Bioinformatics

Abstract Real-time forecasts based on mathematical models can inform critical decision-making during infectious disease outbreaks. Yet, epidemic forecasts are rarely evaluated during or after the event, and there is little guidance on the best metrics for assessment. Here, we propose an evaluation approach that disentangles different components of forecasting ability using metrics that separately assess
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Posted by: RNA-Seq Blog in Webinars, Workshops 8 days ago 597 Views Minnesota Supercomputing Institute – 04/02/19 The RNA-Seq analysis tutorials includes a lecture and a hands-on guided tutorial. The lecture materials cover the basics of differential expression analysis and touches on other RNA-seq topics such as transcriptome assembly. Topics Covered: RNA-Seq vs Microarray technology Experimental Design
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Tissue-specific receptors and adaptations enable localisation of T regulatory cells Mouse b and t cells. To create a detailed picture of T cells, the researchers studied 35,000 individual cells from healthy mouse lymph nodes, spleen, skin and colon, comparing cells across the different tissues. Image credit: Peter Lane and Fiona McConnell, Wellcome Images For the
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Cellular lineage trees can be derived from single-cell RNA sequencing snapshots of differentiating cells. Currently, only datasets with simple topologies are available. To test and further develop tools for lineage tree reconstruction, we need test datasets with known complex topologies. Researchers at Max Planck Institute for Biophysical Chemistry have developed PROSSTT which can simulate scRNA-seq datasets for
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Prototype technology demonstrates a more automated, efficient, and scalable workflow to analyze cells by type A team led by scientists at the Broad Institute, MIT, and Massachusetts General Hospital has developed a prototype device that uses microfluidics to sort cell types extracted from clinical samples for RNA sequencing. “This platform allows us to isolate specific
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The ALS Association and The Tow Foundation are pleased to announce their continuing support of the New York Genome Center’s (NYGC) Center for Genomics of Neurodegenerative Disease (CGND), in recognition of the substantial genomic research being carried out by NYGC scientists. The ALS Association has committed an additional $3.5 million to the NYGC’s CGND, including
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Posted by: RNA-Seq Blog in Publications 10 days ago 600 Views RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here,
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From March 11-13, 2019, the NCBI will help run a bioinformatics hackathon in the North Carolina Research Triangle hosted by the University of North Carolina, Chapel Hill (UNC). Potential topics include: technical metadata homogenization a simple interface for using ontologies to make data searches more sensitive and specific automated data analysis and visualization novel isoform
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Researchers investigating the gut microbiome have isolated more than a hundred bacterial species that have never previously been identified. The discovery has led to the creation of what is now the most comprehensive database of human health-associated intestinal bacteria to date. Yurchanka Siarhei | Shutterstock The new resource will enable researchers to identify the bacteria
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Registered researchers will have rapid access to an “unprecedented scale” of clinical research data through the new Common Infrastructure for National Cohorts in Europe, Canada and Africa (CINECA), launched today. Simon Fraser University professor Fiona Brinkman, the initiative’s Canadian lead, says the project will not only accelerate disease research but will also help to advance
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A University of Oklahoma researcher, Si Wu, and collaborators from the Oklahoma Medical Research Foundation and Indiana University, are developing new strategies leading to diagnosis and early intervention of Lupus, an autoimmune disease that may affect up to 1.5 million Americans. The National Institutes of Health is funding the OU research with a $2 million
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Abstract Constraint-based modeling (CBM) is increasingly used to analyze the metabolism of complex microbial communities involved in ecology, biomedicine, and various biotechnological processes. While CBM is an established framework for studying the metabolism of single species with linear stoichiometric models, CBM of communities with balanced growth is more complicated, not only due to the larger
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Citation: Osthus D, Daughton AR, Priedhorsky R (2019) Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited. PLoS Comput Biol 15(2): e1006599. https://doi.org/10.1371/journal.pcbi.1006599 Editor: David A. Broniatowski, The George Washington University, UNITED STATES Received: May 21, 2018; Accepted: October 30, 2018; Published: February 1, 2019 This is an
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Long non-coding RNAs (lncRNAs) can act as scaffolds that promote the interaction of proteins, RNA, and DNA. There is increasing evidence of sequence-specific interactions of lncRNAs with DNA via triple-helix (triplex) formation. This process allows lncRNAs to recruit protein complexes to specific genomic regions and regulate gene expression. Here researchers at RWTH Aachen University propose a
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Posted by: RNA-Seq Blog in Industry News, Press Release 47 mins ago 56 Views Fluidigm Corporation, a leader in mass cytometry and microfluidics technologies, today announced the introduction of a REAP-seq (RNA expression and protein sequencing) protocol for use with the C1™ system. C1 REAP-seq is a powerful multi-omic single-cell application that enables deep characterization
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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 results in modern and next-generation AI for Drug Discovery on a live episode of the influential CXOTalk Show on February 8, 2019 at 1:00 PM Eastern time. Artificial intelligence (AI) has the potential to
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We propose here an integrative analysis strategy to identify key regulators and pathways in cancers from the TCGA data. By comparing gene expression, genetic variation, and DNA methylation data between normal and cancer samples, we extracted the triple-evidenced genes for 13 cancers and analyzed the characteristics of these genes (Fig. 1a). Fig. 1 The workflow
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1. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013). 2. Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647–661 (2014). 3. Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583–588 (2015). 4. Mali, P. et al.
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Compounding culture factor combinations for TF-1 cells The epMotion 5070 liquid hander (Eppendorf) was used to compound the culture condition “recipe” according to the prescribed algorithm-generated test formulations. Each factor was diluted to the appropriate concentration in a base media of DMEM (Gibco #12430054) supplemented with 1% Penicillin-Streptomycin (Pen-Strep; Gibco #15140122) and distributed into 48-well
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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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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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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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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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