Bioinformatics

Abstract Covalent modification of proteins by ubiquitin or ubiquitin chains is one of the most prevalent post-translational modifications in eukaryotes. Different types of ubiquitin chains are assumed to selectively signal respectively modified proteins for different fates. In support of this hypothesis, structural studies have shown that the eight possible ubiquitin dimers adopt different conformations. However,
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Abstract Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes. Simulations of 15 manually curated genome-scale metabolic models were integrated with 36 large-scale gene
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Long intergenic noncoding RNAs (lincRNAs) have risen to prominence in cancer biology as new biomarkers of disease. Those lincRNAs transcribed from active cis-regulatory elements (enhancers) have provided mechanistic insight into cis-acting regulation; however, in the absence of an enhancer hallmark, computational prediction of cis-acting transcription of lincRNAs remains challenging. Here, University of Chicago researchers introduce
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Citation: Carvalho-Silva D, Garcia L, Morgan SL, Brooksbank C, Dunham I (2018) Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars. PLoS Comput Biol 14(11): e1006419. https://doi.org/10.1371/journal.pcbi.1006419 Editor: Scott Markel, Dassault Systemes BIOVIA, UNITED STATES Published: November 15, 2018 Copyright: © 2018 Carvalho-Silva et al. This is an open
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Citation: Frassl MA, Hamilton DP, Denfeld BA, de Eyto E, Hampton SE, Keller PS, et al. (2018) Ten simple rules for collaboratively writing a multi-authored paper. PLoS Comput Biol 14(11): e1006508. https://doi.org/10.1371/journal.pcbi.1006508 Editor: Fran Lewitter, Whitehead Institute, UNITED STATES Published: November 15, 2018 Copyright: © 2018 Frassl et al. This is an open access article
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Citation: Ebadi H, Perry M, Short K, Klemm K, Desplan C, Stadler PF, et al. (2018) Patterning the insect eye: From stochastic to deterministic mechanisms. PLoS Comput Biol 14(11): e1006363. https://doi.org/10.1371/journal.pcbi.1006363 Editor: Robert Johnston, Johns Hopkins University, UNITED STATES Received: March 23, 2017; Accepted: July 16, 2018; Published: November 15, 2018 Copyright: © 2018 Ebadi
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Abstract Cytoplasmic flows are an ubiquitous feature of biological systems, in particular in large cells, such as oocytes and eggs in early animal development. Here we show that cytoplasmic flows in starfish oocytes, which can be imaged well with transmission light microscopy, are fully determined by the cortical dynamics during surface contraction waves. We first
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The analysis of transcriptome data from non-model organisms contributes to our understanding of diverse aspects of evolutionary biology, including developmental processes, speciation, adaptation, and extinction. Underlying this diversity is one shared feature, the generation of enormous amounts of sequence data. Data availability requirements in most journals oblige researchers to make their raw transcriptome data publicly
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Neural nets supplant marker genes in analyzing single cell RNA sequencing | RNA-Seq Blog Don’t Miss Posted by: RNA-Seq Blog in Commentary 13 hours ago 302 Views CMU’s scQuery Web Server Uses New Method To Determine Cell Types, Identify Key Genes Computer scientists at Carnegie Mellon University say neural networks and supervised machine learning techniques
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Amaryllis Nucleics, a Bay Area biotech company using the most advanced chemistry for RNA sequencing sample prep to provide rapid and accurate RNA sequencing, today launched a new version of their dual-mode (FT+3′-DGE) RNA-seq kit that allows users to do dual-indexed sequencing. The YourSeq Dual RNAseq Library Kit is a versatile, Illumina-compatible RNAseq library kit that can
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In this work, we describe a novel machine learning method to predict protein binding affinity using protein sequence and structure information. Previously, various machine learning models have been developed for this purpose using standard machine learning approaches using sequence or structure information. Typically, structure-based methods generate better predictions than sequence-based ones but are limited by
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Posted by: RNA-Seq Blog in Splicing and Junction Mapping 5 hours ago 33 Views Next generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression and alternative splicing. Key to this is the the accurate identification of exon-exon junctions from RNA sequenced (RNA-Seq) reads. A number
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inDrop™ System selected to generate predictive multi-omic clinical research data for undiagnosed conditions with immune dysfunction 1CellBio Inc., a leading single-cell analysis company serving the biomedical research community, today announced a partnership agreement with the Open Medicine Institute (OMI), a leading independent precision medicine clinical and research organization. Researchers at OMI will apply and validate
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Initially, we perform two simulation studies for assessing how accurately our proposed model identifies true genotype states when hypersegmentation occurs. For these two studies, we generate 500 datasets with true genotype sequences of size N=10,000 based on a Markov chain with a given transition probability, using the R- package markovchain. We consider four genotypes as
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RNA sequencing (RNA-Seq), despite being the choice technique for transcriptome-wide identification of differentially expressed genes, is still rapidly evolving. A number of tools are available for each major processing step in data analysis: read alignment, expression modeling, and differential gene identification [1], but their performance in concert is only beginning to be understood [2–6]. Additionally,
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Abstract Population genetic modeling can enhance Bayesian phylogenetic inference by providing a realistic prior on the distribution of branch lengths and times of common ancestry. The parameters of a population genetic model may also have intrinsic importance, and simultaneous estimation of a phylogeny and model parameters has enabled phylodynamic inference of population growth rates, reproduction
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Measurement noise. For models (such as our core models) where the relationship between reliability (i.e., contrast or ellipse eccentricity) and noise was parametric, we assumed a power law relationship between reliability c and measurement noise variance σ2: σ2(c) = γ + αc−β. We have previously [30] used this power law relationship because it encompasses a
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Introduction Most cellular processes are carried out by interacting proteins. Functional protein-protein interactions allow multi-protein complexes to assemble, and ensure proper signal transduction in various pathways. Hence, mapping functional protein-protein interactions is an important fundamental question. High-throughput experiments have recently elucidated a substantial fraction of protein-protein interactions in a few model organisms [1], but such
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Abstract The efficient coding hypothesis predicts that sensory neurons adjust their coding resources to optimally represent the stimulus statistics of their environment. To test this prediction in the moth olfactory system, we have developed a stimulation protocol that mimics the natural temporal structure within a turbulent pheromone plume. We report that responses of antennal olfactory
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Posted by: RNA-Seq Blog in Publications 1 hour ago 60 Views The usual analysis of RNA-Seq reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly.
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Citation: Henderson JA, Gong P (2018) Functional mechanisms underlie the emergence of a diverse range of plasticity phenomena. PLoS Comput Biol 14(11): e1006590. https://doi.org/10.1371/journal.pcbi.1006590 Editor: Abigail Morrison, Research Center Jülich, GERMANY Received: January 8, 2018; Accepted: October 23, 2018; Published: November 12, 2018 Copyright: © 2018 Henderson, Gong. This is an open access article distributed
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Citation: Giaimo S, Arranz J, Traulsen A (2018) Invasion and effective size of graph-structured populations. PLoS Comput Biol 14(11): e1006559. https://doi.org/10.1371/journal.pcbi.1006559 Editor: Sebastian Schreiber, UC Davis, UNITED STATES Received: February 7, 2018; Accepted: October 9, 2018; Published: November 12, 2018 Copyright: © 2018 Giaimo et al. This is an open access article distributed under the
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Abstract Neurons collect their inputs from other neurons by sending out arborized dendritic structures. However, the relationship between the shape of dendrites and the precise organization of synaptic inputs in the neural tissue remains unclear. Inputs could be distributed in tight clusters, entirely randomly or else in a regular grid-like manner. Here, we analyze dendritic
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Ethics statement All experiments, animal treatment and surgical protocols were carried out with authorization from the Institutional Animal care and Use Committee of the Allen Institute in accordance with the Public Health Service (PHS) Policy on Humane Care and Use of Laboratory Animals. Model building and simulation details All simulations were performed with the parallelized
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Abstract Neural oscillations have been recorded and implicated in many different basic brain and cognitive processes. For example, oscillatory neural activity has been suggested to play a role in binding and in the maintenance of information in working memory. With respect to the latter, the majority of work has focused primarily on oscillations in terms
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Posted by: RNA-Seq Blog in Publications, Workflow 8 hours ago 158 Views Tumor ecosystems are composed of multiple cell types that communicate by ligand-receptor interactions. Targeting ligand-receptor interactions (for instance, with immune checkpoint inhibitors) can provide significant benefits for patients. However, our knowledge of which interactions occur in a tumor and how these interactions affect
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Proteins are involved in almost all life processes. The discovering of protein function is of significance for understanding the underlying molecular mechanism in organisms and diseases. Thanks to the development of high-throughput technologies, computational approaches become a major force to uncover molecular structures and functions [1, 2]. Since then, a large amount to genomics, proteins,
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Abstract GTPases regulate a multitude of essential cellular processes ranging from movement and division to differentiation and neuronal activity. These ubiquitous enzymes operate by hydrolyzing GTP to GDP with associated conformational changes that modulate affinity for family-specific binding partners. There are three major GTPase superfamilies: Ras-like GTPases, heterotrimeric G proteins and protein-synthesizing GTPases. Although they
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DASHR (Database of small human non-coding RNAs) v2.0 provides a complete catalog of annotation, expression, processing, conservation, tissue-specificity and other biological features for all human small non-coding (sncRNA) genes, full sncRNA transcripts and mature products derived from all major small RNA classes, including miRNAs, piRNAs, sc-, sn-, sno- RNAs, tRNAs, tRFs. DASHR v2.0 is freely available
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Join the 9th Gene Quantification Event #GQ2019 qPCR dPCR & NGS 2019Symposium & Industrial Exhibition & Application Workshopsmain.qPCR-dPCR-NGS-2019.netMain topics: Next Generation Biomarkers — Liquid Biopsy, Multi-Omics, MicroGenomics18-22 March 2019, in Freising-Weihenstephan,School of Life Sciences, Technical University of Munich, Weihenstephan, Germany Join qPCR dPCR & NGS Workshops:Workshoptopics & short agendas => http://Workshops.qPCR-dPCR-NGS-2019.net• Basic real-time qPCR Application
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Benchmark data sets As for many other computational methods, the success of binding site comparison methods has to be evaluated using benchmark data sets. Some evaluation sets previously created to test the tools analyzed herein are summarized in the SI (S1 Table). Although we do not claim that our collection is comprehensive, there are no
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Citation: Zhao W, Sher X (2018) Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes. PLoS Comput Biol 14(11): e1006457. https://doi.org/10.1371/journal.pcbi.1006457 Editor: Bjoern Peters, La Jolla Institute for Allergy and Immunology, UNITED STATES Received: January 13, 2018; Accepted: August 22, 2018; Published: November 8, 2018 Copyright: © 2018 Zhao, Sher. This is an
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We begin by laying out the key assumptions underlying both the analytical and simulation models. The predictions of the analytical model are derived using adaptive dynamics. We present the key insights that we are able to derive without the complexities of simulation. The full analytical model can be found in the Supplementary Material. We then
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QIAseq FastSelect: A new revolutionary technology for rRNA depletion For transcriptomic profiling of gene expression using RNA-seq, removal of highly abundant, but unimportant RNA species increases sensitivity and decreases cost- per-sample. Current removal methods are arduous, not well suited for fragmented samples and may result in sample loss or distortion of transcriptomic profiles. This webinar
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The “Genomics of Long Non-Coding RNAs in Disease” Laboratory (GOLD Lab) at the University of Bern has an opportunity for a Bioinformatics Postdoc. The Project: Understanding how long noncoding RNA (lncRNA) functions are encoded in their sequence is a great challenge in biology. Our goal is to discover, classify and characterise lncRNA functional elements by
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The emergence of single-cell RNA sequencing (scRNA-seq) technologies has enabled us to measure the expression levels of thousands of genes at single-cell resolution. However, insufficient quantities of starting RNA in the individual cells cause significant dropout events, introducing a large number of zero counts in the expression matrix. To circumvent this, researchers from the Indraprastha
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The selection of a first-line chemotherapy drug to treat many types of cancer is often a clear-cut decision governed by standard-of-care protocols, but what drug should be used next if the first one fails? That’s where Georgia Institute of Technology researchers believe their new open source decision support tool could come in. Using machine learning
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Advaita Bioinformatics  has announced a new release of iPathwayGuide, the world’s most advanced RNA-seq and gene expression analysis software. This release includes unprecedented gene network analysis and literature mining capabilities. The newly added network analysis capabilities allow the scientists to discover previously unknown mechanisms that explain the conditions they study. Furthermore, the analysis is able
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New findings add to growing evidence that previously dismissed “junk DNA” actually produces RNA molecules with important regulatory functions Scientists have identified an RNA molecule with broad powers to regulate the body’s inflammatory response to infection and injury. Called lincRNA-Cox2, it belongs to a recently discovered, highly abundant class of RNAs whose functions are only
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In silico deconvolution modeling started with partial approaches requiring as available, either the cell/tissue type-specific expression profiles or mixture proportions, but gradually complete semi-supervised and more importantly unsupervised methods have gained ground. The unsupervised ones showed that representative profiles – sufficient to decompose the signal – can be extracted directly from the mixed data alleviating
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Abstract Bacterial lipopolysaccharide (LPS) induces an acute inflammatory response across multiple organs, primarily via Toll-like receptor 4 (TLR4). We sought to define novel aspects of the complex spatiotemporal dynamics of LPS-induced inflammation using computational modeling, with a special focus on the timing of pathological systemic spillover. An analysis of principal drivers of LPS-induced inflammation in
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Citation: H. Heras FJ, Vähäsöyrinki M, Niven JE (2018) Modulation of voltage-dependent K+ conductances in photoreceptors trades off investment in contrast gain for bandwidth. PLoS Comput Biol 14(11): e1006566. https://doi.org/10.1371/journal.pcbi.1006566 Editor: Maxim Bazhenov, University of California San Diego, UNITED STATES Received: June 13, 2018; Accepted: October 16, 2018; Published: November 6, 2018 Copyright: © 2018
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