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Hélène Perrin

CircRNAs in human and mouse tissues

Leng Han and Chunjiang He are the creators of the tissue-specific circular RNA (circRNA) database TSCD. They performed the first global analysis of tissue-specific circRNAs and collected these data in a comprehensive database. Here, they talk about their work and how the TSCD database can help researchers explore their RNA sequencing data. A repository of more than 300,000 tissue-specific RNAs With circRNAs attracting more attention in transcriptome research, we explored the global features of tissue-specific circRNAs in embryo development and organ differentiation. To identify tissue specific circRNAs, 3 algorithms, CIRI, circRNA_finder and find_circ, were applied to RNA-seq data collected from the ENCODE project and the NCBI GEO database.   Based on the major types of circRNA, we identified more than 300,000 tissue-specific circRNAs in different tissues. Our …

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Best bioinformatics software for circos plot generation

With the growing amount of biological data generated, innovative bioinformatics tools have been developed for modelling and synthetizing complex information in comprehensive figures. Several infographics types are now available for an informative and clear representation and analysis of your data, and which differ depending on the specific domain and question you are studying. So how do you choose the best tools to efficiently explore your data and illustrate your scientific findings? To help you answer this key question, we have initiated a series of surveys with users on the main categories of data visualization tools among those which are most used by the OMICtools community. The first of our survey series concerns the Circos plot generation tools. Using Circos plots Circos plots allow …

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6 ways biorepositories support clinical research

Biorepositories help research institutions by providing tissue samples for clinical studies. Human tissue samples play a critical role in disease research by enabling assessments of molecular expression, prediction of toxicity, and identification of biomarkers. They help clarify and expand field-of-use claims, selection of appropriate species for preclinical studies and they assist in the clinical trial stages of drug development. Below is a list of key areas where availability of tissues (both from humans and preclinical species) can support pharmaceutical and other research. Assessment of Molecular Expression Biobanks contain vast libraries of human tissue samples, allowing for the assessment of expression levels of biological target molecules such as proteins and RNA. Methods include immunohistochemistry, in situ hybridization, western blotting, PCR and tissue microarrays, all …

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Evaluating the functional impact of genetic variants with COPE software

Dr Ge Gao, developer of the COPE-PCG software tool, talks here about his tool and how it can assist researchers to analyze sequencing data. COPE: A new framework of context-oriented prediction for variant effects Evaluating functional impacts of genetic variants is a key step in genomic studies. Whilst most popular variant annotation tools take a variant-centric strategy and assess the functional consequence of each variant independently, multiple variants in the same gene may interfere with each other and have different effects in combination than individually (e.g., a frameshift caused by an indel can be “rescued” by another downstream variant). The COPE framework, Context-Oriented Predictor for variant Effect, was developed to accurately annotate multiple co-occurring variants. This new gene-centric annotation tool …

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Evaluating biomedical data production with text mining

Estimating biomedical data Evaluating the impact of a scientific study is a difficult and controversial task. Recognition of the value of a biomedical study is widely measured by traditional bibliographic metrics such as the number of citations of the paper and the impact factor of the journal. However a more relevant critical success criteria for a research study likely lies in the production itself of biological data, both in terms of quality and also how these datasets can be reused to validate (or reject!) hypotheses and support new research projects. Although biological data can be deposited in specific repositories such as the GEO database, ImmPort, ENA, etc., most data are primarily disseminated in articles within the text, figures and tables. This raises the …

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Best CRISPR/Cas9 software tools

The development of CRISPR-Cas9 systems has revolutionized genome engineering in living organisms. This novel technology opens up a new era in genomics, along with a wide range of applications. Several bioinformatics tools have recently been developed for researchers designing CRISPR/Cas9 experiments, and analyzing and evaluating CRISPR/Cas9 genome editing.   A few weeks ago, we asked OMICtools members to choose their top 3 CRISPR/Cas9 favorite tools among those most used by the scientific community. Here are the results of your votes.    First position for CRISPR-GA, CROP-IT and CRISPRTarget tools   Three web applications came out equally on top – each voted as a number #1 tool by 45% of the users surveryed: CRISPR-GA (CRISPR Genome Analyzer), CROP-IT (CRISPR/Cas9 Off-target Prediction and Identification Tool) and …

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Analyzing population genomics using ENDOG software

Dr. Juan Pablo Gutiérrez, developer of the ENDOG software, talks here about his tool and how you can use it to perform various demographic and genealogical analyses of genomics data. ENDOG: one of the most popular softwares for genealogical analysis The program ENDOG has become one of the most popular software tools  for genealogical analyses. It includes not only computation of classical parameters in population genetics but also new parameters based on computation of individual increase of inbreeding or co-ancestry. Inbreeding per Generation submenu screen ENDOG allows you to conduct several demographic and genetic analyses including: Individual inbreeding and average relatedness coefficients Effective population size Parameters characterizing the concentration of both gene and individuals origin, such as the effective number of founders and …

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How to visualize biological data using R

Data visualization is one of the key steps of any data science related process. There are hundreds of possibilities available when it comes to visualizing data, and choosing and using the right one are determining factors in accurately getting your message across. R programming language is one of the most common tools used for this process. Data visualization and R R is fabulous for creating charts. It allows you to create all types of visualizations and lots of libraries are developed to help users scan them quicker. However, it can sometimes be challenging – and extremely frustrating – to look for the right code to compute a desired plot. The R Graph Gallery by its creator, Yan Holtz The R graph …

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