Bioinformatics

1. Zamanian, J. L. et al. Genomic analysis of reactive astrogliosis. J. Neurosci. 32, 6391–6410 (2012). 2. Liddelow, S. A. et al. Neurotoxic reactive astrocytes are induced by activated microglia. Nature 541, 481–487 (2017). 3. Fawcett, J. W. & Asher, R. A. The glial scar and central nervous system repair. Brain Res. Bull. 49, 77–391
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Posted by: RNA-Seq Blog in Statistical Analysis 5 hours ago 81 Views Analysis of single-cell RNA sequencing (scRNA-Seq) data often involves filtering out uninteresting or poorly measured genes and dimensionality reduction to reduce noise and simplify data visualization. However, techniques such as principal components analysis (PCA) fail to preserve non-negativity and sparsity structures present in
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Modern technology makes it possible to sequence individual cells and to identify which genes are currently being expressed in each cell. These methods are sensitive and consequently error prone. Devices, environment and biology itself can be responsible for failures and differences between measurements. Researchers at Helmholtz Zentrum München joined forces with colleagues from the Technical
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One of the main obstacles to successfully treating breast cancer is the cells’ ability to change in ways that make them resistant to treatment. Understanding the cellular mechanisms that mediate this cancer cell plasticity may lead to improved treatments. Taking a step in that direction, a team led by researchers at Baylor College of Medicine
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An Osaka University-centered research team has performed fine-mapping of the key immunity-related part of the genome, revealing associations between gene variants and over 50 different phenotypes in the Japanese Although different genes are distributed widely across chromosomes, many genes related to the immune system are clustered together on human chromosome 6, in a segment called
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Inside the cell, DNA is tightly wrapped around proteins and packed in a complex, 3D structure that we call “chromatin”. Chromatin not only protects our genetic material from damage, but also organizes the entire genome by regulating the expression of genes in three dimensions, unwinding them to be presented to the cell’s gene-expression machinery and
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Asuragen, Inc., a molecular diagnostics company delivering easy-to-use products for complex testing in genetics and oncology, today announced that the results of a five-site study using the QuantideX NGS RNA Lung Cancer Kit* have been published as an article in press by The Journal of Molecular Diagnostics (see https://doi.org/10.1016/j.jmoldx.2018.10.003). The peer-reviewed article, titled “Design, Optimization,
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1. Hong, X. et al. Molecular signatures of circulating melanoma cells for monitoring early response to immune checkpoint therapy. Proceedings of the National Academy of Sciences of the United States of America 115, 2467–2472, https://doi.org/10.1073/pnas.1719264115 (2018). 2. Tsang, J. C. H. et al. Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics. Proceedings
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The correlation matrix (Figs 2, S1) demonstrates that spectra of different fragments of the same tissue sample correlate better with each other than with the spectra of fragments of other tissue samples. There are also white lines on the figure, which are associated with electrospray instability (these lines in the correlogram correspond to anomalous local maxima or
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Abstract Birdsong is a complex vocal communication signal, and like humans, birds need to discriminate between similar sequences of sound with different meanings. The caudal mesopallium (CM) is a cortical-level auditory area implicated in song discrimination. CM neurons respond sparsely to conspecific song and are tolerant of production variability. Intracellular recordings in CM have identified
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Citation: Guerfali FZ, Laouini D, Boudabous A, Tekaia F (2019) Designing and running an advanced Bioinformatics and genome analyses course in Tunisia. PLoS Comput Biol 15(1): e1006373. https://doi.org/10.1371/journal.pcbi.1006373 Editor: Francis Ouellette, Genome Quebec, CANADA Published: January 28, 2019 Copyright: © 2019 Guerfali et al. This is an open access article distributed under the terms of
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Abstract Within influenza virus infected cells, viral genomic RNA are selectively packed into progeny virions, which predominantly contain a single copy of 8 viral RNA segments. Intersegmental RNA-RNA interactions are thought to mediate selective packaging of each viral ribonucleoprotein complex (vRNP). Clear evidence of a specific interaction network culminating in the full genomic set has
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As parents of identical twins will tell you, they are never actually identical, even though they have the same genes. This is also true in the plant world. Now, new research by the University of Cambridge is helping to explain why ‘twin’ plants, with identical genes, grown in identical environments continue to display unique characteristics
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Posted by: RNA-Seq Blog in Conferences 15 hours ago 259 Views The 6th annual Genomic Medicine 2019 Edinburgh conference will take place on 15th & 16th May 2019 at the Radisson Blu Hotel in Edinburgh.  As usual we will focus on high throughput genomic technologies with a special focus on Next Generation Sequencing in the research and
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1CellBio and Partek DeliverEasy-to-use Single Cell Analysis Solution Powerful Single Cell Bioinformatics Solution in a Graphical User Interface LOUIS and CAMBRIDGE — 1/24/2019 — 1CellBio Inc. and Partek Incorporated have partnered to deliver a data analysis pipeline for the inDrop™ System for use within Partek® Flow® bioinformatics software. The pipeline allows users to pre-process raw
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The oscillons We implemented a “Short Time Padé Transform” (STPT), in which a short segment of the time series (that fits into a window of a width TW) is analyzed at a time. This allows us to follow the signal’s spectral composition on moment-to-moment basis and to illustrate its spectral dynamics using Padé spectrograms (the
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1. He, K., Zhang, X., Ren, S. & Sun, J. Deep residual learning for image recognition. Proc. IEEE Conference on Computer Vision and Pattern Recognition 770–778 (IEEE, 2016). 2. Pinheiro, P. O., Collobert, R. & Dollár, P. Learning to segment object candidates. Proc. 28th International Conference on Neural Information Processing Systems 2, 1990–1998 (2015). 3.
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Different mutations were found after selection of phage-displayed IL-2 variants on CD25 Selection from a phage library of 109 members displaying hIL-2 with controlled diversity at the IL-2R alpha subunit interface (see Supplementary Table S1 for library design) on immobilized human CD25 rendered phage mixtures with growing reactivity to the selector molecule (Supplementary Fig. S1a). Sequencing of
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Workflow COMMAND>_ is a multi-user application. From the web interface it is possible to create users and groups and grant privileges. Admin users have unlimited access, while normal users might be limited to work only on specific compendia and/or with a subset of functionalities. The typical workflow can be divided into three steps: i) search
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In order to perform our tests, we downloaded expression data from the GTEx consortium [13, 15] (http://www.gtexportal.org). We chose the “Whole blood” data set (with data for 23,152 genes), as it contains a very large amount of measurements per gene (338), which allows us to use the full data set as a reasonably accurate reference
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The parcellation protocol we followed while segmenting the ground truth parcels enabled us to consistently identify and address any visible anatomical variability (see Additional file 1, [21]). Because of this, the parcels’ shapes varied greatly across the cohort, creating large dispersions in the ground truth volumes (Fig. 1) and surface areas (Fig. 3). Using this as a
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ModelExplorer allows the visualization of a metabolic reconstructed networks as bipartite graphs: Metabolites and reactions are represented by nodes, and links (shown as arrows) only connect metabolites to reactions and vice versa. The arrows may be unidirectional or bidirectional, depending on the encoded reaction reversibility in the metabolic reconstruction. Metabolites and reactions are automatically grouped
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I’m trying to teach myself to use the FlowCore package to analyze flow cytometry data. I’ve attached a screenshot of a PDF that the CytExpert software spits out. However, I work in a 96 well plate format, so I’ve got 96 PDFs and 96 .fcs files per experiment. I’d like to use FlowCore to read
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Citation: Monaco JD, De Guzman RM, Blair HT, Zhang K (2019) Spatial synchronization codes from coupled rate-phase neurons. PLoS Comput Biol 15(1): e1006741. https://doi.org/10.1371/journal.pcbi.1006741 Editor: Daniel Bush, University College London, UNITED KINGDOM Received: August 14, 2018; Accepted: December 21, 2018; Published: January 25, 2019 Copyright: © 2019 Monaco et al. This is an open access
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Posted by: RNA-Seq Blog in Publications 3 hours ago 89 Views Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression and treatment response remain unclear due to significant heterogeneity. Here, following a negative selection strategy combined with single-cell RNA sequencing of 768 transcriptomes
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Insilico Medicine, a Rockville-based company developing the end-to-end drug discovery pipeline utilizing the next generation artificial intelligence, will present its latest advances in human aging biomarker development at the Longevity Leaders Conference in London, 4 of February. Artificial Intelligence (AI) techniques, such as deep learning (DL) and reinforcement learning (RL) play a pivotal role in
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1. Zhang H, Zhao Z, Pang X, Yang J, Yu H, Zhang Y, et al. Genistein detection protects against Ox-LDL-induced inflammation through microRNA-155/SOCS1-mediated repression of NF-kB signaling pathway in HUVECs. Inflammation. 2017;40:1450–9. 2. Yu X, Xing C, Pan Y, Ma H, Zhang J, Li W. IGF-1 alleviates ox-LDL-induced inflammation via reducing HMGB1 release in HAECs.
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1. Kamps R, Brandao RD, Bosch BJ, Paulussen AD, Xanthoulea S, Blok, et al. Next-generation sequencing in oncology: genetic diagnosis, risk prediction and cancer classification. Int J Mol Sci. 2017;18:308. 2. Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L, et al. Identification and correction of systematic error in high-throughput sequence data.
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Gene expression is known to be subject to sophisticated and fine-grained regulation. Besides underlying the developmental processes and morphogenesis of every multicellular organism, gene regulation represents an integral component of cellular operation by allowing for adaptation to new environments through protein expression on demand [1–4]. While the basic principles of gene regulation have been discovered
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Citation: Küken A, Eloundou-Mbebi JMO, Basler G, Nikoloski Z (2019) Cellular determinants of metabolite concentration ranges. PLoS Comput Biol 15(1): e1006687. https://doi.org/10.1371/journal.pcbi.1006687 Editor: Costas D. Maranas, The Pennsylvania State University, UNITED STATES Received: February 16, 2018; Accepted: November 29, 2018; Published: January 24, 2019 Copyright: © 2019 Küken et al. This is an open access
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Abstract Gene regulatory networks are composed of sub-networks that are often shared across biological processes, cell-types, and organisms. Leveraging multiple sources of information, such as publicly available gene expression datasets, could therefore be helpful when learning a network of interest. Integrating data across different studies, however, raises numerous technical concerns. Hence, a common approach in
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Citation: Hu X, Wang Y, Hunkele A, Provasi D, Pasternak GW, Filizola M (2019) Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis. PLoS Comput Biol 15(1): e1006689. https://doi.org/10.1371/journal.pcbi.1006689 Editor: Alexander MacKerell, University of Maryland School of Pharmacy, UNITED STATES Received: October 4, 2018; Accepted:
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Abstract Osteoarthritis (OA) is a degenerative condition caused by dysregulation of multiple molecular signalling pathways. Such dysregulation results in damage to cartilage, a smooth and protective tissue that enables low friction articulation of synovial joints. Matrix metalloproteinases (MMPs), especially MMP-13, are key enzymes in the cleavage of type II collagen which is a vital component
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Citation: Sarkar D, Mueller TJ, Liu D, Pakrasi HB, Maranas CD (2019) A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism. PLoS Comput Biol 15(1): e1006692. https://doi.org/10.1371/journal.pcbi.1006692 Editor: Ralf Steuer, Humboldt University Berlin, GERMANY Received: October 9, 2017; Accepted: December 3, 2018; Published: January 24, 2019 Copyright: © 2019 Sarkar et al. This
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Dear colleagues, with the growing computational power and development of new computational methods importance of computer simulations in the polymer science is increasing, complementing classical theory and experiment. Therefore, following the long-term tradition of Bratislava International Conferences on Macromolecules, this year the conference is going to cover research fields dealing with computer modeling of macromolecules
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Posted by: RNA-Seq Blog in Splicing and Junction Mapping 3 hours ago 94 Views The splicing of pre-mRNAs into mature transcripts is remarkable for its precision, but the mechanisms by which the cellular machinery achieves such specificity are incompletely understood. Illumina scientists describe a deep neural network that accurately predicts splice junctions from an arbitrary
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Lots of these tools exist actually! A popular alternative is enrichR (https://github.com/wjawaid/enrichR) however it is a bit more restrictive in how background population is determined which can skew p-value corrections. Regarding bypassing the Broad login requirement, one can do so through this super helpful R wrapper (https://github.com/oganm/MSigDB)!
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HSI microscopy Figure 1 shows a diagram of the HSI microscopy used in this study. The tunable bandpass filter and camera were connected to the port of the microscope on the left side, with two adapters in front of and behind the tunable bandpass filter. In the adapter in front of the tunable bandpass filter (Fig. 1
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Dynamics behavior of HLA-DR complexed to Top1 peptide Root-mean-square displacement (RMSD) calculations were performed to monitor the conformational stability in the overall MD simulation, as shown in Fig. 2. RMSD along simulated time was evaluated from the geometrical coordinates of protein backbone (N-Cα-C-O) with respect to those of the initial structure. For HLA-DRs without Top1, RMSDs
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Synthesis of IgG using the standard PURE system All experiments in this paper used the commercially-available PUREfrex® 2.0 kit as the standard PURE system. The well-known anti-HER2 antibody trastuzumab19 was selected as a model IgG for the optimization of synthesis conditions. Since the PURE system does not contain nuclease activity, linear (e.g., PCR product) or
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Transcriptomic analysis We identified 1,817 signature genes with significant differences in expression (p < 0.015 in t-test) between the 10 DHF patients and 8 normal controls from the GSE18090 dataset. A heat map of the expression data is shown in Supplementary Fig. S1. We also identified 1,809 and 1,018 signature genes with significant differences in expression between DHF
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1. Garellick, G., Kärrholm, J., Rogmark, C. & Herberts, P. Swedish Hip Arthroplasty Register: Annual Report, 2008. Department of Orthopaedics, Sahlgrenska University Hospital (2009). 2. Streit, M. R. et al. Long-term (20-to 25-year) results of an uncemented tapered titanium femoral component and factors affecting survivorship. Clin Orthop Relat Res 471, 3262–3269, https://doi.org/10.1007/s11999-013-3033-4 (2013). 3. Taylor,
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