Bioinformatics

Gene expression data can reflect gene activities and physiological status in a biological system at the transcriptome level. Gene expression data typically includes small samples but with high dimensions and noise [1]. A single gene chip or next generation sequencing technology can detect at least tens of thousands of genes for one sample, but when
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Abstract Recent studies suggest that deep Convolutional Neural Network (CNN) models show higher representational similarity, compared to any other existing object recognition models, with macaque inferior temporal (IT) cortical responses, human ventral stream fMRI activations and human object recognition. These studies employed natural images of objects. A long research tradition employed abstract shapes to probe
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Abstract Substrate permissiveness has long been regarded as the raw materials for the evolution of new enzymatic functions. In land plants, hydroxycinnamoyltransferase (HCT) is an essential enzyme of the phenylpropanoid metabolism. Although essential enzymes are normally associated with high substrate specificity, HCT can utilize a variety of non-native substrates. To examine the structural and dynamic
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Posted by: RNA-Seq Blog in RNA Extraction 5 hours ago 99 Views Researchers from the RIKEN Cluster for Pioneering Research have developed a microfluidic method for electrical lysis and RNA extraction from single fixed cells leveraging reversible cross-linker dithiobis(succinimidyl propionate) (DSP). The microfluidic system captures a single DSP-fixed cell at a hydrodynamic trap, reverse-cross-links the
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Resistance to therapy is common in estrogen receptor positive (ER+) breast cancer, the most common type of breast cancer, and eventual development of metastatic disease is a leading cause of death. Exploring what sets breast cancer cells on a path toward becoming resistant to therapy has led researchers at Baylor College of Medicine to discover
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Abstract Although a standard reinforcement learning model can capture many aspects of reward-seeking behaviors, it may not be practical for modeling human natural behaviors because of the richness of dynamic environments and limitations in cognitive resources. We propose a modular reinforcement learning model that addresses these factors. Based on this model, a modular inverse reinforcement
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A deep neural network algorithm called BOTA uses bacterial genomes to identify unrecognized bacterial antigens. The immune system keeps T cells under control by regulating precisely when they can respond to a pathogen. For instance, helper T cells only turn “on” if other immune cells, such as antigen-presenting cells (APCs) present bacterial peptides (protein fragments)
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Abstract Multicellular tumour spheroids capture many characteristics of human tumour microenvironments, including hypoxia, and represent an experimentally tractable in vitro model for studying interactions between radiotherapy and anticancer drugs. However, interpreting spheroid data is challenging because of limited ability to observe cell fate within spheroids dynamically. To overcome this limitation, we have developed a hybrid
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Abstract The size of a cell sets the scale for all biochemical processes within it, thereby affecting cellular fitness and survival. Hence, cell size needs to be kept within certain limits and relatively constant over multiple generations. However, how cells measure their size and use this information to regulate growth and division remains controversial. Here,
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Abstract Thermodynamics dictates the structure and function of metabolism. Redox reactions drive cellular energy and material flow. Hence, accurately quantifying the thermodynamics of redox reactions should reveal design principles that shape cellular metabolism. However, only few redox potentials have been measured, and mostly with inconsistent experimental setups. Here, we develop a quantum chemistry approach to
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Posted by: RNA-Seq Blog in Publications, Workflow 4 hours ago 107 Views Ribonucleoprotein particles (mRNPs) are complexes consisting of mRNAs and RNA-binding proteins (RBPs) which control mRNA transcription localization, turnover, and translation. Some mRNAs within the mRNPs have been shown to undergo degradation or storage. Those transcripts can lack general mRNA elements, like the poly(A)
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Posted by: RNA-Seq Blog in Industry News, Press Release 15 hours ago 211 Views Proteona Pte. Ltd. has entered into an exclusive worldwide licensing agreement with the National University of Singapore (NUS) for Enhanced Single Cell Analysis with Protein Expression (ESCAPE™) RNA sequencing technology, an innovative multifaceted single-cell sequencing platform for simultaneous protein and RNA
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The representation of interactions between a set of nodes by the wTO method [10–12] takes into account the overall commonality of all the links a node has, instead of basing the analysis only on calculating raw correlations among the nodes. It thus provides a more comprehensive understanding of how two nodes are related. Therefore, it
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Simulation settings In the following simulation studies, we compare the Bayesian approach with other methods such as GSEA, ORA, global test, frequentist logistic regression with the proposed pathway score (denoted as Logistic (ps)), frequentist logistic regression with the average expression level as the pathway score (Logistic (sum)), and the Fisher’s method. First we generated either
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University of Kentucky researchers have developed SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets. The query recovers 92.7% of tier-1
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In ageing research, the lifespan of an organism is an indicator for determining factors that play a role in this process. These ageing factors (AFs) can be genes, chemical compounds or other factors like dietary restriction. Usually, they are examined under different experimental conditions in model organisms like the worm (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae),
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Citation: Brinkman BAW, Rieke F, Shea-Brown E, Buice MA (2018) Predicting how and when hidden neurons skew measured synaptic interactions. PLoS Comput Biol 14(10): e1006490. https://doi.org/10.1371/journal.pcbi.1006490 Editor: Jeff Beck, Duke University, UNITED STATES Received: December 7, 2017; Accepted: September 5, 2018; Published: October 22, 2018 Copyright: © 2018 Brinkman et al. This is an open
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Abstract We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) identifies phenotype-specific k-mers, (b) generates a k-mer-based statistical model for predicting a given phenotype and (c) predicts the phenotype from the sequencing data of a given bacterial isolate. The method was validated on 167 Klebsiella pneumoniae isolates (virulence), 200 Pseudomonas aeruginosa isolates
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Abstract The development of novel therapeutics is urgently required for diseases where existing treatments are failing due to the emergence of resistance. This is particularly pertinent for parasitic infections of the tropics and sub-tropics, referred to collectively as neglected tropical diseases, where the commercial incentives to develop new drugs are weak. One such disease is
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Posted by: RNA-Seq Blog in Statisitcal Analysis 3 hours ago 89 Views High-throughput expression profiling experiments with ordered conditions (e.g. time-course or spatial-course) are becoming more common for studying detailed differentiation processes or spatial patterns. Identifying dynamic changes at both the individual gene and whole transcriptome level can provide important insights about genes, pathways, and
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The ability to translate the genetic code into proteins is an essential step in all living organisms. A cornerstone of this molecular process is the ability of transfer RNA (tRNA) molecules to couple recognition of the genetic code with the cognate amino acid, which are the building blocks of proteins. Chemical modification of individual tRNAs
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Determining ‘who infected whom’ during an outbreak can yield precious insights into transmission dynamics of an infectious disease and subsequently inform infection control policies. Transmission tree reconstruction has been used to specify the contribution of individual cases and locations to overall transmission [1], characterise heterogeneous infectiousness within outbreaks [2, 3], evaluate the impact of control
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Human Immunodeficiency Virus (HIV) is a major pandemic disease [1]. More than 36 million people have been infected and about half of these people receive anti-retroviral therapy [2]. However, retroviruses like HIV mutate rapidly since the conversion from the RNA genome to DNA is error-prone [3]. They readily form quasi-species and distinct viral strains. Therefore,
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Visualizations include display of nucleotide and amino acid substitutions occurring along a user-defined sequence interval (summary plots via baseml) and along the phylogenetic tree (via codeml). Transition (Ts: A↔G, C↔T) and transversion (Tv: A↔C, A↔T, G↔C, G↔T) substitutions are analyzed by codon position (Fig. 1) and then frequency plots summarize the overall accumulation of Ts and
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The design presented in this paper should be regarded as one acceptable approach with respect to the the aforementioned requirements. However, numerous other frameworks, architectures, and configurations could potentially prove adequate. In this section, our reasons for favoring this system will be explained more thoroughly. The research conducted during the course of this project resulted
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Cancer is a genetic disease that is driven by changes to genes controlling cellular function [1]. Characterizing the disease at the molecular level is essential for early detection, personalized therapy based on tumor genomic profiles, monitoring tumor progression and response to treatment and the identification of resistant mechanisms [2]. For solid tumors, tumor tissue biopsies
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Gene expression profiling can uncover biologic mechanisms underlying disease and is important in drug development. RNA sequencing (RNA-seq) is routinely used to assess gene expression, but costs remain high. Sample multiplexing reduces RNAseq costs; however, multiplexed samples have lower cDNA sequencing depth, which can hinder accurate differential gene expression detection. The impact of sequencing depth
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Pathways are sets of genes corresponding to functionally related interacting proteins. Pathway data is available from many databases dependent on biological focus. The fragmented nature of pathways across multiple databases makes it difficult to perform inclusive analysis of all known data. To address this issue, many attempts have been made to consolidate pathway databases such
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Abstract Cortical activity has distinct features across scales, from the spiking statistics of individual cells to global resting-state networks. We here describe the first full-density multi-area spiking network model of cortex, using macaque visual cortex as a test system. The model represents each area by a microcircuit with area-specific architecture and features layer- and population-resolved
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Abstract RAVEN is a commonly used MATLAB toolbox for genome-scale metabolic model (GEM) reconstruction, curation and constraint-based modelling and simulation. Here we present RAVEN Toolbox 2.0 with major enhancements, including: (i) de novo reconstruction of GEMs based on the MetaCyc pathway database; (ii) a redesigned KEGG-based reconstruction pipeline; (iii) convergence of reconstructions from various sources;
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Citation: Xu S, Kim S, Chen ISY, Chou T (2018) Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque. PLoS Comput Biol 14(10): e1006489. https://doi.org/10.1371/journal.pcbi.1006489 Editor: Thomas Höfer, German Cancer Research Center, GERMANY Received: March 23, 2017; Accepted: September 5, 2018; Published:
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Abstract Data from SIV-infected macaques indicate that virus-specific cytotoxic T lymphocytes (CTL) are mostly present in the extrafollicular (EF) compartment of the lymphoid tissue, with reduced homing to the follicular (F) site. This contributes to the majority of the virus being present in the follicle and represents a barrier to virus control. Using mathematical models,
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Posted by: RNA-Seq Blog in Publications 2 hours ago 60 Views Spatially resolved single-cell RNA sequencing (scRNAseq) is a powerful approach for inferring connections between a cell’s identity and its position in a tissue. Researchers at the Weizmann Institute of Science recently combined scRNAseq with spatially mapped landmark genes to infer the expression zonation of hepatocytes.
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Abstract The relationship between brain structure and function has been probed using a variety of approaches, but how the underlying structural connectivity of the human brain drives behavior is far from understood. To investigate the effect of anatomical brain organization on human task performance, we use a data-driven computational modeling approach and explore the functional
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Abstract Elucidating the complete network of protein-protein interactions, or interactome, is a fundamental goal of the post-genomic era, yet existing interactome maps are far from complete. To increase the throughput and resolution of interactome mapping, methods for protein-protein interaction discovery by co-migration have been introduced. However, accurate identification of interacting protein pairs within the resulting
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MicroRNAs (miRNAs) function as master regulators of gene expression. Recent studies demonstrate that miRNA isoforms (isomiRs) play a unique role during cancer development. National Cancer Institute researchers have developed QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designed for the detection and annotation
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In a study published in iScience, Professor Akiyoshi Fukamizu of the Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (University of Tsukuba, JAPAN) and the research group reported a new work on discovery of the important role of PRMT1 in dilated cardiomyopathy (DCM). The heart pumps blood to all organs and tissues of
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Recent advances in Next-Generation Sequencing (NGS) technologies provided new tools to sequence large amounts of DNA at a reasonable cost and in a limited period [1]. This technological breakthrough is expected to significantly modify the landscape and practices in the field of clinical microbiology. Microorganisms can now be characterized with unprecedented resolution, which can have
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When different types of functional genomics data are generated on single cells from different samples of cells from the same heterogeneous population, the clustering of cells in the different samples should be coupled. Stanford University researchers formulate this “coupled clustering” problem as an optimization problem and propose the method of coupled nonnegative matrix factorizations (coupled
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To avoid diabetes, we need healthy populations of the pancreatic “beta” cells that produce insulin for us. Research at Joslin Diabetes Center in Boston now has shown that the health of these crucial cell populations can be regulated in part by an unexpected biological route—dynamic modifications of RNA involved in the biological pathways that signal
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Genialis, which provides AI-driven, platform-enabled data integration solutions to help accelerate drug discovery, today announced a partnership with Roche to provide researchers with a complete, streamlined next-generation sequencing (NGS) workflow for gene expression profiling. By using Genialis, Roche KAPA RNA HyperPrep Kit* customers now have end-to-end support from sample through analysis. Genialis and Roche are
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