vrugt and ter Braak (2008) and Laloy and Vrugt (2012)...
October 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028892/nephele-a-cloud-platform-for-simplified-standardized-and-reproducible-microbiome-data-analysis
#11
Nick Weber, David Liou, Jennifer Dommer, Philip MacMenamin, Mariam Quiñones, Ian Misner, Andrew Oler, Joe Wan, Lewis Kim, Meghan Coakley McCarthy, Samuel Ezeji, Karlynn Noble, Darrell E Hurt
Motivation: Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results: The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028886/analysis-of-protein-targets-in-pathogen-host-interaction-in-infectious-diseases-a-case-study-on-plasmodium-falciparum-and-homo-sapiens-interaction-network
#12
Sovan Saha, Kaustav Sengupta, Piyali Chatterjee, Subhadip Basu, Mita Nasipuri
Infection and disease progression is the outcome of protein interactions between pathogen and host. Pathogen, the role player of Infection, is becoming a severe threat to life as because of its adaptability toward drugs and evolutionary dynamism in nature. Identifying protein targets by analyzing protein interactions between host and pathogen is the key point. Proteins with higher degree and possessing some topologically significant graph theoretical measures are found to be drug targets. On the other hand, exceptional nodes may be involved in infection mechanism because of some pathway process and biologically unknown factors...
September 23, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028878/web-based-drug-repurposing-tools-a-survey
#13
Elizabeth Sam, Prashanth Athri
Drug repurposing (a.k.a. drug repositioning) is the search for new indications or molecular targets distinct from a drug's putative activity, pharmacological effect or binding specificities. With the ever-increasing rates of termination of drugs in clinical trials, drug repositioning has risen as one of the effective solutions against the risk of drug failures. Repositioning finds a way to reverse the grim but real trend that Eroom's law portends for the pharmaceutical and biotech industry, and drug discovery in general...
October 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29028318/a-combination-of-c%C3%AE-h-hydrogen-bonds-and-van-der-waals-packing-modulates-the-stability-of-gxxxg-mediated-dimers-in-membranes
#14
Samantha M Anderson, Benjamin Keymar Mueller, Evan Lange, Alessandro Senes
The GxxxG motif is frequently found at the dimerization interface of a transmembrane structural motif called GASright, which is characterized by a short inter-helical distance and a right-handed crossing angle between the helices. In GASright dimers - such as glycophorin A (GpA), BNIP3, and members of the ErbB family - the backbones of the helices are in contact, and they invariably display networks of 4 to 8 weak hydrogen bonds between Cα-H carbon donors and carbonyl acceptors on opposing helices (Cα-H∙∙∙O=C hydrogen bonds)...
October 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29028265/stereogene-rapid-estimation-of-genome-wide-correlation-of-continuous-or-interval-feature-data
#15
Elena D Stavrovskaya, Tejasvi Niranjan, Elana J Fertig, Sarah J Wheelan, Alexander V Favorov, Andrey A Mironov
Motivation: Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required. Results: Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028264/teacheng-a-teaching-engine-for-genomics
#16
Minji Kim, Yeonsung Kim, Lei Qian, Jun S Song
Motivation: Bioinformatics is a rapidly growing field that has emerged from the synergy of computer science, statistics and biology. Given the interdisciplinary nature of bioinformatics, many students from diverse fields struggle with grasping bioinformatic concepts only from classroom lectures. Interactive tools for helping students reinforce their learning would be thus desirable. Here, we present an interactive online educational tool called TeachEnG (acronym for Teaching Engine for Genomics) for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028065/a-bayesian-approach-for-estimating-protein-protein-interactions-by-integrating-structural-and-non-structural-biological-data
#17
Hafeez Ur Rehman, Inam Bari, Anwar Ali, Haroon Mahmood
Accurate elucidation of genome wide protein-protein interactions is crucial for understanding the regulatory processes of the cell. High-throughput techniques, such as the yeast-2-hybrid (Y2H) assay, co-immunoprecipitation (co-IP), mass spectrometric (MS) protein complex identification, affinity purification (AP) etc., are generally relied upon to determine protein interactions. Unfortunately, each type of method is inherently subject to different types of noise and results in false positive interactions. On the other hand, precise understanding of proteins, especially knowledge of their functional associations is necessary for understanding how complex molecular machines function...
October 13, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29026678/statistical-model-for-oct-image-denoising
#18
Muxingzi Li, Ramzi Idoughi, Biswarup Choudhury, Wolfgang Heidrich
Optical coherence tomography (OCT) is a non-invasive technique with a large array of applications in clinical imaging and biological tissue visualization. However, the presence of speckle noise affects the analysis of OCT images and their diagnostic utility. In this article, we introduce a new OCT denoising algorithm. The proposed method is founded on a numerical optimization framework based on maximum-a-posteriori estimate of the noise-free OCT image. It combines a novel speckle noise model, derived from local statistics of empirical spectral domain OCT (SD-OCT) data, with a Huber variant of total variation regularization for edge preservation...
September 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/29026602/re-phrasing-the-question-a-simple-tool-for-evaluation-of-adherence-to-therapy-in-patients-with-inflammatory-bowel-disease
#19
T Engel, B Ungar, G Ben-Haim, N Levhar, R Eliakim, S Ben-Horin
BACKGROUND: Non-adherence to medication in patients with inflammatory bowel disease (IBD) is a challenging problem which is often overlooked or under-estimated by the physician or denied by the patient. We aimed to examine if re-phrasing the wording of the question used by the physician could help in revealing more patients who are non-adherent, and for whom appropriate counseling may be instituted. METHODS: A cross-sectional questionnaire-based study of IBD patients treated in a tertiary center was conducted...
October 2017: United European Gastroenterology Journal
https://www.readbyqxmd.com/read/29026441/modeling-the-architecture-of-the-regulatory-system-controlling-methylenomycin-production-in-streptomyces-coelicolor
#20
Jack E Bowyer, Emmanuel Lc de Los Santos, Kathryn M Styles, Alex Fullwood, Christophe Corre, Declan G Bates
BACKGROUND: The antibiotic methylenomycin A is produced naturally by Streptomyces coelicolor A3(2), a model organism for streptomycetes. This compound is of particular interest to synthetic biologists because all of the associated biosynthetic, regulatory and resistance genes are located on a single cluster on the SCP1 plasmid, making the entire module easily transferable between different bacterial strains. Understanding further the regulation and biosynthesis of the methylenomycin producing gene cluster could assist in the identification of motifs that can be exploited in synthetic regulatory systems for the rational engineering of novel natural products and antibiotics...
2017: Journal of Biological Engineering
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