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Bioinformatics

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https://www.readbyqxmd.com/read/29029016/an-r-package-to-compute-diffusion-based-scores-on-biological-networks-diffustats
#1
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/29028961/towards-unified-quality-verification-of-synthetic-count-data-with-countsimqc
#2
Charlotte Soneson, Mark D Robinson
Summary: Statistical tools for biological data analysis are often evaluated using synthetic data, designed to mimic the features of a specific type of experimental data. The generalizability of such evaluations depends on how well the synthetic data reproduce the main characteristics of the experimental data, and we argue that an assessment of this similarity should accompany any synthetic data set used for method evaluation. We describe countsimQC, which provides a straightforward way to generate a stand-alone report that shows the main characteristics of (e...
October 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028896/pydream-high-dimensional-parameter-inference-for-biological-models-in-python
#3
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/29028890/maldirppa-quality-control-and-robust-analysis-for-mass-spectrometry-data
#4
Javier Palarea-Albaladejo, Kevin Mclean, Frank Wright, David G E Smith
Summary: This R package helps to implement a robust approach to deal with mass spectrometry (MS) data. It is aimed at alleviating reproducibility issues and pernicious effects of deviating signals on both data pre-processing and downstream data analysis. Based on robust statistical methods, it facilitates the identification and filtering of low-quality mass spectra and atypical peak profiles, as well as monitoring and data handling through pre-processing, which extends existing computational tools for high-throughput data...
October 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028907/oncomir-an-online-resource-for-exploring-pan-cancer-microrna-dysregulation
#5
Nathan W Wong, Yuhao Chen, Shuai Chen, Xiaowei Wang
Summary: Dysregulation of microRNAs (miRNAs) is extensively associated with cancer development and progression. miRNAs have been shown to be biomarkers for predicting tumor formation and outcome. However, identification of the relationships between miRNA expression and tumor characteristics can be difficult and time-consuming without appropriate bioinformatics expertise. To address this issue, we present OncomiR, an online resource for exploring miRNA dysregulation in cancer. Using combined miRNA-seq, RNA-seq, and clinical data from The Cancer Genome Atlas, we systematically performed statistical analyses to identify dysregulated miRNAs that are associated with tumor development and progression in most major cancer types...
October 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028986/a-new-haplotype-block-detection-method-for-dense-genome-sequencing-data-based-on-interval-graph-modeling-of-clusters-of-highly-correlated-snps
#6
Sun Ah Kim, Chang-Sung Cho, Suh-Ryung Kim, Shelley B Bull, Yun Joo Yoo
Motivation: Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation...
September 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028898/diffloop-a-computational-framework-for-identifying-and-analyzing-differential-dna-loops-from-sequencing-data
#7
Caleb A Lareau, Martin J Aryee
Summary: The three-dimensional architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops...
September 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028931/deepgo-predicting-protein-functions-from-sequence-and-interactions-using-a-deep-ontology-aware-classifier
#8
Maxat Kulmanov, Mohammed Asif Khan, Robert Hoehndorf
Motivation: A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often only done rigorously for few selected model organisms. Computational function prediction approaches have been suggested to fill this gap. The functions of proteins are classified using the Gene Ontology (GO), which contains over 40,000 classes...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028927/tumor-origin-detection-with-tissue-specific-mirna-and-dna-methylation-markers
#9
Wei Tang, Shixiang Wan, Zhen Yang, Andrew E Teschendorff, Quan Zou
Motivation: A clear identification of the primary site of tumor is of great importance to the next targeted site-specific treatments and could efficiently improve patient's overall survival. Even though many classifiers based on gene expression had been proposed to predict the tumor primary, only a few studies focus on using DNA methylation profiles to develop classifiers, and none of them compares the performance of classifiers based on different profiles. Results: We introduced novel selection strategies to identify highly tissue-specific CpG sites and then used the random forest approach to construct the classifiers to predict the origin of tumors...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028892/nephele-a-cloud-platform-for-simplified-standardized-and-reproducible-microbiome-data-analysis
#10
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/29028887/identification-of-cancer-driver-genes-in-focal-genomic-aberrations-from-whole-exome-sequencing-data
#11
Ho Jang, Hyunju Lee
Summary: Whole-exome sequencing (WES) data have been used for identifying copy number aberrations in cancer cells. Nonetheless, the use of WES is still challenging for identification of focal aberrant regions in multiple samples that may contain cancer driver genes. In this study, we developed a wavelet-based method for identifying focal genomic aberrant regions in the WES data from cancer cells (WIFA-X). When we applied WIFA-X to glioblastoma multiforme and lung adenocarcinoma datasets, WIFA-X outperformed other approaches on identifying cancer driver genes...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29029024/diversepathsj-diverse-shortest-paths-for-bioimage-analysis
#12
Virginie Uhlmann, Carsten Haubold, Fred A Hamprecht, Michael Unser
Motivation: We introduce a formulation for the general task of finding diverse shortest paths between two end-points. Our approach is not linked to a specific biological problem and can be applied to a large variety of images thanks to its generic implementation as a user-friendly ImageJ/Fiji plugin. It relies on the introduction of additional layers in a Viterbi path graph, which requires slight modifications to the standard Viterbi algorithm rules. This layered graph construction allows for the specification of various constraints imposing diversity between solutions...
September 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028909/the-systematic-analysis-of-ultraconserved-genomic-regions-in-the-budding-yeast
#13
Zhi-Kai Yang, Feng Gao
Motivation: In the evolution of species, a kind of special sequences, termed ultraconserved sequences (UCSs), have been inherited without any change, which strongly suggests those sequences should be crucial for the species to survive or adapt to the environment. However, the UCSs are still regarded as mysterious genetic sequences so far. Here, we present a systematic study of ultraconserved genomic regions in the budding yeast based on the publicly available genome sequences, in order to reveal their relationship with the adaptability or fitness advantages of the budding yeast...
September 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028893/canvas-spw-calling-de-novo-copy-number-variants-in-pedigrees
#14
Sergii Ivakhno, Eric Roller, Camilla Colombo, Philip Tedder, Anthony J Cox
Motivation: Whole genome sequencing is becoming a diagnostics of choice for the identification of rare inherited and de novo copy number variants in families with various pediatric and late-onset genetic diseases. However, joint variant calling in pedigrees is hampered by the complexity of consensus breakpoint alignment across samples within an arbitrary pedigree structure. Results: We have developed a new tool, Canvas SPW, for the identification of inherited and de novo copy number variants from pedigree sequencing data...
September 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028891/on-the-mechanisms-of-protein-interactions-predicting-their-affinity-from-unbound-tertiary-structures
#15
Manuel Alejandro Marín-López, Joan Planas-Iglesias, Joaquim Aguirre-Plans, Jaume Bonet, Javier Garcia-Garcia, Narcis Fernandez-Fuentes, Baldo Oliva
Motivation: The characterization of the protein-protein association mechanisms is crucial to understanding how biological processes occur. It has been previously shown that the early formation of non-specific encounters enhances the realization of the stereospecific (i.e. native) complex by reducing the dimensionality of the search process. The association rate for the formation of such complex plays a crucial role in the cell biology and depends on how the partners diffuse to be close to each other...
September 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028926/structure-based-prediction-of-protein-peptide-binding-regions-using-random-forest
#16
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/29028901/a-collaborative-filtering-based-approach-to-biomedical-knowledge-discovery
#17
Jake Lever, Sitanshu Gakkhar, Michael Gottlieb, Tahereh Rashnavadi, Santina Lin, Celia Siu, Maia Smith, Martin Jones, Martin Krzywinski, Steven J Jones
Motivation: The increase in publication rates makes it challenging for an individual researcher to stay abreast of all relevant research in order to find novel research hypotheses. Literature-based discovery methods make use of knowledge graphs built using text mining and can infer future associations between biomedical concepts that will likely occur in new publications. These predictions are a valuable resource for researchers to explore a research topic. Current methods for prediction are based on the local structure of the knowledge graph...
September 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028987/in-silico-structural-modelling-of-multiple-epigenetic-marks-on-dna
#18
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/29028984/a-bayesian-framework-for-the-inference-of-gene-regulatory-networks-from-time-and-pseudo-time-series-data
#19
M Sanchez-Castillo, D Blanco, I M Tienda-Luna, M C Carrion, Yufei Huang
Motivation: Molecular profiling techniques have evolved to single-cell assays, where dense molecular profiles are screened simultaneously for each cell in a population. High-throughput single-cell experiments from a heterogeneous population of cells can be experimentally and computationally sorted as a sequence of samples pseudo-temporally ordered samples. The analysis of these data sets, comprising a large number of samples, has the potential to uncover the dynamics of the underlying regulatory programmes...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028963/zcchc17-is-a-master-regulator-of-synaptic-gene-expression-in-alzheimer-s-disease
#20
Zeljko Tomljanovic, Mitesh Patel, William Shin, Andrea Califano, Andrew F Teich
Motivation: In an effort to better understand the molecular drivers of synaptic and neurophysiologic dysfunction in Alzheimer's disease (AD), we analyzed neuronal gene expression data from human AD brain tissue to identify master regulators of synaptic gene expression. Results: Master regulator analysis identifies ZCCHC17 as normally supporting the expression of a network of synaptic genes, and predicts that ZCCHC17 dysfunction in AD leads to lower expression of these genes...
September 25, 2017: Bioinformatics
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