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Hi, There! This week marks a transformational moment for computational biology and precision medicine. We're witnessing the convergence of genomic science and large language models—what researchers are calling the "biological GPT" era. The landmark collaboration between Sheba Medical Center, Mount Sinai, and NVIDIA to decode the previously dismissed 98% of human DNA represents a paradigm shift in how we understand genetic regulation and disease.
🚀 EVENT OF THE WEEK
In a landmark three-year collaboration announced November 18, 2025, Sheba Medical Center, Mount Sinai's Icahn School of Medicine, and NVIDIA are building a Genomic Foundation Model (gFM) to decode the 98% of the human genome previously dismissed as "junk DNA."
Why this matters: This Genomic LLM promises to unlock regulatory logic hidden across vast genomic regions, enabling researchers to understand how genetic variants influence disease susceptibility and drug response.
Key takeaways:
- Genomic foundation models now scale to analyze regulatory regions previously inaccessible to traditional methods
- Clinical partnerships ensure AI models are validated against real patient outcomes
- Open global access could democratize precision medicine worldwide
📚 Top Research Papers
Publisher: Nature Methods | Published: November 28, 2024
Landmark paper introducing Nucleotide Transformer, a series of genomics foundation models for predicting protein structure, function, and genomic features.
Publisher: arXiv | Posted: November 18, 2025
Critical analysis examining whether toxicity prediction has improved, revealing surprising stagnation in this crucial field.
Publisher: National Science Review | Published: March 7, 2025
Comprehensive review examining foundation models across genomics, transcriptomics, proteomics, drug discovery, and single-cell analysis.
Publisher: arXiv | Posted: February 11, 2025
Transformer decoder-based generative model with 98k base pair context for designing novel DNA sequences.
💻 Top GitHub Repos of the Week
⭐ 6,800+ | Official OpenAI
Lightweight framework for multi-agent workflows. Ideal for healthcare coordination between diagnostic imaging AI, drug interaction checkers, and treatment planners.
⭐ 20,000+ | Microsoft Research
Graph-based RAG excels at biomedical knowledge - disease-gene-drug interactions, metabolic pathways, protein networks.
⭐ 8,500+ | EMNLP 2025
Simple and fast RAG ideal for resource-constrained clinical settings and real-time clinical decision support.
⭐ 1,200+ | InstaDeep/BioNTech
Essential genomics AI tool. Pre-trained for genomic analysis, enabling precision medicine research globally.
⭐ 11,000+ | Official Pydantic
Type-safe AI agent framework crucial for medical data handling and EHR integration.
📖 Learning Blog of the Week
The Rise of Genomic Foundation Models: From "Junk DNA" to Precision Medicine
Focus: Computational Genomics | Relevance: Clinical Translation
The convergence of transformer architectures with genomic science is reshaping modern biology. Today's genomic foundation models are learning regulatory logic from unlabeled DNA at scale, transforming how we understand genetic disease.
What computational biologists should understand:
- Foundation models use transfer learning—pre-training on massive data, then fine-tuning for tasks
- These models capture patterns across regulatory regions that traditional approaches miss
- Interpretability remains crucial for clinical applications
- Validation requires connecting predictions to functional experiments and outcomes
🛠️ Top AI Products of the Week
Healthcare Integration | HIPAA Compliant
Make medical databases and clinical tools accessible in ChatGPT & Claude with built-in HIPAA compliance.
Health Research | Longitudinal Data
Continuous sleep, activity, and physiological tracking for research on circadian rhythms and health trends.
Practice Management | Multi-specialty
Integrated appointment scheduling, patient records, and insurance claims for healthcare practices.
Clinical Documentation | HIPAA Compliant
Bot-free transcription for sensitive medical consultations and clinical documentation.
⚠️ AI Criticism & Concerns
OpenAI Downgrades Manipulation Risks
OpenAI no longer classifies mass manipulation as "critical risk." Experts warn this signals competitive pressure overrides safety in healthcare AI applications.
AI Transparency and Bias in Medical Applications
AI systems as "black boxes" are problematic in healthcare. AI can amplify training data biases, leading to dangerous clinical outcomes. Clinicians need understanding of AI reasoning.
AI Chatbots Violate Mental Health Ethics
Research shows AI chatbots routinely violate mental health ethics standards. Concerning as people increasingly turn to AI for mental health support.
Closing Note
This week represents a pivotal transition in computational biology. We're moving beyond AI as research tool toward AI as clinical infrastructure. The Genomic LLM collaboration bridges academic development and clinical deployment.
Thank you for reading PythRaSh's AI Newsletter! Share with colleagues interested in AI applications in biology and healthcare.
Have feedback? Reply to this email - I read every response!
See you next week!
Md Rasheduzzaman
Bioinformatics Researcher & AI Educator
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Twitter: "🧬 This week in AI + Biology (Nov 19): Genomic LLM to decode 98% of human DNA by Sheba/Mount Sinai/NVIDIA. AI drugs in clinical trials. Foundation models revolutionizing precision medicine. #AIinBiology #ComputationalGenomics"
LinkedIn: "Exciting AI + healthcare developments this week. Genomic LLM collaboration represents paradigm shift in understanding genetic disease. Combined with AI therapeutics reaching clinical trials—we're witnessing transition from research tools to clinical infrastructure."
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