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https://www.readbyqxmd.com/read/29040919/functional-analyses-of-the-interaction-of-chicken-interleukin-23-subunit-p19-with-il-12-subunit-p40-to-form-the-il-23-complex
#1
Anh Duc Truong, Cong Thanh Hoang, Yeojin Hong, Janggeun Lee, Kyungbaek Lee, Hyun S Lillehoj, Yeong Ho Hong
This study represents the first description of the cloning of chicken IL-23p19 (ChIL-23α) and the function of the IL-23 complex in birds. Multiple alignment of ChIL-23α with other known IL-23α amino acid sequences revealed regions of amino acid conservation. The homologies of ChIL-23α, IL-12p35, and similar mammalian subunits ranged between 26% and 42%. ChIL-23α consisted of four exons and three introns; similar to those in humans and mice, and limited conservation of synteny between the human and chicken genomes was observed...
October 14, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29040908/predicting-lysine-glycation-sites-using-bi-profile-bayes-feature-extraction
#2
Zhe Ju, Juhe Sun, Yanjie Li, Li Wang
Glycation is a nonenzymatic post-translational modification which has been found to be involved in various biological processes and closely associated with many metabolic diseases. The accurate identification of glycation sites is important to understand the underlying molecular mechanisms of glycation. As the traditional experimental methods are often labor-intensive and time-consuming, it is desired to develop computational methods to predict glycation sites. In this study, a novel predictor named BPB_GlySite is proposed to predict lysine glycation sites by using bi-profile bayes feature extraction and support vector machine algorithm...
October 12, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29040639/the-medical-science-dmz-a-network-design-pattern-for-data-intensive-medical-science
#3
Sean Peisert, Eli Dart, William Barnett, Edward Balas, James Cuff, Robert L Grossman, Ari Berman, Anurag Shankar, Brian Tierney
Objective: We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods: High-end networking, packet-filter firewalls, network intrusion-detection systems. Results: We describe a "Medical Science DMZ" concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs...
October 6, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29040613/dna-data-bank-of-japan-30th-anniversary
#4
Yuichi Kodama, Jun Mashima, Takehide Kosuge, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
The DNA Data Bank of Japan (DDBJ) Center (http://www.ddbj.nig.ac.jp) has been providing public data services for 30 years since 1987. We are collecting nucleotide sequence data and associated biological information from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with the US National Center for Biotechnology Information and the European Bioinformatics Institute. The DDBJ Center also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database Center to collect genotype and phenotype data of human individuals...
October 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040493/releasing-the-geni-integrating-authentic-microbial-genomics-research-into-the-classroom-through-geni-act
#5
Karobi Moitra
The integration of genomics research into the undergraduate biology curriculum provides students with the opportunity to become familiar with bioinformatics tools and answer original research questions. Our purpose with this research project was to upscale the research experience through integration with classroom experience giving students access to authentic research projects. Students annotated 60 predicted ABC genes of Methanothermobacter thermautotrophicus and Methanobacterium sp. SWAN-1 and they were required to present a research poster to demonstrate their understanding of the project...
October 11, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29040459/uc2-search-using-unique-connectivity-of-uncharged-compounds-for-metabolite-annotation-by-database-searching-in-mass-spectrometry-based-metabolomics
#6
Nozomu Sakurai, Takafumi Narise, Joon-Soo Sim, Chang-Muk Lee, Chiaki Ikeda, Nayumi Akimoto, Shigehiko Kanaya
Summary: For metabolite annotation in metabolomics, variations in the registered states of compounds (charged and multiple components such as salts) and their redundancy among compound databases could be the cause of misannotations and hamper immediate recognition of the uniqueness of metabolites while searching by mass values measured using mass spectrometry. We developed a search system named UC2 (Unique Connectivity of Uncharged Compounds) where compounds are tentatively neutralized into uncharged states and stored on the basis of their unique connectivity of atoms after removing their stereochemical information using the first block in the hash of the IUPAC International Chemical Identifier, by which false-positive hits are remarkably reduced, both charged and uncharged compounds are properly searched in a single query and records having a unique connectivity are compiled in a single search result...
October 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040453/detection-of-sputum-by-interpreting-the-time-frequency-distribution-of-respiratory-sound-signal-using-image-processing-techniques
#7
Jinglong Niu, Yan Shi, Maolin Cai, Zhixin Cao, Dandan Wang, Zhaozhi Zhang, Xiaohua Douglas Zhang
Motivation: Sputum in the trachea is hard to expectorate and detect directly for the patients who are unconscious, especially those in Intensive Care Unit (ICU). Medical staff should always check the condition of sputum in the trachea. This is time-consuming and the necessary skills are difficult to acquire. Currently, there are few automatic approaches to serve as alternatives to this manual approach. Results: We develop an automatic approach to diagnose the condition of the sputum...
October 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040451/an-omnibus-test-for-differential-distribution-analysis-of-microbiome-sequencing-data
#8
Jun Chen, Emily King, Rebecca Deek, Zhi Wei, Yue Yu, Diane Grill, Karla Ballman
Motivation: One objective of human microbiome studies is to identify differentially abundant microbes across biological conditions. Previous statistical methods focus on detecting the shift in the abundance and/or prevalence of the microbes and treat the dispersion (spread of the data) as a nuisance. These methods also assume that the dispersion is the same across conditions, an assumption which may not hold in presence of sample heterogeneity. Moreover, the widespread outliers in the microbiome sequencing data make existing parametric models not overly robust...
October 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040432/machine-learning-accelerates-md-based-binding-pose-prediction-between-ligands-and-proteins
#9
Kei Terayama, Hiroaki Iwata, Mitsugu Araki, Yasushi Okuno, Koji Tsuda
Motivation: Fast and accurate prediction of protein-ligand binding structures is indispensable for structure-based drug design (SBDD) and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose prediction methods based on short-MD simulations such as MM-PBSA and MM-GBSA among generated docking poses have been used. Since molecular structures obtained from MD simulation depends on the initial condition, taking the average over different initial conditions leads to better accuracy...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040406/matam-reconstruction-of-phylogenetic-marker-genes-from-short-sequencing-reads-in-metagenomes
#10
Pierre Pericard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet
Motivation: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040399/toward-completion-of-the-earth-s-proteome-an-update-a-decade-later
#11
Pablo Mier, Miguel A Andrade-Navarro
Protein databases are steadily growing driven by the spread of new more efficient sequencing techniques. This growth is dominated by an increase in redundancy (homologous proteins with various degrees of sequence similarity) and by the incapability to process and curate sequence entries as fast as they are created. To understand these trends and aid bioinformatic resources that might be compromised by the increasing size of the protein sequence databases, we have created a less-redundant protein data set. In parallel, we analyzed the evolution of protein sequence databases in terms of size and redundancy...
October 12, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29040390/robust-and-sparse-correlation-matrix-estimation-for-the-analysis-of-high-dimensional-genomics-data
#12
Angela Serra, Pietro Coretto, Michele Fratello, Roberto Tagliaferri
Motivation: Microarray technology can be used to study the expression of thousands of genes across a number of different experimental conditions, usually hundreds. The underlying principle is that genes sharing similar expression patterns, across different samples, can be part of the same co-expression system, or they may share the same biological functions. Groups of genes are usually identified based on cluster analysis. Clustering methods rely on the similarity matrix between genes...
October 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040385/a-benchmarking-of-workflows-for-detecting-differential-splicing-and-differential-expression-at-isoform-level-in-human-rna-seq-studies
#13
Gabriela A Merino, Ana Conesa, Elmer A Fernández
Over the last few years, RNA-seq has been used to study alterations in alternative splicing related to several diseases. Bioinformatics workflows used to perform these studies can be divided into two groups, those finding changes in the absolute isoform expression and those studying differential splicing. Many computational methods for transcriptomics analysis have been developed, evaluated and compared; however, there are not enough reports of systematic and objective assessment of processing pipelines as a whole...
October 13, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29040382/generalized-correlation-measure-using-count-statistics-for-gene-expression-data-with-ordered-samples
#14
Y X Rachel Wang, Ke Liu, Elizabeth Theusch, Jerome I Rotter, Marisa W Medina, Michael S Waterman, Haiyan Huang
Motivation: Capturing association patterns in gene expression levels under different conditions or time points is important for inferring gene regulatory interactions. In practice, temporal changes in gene expression may result in complex association patterns that require more sophisticated detection methods than simple correlation measures. For instance, the effect of regulation may lead to time-lagged associations and interactions local to a subset of samples. Furthermore, expression profiles of interest may not be aligned or directly comparable (e...
October 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040376/aegs-identifying-aberrantly-expressed-gene-sets-for-differential-variability-analysis
#15
Jinting Guan, Moliang Chen, Congting Ye, James J Cai, Guoli Ji
Motivation: In gene expression studies, differential expression (DE) analysis has been widely used to identify genes with shifted expression mean between groups. Recently, differential variability (DV) analysis has been increasingly applied as analyzing changed expression variability (e.g., the changes in expression variance) between groups may reveal underlying genetic heterogeneity and undetected interactions, which has great implications in many fields of biology. An easy-to-use tool for DV analysis is needed...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040374/beyond-similarity-assessment-selecting-the-optimal-model-for-sequence-alignment-via-the-factorized-asymptotic-bayesian-algorithm
#16
Taikai Takeda, Michiaki Hamada
Motivation: Pair Hidden Markov Models (PHMMs) are probabilistic models used for pairwise sequence alignment, a quintessential problem in bioinformatics. PHMMs include three types of hidden states: match, insertion and deletion. Most previous studies have used one or two hidden states for each PHMM state type. However, few studies have examined the number of states suitable for representing sequence data or improving alignment accuracy. Results: We developed a novel method to select superior models (including the number of hidden states) for PHMM...
October 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040360/elucidating-the-editome-bioinformatics-approaches-for-rna-editing-detection
#17
Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi
RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites...
October 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29036655/mfib-a-repository-of-protein-complexes-with-mutual-folding-induced-by-binding
#18
Erzsébet Fichó, István Reményi, István Simon, Bálint Mészáros
Motivation: It is commonplace that intrinsically disordered proteins (IDPs) are involved in crucial interactions in the living cell. However, the study of protein complexes formed exclusively by IDPs is hindered by the lack of data and such analyses remain sporadic. Systematic studies benefited other types of protein-protein interactions paving a way from basic science to therapeutics; yet these efforts require reliable datasets that are currently lacking for synergistically folding complexes of IDPs...
August 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036643/glass-assisted-and-standardized-assessment-of-gene-variations-from-sanger-sequence-trace-data
#19
Karol Pal, Vojtech Bystry, Tomas Reigl, Martin Demko, Adam Krejci, Tasoula Touloumenidou, Evangelia Stalika, Boris Tichy, Paolo Ghia, Kostas Stamatopoulos, Sarka Pospisilova, Jitka Malcikova, Nikos Darzentas
Motivation: Sanger sequencing is still being employed for sequence variant detection by many laboratories, especially in a clinical setting. However, chromatogram interpretation often requires manual inspection and in some cases, considerable expertise. Results: We present GLASS, a web-based Sanger sequence trace viewer, editor, aligner and variant caller, built to assist with the assessment of variations in 'curated' or user-provided genes. Critically, it produces a standardized variant output as recommended by the Human Genome Variation Society...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036627/using-uncertainty-to-link-and-rank-evidence-from-biomedical-literature-for-model-curation
#20
Chrysoula Zerva, Riza Batista-Navarro, Philip Day, Sophia Ananiadou
Motivation: In recent years, there has been great progress in the field of automated curation of biomedical networks and models, aided by text mining methods that provide evidence from literature. Such methods must not only extract snippets of text that relate to model interactions, but also be able to contextualize the evidence and provide additional confidence scores for the interaction in question. Although various approaches calculating confidence scores have focused primarily on the quality of the extracted information, there has been little work on exploring the textual uncertainty conveyed by the author...
July 24, 2017: Bioinformatics
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