IMMUNO-model COST ACTION’s Post

We are excited to announce a new publication with a superstar team at MD Anderson Cancer Center lead by the fearless Drs Sammy Ferri Borgogno, Jared K. Burks and Mok Samuel C, who had the audacious goal to fuse Complete Genomics #stereoseq STOmics #spatialtranscriptomics with Bruker MALDI-MSI mass spectrometry #spatialmetabolomics with Lunaphore #COMET #spatialproteomics datasets. Our team at Pathomics.io helped to develop a methodology using a bin50 down sampled #Leidencluster "image" generated from the #spatialtranscriptomics as the common coordinate system to move between the different modalities, using a mix of Visiopharm and #opensource tools such as #QuPath, as well as custom in-house #dataanalytics tools to interrogate this rich #dataresource. Shown here is a figure I like to call “One ring to rule them all” 💍 - how spatial clustering can help to be the key to translate between modalities. We are excited to add these hot new techniques of #spatialtranscriptomics and #spatialmetabolomics to our growing arsenal of #spatialbiology #singlecellmultiomics tools - please reach out if you are encountering challenges in #spatialanalysis of your biological datasets, to see how we can help you achieve similar goals! Paper link here: https://lnkd.in/gK3rRkDK #medtech #multiplex #immunofluorescence #dataintegration #digitalpathology #analytics

Happy to share a new #publication, hot off the presses, on #spatialtranscriptomics analysis! Our team put in an intense amount of effort getting all the pipelines working, but we are thrilled with the results! Thanks to everyone on the Pathomics.io team for their help in putting this together so quickly. #medtech #pathomics #pathologyinformatics #multiomics #COMET #STOmics #MALDIMSI

🥁 “CellCharter is a remarkable tool to identify, characterize and compare cell communities in spatial -omics datasets. It integrates existing approaches and provides a generally applicable, performant method.” Decoding the link between tissue architecture and cell plasticity’ is one of the #SIBRemarkableOutputs 2023 👏This work joins the yearly list of outstanding contributions from SIB Members across Switzerland to the field of #bioinformatics. 👉 Find out more about this and the other outputs: https://lnkd.in/eqseYkeP #spatialcellsniches #spatialtranscriptomics 💡The SIB Remarkable Outputs gather on a shortlist the most outstanding works produced by SIB members each year. These contributions showcase the latest advances in the Swiss bioinformatics field and include innovative solutions to share with the life science community. BioAlps - Swiss Health Valley, ELIXIR, Life Sciences Switzerland (LS2) Luciano Cascione Laurent Falquet Robert Ivánek Charlotte Soneson Patricia Palagi Graf Frederique Lisacek Robert Waterhouse Marco Varrone Giovanni Ciriello Daniele Tavernari Université de Lausanne Oncologie | UNIL-CHUV Ludwig Cancer Research

SOPHiA GENETICS’ VP, Multimodal R&D, Thierry Colin, will share his team's innovative work on multimodal research at ESTIA-Recherche tomorrow in Amphi 21 at ESTIA 2 campus, ESTIA Institute of technology. When a patient is diagnosed with cancer, they undergo numerous medical examinations (biopsy, imaging, biological, genomic analyses) so that doctors can propose a treatment plan. The decision regarding the type of treatment offered is made during a multidisciplinary consultation meeting (MCM) based on recommendations from various health agencies and/or professional societies. 💡 The results of the various medical examinations form a dataset whose richness is only partially exploited. In his presentation, Thierry will show how these data can be used to develop algorithms for personalized prediction of treatment response, focusing on localized kidney cancer and metastatic lung cancer. The talk will go beyond sharing our breakthroughs, and we look forward to sparking conversations. Thierry is eager to dive into discussions with ESTIA students, contributing to SOPHiA GENETICS's mission to nurture the next generation of talent right here in our local communities. #BasqueCountry #DataDrivenMedicine #FutureOfHealthcare

Congratulations to Dr Megan Mitchell Dr Olivier Loudig from the Center for Discovery and Innovation New Jersey, and to their colleagues, for the recent publication Exhaled breath condensate contains extracellular vesicles (EVs) that carry miRNA cargos of lung tissue origin that can be selectively purified and analyzed. This work presents an innovative approach for isolating EVs from exhaled aerosolized droplets and analyzing their content. By capturing the EVs, the scientists could intercept the "instant bio-messages" that cells use to communicate with one another in the lungs. They used several methods to assess the captured EVs, among them ONI's #EVProfiler kit, depicted in the attached image. This enabled them to not only identify the cells that generated the EVs, but also to carefully characterize the RNA molecules inside the EVs, and study them as diagnostic markers for various diseases, among them lung cancer. Read the full paper here: https://hubs.li/Q02vjXhf0 This paper is a fine example for the potential that EVs hold for the future of biomedical research. There is no doubt that EVs will play a major role in diagnostics and therapeutics, and we are very excited to see what new technologies are coming next. ONI scientists will attend #ISEV2024, where they will present our latest development in EV research, #EVProfiler2 with #AutoEV, as well as #AploFlow, our next generation end-to-end solution for EV capture, analysis and reporting. #Nanoimager #SuperResolution #microscopy #research #ExtraCellularVesicles #Biology #Biophysics #SingleMolecule #SMLM #dSTORM #LifeSciences #diagnostics

🔎 🧐 How CAN clinicians apply #GenAI to build #SyntheticData in different hematologic neoplasms? 💡🧠 Let Anders, Iñigo, and company tell you in their paper, as highlighted by GenoMed4All!

“For computational scientists the Hartwig Medical Database is foundational. It means that we can focus on creating the best possible algorithm rather than spending time on gathering, normalizing, and unifying data from various sources. This already happened from the ground up, with re-use in mind. This is the way forward in my opinion”: Jeroen de Ridder, Principal Investigator UMC Utrecht and Oncode Institute Would you like to use this data, too? https://lnkd.in/excwE-kp.  The data is pseudonymized and made available free of charge to cancer research institutes and hospitals. It is used by research groups all over the world. Hartwig Medical Foundation is a not-for-profit organization that promotes scientific research in the fight against and treatment of cancer and other diseases, in the broadest sense and provided it is in the public interest.   #cancerresearch #cancergenomics #bioinformatics 

🔬 IX RSG-Spain Symposium & 1st SEBBiC Congress 🧬 During the past three days, I had the wonderful opportunity to attend the IX RSG-Spain Symposium and the Sociedad Española de Bioinformática y Biología Computacional (SEBiBC) Congress 2024. This events were not just about sharing research—they were about connecting with a vibrant community of scientists and colleagues, gaining insights into the latest advances in bioinformatics and computational biology, and being inspired by the incredible work happening across different domains. It was an enriching experience that reinforced the value of collaboration and continuous learning in our field. 🎤 My Contribution: I presented our work titled PDAConsensus in a Poster Flash Talk. PDAConsensus is a consensus molecular classifier designed for Pancreatic Ductal Adenocarcinoma (PDAC), aimed at integrating multiple existing classification systems to better stratify patients. By leveraging gene expression data and using advanced Machine Learning techniques, we developed a classifier that identifies key tumor and stroma subtypes, offering a nuanced understanding of PDAC biology. 📈 Key Findings: The PDAConsensus classifier achieved impressive accuracy (96.43% for tumor and 98.86% for stroma) and provides valuable prognostic insights. It is now available in the PDACMOC R package and a Shiny app to facilitate the classification of new PDAC cases, ultimately contributing to improved clinical outcomes. Attending these congresses was a fantastic experience, and I am excited to take the ideas and connections made here into future projects. Looking forward to continuing to push the boundaries of cancer research! #SEBiBC2024 #PancreaticCancer #PDAC #MachineLearning #Bioinformatics #ComputationalBiology #CancerResearch #PrecisionMedicine #Collaboration #ContinuousLearning

It's quite common to have a packed schedule in academia, isn't it? And we get it too! That's why we've prepared a #WeeklyDigest of recent posts to help you stay in the loop and make sure you haven't missed out on anything important. 1️⃣ This week, we've unveiled groundbreaking advancements in cancer treatment. Stay tuned for updates on the progress of ten promising drugs fighting solid tumors. These drugs are pushing the boundaries of medical innovation as they make their way toward approval by the FDA and European Medicines Agency. 👉 https://lnkd.in/gWy34f2V 👈 2️⃣ Take a look back at the ACS Nano Summit hosted by City University of Hong Kong. This event is a cornerstone for the global scientific community, focusing on the latest developments in nanotechnology and its applications. Discover who attended this significant gathering. 👉 https://lnkd.in/ge8XvfSD 👈 3️⃣ Explore a revolutionary tool that combines deep learning with histopathology and methylation data. This tool offers rapid tumor classification, bypassing the need for DNA methylation profiling. With an impressive accuracy of 95%, it promises to transform neuro-oncology, enabling swift and precise diagnoses for improved patient outcomes. Curious about this game-changing breakthrough? Don't miss out! 👉 https://lnkd.in/gZ7HDPdq 👈 4️⃣ Join us in celebrating the unity of science and art! Let’s honor 7 prominent polymaths who excelled in both science and the arts. 👉 https://lnkd.in/gzvQuPs9 👈 #StayTuned #theBabakLab

In #cancerresearch, time is of the essence. In this article, discover how Essential Software Inc. supported the National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology to create FORGEdb, a #cloudbasedsoftware that helps scientists import data sets, check variants’ scores, and see which ones are likely to have a significant impact on a disease: https://lnkd.in/efxvt32v #EssentialSoftwareInc #EssentialSolutions #NCI #NationalCancerInstitute #CBIIT #bioinformatics #datascience #datasharing #lifesciences