PANORAMICS - A Vision

We’re excited to share that ‘Controversies and Challenges in Dimensional Reduction in Single-Cell Experiments’ is officially back on the calendar! Don’t miss this insightful event—register now using the link or by scanning the QR code: https://lnkd.in/e4ZHYhg9 📅 And that’s not all! Keep an eye out as we unveil our 2025 event lineup in the coming weeks. hashtag #SingleCell #DataAnalysis #ScientificEvents

🚀 Opportunity for Beginner Biologists and Computational Researchers! 🚀 Join us for the Introductory Spatial 'Omics Analysis: Visium HD workshop, part of the Canadian Bioinformatics Workshop Series 2025! 🗓️ Date: February 20-21, 2025 📍 Location: Toronto, Ontario & Online 💡 Free Registration: Apply by January 21 (Meals provided for on-site admissions) 🔬 Course Highlights: Visium HD Sample Preparation: Learn to prepare samples for Visium HD processing. Computational Transformations: Master pre-processing and computational transformations. Clustering Methods: Understand spatial and non-spatial clustering methods. Differential Expression Analysis: Perform differential expression analysis. Image Integration: Integrate images with gene expression datasets. 💡 Why Attend? Gain hands-on experience and valuable insights into Visium HD technology, guided by experts in the field. This workshop is perfect for those looking to build their skills in spatial 'omics analysis and computational biology. 🎓 Funding and Support: Thanks to the Brain Single Cell Initiative and the Canada Brain Research Fund, this workshop is offered free of charge. Priority will be given to brain researchers in Canada. 📅 Apply by January 21 for guaranteed consideration. For registration details, visit our website: https://lnkd.in/e8WwZJwa Don't miss this opportunity to advance your knowledge and network with peers in the bioinformatics community! #Bioinformatics #OmicsAnalysis #ComputationalBiology #VisiumHD #Panoramics #CanadianBioinformaticsWorkshops #BrainResearch #CanadaResearch

As a former researcher in the field of quantitative biology and stem cell biology, I am always keen to see how computational methods can help us better understand stem cells and aging. The research paper in Nature Communications by Hartmut Geiger and colleagues introduces a new tool called #CellDetail, which is designed to analyse the distribution of biomolecules within single cells. This tool is particularly useful for studying how the arrangement of these molecules changes as cells age or in response to diseases. CellDetail uses a concept similar to the dipole moment in physics to calculate the polarity of biomolecules within cells. Polarity refers to the uneven distribution of molecules, which is crucial for many cellular processes. The tool was tested on hematopoietic stem cells (HSCs), which are responsible for producing blood cells. The study found that the organization of certain proteins, like Cdc42 and Tubulin, becomes less polar as these cells age. This loss of polarity is linked to aging and can be reversed by reducing the activity of a protein called Cdc42. The researchers also explored the organisation of a group of proteins called Septins, which help maintain cell structure. They discovered that the Septin network is less organized in aged cells, but this can be restored to a youthful state by targeting Cdc42 activity. The study suggests that changes in the Septin network might be a common feature of aging across different cell types, including human fibroblasts. Overall, the paper highlights the importance of understanding the spatial distribution of biomolecules in cells and provides a new tool to study these changes quantitatively. This research could have implications for understanding aging and developing treatments for age-related diseases.

We are still looking for applicants for a new faculty position! Please share this opportunity with others. 📅Application deadline: December 19. Apply here: https://lnkd.in/eq8wsR9f

Ever wondered who the thought leaders in academic writing are? Discover top-notch academic researchers transforming LinkedIn 👇 Navigating academia can be a daunting journey, especially when it comes to academic writing. But don't worry, I've got you covered! Here are some top LinkedIn accounts you should be following to elevate your academic writing game. For PhD Thesis Writing: → Ali Hindi - Ali M K Hindi 🇵🇸🇮🇶 : Offers insights and tips for structuring your thesis. → Iain Jackson - Iain Jackson: Shares advice on how to communicate complex ideas clearly. → Caroline Dale Caroline Dale: Provides strategies for time management in writing. For Research Papers: → Samira Hosseini - Samira Hosseini: Discusses techniques for impactful writing. → Asad Naveed - Asad Naveed : Focuses on methodological rigor and clarity. → Lennart Nacke - Lennart Nacke : Specialises in storytelling with data. For Using AI in Writing: → Razia Aliani - Razia Aliani : Explores AI tools that can streamline the writing process. → Sowmiya Rani - Sowmiya Rani Ph.D. : Offers guidance on integrating AI insights into research. → Muhammad Irfan - Muhammad Irfan 🧬 : Shares tips on using AI for data analysis. For PhD Scholarships & Jobs: → Banda Khalifa - Banda Khalifa MD, MPH, MBA : Provides updates on available scholarships. → Elena Hoffer - Elena Hoffer, PhD : Shares job opportunities and networking tips. → Rima Dey - Rima Dey Ph.D📘 : Offers advice on crafting effective applications. Following these experts can transform your writing journey. They offer valuable insights that can save you time and enhance the quality of your work. Which other accounts would you add? #AI #academia #phd #postdoc #racwri 🔄 repost to help a friend :) -------------------- If you enjoyed this, then you'd love my exclusive weekly newsletter that teaches you how to secure a tenure-track job and navigate academia as an early career researcher: https://lnkd.in/eNAjgrY9

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Submit your research to the collection, 'Virtual Human Development: Merging Experiments and Theory.' This collection seeks original articles, perspectives, and reviews on experimental and computational models for understanding #EarlyHumanDevelopment. ⬇️ https://lnkd.in/ebVX4t_n

We’re looking for a researcher to help us report on the Biologists @ 100 conference #biologists100 for FocalPlane. If you are interested in getting more experience in scicomm and report on this unique meeting, check out our post and drop us an email: https://lnkd.in/eFf2DCYk

Join us on October 17th and learn how you can help overcome the reproducibility crisis by characterizing antibodies in your own lab.    Dr. Riham Ayoubi, Director of Operations of the YCharOs project will cover: • The YCharOS mission and platform for antibody characterization. • Good practices and experimental conditions for antibody characterization in various immunoassays. • Challenges and limitations. All attendees will receive a certificate of attendance, recording of the event, and an exclusive product promo code. Follow the link below to register for this event! Register here: https://ow.ly/oBpS50TuIBJ

Our Introductory Spatial ‘OMICS Analysis Workshop (ISO2024 - #CBW workshop) is up now for everyone to watch and learn. https://lnkd.in/efq9hadq Though, we used the Xenium as our model machine of choice, our workshop is applicable to other single molecular platforms (I.e Merscope, CosMX) and many of the ideas are also applicable to array-based spatial platforms (I.e Stereo-seq, VisiumHD). 🔲 Module 1 - Garbage-in, garbage-out The focus was on bench-work, the challenges in tissue-prep and the due-diligence required. We had experts sharing real world experience into the art of tissue management and preparation, including a guide to panel design. 🔲 Module 2 - Pre-processing steps Where we took a deeper-dive than usual in understanding transcript quality & distribution and how these have an impact on downstream modelling. 🔲 Module 3 - Building your spatial model In spatial analysis, the beauty lies in capturing the spatial patterns of distributions. Using #Banksy as our method of choice, we challenged our participants to think critically and logically the choices they make when deciding on a spatial model. 🔲 Module 4 - Drawing Boundaries The aim was to encourage participants to understand their images and the nature of tissue structure and to introduce the principles behind segmentation. We compared a publicly available deep-learning image based segmentation output, from 10x, with a transcript guided alternative (#Baysor) 🔲 Module 5/6 - Realizing the spatial potential in your dataset.  We wanted to introduce the fundamental concepts behind statistically evaluating the spatial patterns in your dataset. Our eyes can be mis-leading and seemingly non-random patterns can be truly just random constructions. Touching upon this topic briefly to give a taste to our participants to think beyond the end results of their analysis. ---------------------------------------- 1️⃣ This was alot over two days. If we had intentionally made some modules brief and left out some areas, it was to avoid overwhelming our diverse audience. At the same time, we tried to find a sweet spot in our teaching speed. Therefore, feedback is always welcome. Please leave us a note, email, comment if you found the materials useful and on how we can improve. 2️⃣Github : There are some additional scripts that has been included post-workshop and we will continue to improve on this from time to time. 3️⃣We thank our organizers from the Brain Single Cell Initiative(Princess Margaret Genomics Centre) and Bioinformatics.ca (Canadian Bioinformatics Workshops) who provided this opportunity for Panoramics-A Vision to develop the course content for this workshop. 🔆 We are incredibly proud to share that this was an all-women team of instructors and TAs and we are confident this will only encourage more members from all communities to join us to lead the way in training for a better future. 🔆 Nia Hughes Ashleigh Willis Melanie Peralta Farzaneh Aboualizadeh