Bioinformatics

The ability to record transcriptional events within a cell over time would help to elucidate how molecular events give rise to complex cellular behaviours and states. However, current molecular recording technologies capture only a small set of defined stimuli. Researchers at ETH Zurich developed a method they called Record-seq for capturing gene-expression profiles. They genetically engineered the
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Posted by: RNA-Seq Blog in Review Publications 46 mins ago 46 Views Subpopulation identification, usually via some form of unsupervised clustering, is a fundamental step in the analysis of many single-cell RNA-seq data sets. This has motivated the development and application of a broad range of clustering methods, based on various underlying algorithms. Here, researchers
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High throughput (HT) screens in the omics field are typically analyzed by automated pipelines that generate static visualizations and comprehensive spreadsheet data for scientists. However, exploratory and hypothesis driven data analysis are key aspects for the understanding of biological systems, which benefit considerably from customized and dynamic visualization. WIlsON was implemented in R Shiny as
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Abstract Many pathological conditions, such as seizures, stroke, and spreading depression, are associated with substantial changes in ion concentrations in the extracellular space (ECS) of the brain. An understanding of the mechanisms that govern ECS concentration dynamics may be a prerequisite for understanding such pathologies. To estimate the transport of ions due to electrodiffusive effects,
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Citation: Chen L, Fish AE, Capra JA (2018) Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS Comput Biol 14(10): e1006484. https://doi.org/10.1371/journal.pcbi.1006484 Editor: Jian Ma, Carnegie Mellon University, UNITED STATES Received: March 3, 2018; Accepted: September 2, 2018; Published: October 4, 2018 Copyright: © 2018 Chen et al. This is an
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Posted by: RNA-Seq Blog in Data Visualization, Splicing and Junction Mapping 5 hours ago 90 Views Alternative pre-mRNA splicing generates functionally distinct transcripts from the same gene and is involved in the control of multiple cellular processes, with its dysregulation being associated with a variety of pathologies. The advent of next-generation sequencing has enabled global
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Posted by: RNA-Seq Blog in Review Publications 20 mins ago 23 Views Organisms have acquired sophisticated regulatory networks that control gene expression in response to cellular perturbations. Understanding of the mechanisms underlying the coordinated changes in gene expression in response to external and internal stimuli is a fundamental issue in biology. Recent advances in high-throughput
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Advances in high-throughput sequencing (HTS) technologies have facilitated carrying out genome-wide time series experiments which contain more information on the dynamics of biological processes than static experiments do. With these experiments, thousands or millions of genomic elements can be simultaneously measured at a number of time points, allowing us to study the changes in their
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Posted by: RNA-Seq Blog in Data Visualization, Databases 5 hours ago 116 Views The Michigan Portal for the Analysis of NGS data portalis an open-access online resource that provides the scientific community with access to the results of a large-scale computational analysis of thousands of high-throughput RNA sequencing (RNA-seq) samples. The portal provides access to
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Transposable elements (TEs) or mobile DNA are distinct elements of DNA that move around within the host genomes by generating new copies of themselves into new chromosomal positions. TEs are abundant, ancient, and active components of genomes [1–3]. Because of their ability to transpose from one chromosomal location to another, which thereby increases their copy
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The cell is the basic structural, functional and biological unit in all living organisms. The ability to image, extract and study cells and their sub-cellular compartments is essential to various research areas. Examples include cellular dynamics characterization in normal and pathologic conditions [1] as well as drug discovery where it is important to assess the
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Upcoming Webinar – Tumor Intrinsic and Extrinsic Factors Determining Success of Immunotherapy | RNA-Seq Blog Don’t Miss Posted by: RNA-Seq Blog in Webinars 1 hour ago 56 Views Tuesday, October 9, 201810AM PDT Tumor microenvironment plays an important role in regulating the pathogenesis of malignant diseases and circumventing the anti-tumor immune response in the immune-quiescent
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Posted by: RNA-Seq Blog in Publications, Workflow 13 hours ago 247 Views Researchers at UCSD have developed the Rainbow-seq technology to trace cell division history and reveal single-cell transcriptomes. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA sequencing (RNA-seq) experiment to simultaneously decode the lineage marker genes and read single-cell
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The kidney does more than double or even triple duty compared to other organs—it extracts waste, balances body fluids, forms urine, regulates blood pressure, and secretes hormones. Given this complexity, when things go wrong, havoc can ensue, causing a suite of symptoms called chronic kidney disease (CKD), which includes toxin accumulation, fatigue, and high blood
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Abstract For encapsulated bacteria such as Streptococcus pneumoniae, asymptomatic carriage is more common and longer in duration than disease, and hence is often a more convenient endpoint for clinical trials of vaccines against these bacteria. However, using a carriage endpoint entails specific challenges. Carriage is almost always measured as prevalence, whereas the vaccine may act
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Abstract Here we present an open-source R package ‘meaRtools’ that provides a platform for analyzing neuronal networks recorded on Microelectrode Arrays (MEAs). Cultured neuronal networks monitored with MEAs are now being widely used to characterize in vitro models of neurological disorders and to evaluate pharmaceutical compounds. meaRtools provides core algorithms for MEA spike train analysis,
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Citation: Staddon MF, Bi D, Tabatabai AP, Ajeti V, Murrell MP, Banerjee S (2018) Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing. PLoS Comput Biol 14(10): e1006502. https://doi.org/10.1371/journal.pcbi.1006502 Editor: Anand R. Asthagiri, Northeastern University, UNITED STATES Received: April 26, 2018; Accepted: September 11, 2018; Published: October 1, 2018
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Abstract Vaccination is an effective method to protect against infectious diseases. An important consideration in any vaccine formulation is the inoculum dose, i.e., amount of antigen or live attenuated pathogen that is used. Higher levels generally lead to better stimulation of the immune response but might cause more severe side effects and allow for less
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Extending general recognition theory to the study of brain representations GRT is a multivariate extension of signal detection theory to cases in which stimuli vary on more than one dimension [14, 15]. As in signal detection theory, the theory assumes that different presentations of the same stimulus produce slightly different perceptual representations. For example, as
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Posted by: RNA-Seq Blog in Industry News, Press Release 5 hours ago 201 Views New single-cell protocols available for full-length, whole transcriptome sequencing using microfluidics technology Fluidigm Corporation today announced two new total RNA sequencing applications for the C1™ system. Available on Script Hub™, these single-cell workflows provide basic and translational researchers with powerful new
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General Summary/Purpose A research assistant job in statistical analysis (including algorithm design and evaluation) of large-scale single-cell and bulk RNA-seq data. Specific Duties & Responsibilities Design, analysis and evaluation of algorithms for analysis of large-scale single-cell and bulk RNA-seq data. This involves manuscript reading, implementation of algorithms in R, modifications of existing algorithms, methods benchmarking
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Posted by: Sahil Sethi in Jobs, User Submitted Posts 1 day ago 124 Views 3 month training program that will provide an in-depth overview of standard tools and data types when studying Next generation Sequencing (NGS) datasets in oncology, neuroscience and agriculture. Each week, participants will meet online to discuss various aspects of NGS analysis
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Drug discovery and development programs focus on achieving therapeutic efficacy upon modulation of a specific drug target with a molecule in a patient population. A number of computational approaches to aid in target identification have been considered, and along with various bioinformatics resources they also point to the application of cheminformatics based approaches for ligand
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Biotite is divided into four subpackages: sequence and structure provide tools for handling sequences or biomolecular structures, respectively. database is used for fetching files from biological databases and application offers interfaces for external software. Since computational efficiency is one central aim of the Biotite project, the package makes heavy use of NumPy [5], in places
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Experimental datasets setup The performances of the algorithms were evaluated on the BCI Competition IV [27] “Dataset 2a” and “Dataset 2b”1. The two datasets are compared in Table 3. Figure 6 illustrates how the single-trial EEG data were extracted on “Dataset 2a” and “Dataset 2b”. The two datasets share the same procedure. In the motor imagery classification
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Problem constraints As stated in the previous paragraph, an optimal primer-set-pair should simultaneously maximize efficiency and coverage and minimize matching-bias. In the following, we describe how we quantitatively encoded these constraints. Efficiency The perfect primer-set-pairs should satisfy several constraints, aimed at improving PCR efficiency and specificity [7]. However, concurrently satisfying all constraints is often impractical
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Abstract Spontaneous activity is a fundamental characteristic of the developing nervous system. Intriguingly, it often takes the form of multiple structured assemblies of neurons. Such assemblies can form even in the absence of afferent input, for instance in the zebrafish optic tectum after bilateral enucleation early in life. While the development of neural assemblies based
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Posted by: RNA-Seq Blog in Publications 4 hours ago 75 Views Post-transcriptional RNA processing is a core mechanism of gene expression control in cell stress response. The poly(A) tail influences mRNA translation and stability, but it is unclear whether there are global roles of poly(A)-tail lengths in cell stress. To address this, Cornell University researchers
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With an award from the National Institutes of Health, a team led by Dmitry Korkin will develop next-generation machine learning algorithms that could advance our understanding of the molecular biology of disease and the field of personalized medicine A team of computer scientists at Worcester Polytechnic Institute (WPI) has received a two-year, $347,000 award from
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Abstract Biological data sets are typically characterized by high dimensionality and low effect sizes. A powerful method for detecting systematic differences between experimental conditions in such multivariate data sets is multivariate pattern analysis (MVPA), particularly pattern classification. However, in virtually all applications, data from the classes that correspond to the conditions of interest are not
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Abstract Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2–4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple microbial communities and are well-characterized geochemically. Consequently, these communities are excellent model systems for studying the metabolic activity of
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Effective stratification of cancer patients on the basis of their molecular make-up is a key open challenge. Given the altered and heterogenous nature of cancer metabolism, we here propose to use the overall expression of central carbon metabolism as biomarker to characterize groups of patients with important characteristics, such as response to ad-hoc therapeutic strategies
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Abstract Studying a gene’s regulatory mechanisms is a tedious process that involves identification of candidate regulators by transcription factor (TF) knockout or over-expression experiments, delineation of enhancers by reporter assays, and demonstration of direct TF influence by site mutagenesis, among other approaches. Such experiments are often chosen based on the biologist’s intuition, from several testable
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Abstract CD95/Fas/APO-1 is a member of the death receptor family that triggers apoptotic and anti-apoptotic responses in particular, NF-κB. These responses are characterized by a strong heterogeneity within a population of cells. To determine how the cell decides between life and death we developed a computational model supported by imaging flow cytometry analysis of CD95
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Harnessing the immune system to treat cancer shows great promise in some patients, but for many, the response does not last long-term. In an effort to find out why, Fred Hutchinson Cancer Research Center scientists are using a new technology to look at how cancer cells change under the pressure of immunotherapy treatments. In a
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Here, we present results demonstrating the accuracy, scalability, efficiency and applicability of PanTools for detecting homology in large proteomes of bacteria, fungi, plants and Metazoa (Additional file 1: Table S1). We compare PanTools to the BLAST-based orthology detector OrthoFinder [16] and to DIAMOND-based PanX [19], a pipeline dedicated to microbial data (Additional file 1: Tables S2–S5).
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Abstract Cooperation is key for the evolution of biological systems ranging from bacteria communities to human societies. Evolutionary processes can dramatically alter the cooperation level. Evolutionary processes are typically of two classes: comparison based and self-evaluation based. The fate of cooperation is extremely sensitive to the details of comparison based processes. For self-evaluation processes, however,
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Abstract Dynamic models of large-scale brain activity have been used for reproducing many empirical findings on human brain functional connectivity. Features that have been shown to be reproducible by comparing modeled to empirical data include functional connectivity measured over several minutes of resting-state functional magnetic resonance imaging, as well as its time-resolved fluctuations on a
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User Group Meeting Recap We have just completed our first European User Group Meeting in Berlin, Germany. Launch2018 included Thermo Fisher™ Platform for Science™, SampleManager LIMS™, Watson LIMS™, and Nautilus LIMS™ software users. As with all of our Launch events, our customers took center stage. Presenters described how they were using our informatics solutions to
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Posted by: RNA-Seq Blog in Publications, Workflow 3 hours ago 76 Views While a large number of long noncoding RNAs (lncRNAs) are transcribed from the genome of higher eukaryotes, systematic prediction of their functionality has been challenging due to the lack of conserved sequence motifs or structures. Assuming that some lncRNAs function as large ribonucleoprotein
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Dopamine neurons are located in the midbrain, but their tendril-like axons can branch far into the higher cortical areas, influencing how we move and how we feel. New genetic evidence has revealed that these specialized cells may also have far-reaching effects, implicating them in conditions that range from Parkinson’s disease to schizophrenia. Using a new
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We assessed the performance of the candidate-selection strategies in two ways. First, we considered how close the predicted F1 score from a simulated verification experiment is to that from the overall study. We calculated precision in two modes: ‘default’ (as described in Methods) and ‘weighted’. In the ‘weighted’ mode, precision scores are modified so that
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Citation: Hädicke O, von Kamp A, Aydogan T, Klamt S (2018) OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. PLoS Comput Biol 14(9): e1006492. https://doi.org/10.1371/journal.pcbi.1006492 Editor: Herbert Sauro, University of Washington, UNITED STATES Received: April 20, 2018; Accepted: September 7,
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