Simit Patel

#Spatialmultiomics is the next big thing but are you unsure of the hype, why you’d do it and how? Read our blog on the topic! https://lnkd.in/e3eDTsxt #spatialtranscriptomics #spatialproteomics #spatiallipidomics #spatialglycomics #massspectrometryimaging #histology #ai4smox

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🔬 **EUROTOX Congress 2024 Highlight: Ontology-driven and AI-based Repeated Dose Toxicity Testing Panel** 🔬 We were excited to attend the panel, chaired by Nynke Kramer. A presentation from Susana Proença from ESQlabs GmbH focused on the critical role of 👩‍🔬 Biokinetic Frameworks for Hazard Characterization. Biokinetics is essential in risk assessment, particularly in **Next Generation Risk Assessment (NGRA)**, as it highlights systemic availability, organ-specific accumulation, and the effects of exposure in both **general** and **special populations**. The ONTOX project is refining **in silico biokinetic models**, including **Physiologically-Based Kinetic (PBK) models**, to enhance the prediction of internal chemical concentrations after external exposures. Susana’s presentation emphasized the use of **open-source software (PK-Sim® and MoBi®)** for simulating PBK models, along with strategies for incorporating **Quantitative Structure-Activity Relationships (QSARs)** and chemical databases into these models. A key focus was on addressing **uncertainties** in tissue-specific responses and chemical classes, which is crucial for improving the **accuracy and reliability** of the models. By incorporating **uncertainty quantification** and adversity-specific considerations, this approach strengthens hazard characterization and supports better decision-making in chemical safety and regulatory processes. Thank you to Susana and her ONTOX team for showcasing innovative approaches to biokinetics and toxicology! 👏 Read more here: 👉 https://lnkd.in/edkypBbB #EUROTOX2024 #ONTOX #Toxicology #PBKModels #NGRA #ChemicalSafety #Biokinetics #3Rs #AI #NAMs

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Our Technical Genomics team has extensive experience working and innovating with #longread sequencing. In this article, discover how they're working with researchers to generate long and ultra-long reads. https://okt.to/wNZVfU #genomics #sequencing #longreads #DNAreplication

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The next generation of #WikiPathways is here! 🌐 The open-source #biologicalpathway database has undergone major restructuring, improving stability and paving the way for the future of community pathway curation. A big step forward for biological pathway research! Quick Read: https://lnkd.in/gkF3vG-N #Bioinformatics #BiologicalPathways #Database #ScienceNews

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The next generation of #WikiPathways is here! 🌐 The open-source #biologicalpathway database has undergone major restructuring, improving stability and paving the way for the future of community pathway curation. A big step forward for biological pathway research! Quick Read: https://lnkd.in/gkF3vG-N #Bioinformatics #BiologicalPathways #Database #ScienceNews #biotechnology

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Ah, the good old times when we did #CRISPR screens without knowing that CNVs would be such an issue! Luckily, you can now read this nice comparison between the most recent 8 computational tools that correct for biases and pick the one that works best for you. https://lnkd.in/eBtKrVYT

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With the right data, you can make the right decisions. With RightsLink for Scientific Communications, publishers like American Society for Microbiology have the dashboards and reports they need to move their Open Access business forward. Thanks to David Haber for joining us in celebrating 10 years of OA innovation! #RLSC10 #OpenAccess #ScholarlyPublishing

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Stereo-seq Excels in Spatial Transcriptomics Benchmarking Study 📊 🧬   A study in Nature Methods has systematically benchmarked 11 spatial transcriptomics platforms and set evaluation standards, highlighting Stereo-seq’s superior performance.   Learn more about how our complete spatial transcriptomics solutions with Stereo-seq and DNBSEQ technology can achieve true single-cell resolution. >> https://lnkd.in/e9p-e_h7 Read the Nature Methods publication in full here >> https://lnkd.in/gYcfk9z2   #SpatialTranscriptomics #Genomics #Benchmarking #StereoSeq #DNBSEQ

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DEADLINE EXTENDED to June 30 📣 You can still submit your paper on biobank-scale genomic #data analyses to the GSA Journals—#GENETICS or #G3Journal—for launch in early 2025. While the #biobank model, which has revolutionized human genomics research, is becoming the new standard for data collection, substantial heterogeneity that subsists between biobanks across the world creates both new challenges and opportunities for data analysis. This series will highlight theoretical, analytical, and computational advances addressing these challenges and leveraging these opportunities. Get details on the high-quality papers our Series Editors are looking for, how to submit, and more: https://buff.ly/49U2tDY

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Another glimpse in the rearview mirror ✨ In this book chapter from 2018, Nets-within-nets encounter synthetic biology, trying to answer the more general question - how can computational tools can support the top-down design of biological systems? 🖇 https://lnkd.in/dpqE9fMW ✏ Bardini, R., Politano, G., Benso, A., & Di Carlo, S. (2018). 𝑪𝒐𝒎𝒑𝒖𝒕𝒂𝒕𝒊𝒐𝒏𝒂𝒍 𝒕𝒐𝒐𝒍𝒔 𝒇𝒐𝒓 𝒂𝒑𝒑𝒍𝒚𝒊𝒏𝒈 𝒎𝒖𝒍𝒕𝒊-𝒍𝒆𝒗𝒆𝒍 𝒎𝒐𝒅𝒆𝒍𝒔 𝒕𝒐 𝒔𝒚𝒏𝒕𝒉𝒆𝒕𝒊𝒄 𝒃𝒊𝒐𝒍𝒐𝒈𝒚. Synthetic Biology: Omics Tools and Their Applications, 95-112. #ComputationalBiology #Bioinformatics #SystemsBiology #MultiLevelModeling #SyntheticBiologyTools #BiologicalDesign #Omics #GeneticEngineering #Biotech #Research #ScienceInnovation #TopDownDesign #BiologicalSystems #ComputationalTools

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"The Journal of Trial & Error": a tome to highlight “ugly side of science — the parts of the process that have gone wrong”. In my #PhD days whilst seeking solace in the pub, I sardonically suggested a "Journal of Negative Results" would have been a useful journal to publish in! Not quite my thought exactly this but, in this age of huge data generation, much unpublished, with #AI/#ML tools to interrogate, this could be an invaluable resource for progressing #science efficiently & effectively enabling time to be devoted to new innovation rather than unnecessary repetition. "Illuminating ‘the ugly side of science’: fresh incentives for reporting negative results New data repositories and alternative journals and workshops offer routes for sharing negative results — which could help to solve the reproducibility crisis and give machine learning a boost." In Nature Careers https://lnkd.in/e4vBMPVW

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𝗣𝗿𝗲𝗱𝗶𝗰𝘁𝗶𝗻𝗴 #𝗰𝗮𝗻𝗰𝗲𝗿 𝗿𝗶𝘀𝗸𝘀 𝗼𝗻 𝘁𝗵𝗲 𝗯𝗮𝘀𝗶𝘀 𝗼𝗳 𝗻𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗵𝗲𝗮𝗹𝘁𝗵 #𝗱𝗮𝘁𝗮: Scientists from the German cancer Research Center (DKFZ) and the European Bioinformatics Institute EMBL-EBI, Hinxton, UK, are using the Danish health registers to predict individual risks for 20 different types of cancer with a high degree of accuracy. The prediction model can also be transferred to other healthcare systems. It could help to identify people with a high risk of cancer, for whom individualized early detection programs could be tested in studies. If cancers are detected early, the chances of cure are generally higher and patients require less intensive treatment. However, screening programs for the early detection of cancer only exist for a few tumor diseases - and not all people take advantage of these offers. 𝗜𝗳 𝗰𝗮𝗻𝗰𝗲𝗿𝘀 𝗮𝗿𝗲 𝗱𝗲𝘁𝗲𝗰𝘁𝗲𝗱 𝗲𝗮𝗿𝗹𝘆, 𝘁𝗵𝗲 𝗰𝗵𝗮𝗻𝗰𝗲𝘀 𝗼𝗳 𝗰𝘂𝗿𝗲 𝗮𝗿𝗲 𝗴𝗲𝗻𝗲𝗿𝗮𝗹𝗹𝘆 𝗵𝗶𝗴𝗵𝗲𝗿: https://lnkd.in/erGYstF4 DKFZ Deutsches Krebsforschungszentrum, European Bioinformatics Institute | EMBL-EBI, Alex Jung, Peter Christoffer Holm, Kumar Gaurav, Jessica Hjaltelin, Davide Placido, Laust Mortensen, Ewan Birney, Søren Brunak, Moritz Gerstung

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🔬 Exciting discussions at the Systems Biology & Multiomics session! Exploring how integrated multiomics approaches are unlocking new insights into complex biological systems to understand health, disease and everything in between! 🧬🧫 Katri Vaparanta Yaara Oren Xin Lai #SystemsBiology #NCBweek2024 #Finland

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New Blog Alert: "How Can Statistical Methods Reduce Inequalities in Genomics?" 🔍 Our latest entry in the #DSxHE Blog series dives deep into the pivotal role of statistical methods in bridging the gap in genomics research. Discover how innovative statistical techniques are being leveraged to address and reduce inequalities, ensuring fairer health outcomes for all. A must-read for anyone passionate about data science and health equity!! #Genomics #HealthEquity #DataScience #DSxHEBlog https://lnkd.in/gic34icd

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The road to #FP10 is long, but it's time to start raising top issues to solve. I personally stand behind EMBL position on widening shared by Plamena Markova. My own experience working with partners in Central and Eastern Europe leads me to believe that FP10 needs to priorities support to up-and-coming research organisations in the region. I strongly believe in the "excellence first" soul of the Framework Programmes, but I also believe that a more equitable Europe needs to take into consideration structural, long term inequalities in accessing top-notch laboratories, facilities and faculties.

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Excited to be at #GCSB2024, the German Conference on Synthetic Biology, with our fantastic project partners from Leipzig University! 🎉 Our rockstar PhD students, Jule Walter and Leonhard Sidl are showcasing our latest research with a poster titled "Design of synthetic riboswitches that modulate mRNA stability." 🧬🔬 In this study we engineer functional RNAs together with RNA aptamers to form ligand-inducible molecular devices that modulate the expression and degradation of #mRNA. Our findings not only advance the field of #SyntheticBiology but also hold potential implications for future #healthcare applications, particularly in developing more precise gene regulation technologies. Find the full poster here: https://lnkd.in/d9DDfsdJ #RNA #RNAStability #HealthcareResearch #Biotechnology #GeneticEngineering #FutureOfHealthcare #ComputationalBiology #Biochemistry #ViennaRNA

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