The event is open to all Penn State students, postdocs, faculty, and research staff involved in or interested in methods development for bioinformatics. We hope to connect folks and provide a platform for the presentation and discussionof work in methods development.
| Session | Time | Speaker | Title |
|---|---|---|---|
| Breakfast | 8:30 - 9:00 | ||
| Session 1 (Chair: Md. Hasin Abrar) | 9:00 - 9:30 | David Koslicki | Sketching 5 million metagenomes reveals uncharacterized diversity & enables global similarity search |
| 9:30 - 9:40 | Aditya Raj | Projection and Correction: A method for Heritability estimation using summary statistics under Reference target LD mismatch | |
| 9:40 - 9:50 | Adrita Hossain Nakshi | Sketching the SRA: experiment-wide similarity search across 4.8 million metagenomes | |
| 9:50 - 10:00 | Andrew Seacord | Ultra-Deep Cohorts for Planetary Scale Evolution | |
| Coffee break | 10:00 - 10:30 | ||
| Session 2 (Chair: Maxwell Konnaris) | 10:30 - 11:00 | Anton Nekrutenko | Agentic AI from standpoint of biologist |
| 11:00 - 11:10 | TQ Smith | PacBio Best Practices | |
| 11:10 - 11:20 | Julien Victor Mutton | DeepINSIGHT: Integrating learned sequence context with evolutionary selection models for non-coding variant interpretation | |
| Panel & Lunch (Chair: Tinghua Chen) | 11:20 - 1:00 | Shaun Mahony, Istvan Albert, Francesca Chiaromonte, Justin Silverman | Embedding AI into the research process: from idea generation to paper publication |
| Session 3 (Chair: Paul Medvedev) | 1:00 - 1:30 | Xiaoxiao Sun | AI-informed Neural Engineering |
| 1:30 - 1:40 | Baizhou Pan | Graph Priors Improve Seizure Onset Zone Identification in a Graph Convolutional Network of StereoEEG | |
| 1:40 - 1:50 | Devanshi Gupta | DAQnuc: Deep Learning-Based Quality Assessment for Nucleic Acid Models from Cryo-EM Density Maps | |
| Coffee break | 1:50 - 2:15 | ||
| Session 4 (Chair: Tinghua Chen) | 2:15 - 2:25 | Salaar Khan | Deep learning strategies for Predicting Regulatory Activity Across Species |
| 2:25 - 2:35 | Michael Callahan | OneShot: Uncertainty-Aware Experimental Selection of AI-generated Biological Designs | |
| 2:35 - 2:45 | Ke Chen | Minimum flow decomposition guided by saturating subflows | |
| Break | 2:45 - 3:00 | ||
| Keynote Talk | 3:00 - 4:00 | Qunhua Li | What Does It Mean to Be Reproducible? From Genomic Discoveries to Spatial Experiments and AI-Assisted Workflows |
This workshop is funded with the generous support of the Huck Institutes for the Life Sciences.