Bioinformatics

Simulation The simulations in this work were performed as following (unless specifically stated otherwise): We randomly positioned and orientated the designed triangular configurations onto the canvas, and assigned the vertexes as the positions of the “molecules”. Around each of these “molecules”, we simulated the SMLM data by generating multiple localization coordinates that subject to a
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1. Pui C-H, Relling MV, Downing JR. Acute lymphoblastic leukemia. N Engl J Med. 2004;350:1535–48. 2. Burmeister T, Gökbuget N, Schwartz S, Fischer L, Hubert D, Sindram A, et al. Clinical features and prognostic implications of TCF3-PBX1 and ETV6-RUNX1 in adult acute lymphoblastic leukemia. Haematologica. 2010;95:241–6. 3. Geng H, Hurtz C, Lenz KB, Chen Z,
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Abstract S. aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics. Despite growing knowledge of S. aureus metabolic capabilities, our understanding of its systems-level responses to different media types remains incomplete. Here, we develop a manually reconstructed genome-scale model (GEM-PRO) of metabolism with
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Abstract Advancing age is the dominant risk factor for most of the major killer diseases in developed countries. Hence, ameliorating the effects of ageing may prevent multiple diseases simultaneously. Drugs licensed for human use against specific diseases have proved to be effective in extending lifespan and healthspan in animal models, suggesting that there is scope
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I work at the Parker Institute for Cancer Immunotherapy as a software and data engineer. A couple of my coworkers are creating a video series on data science techniques used to analyze large molecular data sets. The first video just went live on YouTube, and I thought it would be well received here! The video
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After trying to read through broad institutes information on analyzing a GSEA plot and piecing together what I could. I still feel like I’m missing something with GSEA plots. Here’s an example I will refer to GSEA From my understanding you have a gene set of interest which you can then analyze a set of
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Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immunoprecipitation sequencing (CLIP-Seq) or RNA immunoprecipitation (RIP-Seq) sequencing, DNA accessibility by assay for transposase-accessible chromatin (ATAC-Seq), DNase or MNase
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Using a unique bioinformatics technique developed at the University of Alabama at Birmingham, UAB researchers have detected the emergence of new strains of microbes in the human fecal microbiota after obesity surgery. These new strains emerged after surgical disruption of the stomach and upper small intestine. In contrast, the researchers found that strains of the
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Tight regulation of protein complexes by translational and post-translational control mechanisms may result in the degradation of more abundant proteins that do not form the complex. Then the proteins of known complexes, such as the ones collected in the CORUM database, will show similar abundance protein profiles when compared across different cell types. Given that
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Canonical correlation analysis (CCA) is a classic and highly versatile statistical approach to investigate the linear relationship between two sets of variables [1, 2]. CCA helps to decode complex dependency structures in multivariate data and to identify groups of interacting variables. Consequently, it has numerous practical applications in molecular biology, for example omics data integration
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NEWS AND VIEWS 09 January 2019 A computational strategy has delivered a redesigned, more stable version of a cytokine protein that mimics the natural protein’s interactions with receptors, opening the way for designer cytokine-based therapeutics. E. Yvonne Jones E. Yvonne Jones is in the Division of Structural Biology, Wellcome Centre for Human Genetics, University of
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Although modern sequencing technologies such as ribonucleic acid sequencing and next-generation sequencing have been developed, microarrays have been a widely used high-throughput technology in gathering large amounts of genomic data [1, 2]. Due to small sample sizes in single microarray studies, microarray studies are combined with meta-analytic techniques to increase statistical power and generalizability of
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There have been many studies on protein interaction at home and abroad [27]. There are also many websites which have unveiled a large protein response Database, such as STRING, GEN, BioGRID, DDBJ, Database of Interacting Proteins, ExPasy, Gepasi, etc. [28]. According to the relevant literature, the current studies on protein interaction data are broadly divided
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Metabolite secretion cost depends on environmental context Understanding whether the secretion of a metabolite by an organism is associated with a decrease in fitness (interpreted here as growth rate) is difficult to assess experimentally, but can be readily calculated using genome-scale models of metabolism (see Methods). For example, one can impose the secretion of a
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Posted by: RNA-Seq Blog in Publications, Workflow 6 hours ago 108 Views Researchers from the Mayo Clinic used single cell RNA-Seq to examine molecular heterogeneity in multiple myeloma (MM) in 597 CD138 positive cells from bone marrow aspirates of 15 patients at different stages of disease progression. 790 genes were selected by coefficient of variation
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Insilico Medicine, an artificial intelligence company developing end-to-end drug discovery pipelines for age-related diseases and TARA Biosystems, Inc. a company offering “heart-on-a-chip” tissue models for drug discovery and risk assessment applications, announced today the launch of a collaboration to discover and develop novel therapies for cardiac disease and diseases associated with cardiac muscle aging. The
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Diffusion depends upon the properties of both the diffusing species and the medium, so a known medium can be used to characterise an unknown molecule or vice versa. On biological surfaces, the primary interest is to characterize the interaction of different molecules with a membrane and to establish whether movement is or is not Brownian
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Proteins that are predicted to be expressed from an open reading frame, but for which there is no experimental evidence of translation are known as hypothetical proteins (HPs). Across the whole genome, approximately 2% of the genes code for proteins, while the remaining are non-coding or still functionally unknown [1]. These known-unknown regions for which
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In vivo model for adenine accumulation and toxicity Purine biosynthesis pathways are crucial for the normal function of cells and are conserved between yeast and humans. Both the adenine phosphoribosyltransferase (APRT) and adenosine deaminase (ADA) enzymes take part in adenine salvage in humans and mutations in their encoding genes can lead to the accumulation of
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Alterations in oncogenes or tumor suppressor genes underlie the driving forces of carcinogenesis. An oncogene is a gene that causes cancer through activating mutation or expression at high levels, while for a tumor suppressor gene, it is the loss or reduction of function that leads to cancer. Research in cancer biology has identified hundreds of
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Abstract Cancer development is driven by series of events involving mutations, which may become fixed in a tumor via genetic drift and selection. This process usually includes a limited number of driver (advantageous) mutations and a greater number of passenger (neutral or mildly deleterious) mutations. We focus on a real-world leukemia model evolving on the
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Abstract Classical decision theory postulates that choices proceed from subjective values assigned to the probable outcomes of alternative actions. Some authors have argued that opposite causality should also be envisaged, with choices influencing subsequent values expressed in desirability ratings. The idea is that agents may increase their ratings of items that they have chosen in
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Abstract The lack of a deep understanding of how proteins interact remains an important roadblock in advancing efforts to identify binding partners and uncover the corresponding regulatory mechanisms of the functions they mediate. Understanding protein-protein interactions is also essential for designing specific chemical modifications to develop new reagents and therapeutics. We explored the hypothesis of
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The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics tools and technologies are enabling genotype-phenotype association studies that identify genetic determinants of pathogen virulence and drug resistance as well as phylogenetic studies designed to track the origin and spread of pathogens during
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The process of mutation and crossing results in reduction of the density of experimentally induced homozygous polymorphisms relative to heterozygous polymorphisms as distance from the causative mutation increases [7, 8]. We assessed the properties of fragmented genome assemblies of Arabidopsis with respect to statistics of allele frequency. The length distribution of scaffolds was modelled and
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1. Herbert, A. et al. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc. Natl Acad. Sci. USA 94, 8421–8426 (1997). 2. Herbert, A. G., Spitzner, J. R., Lowenhaupt, K. & Rich, A. Z-DNA binding protein from chicken blood nuclei. Proc. Natl Acad. Sci. USA 90, 3339–3342 (1993). 3.
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NEWS 07 January 2019 The most-searched keywords in the Scopus database and on Google, revealed. Kelly Oakes Search for this author in: Science search trends have changed.Credit: Diane Keough/Getty Ever wondered what your colleagues are searching for online? ‘Cancer’, ‘blockchain’ and ‘big data’ were among the top search terms in a major science database in
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GeNeCK allows users to construct network using 11 different methods (summarized in Additional file 3: Table S1). Readers can refer to Yu et al. [7] for a comprehensive review of the different network construction methods. Network inference methods Partial correlation-based methods calculate the inverse covariance matrix Ω (also known as the precision matrix) of gene expressions,
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1. Cohen, I. G., Amarasingham, R., Shah, A., Xie, B. & Lo, B. The legal and ethical concerns that arise from using complex predictive analytics in health care. Health Aff. 33, 1139–1147 (2014). 2. Executive Office of the President. Big data: seizing opportunities, preserving values. https://bigdatawg.nist.gov/pdf/big_data_privacy_report_may_1_2014.pdf (2014). 3. Hoffman, S. Electronic Health Records and Medical
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We evaluated the performance of our BO-LSTM model on the SemEval 2013: Task 9 DDI extraction corpus [49]. This gold standard corpus consists of 792 texts from DrugBank [50], describing chemical compounds, and 233 abstracts from the Medline database [51]. DrugBank is a cheminformatics database containing detailed drug and drug target information, while Medline is
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Identification of peptides presented by major histocompatibility complex class I (MHC-I) is important for multiple applications in immunology and cancer therapy. One especially promising area is neoantigen-based immunotherapy for cancer: for example, one patient with cholangiocarcinoma experienced a partial response lasting at least 2 years after infusion of tumor-infiltrating lymphocytes specific to a neoantigen in
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In this section, we report the performance of the proposed algorithm using simulated and real tumor datasets. We compared model estimates, matrices of genotypes and proportions, from the proposed algorithm to those obtained from other similar algorithms. In real tumor datasets, similar to the manual approach considered in [27], we hypothesized phylogenetic trees from the
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On average, it takes over a dozen years and approximately 1.8 billion dollars to develop a drug [1]. In addition, most drugs have strong side effects or undesirable effects on patients, so these drugs cannot be placed on the market. Therefore, many pharmaceutical companies resort to repositioning of existing drugs on the market [2]. Many
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Abstract The locus coeruleus (LC) in the pons is the major source of noradrenaline (NA) in the brain. Two modes of LC firing have been associated with distinct cognitive states: changes in tonic rates of firing are correlated with global levels of arousal and behavioural flexibility, whilst phasic LC responses are evoked by salient stimuli.
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