Bioinformatics

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 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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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 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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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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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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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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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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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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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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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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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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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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