Thinking Ahead in Real-Time Search. - Dana S. Nau; Ugur Kuter; Emre Sefer (ICAPS, 2009)

Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. - Emre Sefer; Carl Kingsford (RECOMB, 2011)

NetVisia: Heat Map & Matrix Visualization of Dynamic Social Network Statistics & Content. - Robert Gove; Nick Gramsky; Rose Kirby; Emre Sefer; Awalin Sopan; Cody Dunne; Ben Shneiderman; Meirav Taieb-Maimon (SocialCom/PASSAT, 2011)

The missing models: a data-driven approach for learning how networks grow. - Rob Patro; Geet Duggal; Emre Sefer; Hao Wang 024; Darya Filippova; Carl Kingsford (KDD, 2012)

Resolving Spatial Inconsistencies in Chromosome Conformation Data. - Geet Duggal; Rob Patro; Emre Sefer; Hao Wang 024; Darya Filippova; Samir Khuller; Carl Kingsford (WABI, 2012)

Parsimonious reconstruction of network evolution. - Rob Patro; Emre Sefer; Justin Malin; Guillaume Marçais; Saket Navlakha; Carl Kingsford (Algorithms Mol. Biol., 2012)

Resolving spatial inconsistencies in chromosome conformation measurements. - Geet Duggal; Rob Patro; Emre Sefer; Hao Wang 024; Darya Filippova; Samir Khuller; Carl Kingsford (Algorithms Mol. Biol., 2013)

Diffusion Archaeology for Diffusion Progression History Reconstruction. - Emre Sefer; Carl Kingsford (ICDM, 2014)

Convex Risk Minimization to Infer Networks from probabilistic diffusion data at multiple scales. - Emre Sefer; Carl Kingsford (ICDE, 2015)

Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments. - Emre Sefer; Ziv Bar-Joseph (RECOMB, 2016)

Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. - Emre Sefer; Geet Duggal; Carl Kingsford (J. Comput. Biol., 2016)

Diffusion archeology for diffusion progression history reconstruction. - Emre Sefer; Carl Kingsford (Knowl. Inf. Syst., 2016)

Semi-nonparametric modeling of topological domain formation from epigenetic data. - Emre Sefer; Carl Kingsford (Algorithms Mol. Biol., 2019)

Joint Modeling of Histone Modifications in 3D Genome Shape Through Hi-C Interaction Graph. - Emre Sefer (COMPLEX NETWORKS (2), 2020)

Hi-C interaction graph analysis reveals the impact of histone modifications in chromatin shape. - Emre Sefer (Appl. Netw. Sci., 2021)

Asset Price and Direction Prediction via Deep 2D Transformer and Convolutional Neural Networks. - Tuna Tuncer; Uygar Kaya; Emre Sefer; Onur Alacam; Tugcan Hoser (ICAIF, 2022)

A Novel GBT-Based Approach for Cross-Channel Fraud Detection on Real-World Banking Transactions. - Ugur Dolu; Emre Sefer (AIAI (1), 2022)

MOCMIN: convex inferring of modular low-rank contact networks over COVID diffusion data. - Emre Sefer (Turkish J. Electr. Eng. Comput. Sci., 2022)

BioCode: A Data-Driven Procedure to Learn the Growth of Biological Networks. - Emre Sefer (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

A comparison of topologically associating domain callers over mammals at high resolution. - Emre Sefer (BMC Bioinform., 2022)

Optimal Reconstruction of Graph Evolution Dynamics for Duplication-Based Models. - Emre Sefer; Samuel Gilmour (COMPLEX NETWORKS (2), 2023)

NFT Primary Sale Price and Secondary Sale Prediction via Deep Learning. - Betul Seyhan; Emre Sefer (ICAIF, 2023)

SGD with Partial Hessian for Deep Recommendation System Optimization. - Gorkem Yencak; Emre Sefer (ICDM (Workshops), 2023)

BERT2OME: Prediction of 2′-O-Methylation Modifications From RNA Sequence by Transformer Architecture Based on BERT. - Necla Nisa Soylu; Emre Sefer (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Deep Transformer-Based Asset Price and Direction Prediction. - Abdul Haluk Batur Gezici; Emre Sefer (IEEE Access, 2024)

Correction: Hi-C interaction graph analysis reveals the impact of histone modifications in chromatin shape. - Emre Sefer (Appl. Netw. Sci., 2024)

Anomaly Detection via Graph Contrastive Learning. - Emre Sefer (SDM, 2025)

The significance of chromosome conformation capture in 3D genome architecture comprehension. - Selinay Cetin; Emre Sefer (Comput. Biol. Chem., 2025)

DRGAT: Predicting Drug Responses Via Diffusion-Based Graph Attention Network. - Emre Sefer (J. Comput. Biol., 2025)