Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication. - Youngchul Kim; Stefan Bekiranov; Jae K. Lee; Taesung Park (Bioinform., 2009)

Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. - Xiaojiang Xu; Stephen Hoang; Marty W. Mayo; Stefan Bekiranov (BMC Bioinform., 2010)

Genome-wide predictors of NF-κB recruitment and transcriptional activity. - Marcin Cieslik; Stefan Bekiranov (BioData Min., 2015)

Analysis of Meta-Learning Approaches for TCGA Pan-cancer Datasets. - Jingyuan Chou; Stefan Bekiranov; Chongzhi Zang; Mengdi Huai; Aidong Zhang (BIBM, 2020)

Implementation of a Hamming distance-like genomic quantum classifier using inner products on ibmqx2 and ibmq_16_melbourne. - Kunal Kathuria; Aakrosh Ratan; Michael McConnell; Stefan Bekiranov (Quantum Mach. Intell., 2020)

Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment. - Hyun Jae Cho; Mia Shu; Stefan Bekiranov; Chongzhi Zang; Aidong Zhang (Bioinform., 2023)

ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq. - Guangzhi Xiong; Stefan Bekiranov; Aidong Zhang (Bioinform., 2023)

DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data. - Guangzhi Xiong; Nathan Leroy; Stefan Bekiranov; Nathan C. Sheffield; Aidong Zhang (Bioinform., 2024)

Improving Scientific Hypothesis Generation with Knowledge Grounded Large Language Models. - Guangzhi Xiong; Eric Xie; Amir Hassan Shariatmadari; Sikun Guo; Stefan Bekiranov; Aidong Zhang (CoRR, 2024)

IdeaBench: Benchmarking Large Language Models for Research Idea Generation. - Sikun Guo; Amir Hassan Shariatmadari; Guangzhi Xiong; Albert Huang; Eric Xie; Stefan Bekiranov; Aidong Zhang (CoRR, 2024)

Toward Reliable Biomedical Hypothesis Generation: Evaluating Truthfulness and Hallucination in Large Language Models. - Guangzhi Xiong; Eric Xie; Corey Williams; Myles Kim; Amir Hassan Shariatmadari; Sikun Guo; Stefan Bekiranov; Aidong Zhang (CoRR, 2025)