Bioinformatics

Abstract Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general
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Abstract It is estimated that the Earth’s biocapacity is unable to meet current demands, which begs the question: is a sustainable future possible for both humans and the environment? The UN projects a human population of approximately 11 billion by the end of the 21st century; requiring additional agricultural land, greater demands for natural resources,
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Abstract The adherens junctions between epithelial cells involve a protein complex formed by E-cadherin, β-catenin, α-catenin and F-actin. The stability of this complex was a puzzle for many years, since in vitro studies could reconstitute various stable subsets of the individual proteins, but never the entirety. The missing ingredient turned out to be mechanical tension:
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Citation: Hamlet CL, Hoffman KA, Tytell ED, Fauci LJ (2018) The role of curvature feedback in the energetics and dynamics of lamprey swimming: A closed-loop model. PLoS Comput Biol 14(8): e1006324. https://doi.org/10.1371/journal.pcbi.1006324 Editor: Philip K. Maini, Oxford, UNITED KINGDOM Received: January 25, 2018; Accepted: June 24, 2018; Published: August 17, 2018 Copyright: © 2018 Hamlet
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Abstract We present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments, a feature unique to this software. Compared to the existing versions of programs generating sashimi plots, it
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Posted by: RNA-Seq Blog in Data Normalization 2 hours ago 61 Views Breast cancer (BC) is increasing in incidence and resistance to treatment worldwide. The challenges in limited therapeutic options and poor survival outcomes in BC subtypes persist because of its molecular heterogeneity and resistance to standard endocrine therapy. Recently, high throughput RNA sequencing (RNA-seq)
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Posted by: RNA-Seq Blog in Publications 13 hours ago 408 Views Regenerative therapeutic approaches for myocardial diseases often involve delivery of stem cells expanded ex vivo. Prior studies indicate that cell culture conditions affect functional and phenotypic characteristics, but relationship(s) of cultured cells derived from freshly isolated populations and the heterogeneity of the cultured population
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Abstract Understanding the epidemiology of seasonal influenza is critical for healthcare resource allocation and early detection of anomalous seasons. It can be challenging to obtain high-quality data of influenza cases specifically, as clinical presentations with influenza-like symptoms may instead be cases of one of a number of alternate respiratory viruses. We use a new dataset
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Abstract Evolve and Resequencing (E&R) studies allow us to monitor adaptation at the genomic level. By sequencing evolving populations at regular time intervals, E&R studies promise to shed light on some of the major open questions in evolutionary biology such as the repeatability of evolution and the molecular basis of adaptation. However, data interpretation, statistical
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Posted by: RNA-Seq Blog in Splicing and Junction Mapping 2 hours ago 59 Views Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-sequencing data rely on preannotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated
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From Advanced Science News by Kerstin Brachhold How stem cells differentiate into the myriad diverse cell types that ultimately form tissues has been an area of extensive research. Studying this process at the population level unfortunately masks rare or transient intermediates. The application of ever more sophisticated single cell technologies, however, is able to address
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Abstract The spread of disease through human populations is complex. The characteristics of disease propagation evolve with time, as a result of a multitude of environmental and anthropic factors, this non-stationarity is a key factor in this huge complexity. In the absence of appropriate external data sources, to correctly describe the disease propagation, we explore
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Differential gene expression (DGE) analysis is one of the most common applications of RNA-sequencing (RNA-seq) data. This process allows for the elucidation of differentially expressed genes across two or more conditions and is widely used in many applications of RNA-seq data analysis. Interpretation of the DGE results can be nonintuitive and time consuming due to
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Research Associate Center for Genomics and Bioinformatics Indiana University The IU Center for Genomics and Bioinformatics (CGB), https://cgb.indiana.edu/, seeks a Research Associate to serve in the bioinformatics core. Responsibilities include computational analysis of genomic sequencing data, developing scripts and pipelines for automating genomic analyses, use of statistics in a genomic context, and the ability to
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Abstract Hebbian plasticity describes a basic mechanism for synaptic plasticity whereby synaptic weights evolve depending on the relative timing of paired activity of the pre- and postsynaptic neurons. Spike-timing-dependent plasticity (STDP) constitutes a central experimental and theoretical synaptic Hebbian learning rule. Various mechanisms, mostly calcium-based, account for the induction and maintenance of STDP. Classically STDP
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Abstract The hippocampus is known to store cognitive representations, or maps, that encode both positional and contextual information, critical for episodic memories and functional behavior. How path integration and contextual cues are dynamically combined and processed by the hippocampus to maintain these representations accurate over time remains unclear. To answer this question, we propose a
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Genomic variants in both coding and non-coding sequences can have functionally important and sometimes deleterious effects on exon splicing of gene transcripts. For transcriptome profiling using RNA-seq, the accurate alignment of reads across exon junctions is a critical step. Existing algorithms that utilize a standard reference genome as a template sometimes have difficulty in mapping
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The new method can be compared to a photo captured with a long exposure, where stationary objects are sharp (in this image first author Gioele La Manno) while objects in motion are blurred (in this image Sten Linnarsson). Photo: Stefan Zimmerman Researchers at Karolinska Institutet and Harvard Medical School report in the journal Nature that
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In order to perform full evolutionary analysis coupled with structural data, the input is minimal: an MSA and a plain text file with any structural/physicochemical data provided by the user (Additional file 1: Figure S1). Both are described exhaustively in the BALCONY manual. Initial data analysis and validation: The package allows to primarily extract, analyse and summarise
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Abstract Manually curating biomedical knowledge from publications is necessary to build a knowledge based service that provides highly precise and organized information to users. The process of retrieving relevant publications for curation, which is also known as document triage, is usually carried out by querying and reading articles in PubMed. However, this query-based method often
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Abstract Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine the trinucleotide periodicity of translating ribosomes, and draw correct conclusions
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Abstract Gene co-expression network analysis is extremely useful in interpreting a complex biological process. The recent droplet-based single-cell technology is able to generate much larger gene expression data routinely with thousands of samples and tens of thousands of genes. To analyze such a large-scale gene-gene network, remarkable progress has been made in rigorous statistical inference
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Citation: Narasumani M, Harrison PM (2018) Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins. PLoS Comput Biol 14(8): e1006349. https://doi.org/10.1371/journal.pcbi.1006349 Editor: Claus O. Wilke, University of Texas at Austin, UNITED STATES Received: February 26, 2018; Accepted: July 7, 2018; Published: August
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Abstract In schizophrenia, increased aberrant salience to irrelevant events and reduced learning of relevant information may relate to an underlying deficit in relevance detection. So far, subjective estimates of relevance have not been probed in schizophrenia patients. The mechanisms underlying belief formation about relevance and their translation into decisions are unclear. Using novel computational methods,
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Abstract Single-cell RNA sequencing (scRNA-seq) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously. Protocols that incorporate both designed and random barcodes have greatly increased the throughput of scRNA-seq, but give rise to a more complex data structure. There is a need for new tools that can handle the various barcoding strategies
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Estrogen receptor positive (ER+) breast cancer is the most common type of breast cancer, but resistance to therapy is common and eventual development of metastatic disease is a leading cause of death. In new research published in Cell Reports, researchers from Baylor College of Medicine and Washington University in St. Louis identify estrogen receptor alpha
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A comprehensive RNA and DNA sequencing platform benefits late-stage and drug-resistant multiple myeloma patients by determining which drugs would work best for them, according to results from a clinical trial published in JCO Precision Oncology in August. The novel platform, created by Mount Sinai cancer, genomics, and precision health researchers, expands on traditional DNA-based approaches
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Restriction fragment length polymorphism (RFLP) is a useful molecular technique that exploits genetic variants and mutations in homologous DNA. It is based on endonuclease cleavage and is relatively inexpensive for genotyping [1]. Many laboratories use polymerase chain reaction (PCR)-RFLP to rapidly detect point mutations after the genomic sequences are amplified, especially in single nucleotide polymorphism
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miREM workflow The miREM workflow is composed of the following five steps (Fig. 1): Fig. 1 miREM Workflow. a The gene-list and setup parameters are entered into the input page. b Each transcript is associated to its targeted miRNA(s) using the selected prediction databases. miRNAs are selected only if their respective HP p-values reach a pre-defined
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Abstract Oscillations are ubiquitous features of brain dynamics that undergo task-related changes in synchrony, power, and frequency. The impact of those changes on target networks is poorly understood. In this work, we used a biophysically detailed model of prefrontal cortex (PFC) to explore the effects of varying the spike rate, synchrony, and waveform of strong
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Citation: Bradley PH, Nayfach S, Pollard KS (2018) Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. PLoS Comput Biol 14(8): e1006242. https://doi.org/10.1371/journal.pcbi.1006242 Editor: Morgan Langille, DAL, CANADA Received: November 23, 2017; Accepted: May 29, 2018; Published: August 9, 2018 Copyright: © 2018 Bradley et al. This is an open access article distributed
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Supporting Information file S1 Text was published in the wrong format. The publisher apologizes for the error. The correct Supporting Information file is available below. Supporting information Reference 1. Boczkowski L, Natale E, Feinerman O, Korman A (2018) Limits on reliable information flows through stochastic populations. PLoS Comput Biol 14(6): e1006195. https://doi.org/10.1371/journal.pcbi.1006195 pmid:29874234 Citation: The
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Discovering new long non-coding RNAs (lncRNAs) has been a fundamental step in lncRNA-related research. Nowadays, many machine learning-based tools have been developed for lncRNA identification. However, many methods predict lncRNAs using sequence-derived features alone, which tend to display unstable performances on different species. Moreover, the majority of tools cannot be re-trained or tailored by users
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They may evolve in ways that dramatically change their responses to drugs Cell lines form the backbone of cancer research. These individual groups of cells, typically collected from patients’ tumor samples and cultured to grow indefinitely in the laboratory, enable everything from basic genetic research to drug discovery. But while scientists have thought that individual
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Posted by: RNA-Seq Blog in Analysis Pipelines 7 hours ago 208 Views The field of small RNA is one of the most investigated research areas since they were shown to regulate transposable elements and gene expression and play essential roles in fundamental biological processes. Small RNA deep sequencing (sRNA-seq) is now routinely used for large-scale
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Polygenic risk scores (PRS) provide an index of the cumulative contribution of common variants to complex traits [1]. The approach has been applied to a large number of phenotypes, including height [2], body mass index [3], and disease risk, most notably in the prediction of psychiatric disorders [4–6]. PRS build on large existing discovery genome-wide
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Advances in DNA sequencing approaches have produced an overwhelming volume of data, followed by new data analysis software and pipelines. Next generation sequencing (NGS) platforms have been used on a wide variety of omics studies for biodiversity assessment but the traditional Sanger method is still broadly used, including genetic testing [1] and DNA barcode generation
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Workflow overview BART contains six modules that enable users to process raw microarray data from GEO or locally into a list of differential genes and associated pathways, enabling everyone to interpret microarray data in terms of underlying biological processes. Figure 1 summarizes the workflow from data import from CEL, GEO accession, or data matrix, through grouping
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Citation: Coelho CAO, Ferreira TL, Kramer-Soares JC, Sato JR, Oliveira MGM (2018) Network supporting contextual fear learning after dorsal hippocampal damage has increased dependence on retrosplenial cortex. PLoS Comput Biol 14(8): e1006207. https://doi.org/10.1371/journal.pcbi.1006207 Editor: Daniel Bush, University College London, UNITED KINGDOM Received: November 30, 2017; Accepted: May 15, 2018; Published: August 7, 2018 Copyright: ©
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Abstract Allosteric regulation has traditionally been described by mathematically-complex allosteric rate laws in the form of ratios of polynomials derived from the application of simplifying kinetic assumptions. Alternatively, an approach that explicitly describes all known ligand-binding events requires no simplifying assumptions while allowing for the computation of enzymatic states. Here, we employ such a modeling
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Webinar Recording Available – Combining scRNA-Seq and Flow Cytometry | RNA-Seq Blog Don’t Miss Posted by: RNA-Seq Blog in Webinars 7 hours ago 189 Views Learn how to use Dimensionality Reduction, Clustering and Hierarchial Gating, and Geneset Enrichment Analysis! Systems biology is poised to revolutionize our understanding of disease models and multi-omics studies as exemplified
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Posted by: RNA-Seq Blog in Uncategorized 2 hours ago 44 Views It has become exceedingly important to understand the precise molecular profiles of the nearly 40 trillion cells in an adult human because of their role in determining health, disease, and therapeutic outcome. The National Institutes of Health (NIH) Common Fund–supported Single Cell Analysis Program
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Nuclear morphology is an important step in identifying aberrant phenotypes in hematoxylin and eosin (H&E) stained histology sections. However, to date, the problem of nuclear segmentation, for every type of nuclear phenotype remains partially unresolved. If nuclear segmentation is preformed robustly, then malignant phenotypes can be stratified across a large cohort of histology sections. The
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Citation: Yu T (2018) A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data. PLoS Comput Biol 14(8): e1006391. https://doi.org/10.1371/journal.pcbi.1006391 Editor: Ilya Ioshikhes, Ottawa University, CANADA Received: March 2, 2018; Accepted: July 24, 2018; Published: August 6, 2018 Copyright: © 2018 Tianwei Yu. This is an open access article
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De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis workflow is the assembly
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