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Pre-Conference Workshop: Empowering Your Microbial Research with Expert Tools and Resources: Unlock the Power of NCBI Data 

Opening General Session

• 4–4:10 p.m. | Opening Remarks
  Todd Treangen, Ph.D., Rice University, Program Committee Co-Chair
• 4:10–5 p.m. | Tumor-Infiltrating Bacteria and Their Impact on the Tumor Microenvironment and Therapeutic Response
  Keynote Speaker: Susan Bullman, Ph.D., University of Texas MD Anderson Cancer Center
• 5–5:50 p.m. | Genome Language Modeling for Biological Discovery and Design
  Keynote Speaker: Brian Hie, Ph.D., Standford University

Tribute Presentation

Welcome Reception

Continental Breakfast

Scientific Session I: Epidemiology, From Global to Local Surveillance

Session Moderator(s): Jasna Kovac, Ph.D., Penn State University; Anne Piantadosi, M.D., Ph.D., Emory University School of Medicine

• 8:30–9 a.m. | The Evolutionary Footprints of Microbial Transmission
  Speaker: Samuel Sheppard, Ph.D., University of Oxford
  • 9–9:15 a.m. | Q&A and Discussion
• 9:15–10 a.m. | Oral Abstract Presentations
  • 9:15–9:30 a.m. | Transmission Dynamics of Multi-Drug-Resistant Bacterial Pathogens in Long-Term Care Facilities
    Presenter: Veda Khadka, Ph.D., Broad Institute of MIT and Harvard
  • 9:30–9:45 a.m. | Extinction of MRSA in the Year Following a SSTI Infection
    Presenter: Katrina Hofstetter, Ph.D., Emory University
  • 9:45–10 a.m. | High-resolution Phylogenetic Analysis of United States (US) Measles Outbreaks, 2025-2026
    Presenter: Jason Caravas, Ph.D., Centers for Disease Control and Prevention

Poster Session #1 With Refreshments

An Overview of the NIH Human Virome Program

• 11:30–11:40 a.m. | NIH HVP Program
  Speaker: Liliana Brown, Ph.D., National Institute of Allergy and Infectious Diseases
• 11:40–11:55 a.m. | HVP Coordinating Center and Consortium Activities
  Speaker: Kemi Ifeonu, Ph.D., University of Maryland
• 11:55 a.m.–12:10 p.m. | Viral Characterization Centers
  Speaker: Cesar Arze, Broad Institute
• 12:10–12:25 p.m. | Viral Host Assignment Across the Tree of Life with VHAMSTeR
  Speaker: Susanna Grigson, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory

Lunch Buffet

Sponsored Lunch & Learn Presentation: NGD Infection Prevention

• 1:15–2 p.m. | Models of Antibiotic Resistance Enable the Discovery of Resistance Mechanisms and the Interplay Between Them 
  Speaker: Paul A. Rhodes, Ph.D., CEO and CSO, NGD Infection Prevention

Special Interest Session: Featured Presentations by Travel Award Recipients

Session Moderator(s): Todd Treangen, Ph.D., Rice University; Lee Katz, Ph.D., Centers for Disease Control & Prevention (CDC)

• Disinfection of Hospital Sink Drains Enriches Pseudomonadota and Efflux Pump-Mediated Antibiotic Resistance in Reestablished Biofilms
  Presenter: Kate Bowie, Ph.D., Yale University
• A Comprehensive Genomic Characterization of Neonatal Meningitis Escherichia coli
  Presenter: Julie Lima, Ph.D., University of Georgia
• Effects of Copper Sulfate Treatment on Biofiltration in Saltwater Aquaria
  Presenter: Valeria Lugo-Mesa, M.V., Texas A&M University
• Reference-free Hybrid Metagenomics Enables Estimation of Replication Dynamics in Complex Microbial Communities
  Presenter: Tomer Antman, M.S., Weizmann Institute of Science
• Comparative Genomics Reveal Alternative Diversification Strategies in Global Ocular Chlamydia trachomatis Infections
  Presenter: Olusola Olagoke, Ph.D., University of California San Francisco
• Toward a Tumor Microenvironment Digital Twin: Integrating the Microbiome With Host Transcriptomics Improves Cancer Drug-Response Prediction
  Presenter: Bichar Shrestha Gurung, M.S., University of South Dakota
• Uncovering the Distribution of Sialylation Pathways in Microorganisms through Genomic and Metagenomic Analysis
  Presenter: Edson Alexandre Nascimento-Silva, M.S., Ribeirão Preto Medical School, University of São Paulo

Poster Session #2 With Refreshments

Scientific Session II: Multiomics in the Clinic

Session Moderator(s): Elodie Ghedin, Ph.D., National Institute of Allergy and Infectious Diseases; Emily Snavely, Ph.D., University of Virginia

• 5–5:30 p.m. | Resolving Host Response at Cellular Resolution with Multi-Modal Foundation Models
  Speaker: Robert Sebra, Ph.D., Icahn School of Medicine at Mount Sinai
  • 5:30–5:45 p.m. | Q&A and Discussion
• 5:45–6:30 p.m. | Oral Abstract Presentations
  • 5:45–6 p.m. | Characterizing Rates of Gene Gain and Loss in Highly Prevalent Strains of Staphylococcus aureus
    Presenter: Megan Phillips, Emory University
  • 6–6:15 p.m. | microbialARC: A Genome‑Linked Strain Biorepository Integrating Antimicrobial Phenotype and Clinical Metadata to Power Pathogen Surveillance
    Presenter: Erin Theiller, Children's Hospital of Philadelphia
  • 6:15–6:30 p.m. | Systematic Artifacts Produced by Illumina XLEAP-SBS Sequencing Reagents Impact Variant Calling in Clinically Relevant Genes in HSV Whole Genome Sequencing Assays
    Presenter: Pavitra Roychoudhury, M.S., Ph.D., University of Washington

Continental Breakfast

Scientific Session III: Data Sharing, Visualization & AI

Session Moderator(s): Arjun Prasad, Ph.D., National Institutes of Health (NIH), National Center for Biotechnology Information (NCBI); Julie Dunning Hotopp, Ph.D., Institute for Genome Sciences, University of Maryland

• 8:30–9 a.m. | From Data to Discovery: AI-Powered Analysis in BRC Analytics
  Speaker: Michael Schatz, Ph.D., Johns Hopkins
  • 9–9:15 a.m. | Q&A and Discussion
• 9:15–10 a.m. | Oral Abstract Presentations
  • 9:15–9:30 a.m. | A Machine Learning Framework Reduces the Manual Workload for Systematic Reviews on the Prevalence of Campylobacter and Non-Typhoidal Salmonella along Broiler Chicken Production and Distribution Networks
    Presenter: Chen Xin, M.S., Cornell University
  • 9:30–9:45 a.m. | Benchmarking Genome Language Models for Novel Virus Detection in Wastewater Across Evolutionary Distance
    Presenter: Noga Aharony, Columbia University
  • 9:45–10 a.m. | Olivia: AI Enhanced Primer Design for Multiplex Pathogen Detection
    Presenter: Dongwei Li, M.S., Rice University

Poster Session #3 With Refreshments

Featured Oral Abstracts

• 11:30–11:45 a.m. | Sex-Specific Markers and Wolbachia Endosymbiont Variation in Brugia malayi Tissues
  Presenter: Christopher Holt, Ph.D., University of Maryland
• 11:45 a.m.–12 p.m. | Ring Trial v2.0: The Case for Standardizing Phylogenetic WGS Analysis in U.S. Public Health
  Presenter: Sharvari Narendra, M.S., University of Virginia
• 12–12:15 p.m. | Streamlining Plant and Animal Disease Diagnostics Through a Metagenomics-based Pathogen Identification Service
  Presenter: Janet Lorv, Ph.D., Virginia Tech
• 12:15–12:30 p.m. | Characterizing Resistance Associated Accessory Genes and Source Attribution in Vibrio parahaemolyticus through Pangenome Analysis and Machine Learning 
  Presenter: Padmini Ramachandran, Ph.D., FDA

Lunch Buffet

Sponsored Lunch & Learn Presentation: Illumina

• 1:15–2 p.m. | Microbiology Applications with Next Generation Sequencing
  Speaker(s): Jason Smith, Illumina; Christopher J. Grim, Ph.D., U.S. Food and Drug Administration

Special Interest Session: Graph-Based Analysis of Microbial Genomes

Session Moderator(s): Julie Dunning Hotopp, Ph.D., Institute for Genome Sciences, University of Maryland; Lee Katz, Ph.D., Centers for Disease Control & Prevention (CDC)

• 2–2:15 p.m. | Kente: A Graph-Based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes
  Presenter: Natalie Kokroko, Rice University
• 2:15–2:30 p.m. | StrainGraph: Strain-Level Classification of Complex Microbial Communities Using Long-Read 16S-ITS-23S Operon Sequencing and Pangenomic Variation Graphs
  Presenter: Maria Rus, University of Florida
• 2:30–2:45 p.m. | Leveraging the Spectral Energy of Graph Sheaf Laplacian as a Genome-Architecture-Aware Measure of Microbiome Diversity
  Presenter: Nicolae Sapoval, Rice University
• 2:45–3 p.m. | PolkaPox: Graph-Based Assembly and Analyses of Orthopoxvirus Genomes
  Presenter: Michael Weigand, Centers for Disease Control and Prevention

Special Interest Session: Pathogen Detection in Wastewater/National Wastewater Surveillance System

Session Moderator: Todd Treangen, Ph.D., Rice University

• 3–3:30 p.m. | Pathogen Detection in Wastewater/National Wastewater Surveillance System
  Speaker: Rory Welsh, Centers for Disease Control and Prevention

Poster Session #4 With Refreshments

Scientific Session IV: Microbial Ecology, Systems Biology & the Microbiome

Session Moderator(s): Daria Van Tyne, Ph.D., University of Pittsburgh; Timothy Read, Ph.D., Emory University School of Medicine

• 5–5:30 p.m. | The Genomics of Bacterial Adaptation During Human Infections
  Speaker: Vaughn Cooper, Ph.D., University of Pittsburgh
  • 5:30–5:45 p.m. | Q&A and Discussion
• 5:45–6:30 p.m. | Oral Abstract Presentations
  • 5:45–6 p.m. | Agnostic High-Throughput Sequencing to Perform Bioinformatic Surveillance for the Presence of Human Pathogens Associated with Acute Febrile Illness (AFI) in Sand Flies Collected in the Country of Georgia
    Presenter: Adrian Paskey, Ph.D., Naval Medical Research Command
  • 6–6:15 p.m. | ��ྱ�����DZ�������Բ�” Salmonella From an Outbreak Using Metagenomics and Binning: A Public Health Pathogen Discovery Example from the Undetermined Outbreaks (UnO) Project
    Presenter: Andrew Huang, Ph.D., Centers for Disease Control and Prevention
  • 6:15–6:30 p.m. | Interrogating the Genomic Signatures of Mutation Rate Variability Linked to Candida auris Drug Resistance
    Presenter: David Firer, M.S., Brown University

Continental Breakfast

Sponsored Breakfast Symposium: ATCC

• 8:15–9 a.m. | From Materials to Models: Building Community Benchmarks and Standards for Sequencing-Based AMR Prediction 
  Speaker: Jonathan Jacobs, Ph.D., Senior Director of Bioinformatics, ATCC

Scientific Session V: Methods, Tools & Algorithms

Session Moderator(s): Laura Carroll, Ph.D., Umeå University; Todd Treangen, Ph.D., Rice University

• 9–9:30 a.m. | Computational Challenges in Population-Scale Microbial Genomics
  Speaker: Christina Boucher, Ph.D., University of Florida
  • 9:30–9:45 a.m. | Q&A and Discussion
• 9:45–10:15 a.m. | Oral Abstract Presentations
  • 9:45–10 a.m. | MetaOmpA (Metagenomic OmpA-typer): Direct ompA Genotyping of Chlamydia trachomatis From Metagenomic Reads Using Discriminatory k-mers
    Presenter: Parul Sharma, Emory University
  • 10–10:15 a.m. | Developing a New Bioinformatic Pipeline for Long-Read Low Biomass Microbial Sequencing Data
    Presenter: Juliette Kudrick, Oregon Health & Science University

Morning Break

NCBI Scientific Session

• 10:30–10:45 a.m. | What’s New for Pathogens and Prokaryotic Genomes at NCBI?
  Speaker: William Klimke, Ph.D., Product Owner for Pathogen Detection and Prokaryotic Genome Annotation Pipeline (PGAP) at NCBI
• 10:45–11 a.m. | Transforming an Archive into a Modern, Sustainable, Petabyte Scale Biomedical Data Sharing Platform 
  Speaker: J. Rodney Brister, Ph.D., Acting Program Head for the Sequence Read Archive (SRA) at NCBI

�������� Health: From Innovation to Impact in Infectious Diseases

Session Moderator: �������� Health Unit

• 11–11:10 a.m. | �������� Health: Advancing the Future of Infectious Disease Management through MultiOmics
  Speaker: Stefano Bertuzzi, Ph.D. CEO, ��������
• 11:10–11:25 a.m. | When Tests Don't Fit the Rules: Regulatory Challenges for Agnostic mNGS Diagnostics in Infectious Diseases
  Speaker: Dev Mittar, Ph.D., Scientific Director, �������� Health Unit
• 11:25–11:40 a.m. | Panel Discussion: From Innovation to Impact in Infectious Diseases
  Speaker(s): Colleen Kraft, M.D., �������� Health Chair; Randall Hayden, M.D., �������� Health Scientific Advisory Council Member; Amy Mathers, M.D., �������� Health Scientific Advisory Council Member 

Meeting Wrap-Up

Julie Dunning Hotopp, Ph.D., Institute for Genome Sciences, University of Maryland
Program Committee Co-Chair