Charlie Hatton

Negar Janani, Ph.D., Yaning Liu, Troy Butler, Erin Austin and co-authors publish "A novel application of data-consistent inversion to overcome spurious inference in genome-wide association studies" in the journal "Genetic Epidemiology". DOI: 10.1002/gepi.22563 In this article, the authors, Negar Janani, Ph.D., Kendra Young, Gregory Kinney, MPH PhD, Matt Strand, John E. Hokanson, Yaning Liu, Troy Butler, and Erin Austin, propose an assumption-free model built upon data-consistent inversion (DCI), which is a recently developed measure-theoretic framework utilized for uncertainty quantification. This proposed DCI-derived model builds a nonparametric distribution on model inputs that propagates to the distribution of observed data without the required normality assumption of residuals in the regression model. This characteristic enables the proposed DCI-derived model to cover all genetic variants without emphasizing on additivity of the classic-GWAS model. Through simulations and a replication GWAS with data from the COPDGene, the authors demonstrate the ability of this model to control the Type-I error rate at least as well as the classic-GWAS (additive linear model) approach while having similar or greater power to discover variants in different genetic modes of transmission. Find the article at: https://lnkd.in/g9w8s7Kr

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Good morning everyone! Do you like AI and graph neural networks? (see what i did there? :-) ) Our blog today helps you discover how SpatialGlue, a groundbreaking model published in Nature Methods, leverages graph neural networks and dual-attention mechanisms to integrate spatial and multi-omics data, providing unprecedented insights into tissue architecture and cellular interactions. Read our blog for a summary of how this innovative approach outperforms traditional models, offering precise mapping of complex structures and advancing research in fields like cancer and neurology. #SpatialTranscriptomics #ComputationalBiology #Bioinformatics #AI

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data cleaning and wrangling (the mundane work) are what you need to be good at. My odyssey of obtaining scRNAseq metadata https://lnkd.in/eB-kDGeD

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Thrilled about our upcoming presentation at ECCMID Annual Meeting. Looking forward to connecting in person and explore the latest updates in infectious disease dosing strategies. 🔬 🦠 🧫 💊 Send me a note if you want to meet and discuss how you are incorporating MIPD into your precision dosing initiatives! 💊🩺👩🏼‍⚕️ #ECCMID #precisionmedicine #mipd

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There are now many providers of metadata of scientific papers: details about license, bibtex, retraction status, author list, COI statements. We aggregated five of these into one client with fallbacks in PaperQA2. We use it for adding context to LLM calls, but this could be a great tool for exploring science of reserach papers

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I'm starting a series of posts on the biotechnology industry starting with three primers on small molecule drugs, biologics, and nanotechnology. My goal is for each of these to serve as a jumping off point into further exploration into the field. For these primers, starting with the first on small molecule drugs, I will provide an overview on what they are, a case study on the history of their development, and briefly touch on some of the major modern innovations involved.

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I made a "gene info" custom GPT. Paste in a list of human gene symbols. It'll run some python code against a custom knowledge base to provide information about those genes (from RefSeq). This blog post describes what it does and how I made it.

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An interesting article about a recent presentation to Congress by a key RNA researchers at the University of Michigan. I am reminded that the field of genomics is really multiple fields - genetics, proteomics, epigenomics, and this effort: The Human RNome Project. I am also reminded that the successful covid vaccines were based on mRNA technology & understanding. It's good to see these efforts seeing daylight, and potential support from our government. #UMichRNA #UMichRNATx #UMich #genomics https://lnkd.in/greF5Xh5

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Hot of the press! Preprint of new single cell method for targeted, sequence-specific capture of transcripts. Capture specific transcripts, transcript regions, fusion gene targets, mutations etc. together with whole transcriptome analysis. This method is only available with Rhapsody Single Cell analysis platform from BD. #singlecellanalysis #multiomics #RoCKseq https://lnkd.in/d4RiRWBv

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I've been preaching for a couple of years that Spatial Transcriptomics Segmentation errors are the dominant biased error term in this field, not FDR (that statistic doesn't even have spatial coordinates in the equation). Check out our brand new and enabling image segmentation "transcript purifier", that significantly eliminates transcripts ending up the WRONG cell. Amazing work from two of my brightest scientists! https://lnkd.in/g2RuMYDG

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Curious how AI classifiers can be used to quantify histologic features to avoid inter-observe variability & uncover data that would be missed with manual scoring? Then don't miss #IndicaLabs' next webinar with Eli Lilly's Dr. Kelly Credille!

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Come visit me at the poster session of BioTechX tomorrow in Philly! My poster is called "Identification and Annotation of Publicly Available Single Cell RNA-sequencing Data". Rancho BioSciences #biotechxphilly #biotechx 

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Allogeneic CAR-T is a popular topic of conversation in the cell therapy space, and for good reason! It offers patients an off-the-shelf option for something they would otherwise have to wait weeks for (if they're able to even secure a manufacturing slot at all). Not only does it have the potential to reduce wait times, but allogeneic CAR-T can expand treatment access to more patients. Companies like Allogene Therapeutics are working hard to make this future a reality. I recently had the pleasure of speaking with CEO and co-founder, David Chang, MD, Ph.D., about the opportunities and challenges in the allogeneic CAR-T space. Read more about the company's mission to change the CAR-T treatment paradigm on Cell & Gene! https://lnkd.in/dSr-9N_m

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Next-generation sequencing (NGS) technologies continue to open new frontiers in #biology. This article, written by RJ Mackenzie for Technology Networks, explores how the latest advances in #NGS have helped researchers explore areas of the #genome that were previously dismissed as uninformative. https://lnkd.in/evhVknZ3

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How I (recently) learned to Embrace Expertise 🧑‍🚀 Transitioning from academia to consulting is not obvious—it’s a personal and professional challenge. After more than a decade in behavioral and preclinical neuroscience, working on 🧠 Behavioral experiment design, 📊 Advanced data analysis pipelines, 🐭 Home-cage monitoring systems, 📂 Metadata management practices and 👩‍🏫 Mentoring and training teams, I asked myself: Do I really have what it takes to be an 'expert'? In academia, expertise often feels like a baseline, not an accomplishment... But I allowed myself to realize that my skills and knowledge are valuable assets that can drive better, faster results for researchers and organizations. Consulting, with NeuroNautix, will allow me to stay connected to the science I love while broadening my impact across labs, projects, and industries. Being an expert isn’t about knowing everything—it’s about offering experience and perspective to deliver meaningful solutions. Thank you to everyone who supported and motivated me during this journey! Special shout-out to Stefano Gaburro, PhD, CCC , for his advice and valuable insights in his recent book on "path beyond academia". This is just the beginning of an exciting adventure! #AcademiaToConsulting #BehavioralNeuroscience #PreclinicalResearch #HomeCageMonitoring #ExpertiseHasValue

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🌍 Expanding the RNA Virosphere with AI: A New Frontier in Virus Discovery** Another example of how artificial intelligence is revolutionizing science and medicine. Researchers used a transformer-based AI model, LucaProt, to analyze 10,487 metatranscriptomes, uncovering **161,979 potential RNA virus species** and expanding the known RNA virosphere from 21 to an astounding 180 supergroups. Check out the details here: (https://buff.ly/3VkyShN). Why does this matter? RNA viruses play crucial roles in ecosystems and human health, yet many remain elusive to traditional methods. By integrating AI with sequence and structural data, this study reveals how technology can illuminate "dark matter" in biology, offering new opportunities for diagnostics, therapeutics, and understanding viral evolution. The future of science isn’t just about discovery—it’s about the tools we use to get there. #ArtificialIntelligence #VirusDiscovery #PrecisionMedicine #ScienceInnovation

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It was indeed a great day! Thank you, @Sophia Kambanis, and @Massachusetts Innovation Network, for the fantastic opportunity. @InnoTech Precision Medicine had the honor of presenting as one of the @EDDIES 2024 finalists. InnoTech Precision Medicine is revolutionizing cancer diagnostics with its cutting-edge, multi-omics, non-invasive point-of-care solutions. Our flagship product, Recognize™-OPSCC, enables the early detection of HPV-driven oropharyngeal cancer through a simple saliva test, integrating advanced multi-omics biomarker detection with AI-driven analysis. By providing rapid, accurate results, we empower healthcare providers to make timely treatment decisions, improving patient outcomes and reducing healthcare costs. With a strong focus on accessibility and scalability, InnoTech is transforming the future of diagnostics for early cancer detection. #MassachusettsInnovationNetwork, #Innotechprecisionmedicine, #Eddies2024

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Excited for Professor Melissa Fullwood's lab's presentation at the EMBO Chromatin Biology in Cancer Workshop! If you're attending, come listen to Dr. Seng Chuan Tang's talk in Session 6, April 26th. Dr. Tang will discuss epigenetic therapies and drug resistance, providing insight into the disruption of super-silencers by EZH2 and REST inhibition, altering chromatin interactions, and impeding cancer growth. #CancerResearch

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Today, I published my first open-source Python package, DrSyn! 💊 It's currently in Beta pre-release and ready for public testing. This has been quite the undertaking, especially as a self-taught programmer tackling a project of this magnitude. I'm grateful for my position at Precision Genetics, giving me the opportunity to create this tool, which aims to further the goal of improving healthcare. I'll post the link and description below. I'd love if you tested it out, gave some feedback, or shared your ideas with me! #OpenSource #Python #Healthcare #DrugRecognition #BetaRelease #PrecisionGenetics #ProudMoment --- DrSyn: A Python Package for Drug Name Identification and Standardization --- DrSyn is a powerful Python package designed to identify drug names within medical texts, extract them, and convert them to their common names based on MeSH standards. This tool is essential for standardizing drug names across various textual sources, making it invaluable for both healthcare and research purposes.

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