| 2026 | SIGIR | Diagnosing LLM Reranker Behavior Under Fixed Evidence Pools. | Baris Arat, Emre Sefer |
| 2025 | SDM | Anomaly Detection via Graph Contrastive Learning. | Emre Sefer |
| 2023 | ICDM | SGD with Partial Hessian for Deep Recommendation System Optimization. | Gorkem Yencak, Emre Sefer |
| 2016 | RECOMB | Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments. | Emre Sefer, Ziv Bar-Joseph |
| 2015 | ICDE | Convex Risk Minimization to Infer Networks from probabilistic diffusion data at multiple scales. | Emre Sefer, Carl Kingsford |
| 2015 | RECOMB | Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. | Emre Sefer, Geet Duggal, Carl Kingsford |
| 2015 | WABI | Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic Data. | Emre Sefer, Carl Kingsford |
| 2014 | ICDM | Diffusion Archaeology for Diffusion Progression History Reconstruction. | Emre Sefer, Carl Kingsford |
| 2012 | KDD | The missing models: a data-driven approach for learning how networks grow. | Rob Patro, Geet Duggal, Emre Sefer, Hao Wang, Darya Filippova, Carl Kingsford |
| 2012 | WABI | Resolving Spatial Inconsistencies in Chromosome Conformation Data. | Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford |
| 2011 | RECOMB | Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. | Emre Sefer, Carl Kingsford |
| 2011 | WABI | Parsimonious Reconstruction of Network Evolution. | Rob Patro, Emre Sefer, Justin Malin, Guillaume Marais, Saket Navlakha, Carl Kingsford |