Bioinformatics

Cell lines All cells were grown on tissue culture dishes or multi-well plates (Corning) at 37 °C and 5% CO2. CHO-K1 cells (ATCC CCL-61) were phenotypically validated as proline auxotrophs and their Cricetulus griseus origin was confirmed by genomic sequencing. CHOP:GFP and XBP1s:Turquoise reporters were introduced sequentially under G418 and puromycin selection to generate the previously
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Challenges of diagnosing using EMR data An integrated electronic medical record system is becoming an essential part of the fabric of modern healthcare, which can collect, store, display, transmit and reproduce patient information [1, 2]. The current studies show that medical information provided by Electronic Medical Records (EMRs) is more complete and faster to retrieve
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Citation: Marković D, Reiter AMF, Kiebel SJ (2019) Predicting change: Approximate inference under explicit representation of temporal structure in changing environments. PLoS Comput Biol 15(1): e1006707. https://doi.org/10.1371/journal.pcbi.1006707 Editor: Jill O’Reilly, Oxford University, UNITED KINGDOM Received: April 8, 2018; Accepted: December 11, 2018; Published: January 31, 2019 Copyright: © 2019 Marković et al. This is an
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Abstract The circadian oscillator, an internal time-keeping device found in most organisms, enables timely regulation of daily biological activities by maintaining synchrony with the external environment. The mechanistic basis underlying the adjustment of circadian rhythms to changing external conditions, however, has yet to be clearly elucidated. We explored the mechanism of action of nicotinamide in
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RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. Researchers at South Dakota State University aimed to streamline the bioinformatic analyses of gene-level data by developing a user-friendly, interactive web application for exploratory data analysis, differential expression, and pathway analysis. iDEP (integrated
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Exploring cellular responses to stimuli using extensive gene expression profiles has become a routine procedure performed on a daily basis. Raw and processed data from these studies are available on public databases but the opportunity to fully exploit such rich datasets is limited due to the large heterogeneity of data formats. In recent years, several
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New technologies for analyzing the three-dimensional chromosome organization in a genome-wide manner have revealed mechanisms by which chromosome communication is established [1]. By using different types of high-throughput techniques, such as ChIP-sequencing sensitive for different types of histone modifications, whole genome bisulfite sequencing, ATAC-sequencing, and DNase-Seq, many studies have discovered a large number of enhancers
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The advent of high throughput sequencing technologies has greatly accelerated the identification of variants that underlie Mendelian and complex diseases [1–7]. With the cost of sequencing decreasing and sequencing accuracy improving, an increasing number of research laboratories/projects have adopted these technologies to interrogate variants from a few or even hundreds to thousands of human samples
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Architecture of the LCM For the reader’s convenience, we introduce the structure of the LCM (see Fig. 1). The LCM represents a small region in the visual cortex of the cat as a sheet of cortical columns, within which neuron groups are situated (see Methods and Fig. 1B). Neuronal dynamics are modelled using a ‘mean field approximation’
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Simulation model CERONCO is a predominantly discrete multiscale computational model of cervical cancer response to treatment (external beam radiotherapy with concomitant weekly cisplatin, followed by pulsed dose rate brachytherapy) in the patient-individualized context. It makes use of the available multiscale (e.g. imaging, histological, treatment) longitudinal data of the patient. CERONCO follows a cellular automaton approach.
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1. Reck M, Heigener DF, Mok T, Soria JC, Rabe KF. Management of non-small-cell lung cancer: recent developments. Lancet. 2013;382:709–19. 2. Oltean S, Bates DO. Hallmarks of alternative splicing in cancer. Oncogene. 2014;33:5311–8. 3. David CJ, Manley JL. Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev. 2010;24:2343–64. 4. Wahl MC, Will
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PPAR-δ agonists dataset Agonists (789) were collected from different literature sources including CHEMBL29 and WOMBAT30. The range of their agonist activities (EC50) was 0.03–1000 nM. Figures S1–S3 present some characteristics of those 789 PPAR-δ agonists. They partially obey Lipinski’s Rule of Five (ROF) for Oral availability of drugs31 and Oprea’s rules for “Lead like molecules”30 (63% and
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Synthetic data In this section, we examine the performance of MuClone on simulated data. In what follows, we generate N loci from M samples with K underlying tumour mutation clusters with sequencing error rate (epsilon) and tumour content tm. We first randomly generate an evolutionary relationship between clusters, viewed as a binary phylogenetic tree. Each
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Abstract Drug combinations are a promising approach to achieve high efficacy at low doses and to overcome resistance. Drug combinations are especially useful when drugs cannot achieve effectiveness at tolerable doses, as occurs in cancer and tuberculosis (TB). However, discovery of effective drug combinations faces the challenge of combinatorial explosion, in which the number of
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Citation: Duwal S, Dickinson L, Khoo S, von Kleist M (2019) Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis. PLoS Comput Biol 15(1): e1006740. https://doi.org/10.1371/journal.pcbi.1006740 Editor: Sebastian Bonhoeffer, ETH Zürich, SWITZERLAND Received: December 22, 2017; Accepted: December 20, 2018; Published: January 30, 2019 Copyright: © 2019 Duwal et al. This is an
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Abstract Gut microbiota and human relationships are strictly connected to each other. What we eat reflects our body-mind connection and synchronizes with people around us. However, how this impacts on gut microbiota and, conversely, how gut bacteria influence our dietary behaviors has not been explored yet. To quantify the complex dynamics of this interplay between
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Citation: Clark JJ, Benson ML, Smith RD, Carlson HA (2019) Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PLoS Comput Biol 15(1): e1006705. https://doi.org/10.1371/journal.pcbi.1006705 Editor: Charlotte M. Deane, University of Oxford, UNITED KINGDOM Received: July 3, 2018; Accepted: December 7, 2018; Published: January 30, 2019 Copyright: © 2019 Clark et
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Scientists are making important progress in the battle against a class of devilishly complex human pediatric brain cancers thanks to a new study from a team of Florida State University students and faculty. Among young children, there’s no brain tumor more common than medulloblastoma. But no specific and effective therapy yet exists for this dangerous
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In recognition of its dedication to advocating for customers, Integrated DNA Technologies (IDT), has won a prestigious Life Science Industry Award for Best Overall Customer Experience, as well as a Gold award for Most Useful Website. The awards—entirely nominated and voted for by scientists—validate IDT’s continued efforts to support scientists at every stage of their
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Posted by: RNA-Seq Blog in Workflow 5 hours ago 106 Views The analysis of single cell gene expression across thousands of individual cells within a tissue or microenvironment is a valuable tool for identifying cell composition, discrimination of functional states, and molecular pathways underlying observed tissue functions and animal behaviors. However, the isolation of intact,
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Posted by: RNA-Seq Blog in Review Publications 16 hours ago 338 Views For the last 40 years, “Sanger sequencing” allowed to unveil crucial secrets of life. However, this method of sequencing has been time-consuming, laborious and remains expensive even today. Human Genome Project was a huge impulse to improve sequencing technologies, and unprecedented financial and
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looking for basic help you guys must know like the back of your hand. was given five sequences and was told to align them. some have 12bp some have 9. how would i go about aligning these, how do i know when to align homologous positions? is there a case where homologous nucleotides are aligned?
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1. Tomasetti, C., Marchionni, L., Nowak, M. A., Parmigiani, G. & Vogelstein, B. Only three driver gene mutations are required for the development of lung and colorectal cancers. Proc Natl Acad Sci USA 112, 118–123 (2015). 2. Zhang, X. & Simon, R. Estimating the number of rate limiting genomic changes for human breast cancer. Breast
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Animals and experimental infection All the protocols of animal handling and sampling were approved by the Animal Care and Ethics Committee, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences. All the methods were carried out in accordance with the approved protocols and relevant guidelines. Four hundred virus-free H. diversicolor supertexta (size range between
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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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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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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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