Bioinformatics

Lots of these tools exist actually! A popular alternative is enrichR (https://github.com/wjawaid/enrichR) however it is a bit more restrictive in how background population is determined which can skew p-value corrections. Regarding bypassing the Broad login requirement, one can do so through this super helpful R wrapper (https://github.com/oganm/MSigDB)!
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Synthesis of IgG using the standard PURE system All experiments in this paper used the commercially-available PUREfrex® 2.0 kit as the standard PURE system. The well-known anti-HER2 antibody trastuzumab19 was selected as a model IgG for the optimization of synthesis conditions. Since the PURE system does not contain nuclease activity, linear (e.g., PCR product) or
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Transcriptomic analysis We identified 1,817 signature genes with significant differences in expression (p < 0.015 in t-test) between the 10 DHF patients and 8 normal controls from the GSE18090 dataset. A heat map of the expression data is shown in Supplementary Fig. S1. We also identified 1,809 and 1,018 signature genes with significant differences in expression between DHF
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1. Garellick, G., Kärrholm, J., Rogmark, C. & Herberts, P. Swedish Hip Arthroplasty Register: Annual Report, 2008. Department of Orthopaedics, Sahlgrenska University Hospital (2009). 2. Streit, M. R. et al. Long-term (20-to 25-year) results of an uncemented tapered titanium femoral component and factors affecting survivorship. Clin Orthop Relat Res 471, 3262–3269, https://doi.org/10.1007/s11999-013-3033-4 (2013). 3. Taylor,
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In the best case, the performance of single machines can be doubled in every 1.5 years with respect to Moore’s law. Moreover, a two times faster machine is four times more expensive while distributed systems cost to performance ratio is almost constant. For having an unlimited (theoretically) processing power, we need a distributed system that
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The scientific literature is the principal medium for disseminating original research. The public availability of peer-reviewed articles is essential to progress, allowing access to new findings, evaluation of results, reproduction of experiments, and continuous technological improvement. The biomedical community devotes a substantial investment to extracting knowledge and data from publications to facilitate their reuse towards
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Learning times Lowering the characteristic probability of spike transmissions and the characteristic probability of the readout neurons’ responses produces an uneven delay in spatial learning times (Fig. 4A). If the spike transmission probability is high (typically (0.9le hat{p}le 1)), then the small variations of (hat{p}) do not inflict a strong impact on Tmin, i.e., the time
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HSI microscopy Figure 1 shows a diagram of the HSI microscopy used in this study. The tunable bandpass filter and camera were connected to the port of the microscope on the left side, with two adapters in front of and behind the tunable bandpass filter. In the adapter in front of the tunable bandpass filter (Fig. 1
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Dynamics behavior of HLA-DR complexed to Top1 peptide Root-mean-square displacement (RMSD) calculations were performed to monitor the conformational stability in the overall MD simulation, as shown in Fig. 2. RMSD along simulated time was evaluated from the geometrical coordinates of protein backbone (N-Cα-C-O) with respect to those of the initial structure. For HLA-DRs without Top1, RMSDs
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Abstract Infections of stratified epithelia contribute to a large group of common diseases, such as dermatological conditions and sexually transmitted diseases. To investigate how epithelial structure affects infection dynamics, we develop a general ecology-inspired model for stratified epithelia. Our model allows us to simulate infections, explore new hypotheses and estimate parameters that are difficult to
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Hi all, I’m wondering if anyone knows if there is a command line based version (non-graphical output) of this virus genotyping tool from NCBI: https://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi Ideally, just looking to generate the raw output table from any given run (don’t need the graphics). I am processing a large number of viral contigs and want to do
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Posted by: RNA-Seq Blog in Presentations 3 hours ago 69 Views [embedded content] This lecture was recorded at the ITN CONTRA workshop in Warsaw, Poland 2018. CONTRA (Computational ONcology TRaining Alliance) is an European Union funded Innovative Training Network consisting of 8 principal investigators from equally many major European universities as well as partners from
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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 at the 3rd Annual SABPA FTD Forum in San Diego, California, 2 of February. Artificial Intelligence (AI) techniques, such as deep learning (DL) and reinforcement
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Research governance Frozen brains from mice with clinical prion disease were used to generate purified prion samples. These brain samples were generated by us as part of a previous study8 in which work with animals was performed in accordance with licences approved and granted by the UK Home Office (Project Licences 70/6454 and 70/7274) and
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Insight into the de novo transcriptome assembly and sequence annotation Drought tolerance is a multi-pronged mechanism orchestrated by a complex set of gene actions in plants. Its understanding requires a comprehensive approach to explore gene expression and physiological and biochemical pathways. To investigate the dynamic variation of A. sisalana transcriptome to drought conditions, we employed
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With sequencing technologies becoming cheaper and more accessible, genomic sequencing is becoming increasingly widespread. Smaller groups are generating more sequencing data than they can analyze alone. In order to extract maximal scientific and public health value out of these data, sharing of assembled consensus genomes and raw sequence data is critical. The democratization of genomics
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Post-translational modifications (PTMs) refer to the chemical modification of a protein after translation. PTMs play a crucial role in regulating many biological functions, such as protein localization in the cell, protein stabilization, and the regulation of enzymatic activity [1]. Studies have shown that 50–90% of the proteins in the human body undergo PTMs, mainly through
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Abstract Much of the computational power of the mammalian brain arises from its extensive top-down projections. To enable neuron-specific information processing these projections have to be precisely targeted. How such a specific connectivity emerges and what functions it supports is still poorly understood. We addressed these questions in silico in the context of the profound
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Abstract Patterns of trait distribution among competing species can potentially reveal the processes that allow them to coexist. It has been recently proposed that competition may drive the spontaneous emergence of niches comprising clusters of similar species, in contrast with the dominant paradigm of greater-than-chance species differences. However, current clustering theory relies largely on heuristic
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Abstract Infectious disease transmission in animals is an inherently spatial process in which a host’s home location and their social mixing patterns are important, with the mixing of infectious individuals often different to that of susceptible individuals. Although incidence data for humans have traditionally been aggregated into low-resolution data sets, modern representative surveillance systems such
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I am trying to do some work with HLA alleles, and am interested in exploring the IMGT/HLA database. Their data comes in the form of these alignment files (https://github.com/ANHIG/IMGTHLA/blob/Latest/alignments/A_gen.txt) and I can’t find any documentation on what this format is. Is this a standard file format? I could probably make my own tool to parse
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Posted by: RNA-Seq Blog in Clouding Platforms 2 hours ago 80 Views The availability of low-cost small-factor sequencers, such as the Illumina MiSeq, MiniSeq, or iSeq, have paved the way for democratizing genomics sequencing, providing researchers in minority universities with access to the technology that was previously only affordable by institutions with large core facilities.
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Patient specific stem cell-derived motor neurons stained for the neuronal marker III-Tubulin (green) and the ALS-implicated protein TDP-43 (magenta). In this study, the authors determined that TDP-43 sustains normal levels of the microtubule destabilizing protein STMN2, which helps neurons grow and regenerate axons. Credit: Joseph Klim Research led by stem cell scientists at Harvard University
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The Allen Institute for Brain Science, located in Seattle, Washington, has an ambitious, multi-disciplinary effort to reverse engineer complex neural circuits by understanding their diverse cellular parts. A key component of this effort is to define and characterize neural cell types based on shared features. Single nucleus RNA-seq has revolutionized this field by allowing a high-throughput
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Strains, media and growth conditions All Saccharomyces cerevisiae strains used in this study were derived from the wildtype haploid BY4741 (MATa his3∆1 leu2∆0 met15∆0 ura3∆0) strain as previously described5,7. All experiments were conducted in acidic YPD media as originally described5. Normally cells were grown to mid-logarithmic phase (T1; OD660 0.5–0.6) at 30 °C. For heat shock
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Quantification of precursor autoprocessing by amplified luminescent proximity homogeneous assay ELISA (AlphaLISA) We previously established a cell-based assay to study the precursor autoprocessing mechanism inside mammalian cells by expressing fusion precursors with the p6*-PR miniprecursor sandwiched between various fusion tags32,33,34,38,42,43. Domain organization of a typical fusion precursor is illustrated in Fig. 1A. The NL4-3 derived p6*-PR has
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Correction to: BMC Bioinformatics 2018, 19 (Suppl 18): 487. https://doi.org/10.1186/s12859-018-2502-x It was highlighted that the original article [1] contained errors. The list of authors and submissions for the supplement contained some outdated information and could be improved for readability and clarity. Below is the reformatted and corrected list. CAT: computer aided triage improving upon the
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When examining the global trabecular bone changes, we found a significant decrease in Tb.BMD of 38.1% from the 9th to the 10th decade of life. Previous studies report similar changes when measuring the BV/TV which, comparably to Tb.BMD, expresses the bone mineral content in the examined region or sample. Cui et al.12 showed that the
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During the last decade, Genome-Wide Association Studies (GWAS) have greatly advanced our understanding of the impact of common variants on complex traits. The associations of alleles with frequency more than 1–5% have provided important insights into research and clinical practice [1, 2]. Despite GWAS revealing novel disease associations, limited genetic heritability has been explained by
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The inherent heterogeneity of cancers always makes the same cancer patients exhibiting different anticancer drug responses, which is a major difficulty in cancer treatment. It is critical to accurately predict the therapy responses of patients based on their molecular and clinical profiles [1, 2]. With the rapid development of high-throughput technology, a huge number of
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The investigation of DNA polymorphisms is a cornerstone of modern genetics research. Next generation sequencing (NGS) is widely used for the determination of polymorphisms and estimation of their frequency, yet the cost of large-scale DNA sequencing remains prohibitively high. Sample pooling (i.e., mixing DNA samples into pools for library preparation) substantially reduces the costs of
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Could anyone recommend a good algorithms MOOC or book? Even better if it is focused on bioinformatics/computational biology algorithms. I was going to start EdX’s UCSD Algorithm Designs and Techniques, but apparently the course is going to be archived by the end of this month so I was afraid it might not be up-to-date. Thanks.
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Posted by: RNA-Seq Blog in Presentations 2 hours ago 59 Views Next-generation sequencing has evolved into a powerful diagnostic tool helping thousands get answers to the most challenging disease diagnoses. Even with today’s newest equipment, many diagnostic reports may include one or more VUS that are hard to interpret as being potentially pathogenic or uninvolved.
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Posted by: Klemen Hrovat in Publications, User Submitted Posts 2 hours ago 39 Views Huntington’s disease (HD) is characterized by hypomyelination and neuronal loss. To assess the basis for myelin loss in HD, we generated bipotential glial progenitor cells (GPCs) from human embryonic stem cells (hESCs) derived from mutant Huntingtin (mHTT) embryos or normal controls
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Yeast strains and insect cells Saccharomyces cerevisiae strain LJ1450 (MATa ade1-14 trp1-289 his3D-200 ura3-52 leu2-3,112 SUP35::loxP p[SUP35-URA3][PSI+]) was used for shuffling experiments and phenotypic assays. LJ14-derived strains made in this study for yeast phenotypic experiments are listed in Supplementary Table 2. Standard rich (YPD) and Synthetic Dropout (SD) Media were used to culture yeast cells at
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1. Fuster, J. M. & Alexander, G. E. Neuron activity related to short-term memory. Science 173, 652–654 (1971). 2. Wang, X. J. Synaptic reverberation underlying mnemonic persistent activity. Trends Neurosci. 24, 455–463 (2001). 3. Goldman, M. S. Memory without feedback in a neural network. Neuron 61, 621–634 (2009). 4. Druckmann, S. & Chklovskii, D. B.
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Abstract In the field of assisted reproductive techniques (ART), computer-assisted sperm analysis (CASA) systems have proved their utility and potential for assessing sperm quality, improving the prediction of the fertility potential of a seminal dose. Although most laboratories and scientific centers use commercial systems, in the recent years certain free and open-source alternatives have emerged
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Posted by: RNA-Seq Blog in Webinars 4 hours ago 105 Views 28 Feb 2019 at 11:00 (GMT -06:00) Jonathan Göke – Senior Research Scientist (PI) Genome Institute of Singapore (A*STAR) The ability of RNA-sequencing to generate a high-dimensional, quantitative readout of cells and tissues has made it arguably the most successful functional genomics assay in
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