Bioinformatics

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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Biomedical ontology and terminology libraries In the biomedical domain, multiple ontology libraries (or repositories) have been developed. The OBO Foundry [18] is a reference community effort to help the biomedical and biological communities build their ontologies with an enforcement of design and reuse principles, which has been a tremendous success. The OBO Foundry web application
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Recent advances in high-throughput sequencing have led to the discovery of a substantial transcriptome portion, across different species, that does not show encoding potential [1]. Long non-coding RNAs (lncRNAs) have emerged as important players in different biological processes, from development and differentiation to multilevel regulation and tumor progression [2]. The rapidly increasing number of evidence
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Probabilistic networks of blood metabolites associated to latent cardiovascular risk Comparison of networks extracted under different clinical conditions, such as health and disease, might help uncover key mechanisms of disease physiology, especially in conditions whose outcome is presumably affected by a multitude of risk factors. Cardiovascular diseases (CVD), one of the leading causes of death
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We have described a rank-based single sample gene set scoring method, implemented in the R/Bioconductor package singscore. Our method can easily be applied on any high throughput transcriptional data from microarray or RNA-seq experiments. While our method is non-parametric, genes with low read counts should be filtered out, adjusted for gene length [24, 25], and
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Citation: Vorberg S, Seemayer S, Söding J (2018) Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Comput Biol 14(11): e1006526. https://doi.org/10.1371/journal.pcbi.1006526 Editor: Björn Wallner, Linköping University, SWEDEN Received: June 27, 2018; Accepted: September 24, 2018; Published: November 5, 2018 Copyright: © 2018 Vorberg et al. This is an open access article
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Citation: Brandani GB, Takada S (2018) Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA. PLoS Comput Biol 14(11): e1006512. https://doi.org/10.1371/journal.pcbi.1006512 Editor: Alexey Onufriev, Virginia Tech, UNITED STATES Received: May 18, 2018; Accepted: September 13, 2018; Published: November 5, 2018 Copyright: © 2018 Brandani, Takada. This is an open access article distributed
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Abstract Modeling the complex collective behavior is a challenging issue in several material and life sciences. The collective motion has been usually modeled by simple interaction rules and explained by global statistics. However, it remains difficult to bridge the gap between the dynamic properties of the complex interaction and the emerging group-level functions. Here we
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The abundance of cheap and accurate genomic technologies has led to a multitude of different approaches for classifying breast cancer patients into different prognostic groups based on their transcriptomic profiles. These risk classifications are clinically useful because they allow the targeting of aggressive treatment on patients most vulnerable to tumour recurrence or mortality while avoiding
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Simple simulation data We first evaluated the proposed method on simple simulation data. The simulation data contain two groups of genes:Group I consists of G = 1000 non-differentially expressed genes between two classes of samples while group II consists of G = 1000 differentially expressed genes. For group I, the expression values of genes in all samples were randomly
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Abstract Multiscale modeling provides a very powerful means of studying complex biological systems. An important component of this strategy involves coarse-grained (CG) simplifications of regions of the system, which allow effective exploration of complex systems. Here we studied aspects of CG modeling of the human zinc transporter ZnT2. Zinc is an essential trace element with
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Citation: Luccioli S, Angulo-Garcia D, Cossart R, Malvache A, Módol L, Sousa VH, et al. (2018) Modeling driver cells in developing neuronal networks. PLoS Comput Biol 14(11): e1006551. https://doi.org/10.1371/journal.pcbi.1006551 Editor: Michele Giugliano, BELGIUM Received: February 6, 2018; Accepted: October 7, 2018; Published: November 2, 2018 Copyright: © 2018 Luccioli et al. This is an open
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Illumina will acquire Pacific Biosciences for approximately $1.2 billion, broadening access to long-read sequencing and accelerating scientific discovery. Brings Together Highly Accurate Short- and Long-Read Sequencing Technologies, Paving the Path to a More Perfect View of a Genome Pacific Biosciences’ Recent Advances with its Sequel SMRT® Technology, Combined with Illumina’s Infrastructure, will Expand Biological Discovery and Clinical
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Posted by: RNA-Seq Blog in Publications 15 hours ago 182 Views Extracellular microRNAs (miRNAs) and other small RNAs are implicated in cellular communication and may be useful as disease biomarkers. UCSF researchers systematically compared small RNAs in 12 human biofluid types using RNA sequencing (RNA-seq). miRNAs and tRNA-derived RNAs (tDRs) accounted for the majority of
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In-depth analysis sorts cells from the cerebral cortex into 133 types, lays groundwork to explore function Neuroscientists used a new, gene-based classification of mouse brain cell types and additional information about neuron shape to uncover two new types of neurons involved in movement Neuroscientists at the Allen Institute have moved one step closer to understanding
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Abstract In this paper we describe how to efficiently record the entire genetic history of a population in forwards-time, individual-based population genetics simulations with arbitrary breeding models, population structure and demography. This approach dramatically reduces the computational burden of tracking individual genomes by allowing us to simulate only those loci that may affect reproduction (those
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Abstract Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence motifs is still difficult to achieve, due to the fact that the contribution of these typically short fragments is
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Citation: Basak R, Narayanan R (2018) Active dendrites regulate the spatiotemporal spread of signaling microdomains. PLoS Comput Biol 14(11): e1006485. https://doi.org/10.1371/journal.pcbi.1006485 Editor: Joanna Jedrzejewski-Szmek, Instytut Biologii Doswiadczalnej im M Nenckiego Polskiej Akademii Nauk, POLAND Received: June 22, 2017; Accepted: September 3, 2018; Published: November 1, 2018 Copyright: © 2018 Basak, Narayanan. This is an open
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Researchers from the Max Delbrück Center for Molecular Medicine present omniCLIP, a probabilistic approach to identify RBB-RNA interaction sites from CLIP-data. The model presents a principled framework for the analysis of CLIP-Seq assays and takes into account several important new aspects. First, it jointly models the CLIP-Seq and background data in all replicates and accounts for confounding factors
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The TASSEL-GBS pipeline modified for polyploids Earlier implementations of TASSEL-GBS (v.3 and 4) output truncated read counts per allele in the VCF file. The most recent version (v.5) of the pipeline addressed this limitation, but provides only approximate values for higher read counts [7]. The read counts are then used for genotype calling [6], which
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The Iowa State University Veterinary Diagnostic Laboratory The ISU VDL provided IAV diagnostic and sequencing services from 2003 to present, with significant increases in the past 2 years: since 2015, the ISU VDL processed over 1,000 IAV-related cases annually collected from 38 states across the continental US. The IAV diagnostic results and related sequences are stored
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Abstract Malaria is a life-threatening disease spread by mosquitoes. Plasmodium falciparum M1 alanyl aminopeptidase (PfM1-AAP) is a promising target for the treatment of malaria. The recently solved crystal structures of PfM1-AAP revealed that the buried active site can be accessed through two channel openings: a short N-terminal channel with the length of 8 Å and
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Abstract Effective cancer treatment is crucially dependent on the identification of the biological processes that drive a tumor. However, multiple processes may be active simultaneously in a tumor. Clustering is inherently unsuitable to this task as it assigns a tumor to a single cluster. In addition, the wide availability of multiple data types per tumor
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Citation: Nöh K, Niedenführ S, Beyß M, Wiechert W (2018) A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments. PLoS Comput Biol 14(10): e1006533. https://doi.org/10.1371/journal.pcbi.1006533 Editor: Vassily Hatzimanikatis, Ecole Polytechnique Fédérale de Lausanne, SWITZERLAND Received: May 16, 2018; Accepted: September 27, 2018; Published: October 31,
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Posted by: RNA-Seq Blog in Review Publications 6 hours ago 116 Views Transcriptome profiling has become routine in studies of many biological processes. However, favored approaches such as short-read Illumina RNA sequencing are giving way to long-read sequencing platforms better suited to interrogating the complex transcriptomes typical of many RNA and DNA viruses. Here, researchers
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Posted by: RNA-Seq Blog in Publications 56 mins ago 35 Views Cancers acquire resistance to systemic treatment with platinum-based chemotherapy (eg, cisplatin [CDDP]) as a result of a dynamic intratumoral heterogeneity (ITH) and clonal repopulation. However, little is known about the influence of chemotherapy on ITH at the single-cell level. Here, mapping the transcriptome of
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Abstract Chemical-genetic interactions–observed when the treatment of mutant cells with chemical compounds reveals unexpected phenotypes–contain rich functional information linking compounds to their cellular modes of action. To systematically identify these interactions, an array of mutants is challenged with a compound and monitored for fitness defects, generating a chemical-genetic interaction profile that provides a quantitative, unbiased
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Abstract The gut microbiota represent a highly complex ecosystem comprised of approximately 1000 species that forms a mutualistic relationship with the human host. A critical attribute of the microbiota is high species diversity, which provides system robustness through overlapping and redundant metabolic capabilities. The gradual loss of bacterial diversity has been associated with a broad
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Single cell transcriptomics is critical for understanding cellular heterogeneity and identification of novel cell types. Leveraging the recent advances in single cell RNA sequencing (scRNA-Seq) technology requires novel unsupervised clustering algorithms that are robust to high levels of technical and biological noise and scale to datasets of millions of cells. University of Connecticut researchers present
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AMPEL BioSolutions announced proof-of-principle for a multi-pronged approach to rank small molecules and biologics for safe, effective treatment of patients with Systemic Lupus Erythematosus (SLE) and reduce the risk of trial failure that has plagued the lupus community for years. AMPEL’s approach combines an evidence-based CoLT® scoring system with validation of the pathway inhibited by a drug
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Abstract Protein signaling networks are static views of dynamic processes where proteins go through many biochemical modifications such as ubiquitination and phosphorylation to propagate signals that regulate cells and can act as feed-back systems. Understanding the precise mechanisms underlying protein interactions can elucidate how signaling and cell cycle progression occur within cells in different diseases
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Posted by: RNA-Seq Blog in Statistical Analysis 5 hours ago 118 Views Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Researchers at the University of North Carolina at Chapel Hill have developed a simple workflow using a set of existing R/Bioconductor packages for
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In this section, we first present simulation studies to demonstrate the performance of ConMod to detect conserved modules in synthetic multiple networks. We compare ConMod with four state-of-the-art methods, including NetsTensor [11], SC-ML [16], multi-view pairwise co-regularized spectral clustering (pairwiseCRSC) [15] and multi-view centroid-based co-regularized spectral clustering (centroidCRSC) [15]. NetsTensor introduced a tensor-based computational framework
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