Bioinformatics

Our body’s cells are constantly changing. But which of these changes are healthy developments and which lead to serious diseases? This is what LifeTime, a new transnational and interdisciplinary initiative of leading European researchers, aims to discover. The consortium is jointly coordinated by the Max Delbrück Center in Berlin and the Institut Curie in Paris,
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The U.S. Department of Defense has turned to the University of Nebraska to jumpstart the development of drug therapies to protect military service members from the effects of radiation exposure. In an environment where for-profit pharmaceutical companies are often reluctant to embark upon financially risky drug discovery efforts, the unique four-pronged partnership established by the
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USP7 activation requires the C-terminal tail in cis The activation of USP7 requires interaction between the CD and the C-terminal peptide (see Fig. 1a for domain definitions and nomenclature). The details of this interaction were described in a recent crystal structure (PDB: 5JTV) of Ubl45 and CD36. This structure clarifies how the activating C-terminal peptide binds,
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Due to the presented used decoupling strategies, the fitting framework is very flexible in terms of which use-case can be addressed and how the use-case is implemented. The first aspect (what/which) is possible due to abstraction between model, data and fit representation (see abstraction strategy 1 and 3). Thus, the framework can be applied to
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Image-based data for a quantitative model selection approach It is currently impossible to obtain time-lapse data of kidney branching morphogenesis in utero. We therefore cultured the dissected wild type (Fig. 2a, Supplementary Movie 1) and mutant kidneys (Supplementary Movies 2, 3) under a fluorescent microscope and imaged the branching process once per hour (for details see “Methods”—Kidney cultures
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Abstract Modern optical imaging experiments not only measure single-cell and single-molecule dynamics with high precision, but they can also perturb the cellular environment in myriad controlled and novel settings. Techniques, such as single-molecule fluorescence in-situ hybridization, microfluidics, and optogenetics, have opened the door to a large number of potential experiments, which begs the question of
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Citation: Dube D, Ahalawat N, Khandelia H, Mondal J, Sengupta S (2019) On identifying collective displacements in apo-proteins that reveal eventual binding pathways. PLoS Comput Biol 15(1): e1006665. https://doi.org/10.1371/journal.pcbi.1006665 Editor: Anders Wallqvist, US Army Medical Research and Materiel Command, UNITED STATES Received: July 3, 2018; Accepted: November 23, 2018; Published: January 15, 2019 Copyright: ©
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Posted by: RNA-Seq Blog in Splicing and Junction Mapping 8 hours ago 115 Views While the reconstruction of transcripts from a sample of RNA-Seq data is a computationally expensive and complicated task, the detection of splicing events from RNA-Seq data and a gene annotation is computationally feasible. This latter task, which is adequate for many
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MicroRNAs, the tiny bits of genetic material that regulate gene expression, play a significant – but poorly understood – role in controlling the differences between individual cells. Yale researchers have developed a technology that sheds light on the workings responsible for these differences – a breakthrough that could lead to new insights about cancer development.
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BioTuring Inc. has officially launched BioTuring Browser, the software that integrates state-of-the-art analyses for single-cell RNA-seq data, from transcript quantification, batch effect removal to downstream analyses, all delivered in an interactive visualization dashboard. Latest advances in single-cell RNA-seq (scRNA-seq) technologies have enabled scientists to look at individual transcriptomic profiles of millions of cells at a
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Numerous NGS workflows have been adapted to HPC systems with various methods. For example, HugeSeq [18] detects and annotates genetic variations by applying a MapReduce [19] approach, NGSANE [20] uses bash scripting with extensible logging and checkpointing measures, SIMPLEX [21] offers a fully functional VirtualBox Image to reduce installation issues. While they describe the analysis
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SMLM data consist of Cartesian coordinates of molecules and their respective precision along with all possible extra information that is desired in a specific experiment (i.e. time or frame of detection, channel, estimated number of photons detected etc.). The localization data together with these additional parameters can be imported into SMoLR in different formats obtained
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PolyQ-expanded AR exhibits reduced nuclear export To compare the nuclear export of polyQ-expanded AR with wildtype AR, we utilized a well-characterized PC12 cell model of SBMA in which rat pheochromocytoma-derived PC12 cells express full-length human AR under the control of a tetracycline-inducible promoter17,19,49,50,51,52,53,54,55. Using PC12 cells expressing AR10Q (wildtype) or AR112Q (polyQ-expanded), we performed a
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Comparison with other genetic variants simulators We compared sim1000G to two other competing and well established genetic variants simulators: hapgen2 [6] and simuGWAS [14]. We assessed how these simulators preserve the allele frequency distribution and correlation structure across genetic variants in a real genomic region. We used the default parameters specified by each software (Additional file 1)
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To perform this study, we received a large administrative dataset of anonymized blood biochemistry and cell count results linked to individuals’ chronological age, sex, and confirmed smoking status. The dataset was representative of the entire Alberta population, both rural and urban, with proportional representation of individuals of all ethnic origins. We then trained a set
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Image Capture Black, 96-well, flat-bottom, polystyrene microplates (Greiner Bio-One North America Inc., Monroe, NC) were covered with a one mm thick light scattering panel (Nikon SW-12 Diffuser Panel, Nikon Instruments, Melville, NY) employed to cast a consistent field of illumination throughout the well. Images were captured using an Andor Zyla 4.2 sCMOS (Andor Technologies, Belfast,
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Blat [1] is a sequence alignment tool designed to map DNA, RNA and protein sequences to reference genomes. It is commonly used to locate sequences in a reference genome, find homologous sequences from genomes of closely related species, identify exon-intron boundaries from mRNA sequences and determine gene structures, and to help assemble and annotate genome
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Analytical approach to identify key miRNAs associated with progression to PDAC We performed an integrative meta-analysis on miRNA and mRNA data from CP and PDAC cases to identify the miRNAs that are putatively associated with pathophysiology of CP to PDAC. In order to identify the miRNAs originating from the pancreas and circulating in blood, we
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Abstract Metabolomics is a powerful approach for discovering biomarkers and for characterizing the biochemical consequences of genetic variation. While untargeted metabolite profiling can measure thousands of signals in a single experiment, many biologically meaningful signals cannot be readily identified as known metabolites nor compared across datasets, making it difficult to infer biology and to conduct
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Abstract The mental contents of perception and imagery are thought to be encoded in hierarchical representations in the brain, but previous attempts to visualize perceptual contents have failed to capitalize on multiple levels of the hierarchy, leaving it challenging to reconstruct internal imagery. Recent work showed that visual cortical activity measured by functional magnetic resonance
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Hello folks, We are proud to announce the second genomics workshop for Asia Pacific! Held at the North Bangkok campus of the prestigious Kasetsart University, Empowering agricultural research through (meta)genomics will be held in Bangkok on the 25-28th June 2019. We’re sponsored by Illumina, Custom Science, the Hawkesbury Institute, University of Technology Sydney, as well
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Development and delivery of anti-HIV drugs are essential in prevention as well as therapeutic strategies against HIV/AIDS. Several drug delivery systems are currently in development for prevention, employing oral, intravenous, subcutaneous, and topical routes of administration1,2,3,4. Epidemiologically, oral PrEP (pre-exposure prophylaxis) has achieved a key role in overall prevention strategies5,6,7. However, topically delivered and acting
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Prions are proteins able to adopt multiple structural conformations from which at least one has self-propagating properties [1]. Yeast prions are the best understood subset of functional prions. A common feature of most yeast prions is the presence of an intrinsically disordered and low complexity prion domain (PrD), which is necessary and sufficient for prion
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The software package optiSel is implemented in R and C++. This section demonstrates the functionality of the package. This includes the estimation of genetic parameters and their use in OCS. Exact mathematical formulas for objective functions and constraints in OCS and their derivations can be found in (Wellmann R, Bennewitz J: Key genetic parameters for
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Participants A total of 49 volunteers (39 female; mean age 20.02 ± 1.55 years) took part in behavioural Experiment 1. Twenty-six of them (19 female; mean age 20.62 ± 1.62 years) participated in the memory reaction time task. Five out of these 26 participants were not included in the final analysis due to poor memory performance (<66% general accuracy)
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Place of introduction First we considered the effect of place of introduction of BTV on the final outbreak size. Figure 1a reveals the spatial distribution of the chance of an outbreak (i.e. the percentage of simulations which result in at least one farm becoming infected), while Fig. 1b shows the spatial distribution of the median outbreak size
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Researchers uncover novel immune cell populations that respond to immunotherapy treatment as well as key molecular factor required for therapy to succeed There have been many success stories for checkpoint blockade therapies both in preclinical models and in patients with cancer. But many questions remain about exactly how such immunotherapies elicit their response and what
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Earlier detection of cardiovascular disease is a step closer thanks to the findings of a research team at the Centro Nacional de Investigaciones Cardiovasculares (CNIC) led by Francisco Sánchez-Madrid and Pilar Martín. The scientists have found that the expression level of the molecule CD69 in blood cells inversely predicts the appearance of subclinical atherosclerosis (developing
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Data acquisition Three data sources were used in our models: influenza-like illness rates from ILINet, Internet search frequencies from Google Trends, and electronic health records from athenahealth, as described below. Weekly information from each data source was collected for the time period of October 4, 2009 to May 14, 2017. Influenza-like illness rates Weekly influenza-like
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1. Giaever, G. et al. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat. Genet. 21, 278–283 (1999). 2. Parsons, A. B. et al. Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat. Biotechnol. 22, 62–69 (2004). 3. Parsons, A. B. et al. Exploring the mode-of-action of bioactive compounds
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The Gene Ontology (GO) is a controlled vocabulary of gene annotations, which was founded in 1998 to provide interpretation of biological functions that are associated with individual genes [1, 2]. The GO terms were placed in a hierarchy and are structured as an acyclic directed graph. They are classified into three vocabularies: Biological Processes, Molecular
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Selection of platin drug-related genes We documented genes in the peer-reviewed literature associated with drug effectiveness or responses (Supplementary References, Section B). For cisplatin, carboplatin, and oxaliplatin, 179, 90, and 288 genes were implicated, respectively (Supplementary Table S1). Multiple factor analysis (MFA) was used to determine which genes correlated with the GI50 in breast cancer cell
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De novo assembly of the A. auricula-judae transcriptome Each of the individual RNA samples from Quanjin (n = 3), Banjin (n = 3), and Wujin (n = 3) (Fig. 1) were used to construct cDNA libraries for sequencing on an Illumina HiSeq2000 system. After removal of low quality reads, 69,814,486 reads, 62,918,023 reads, and 69,589,663 reads were obtained for Quanjin, Banjin, and
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Abstract Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis among solid malignancies and improved therapeutic strategies are needed to improve outcomes. Patient-derived xenografts (PDX) and patient-derived organoids (PDO) serve as promising tools to identify new drugs with therapeutic potential in PDAC. For these preclinical disease models to be effective, they should both recapitulate the molecular
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Abstract The high failure rate of therapeutics showing promise in mouse models to translate to patients is a pressing challenge in biomedical science. Though retrospective studies have examined the fidelity of mouse models to their respective human conditions, approaches for prospective translation of insights from mouse models to patients remain relatively unexplored. Here, we develop
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Gene signature may allow clinicians to better stratify patients and reduce treatment intensity to lower side effects By analyzing variations in the level of human papillomavirus (HPV) in head and neck cancers, researchers at The University of Texas MD Anderson Cancer Center have discovered a gene signature associated with treatment response and survival in patients.
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Jan 10 2019 In response to current regulatory guidance a Mass Spectrometry (MS) based Host Cell Protein (HCP) detection approach with faster, more accurate and wider-ranging detection is essential. In order to meet the newly prevailing demands Protagen Protein Services (PPS) recently invested in more far-reaching MS capabilities: The new high-performing mass spectrometer ThermoFisher Q
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RESEARCH HIGHLIGHT 10 January 2019 Megan Cully Search for this author in: Credit: Jack Walters/Alamy Stock Photo GABAA (γ-aminobutyric acid, type A) receptors are targeted by numerous small-molecule drugs, many of which were discovered before their target was known. Using single particle cryo-electron microscopy (cryo-EM), the first structure of a GABAA receptor in a physiological
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NMR assignments of the channels at near-native conditions We assigned the 1H, 13C, and 15N ssNMR chemical shifts of WT KcsA and the E71A, E71I, E71Q mutants in order to analyse their conformational dynamics in membranes. First, we prepared uniformly [13C,15N]-labelled inversely Fractionally Deuterated17 channels in liposomes composed of Escherichia coli lipids. Samples were prepared
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Model A non-spontaneous metabolic reaction is catalyzed by one or several enzymes. A given enzyme can be encoded by one or several genes. We regard metabolic pathways and genomic context as networks of reactions and genes, respectively. We represent the relation between metabolic pathways and their encoding genes using a classical model involving two graphs
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