Bioinformatics

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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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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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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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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Researchers have identified a rare cell type in airway tissue, previously uncharacterized in the scientific literature, that appears to play a key role in the biology of cystic fibrosis. Using new technologies that enable scientists to study gene expression in thousands of individual cells, the team comprehensively analyzed the airway in mice and validated the
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Abstract Glycosyltransferases are a class of enzymes that catalyse the posttranslational modification of proteins to produce a large number of glycoconjugate acceptors from a limited number of nucleotide-sugar donors. The products of one glycosyltransferase can be the substrates of several other enzymes, causing a combinatorial explosion in the number of possible glycan products. The kinetic
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Citation: Tse MJ, Chu BK, Gallivan CP, Read EL (2018) Rare-event sampling of epigenetic landscapes and phenotype transitions. PLoS Comput Biol 14(8): e1006336. https://doi.org/10.1371/journal.pcbi.1006336 Editor: Ilya Ioshikhes, Ottawa University, CANADA Received: December 9, 2017; Accepted: June 29, 2018; Published: August 3, 2018 Copyright: © 2018 Tse et al. This is an open access article distributed
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Posted by: RNA-Seq Blog in Publications 6 hours ago 110 Views Tumor-propagating glioblastoma (GBM) stem-like cells (GSCs) of the proneural and mesenchymal molecular subtypes have been described. However, it is unknown if these two GSC populations are sufficient to generate the spectrum of cellular heterogeneity observed in GBM. The lineage relationships and niche interactions of
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Circular RNAs (circRNAs) are a large class of regulatory RNAs that were identified in the early 1990s, and in the following years, they were considered to be molecular flukes or products of aberrant RNA splicing [1, 2]. Recently, with advances in high-throughput RNA sequencing (RNA-seq) technology, circRNAs were revealed to post-transcriptionally regulate gene expression and
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Abstract Cellular morphology and associated morphodynamics are widely used for qualitative and quantitative assessments of cell state. Here we implement a framework to profile cellular morphodynamics based on an adaptive decomposition of local cell boundary motion into instantaneous frequency spectra defined by the Hilbert-Huang transform (HHT). Our approach revealed that spontaneously migrating cells with approximately
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Abstract Several channels, ranging from TRP receptors to Gap junctions, allow the exchange of small organic solute across cell membrane. However, very little is known about the molecular mechanism of their permeation. Cyclic Nucleotide Gated (CNG) channels, despite their homology with K+ channels and in contrast with them, allow the passage of larger methylated and
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Abstract Annual incidence rates of varicella infection in the general population in France have been rather stable since 1991 when clinical surveillance started. Rates however show a statistically significant increase over time in children aged 0–3 years, and a decline in older individuals. A significant increase in day-care enrolment and structures’ capacity in France was
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Citation: Insel N, Guerguiev J, Richards BA (2018) Irrelevance by inhibition: Learning, computation, and implications for schizophrenia. PLoS Comput Biol 14(8): e1006315. https://doi.org/10.1371/journal.pcbi.1006315 Editor: Samuel J. Gershman, Harvard University, UNITED STATES Received: July 27, 2017; Accepted: June 15, 2018; Published: August 1, 2018 Copyright: © 2018 Insel et al. This is an open access article
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Recently, long noncoding RNA molecules (lncRNA) captured widespread attentions for its critical roles in diverse biological process and important implications in variety of human diseases and cancers. Identification and profiling of lncRNAs is a fundamental step to advance our knowledge on their function and regulatory mechanisms. However, RNA sequencing based lncRNA discovery is limited due
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10x Genomics, Inc., a company focused on accelerating genomic discovery, today announced that BioLegend and Immudex will be the first 10x Compatible Partners providing products for its new single cell Feature Barcoding Technology, which was revealed at the 2018 Advances in Genome Biology and Technology meeting in February this year. The resulting product innovations, available
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Posted by: Damini Jawaheer in Jobs, User Submitted Posts 2 days ago 167 Views Job Description: A postdoctoral position is available at the UCSF Benioff Children’s Hospital Oakland Research Institute (Oakland, CA) on an ongoing NIH-funded project to examine disease pathways in rheumatoid arthritis (RA). The successful candidate is expected to take a lead role
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Abstract Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and theoretical modeling to study the factors that control the size and morphology of a protein shell assembling around hundreds to thousands of molecules. We perform
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RStudio tools for data science development and publishing, are now integrated into Thermo Fisher™ Platform for Science™ software, a leading cloud-based platform supporting scientific data management. Data scientists can use the popular RStudio integrated development environment (IDE) and publish their Shiny apps to RStudio Connect and access these applications from the Platform for Science software. The…
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Posted by: RNA-Seq Blog in Library Preparation, Sequencing Protocols, Workflow 4 hours ago 113 Views Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. Stanford University researchers have developed and applied a technology for 3D intact-tissue RNA
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A panel of 19 microRNAs identified using next-generation sequencing could categorize indeterminate thyroid nodule samples into malignant and benign, according to results published in Cancer Epidemiology, Biomarkers & Prevention, a journal of the American Association for Cancer Research. “Thyroid nodules are extremely common and occasionally harbor cancer,” explained first author Haggi Mazeh, MD, FACS, chief
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Hi-C data representation and properties HiCcompare focuses on the joint analysis of multiple Hi-C datasets represented by chromatin interaction matrices, where rows and columns represent genomic regions (bins), and cells contain interaction counts (frequencies). A chromosome-specific Hi-C matrix is a square matrix of size N × N, where N is the number of genomic regions (bins) of
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We presented TOPAZ, a protein homology search method based on asymmetric suffix array neighbourhood search, scored seeds and optimal substitution ordering. All BLAST alternatives trade-off sensitivity in exchange for speed. In doing so, database search can be used in high-throughput and time-sensitive applications that would have otherwise taken a prohibitively long time. This trade-off was
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High throughput genotyping data have been used extensively in many contexts to explain phenotypic variation of complex traits in a wide range of Genome Wide Association Studies (GWAS). GWAS can however, only partially explain observed phenotypic variation [1], and phenotypic variation has been shown to eclipse genotypic variation in the same population [2]. For example,
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Introduction In everyday life, we are continuously engaged in selecting visual information to achieve our action goals, as the amount of information we receive at any time exceeds the available processing capacity. The mechanisms mediating attentional selection enable us to act efficiently by prioritizing task-relevant, and deprioritizing irrelevant, information. Of importance for the question at
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Abstract The accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good ground truth data typically involves trained professionals; however, this can be costly in time, effort, and money. Here we explore the use of crowdsourcing to generate a large number of training data of good
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Citation: Acerbi L, Dokka K, Angelaki DE, Ma WJ (2018) Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception. PLoS Comput Biol 14(7): e1006110. https://doi.org/10.1371/journal.pcbi.1006110 Editor: Samuel J. Gershman, Harvard University, UNITED STATES Received: July 26, 2017; Accepted: March 28, 2018; Published: July 27, 2018 Copyright: © 2018 Acerbi et al.
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Posted by: RNA-Seq Blog in Analysis Pipelines, Workflow 3 hours ago 91 Views Assay for Transposase-Accessible Chromatin (ATAC)-cap-seq is a high-throughput sequencing method that combines ATAC-seq with targeted nucleic acid enrichment of precipitated DNA fragments. There are increased analytical difficulties arising from working with a set of regions of interest that may be small in
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Posted by: RNA-Seq Blog in Industry News, Press Release 14 hours ago 334 Views Becton Dickinson today announced the commercial release of the BD® AbSeq assay to analyze protein expression at the single-cell level using high-throughput sequencing. The assay brings together high-quality antibodies from the BD Pharmingen™ portfolio with oligonucleotides, allowing researchers to perform single-cell
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Abstract With remarkable spatial and temporal specificities, peripheral membrane proteins bind to biological membranes. They do this without compromising solubility of the protein, and their binding sites are not easily distinguished. Prototypical peripheral membrane binding sites display a combination of patches of basic and hydrophobic amino acids that are also frequently present on other protein
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Abstract Movement is fundamental to human and animal life, emerging through interaction of complex neural, muscular, and skeletal systems. Study of movement draws from and contributes to diverse fields, including biology, neuroscience, mechanics, and robotics. OpenSim unites methods from these fields to create fast and accurate simulations of movement, enabling two fundamental tasks. First, the
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Output The software has two primary functions: (1) to unfold the full CES of a discrete dynamical system of interacting elements and compute its Φ value, and (2) to compute the maximally-irreducible cause-effect repertoires of a particular set of elements within the system. The first is function is implemented by pyphi.compute.major_complex(), which returns a SystemIrreducibilityAnalysis
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Posted by: RNA-Seq Blog in Data Normalization, Data Visualization, Publications 2 hours ago 81 Views With the surge of next generation high-throughput technologies, RNA-seq data is playing an increasingly important role in disease diagnosis, in which normalization is assumed as an essential procedure to produce comparable samples. Recent studies have seen different normalization methods proposed
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