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Added team members to all projects
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‎src/content/projects/RDF-knowledge-graph-construction.md‎

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**Team Members (4-6 members recommended):**
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| Name | Affiliation | Role / Expertise |
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| ----------------- | --------------------------------------- | ---------------- |
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| Panayiotis Smeros | Swiss Institute of Bioinformatics (SIB) | LLM, RDF, SPARQL |
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| Imane Lboukili | Swiss Institute of Bioinformatics (SIB) | LLM |
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| TBD | - | - |
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| TBD | - | - |
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| Name | Affiliation | Role / Expertise |
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| ------------------------- | ------------------------------------------------ | ---------------- |
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| David/Yu Yuan | European Bioinformatics Institute (Non-BRC) | |
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| Douglas Fils | University of California San Diego (Non-BRC) | |
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| Imane Lboukili | SIB Swiss Institute of Bioinformatics, PDN | LLM |
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| Panayiotis Smeros | Swiss Institute of Bioinformatics (Non-BRC) | LLM, RDF, SPARQL |
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| Senthilnathan Vijayaraja* | European Bioinformatics Institute (Non-BRC) | |
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\*\*Project Summary
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‎src/content/projects/ai-dataset-and-analysis-discovery.md‎

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**Suggested Team Members and Roles [4-6 members]**
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| Name | Affiliation | Role / Expertise |
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| ---------- | ------------- | ----------------------------------- |
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| [Member 1] | [Institution] | AI/ML Engineer - LLM Integration |
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| [Member 2] | [Institution] | Bioinformatician - Domain Knowledge |
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| [Member 3] | [Institution] | Backend Developer - API Integration |
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| [Member 4] | [Institution] | Frontend Developer - User Interface |
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| [Member 5] | [Institution] | Data Scientist - Query Optimization |
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| Name | Affiliation | Role / Expertise |
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| ------------------ | ---------------------------------------- | ----------------------------------- |
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| Anton Nekrutenko | Penn State, BRC Analytics | AI/ML Engineer - LLM Integration |
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| Danielle Callan | Temple University, BRC Analytics | Bioinformatician - Domain Knowledge |
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| Dannon Baker | Johns Hopkins, BRC Analytics | Backend Developer - API Integration |
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| Dave Rogers | Penn State/Clever Canary, BRC Analytics | Frontend Developer - User Interface |
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| Jonathan Livny | Genomic Center for Infectious Disease, NIAID (Non-BRC) | Data Scientist - Query Optimization |
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| Steven Weaver | Temple University, BRC Analytics | Data Scientist - Query Optimization |
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**Project Summary**
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‎src/content/projects/gene-function-prediction.md‎

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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| --------------- | --------------------- | -------------------------------- |
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| Marcus Nguyen | University of Chicago | Model building and data cleaning |
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| Justin Podowski | University of Chicago | Model building and data cleaning |
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| Alex Brace??? | University of Chicago | LLM modeling |
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| James Davis??? | University of Chicago | Model building and data cleaning |
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| Name | Affiliation | Role / Expertise |
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| --------------- | -------------------------------------------- | -------------------------------- |
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| Alex Brace | Argonne National Laboratory, BV-BRC/ANL | LLM modeling |
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| Gary Olsen | UIUC, BV-BRC/ANL | Model building and data cleaning |
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| James Davis | Argonne National Laboratory, BV-BRC | Model building and data cleaning |
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| Justin Padowski | Argonne National Laboratory, BV-BRC/ANL | Model building and data cleaning |
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| Marcus Nguyen | Argonne National Laboratory, BV-BRC | Model building and data cleaning |
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| Raleigh Butler | Argonne National Laboratory, BV-BRC/ANL | Model building and data cleaning |
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| Ross Overbeek | Argonne National Laboratory, BV-BRC/ANL | Model building and data cleaning |
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**Project Summary**
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‎src/content/projects/hiperrag-literature-extraction.md‎

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---
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title: "HiPerRAG for Literature-based Data Extraction on Priority Pathogens"
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description: "Leveraging high-performance retrieval-augmented generation to extract and curate structured biological data for CEPI priority pathogens from scientific literature"
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description: "Leveraging high-performance retrieval-augmented generation to extract and curate structured biological data for priority pathogens from scientific literature"
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tags:
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[
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"HiPerRAG",
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**Team Lead(s):**
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- Name: Ozan
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- Affiliation: Argonne National Laboratory, BV-BRC
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- Email: [To be added]
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- Name: Ozan Gokdemir
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- Affiliation: Argonne National Laboratory, BV-BRC/ANL
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- Email: ogokdemir@anl.gov
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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| ------------------ | --------------------------- | ---------------------------------- |
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| Ozan | Argonne National Laboratory | AI/ML Engineer, Data Curation Lead |
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| Arvind Ramanathan | Argonne National Laboratory | Scientific Advisor |
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| BV-BRC Analysts | - | Data integration and validation |
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| CEPI collaborators | - | Priority Pathogen Data Alignment |
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| Name | Affiliation | Role / Expertise |
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| ----------------- | ------------------------------------------- | ---------------------------------- |
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| Blessy Antony | Virginia Tech (Non-BRC) | Data integration and validation |
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| James McFeeters | CViSB (Non-BRC) | Scientific Advisor |
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| Maliha Aziz | George Washington University (Non-BRC) | Data integration and validation |
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| Ozan Gokdemir | Argonne National Laboratory, BV-BRC/ANL | AI/ML Engineer, Data Curation Lead |
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| Yitian Chen | Scripps Research (Non-BRC) | Priority Pathogen Data Alignment |
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**Project Summary**
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This project leverages HiPerRAG—a high-performance retrieval-augmented generation system optimized for large scientific corpora—to extract and curate structured data for priority pathogens. By targeting key relationship types such as protein–protein interactions (PPIs), host–pathogen interactions, and drug–protein binding data, the project aims to produce curated, machine-readable datasets for integration with BV-BRC knowledgebases.
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**Goals and Objectives**
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- Goal 1: Define target data types relevant to CEPI and BV-BRC (e.g., PPIs, drug-protein interactions)
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- Goal 1: Define target data types relevant to BV-BRC (e.g., PPIs, drug-protein interactions)
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- Goal 2: Deploy HiPerRAG on relevant literature corpora to extract structured relationships
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- Goal 3: Generate curated datasets for 1–2 CEPI priority pathogens (e.g., Nipah, Lassa)
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- Goal 3: Generate curated datasets for 1–2 priority pathogens (e.g., Nipah, Lassa)
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**Approach**
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**Expected Outcomes / Deliverables**
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Curated datasets of structured biological relationships for CEPI priority pathogens, integrated into BV-BRC pipelines.
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Curated datasets of structured biological relationships for priority pathogens, integrated into BV-BRC pipelines.
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**Potential Impact and Next Steps**
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This project demonstrates scalable AI-driven literature mining for infectious disease research. It will enable automated knowledge enrichment and accelerate understanding of pathogen biology, supporting CEPI's 100-day mission and BV-BRC's informatics goals.
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This project demonstrates scalable AI-driven literature mining for infectious disease research. It will enable automated knowledge enrichment and accelerate understanding of pathogen biology, supporting BV-BRC's informatics goals.
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**Technical Support Needed**
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‎src/content/projects/outbreak-surveillance-monitoring.md‎

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**Team Lead(s):**
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- Name: Nicholas Chia
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- Affiliation: ANL
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- Affiliation: Argonne National Laboratory, BV-BRC/ANL
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- Email: chia@ANL.gov
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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| ---- | ----------- | ---------------- |
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| ???? | | |
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| | | |
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| Name | Affiliation | Role / Expertise |
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| ------------------ | ------------------------------------------------ | ---------------- |
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| Alexander Taepper | Swiss Institute of Bioinformatics, PDN | |
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| Natalie Kucher | Galaxy (Non-BRC) | |
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| Nicholas Chia | Argonne National Laboratory, BV-BRC/ANL | |
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| Rachel Poretskey | UIC, BV-BRC | |
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| Sam Halabi | Georgetown University, PDN | |
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| Thomas Grys | Mayo Clinic (Non-BRC) | |
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**Project Summary**
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‎src/content/projects/pubmed-miner.md‎

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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| ---------------- | --------------------------------- | --------------------------- |
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| Indresh Singh | J. Craig Venter Institute, BV-BRC | Software engineering, AI/ML |
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| Shubham Deshmukh | J. Craig Venter Institute, BV-BRC | Software engineering, AI/ML |
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| | | |
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| | | |
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| Name | Affiliation | Role / Expertise |
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| -------------------- | -------------------------------------------- | --------------------------- |
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| Allan Dickerman | University of Virginia, BV-BRC | |
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| Gordon Pusch | Argonne National Laboratory, BV-BRC/ANL | |
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| Hasin Rehana | University of North Dakota (Non-BRC) | |
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| Indresh Singh | J. Craig Venter Institute, BV-BRC | Software engineering, AI/ML |
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| Sayed Asaduzzaman | University of North Dakota (Non-BRC) | |
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| Shubham Deshmukh | Virginia Tech (Non-BRC) | Software engineering, AI/ML |
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**Project Summary**
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‎src/content/projects/rhea-workflow-automation.md‎

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- Name: Chris Grams, Oleksandr Narykov
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- Affiliation: Argonne National Laboratory, BV-BRC
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- Email: [To be added]
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- Email: cgrams@anl.gov, onarykov@anl.gov
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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| ------------------ | --------------------------- | ---------------------------------- |
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| Chris Grams | Argonne National Laboratory | Lead Developer, Galaxy Integration |
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| Oleksandr Narykov | Argonne National Laboratory | Workflow Automation Engineer |
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| Arvind Ramanathan | Argonne National Laboratory | AI Systems Integration Advisor |
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| CEPI collaborators | - | Use-case Alignment and Testing |
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| Name | Affiliation | Role / Expertise |
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| --------------------- | -------------------------------------------- | ---------------------------------- |
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| Arvind Ramanathan | Argonne National Laboratory | AI Systems Integration Advisor |
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| Chris Grams | Argonne National Laboratory, BV-BRC/ANL | Lead Developer, Galaxy Integration |
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| Marius van den Beek | SCI-SCALE, BRC Analytics | Workflow Automation Engineer |
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| Maulik Shukla | Argonne National Laboratory, BV-BRC | Use-case Alignment and Testing |
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| Oleksandr Narykov | Argonne National Laboratory, BV-BRC/ANL | Workflow Automation Engineer |
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**Project Summary**
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‎src/content/projects/storyseq-sequence-narrative.md‎

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**Team Lead(s):**
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- Name: Andrew Warren
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- Affiliation: UVA
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- Affiliation: University of Virginia, BV-BRC
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- Email: asw3xp@virginia.edu
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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| ------------------ | ----------- | -------------------- |
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| Dustin Machi | UVA | AI / Software |
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| Curtis Hendrickson | UAB | Software development |
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| Name | Affiliation | Role / Expertise |
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| ------------------ | -------------------------------------------- | -------------------- |
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| Andrew Warren | University of Virginia, BV-BRC | AI / Software |
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| Curtis Hendrickson | University of Alabama at Birmingham, BV-BRC | Software development |
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| Dustin Machi | University of Virginia, BV-BRC | AI / Software |
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| Jason Williams | Cold Spring Harbor Laboratory, PDN | |
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**Project Summary**
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‎src/content/projects/viral-phylogenetics.md‎

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### Team Name: _virAllSpark_
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### Team Leads
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**Team Lead(s):**
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- David Moi, University of Lausanne [✉️](mailto:david.moi@unil.ch)
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- Dongwook Kim, University of Lausanne [✉️](mailto:dongwook.kim@unil.ch)
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- Name: Dave Moi, Dongwook Kim
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- Affiliation: University of Lausanne / SIB, PDN
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- Email: david.moi@unil.ch, dongwook.kim@unil.ch
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### Team Members
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**Suggested Team Members and Roles [4-6 members]**
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| Name | Affiliation | Expected Role / Expertise |
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| ------------ | ---------------------- | --------------------------------------------------------------------------------------------------------------------------- |
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| David Moi | University of Lausanne | Project leader (model development) / AI, ML, snakemake, HPC, docker, structural biology, phylogenetics |
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| Dongwook Kim | University of Lausanne | Project leader (validation and integration) / Phylogenetics, sequence analysis, protein structures, Protein Language Models |
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| TBD | - | Model development part / AI expert(s) on transformer models, biological language models, sequence embeddings |
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| TBD | - | Validation part / Biology and/or Bioinformatics expert(s) on virology, viral taxonomy, sequence analysis, sequence database |
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| Name | Affiliation | Expected Role / Expertise |
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| ---------------- | -------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ |
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| Alex Partin | Argonne National Laboratory, BV-BRC/ANL | Model development part / AI expert(s) on transformer models, biological language models, sequence embeddings |
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| Christian Zmasek | J. Craig Venter Institute, BV-BRC | Validation part / Biology and/or Bioinformatics expert(s) on virology, viral taxonomy, sequence analysis, sequence database |
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| Dave Moi | University of Lausanne / SIB, PDN | Project leader (model development) / AI, ML, snakemake, HPC, docker, structural biology, phylogenetics |
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| Dongwook Kim | University of Lausanne / SIB, PDN | Project leader (validation and integration) / Phylogenetics, sequence analysis, protein structures, Protein Language Models |
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| Jamie Overbeek | Argonne National Laboratory, BV-BRC/ANL | Model development part / AI expert(s) on transformer models, biological language models, sequence embeddings |
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## Project Summary
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‎src/content/projects/workflow-generation-mcp.md‎

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**Team Lead(s):**
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- Name: Clark Cucinell, Bob Olson
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- Affiliation: Argonne National Lab
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- Name: Clark Cucinell
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- Affiliation: Argonne National Laboratory, BV-BRC
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- Email: cucinell@anl.gov
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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| ------------- | -------------------- | ---------------------------- |
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| Nicole Bowers | Argonne National Lab | Bioinformatician |
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| Bruce Parello | Argonne National Lab | Computer Scientist |
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| Chris Grams | Argonne National Lab | PhD Student Computer Science |
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| Name | Affiliation | Role / Expertise |
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| ------------------ | -------------------------------------------- | ---------------------------- |
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| Chris Escobar | Argonne National Laboratory, BV-BRC/ANL | Computer Scientist |
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| Clark Cucinell | Argonne National Laboratory, BV-BRC | PhD Student Computer Science |
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| David Gelerinter | Argonne National Laboratory, BV-BRC/ANL | Computer Scientist |
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| Dylan Pilz | Scripps Research Institute (Non-BRC) | Bioinformatician |
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| Nicole Bowers | Argonne National Laboratory, BV-BRC/ANL | Bioinformatician |
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| Rebecca Wattam | University of Virginia, BV-BRC | Bioinformatician |
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**Project Summary**
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