Bioinformatics

Abstract The dynamic nature of technological developments invites us to rethink the learning spaces. In this context, science education can be enriched by the contribution of new computational resources, making the educational process more up-to-date, challenging, and attractive. Bioinformatics is a key interdisciplinary field, contributing to the understanding of biological processes that is often underrated
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Abstract The dynamic nature of technological developments invites us to rethink the learning spaces. In this context, science education can be enriched by the contribution of new computational resources, making the educational process more up-to-date, challenging, and attractive. Bioinformatics is a key interdisciplinary field, contributing to the understanding of biological processes that is often underrated
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Like going from a pinhole camera to a Polaroid, a significant mathematical update to the formula for a popular bioinformatics data visualization method will allow researchers to develop snapshots of single-cell gene expression not only several times faster but also at much higher-resolution. Published in Nature Methods, this innovation by Yale mathematicians will reduce the rendering
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Posted by: RNA-Seq Blog in Information 21 hours ago 173 Views Sometimes, analyzing our DNA sequences isn’t quite enough. RNA-seq is a next-generation sequencing (NGS)-based technique that looks at the RNA transcripts produced from our DNA, allowing us to look into how our genes are expressed. RNA-seq has shown its worth across many fields, and
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Genetic sequence database searching is a foundational tool in bioinformatics commonly used to make new discoveries, guide annotation, and direct downstream analysis, among many other tasks. Therefore, the performance of database searching tools is crucial to high quality results in many biomedical applications. Benchmarking such tools provides a systematic comparison to aid developers and researchers
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Genetic sequence database searching is a foundational tool in bioinformatics commonly used to make new discoveries, guide annotation, and direct downstream analysis, among many other tasks. Therefore, the performance of database searching tools is crucial to high quality results in many biomedical applications. Benchmarking such tools provides a systematic comparison to aid developers and researchers
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Dissecting the model to predict how landmark learning is achieved Using this model, we can dissect different elements of learning, analyse what information is learnt, and how effective is this information. Initially, we examined whether our model could simulate experimental spatial learning. Rats were simulated in a water maze using 4 trials/day for 10 days.
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This study involved a deep computational investigation of the MOG-antibody complex in aqueous solution. For a significant nanoscale description, available data on MOG structure and its specific antibody6,21 were taken into account together with considerations from the experimental-theoretical interface background of our research group. This study presented the following highlights: (1) Fab portion fluctuation of
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In the past decade, next generation sequencing (NGS) technology has made great progress and personal genome sequencing has also been widely used in human disease research, clinical treatment and new drug research [1]. In the genome analysis process, variant calling is significant step to discover and obtain variants relative to reference genome, which is also
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In the past decade, next generation sequencing (NGS) technology has made great progress and personal genome sequencing has also been widely used in human disease research, clinical treatment and new drug research [1]. In the genome analysis process, variant calling is significant step to discover and obtain variants relative to reference genome, which is also
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Abstract A well-established notion in cognitive neuroscience proposes that multiple brain systems contribute to choice behaviour. These include: (1) a model-free system that uses values cached from the outcome history of alternative actions, and (2) a model-based system that considers action outcomes and the transition structure of the environment. The widespread use of this distinction,
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Abstract A well-established notion in cognitive neuroscience proposes that multiple brain systems contribute to choice behaviour. These include: (1) a model-free system that uses values cached from the outcome history of alternative actions, and (2) a model-based system that considers action outcomes and the transition structure of the environment. The widespread use of this distinction,
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Abstract An important goal of systems medicine is to study disease in the context of genetic and environmental perturbations to the human interactome network. For diseases with both genetic and infectious contributors, a key postulate is that similar perturbations of the human interactome by either disease mutations or pathogens can have similar disease consequences. This
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Abstract An important goal of systems medicine is to study disease in the context of genetic and environmental perturbations to the human interactome network. For diseases with both genetic and infectious contributors, a key postulate is that similar perturbations of the human interactome by either disease mutations or pathogens can have similar disease consequences. This
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Ethics statement All experiments using mice were performed in accordance with the Animal Experimentation Ethics Committee of the Peter MacCallum Cancer Centre (Approval E427) and mice were sacrificed by anaesthetic overdose. Lineage data Data from 3 types of lineages are analyzed in this paper. Experimental data from T cells provide an example of a lineage
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Ethics statement All experiments using mice were performed in accordance with the Animal Experimentation Ethics Committee of the Peter MacCallum Cancer Centre (Approval E427) and mice were sacrificed by anaesthetic overdose. Lineage data Data from 3 types of lineages are analyzed in this paper. Experimental data from T cells provide an example of a lineage
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A team of scientists led by researchers at the University of Georgia Center for Food Safety in Griffin has developed a machine-learning approach that could lead to quicker identification of the animal source of certain Salmonella outbreaks. In the research, published in the January 2019 issue of Emerging Infectious Diseases, Xiangyu Deng and his colleagues
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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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Abstract Electrocorticography (ECoG) is becoming more prevalent due to improvements in fabrication and recording technology as well as its ease of implantation compared to intracortical electrophysiology, larger cortical coverage, and potential advantages for use in long term chronic implantation. Given the flexibility in the design of ECoG grids, which is only increasing, it remains an
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Abstract Electrocorticography (ECoG) is becoming more prevalent due to improvements in fabrication and recording technology as well as its ease of implantation compared to intracortical electrophysiology, larger cortical coverage, and potential advantages for use in long term chronic implantation. Given the flexibility in the design of ECoG grids, which is only increasing, it remains an
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Abstract Prediction of response to specific cancer treatments is complicated by significant heterogeneity between tumors in terms of mutational profiles, gene expression, and clinical measures. Here we focus on the response of Estrogen Receptor (ER)+ post-menopausal breast cancer tumors to aromatase inhibitors (AI). We use a network smoothing algorithm to learn novel features that integrate
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Citation: Zhang Q, Hu X, Hong B, Zhang B (2019) A hierarchical sparse coding model predicts acoustic feature encoding in both auditory midbrain and cortex. PLoS Comput Biol 15(2): e1006766. https://doi.org/10.1371/journal.pcbi.1006766 Editor: Frédéric E. Theunissen, University of California at Berkeley, UNITED STATES Received: April 29, 2018; Accepted: December 21, 2018; Published: February 11, 2019 Copyright:
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Citation: Zhang Q, Hu X, Hong B, Zhang B (2019) A hierarchical sparse coding model predicts acoustic feature encoding in both auditory midbrain and cortex. PLoS Comput Biol 15(2): e1006766. https://doi.org/10.1371/journal.pcbi.1006766 Editor: Frédéric E. Theunissen, University of California at Berkeley, UNITED STATES Received: April 29, 2018; Accepted: December 21, 2018; Published: February 11, 2019 Copyright:
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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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