Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. - Serdar Bozdag; Timothy J. Close; Stefano Lonardi (WABI, 2008)

A compartmentalized approach to the assembly of physical maps. - Serdar Bozdag; Timothy J. Close; Stefano Lonardi (BMC Bioinform., 2009)

FastMEDUSA: a parallelized tool to infer gene regulatory networks. - Serdar Bozdag; Aiguo Li; Stefan Wuchty; Howard A. Fine (Bioinform., 2010)

GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes. - Aiguo Li; Serdar Bozdag; Yuri Kotliarov; Howard A. Fine (BMC Medical Informatics Decis. Mak., 2010)

Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic levels. - Serdar Bozdag; Aiguo Li; Gregory Riddick; Yuri Kotliarov; Mehmet Baysan; Fabio M. Iwamoto; Margaret C. Cam; Svetlana Kotliarova; Howard A. Fine (BCB, 2013)

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. - Stefano Lonardi; Denisa Duma; Matthew Alpert; Francesca Cordero; Marco Beccuti; Prasanna R. Bhat; Yonghui Wu; Gianfranco Ciardo; Burair Alsaihati; Yaqin Ma; Steve Wanamaker; Josh Resnik; et al. (PLoS Comput. Biol., 2013)

A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map. - Serdar Bozdag; Timothy J. Close; Stefano Lonardi (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

A Canonical Correlation Analysis-Based Dynamic Bayesian Network Prior to Infer Gene Regulatory Networks from Multiple Types of Biological Data. - Brittany A. Baur; Serdar Bozdag (J. Comput. Biol., 2015)

Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. - Duc Do; Serdar Bozdag (PLoS Comput. Biol., 2018)

miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer. - Banabithi Bose; Serdar Bozdag (BCB, 2019)

PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks. - Cagatay Dursun; Naoki Shimoyama; Mary Shimoyama; Michael Schläppi; Serdar Bozdag (BCB, 2019)

GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display. - Karl Stamm; Aoy Tomita-Mitchell; Serdar Bozdag (BMC Bioinform., 2019)

CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer. - Banabithi Bose; Serdar Bozdag (BCB, 2020)

NECo: A node embedding algorithm for multiplex heterogeneous networks. - Cagatay Dursun; Jennifer R. Smith; G. Thomas Hayman; Anne E. Kwitek; Serdar Bozdag (BIBM, 2020)

SUPREME: a cancer subtype prediction methodology integrating multiple biological datatypes using graph convolutional neural networks. - Ziynet Nesibe Kesimoglu; Serdar Bozdag (BCB, 2021)

GWAS analysis to compute genetic markers of progression to Alzheimer's disease. - Yashu Vashishath; Serdar Bozdag (BCB, 2021)

Classification of Autism Spectrum Disorder Using rs-fMRI data and Graph Convolutional Networks. - Tianren Yang; Mai A. Al-Duailij; Serdar Bozdag; Fahad Saeed (IEEE Big Data, 2022)

PhenoGeneRanker: Gene and Phenotype Prioritization Using Multiplex Heterogeneous Networks. - Cagatay Dursun; Anne E. Kwitek; Serdar Bozdag (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

PPAD: a deep learning architecture to predict progression of Alzheimer's disease. - Mohammad Al Olaimat; Jared Martinez; Fahad Saeed; Serdar Bozdag (Bioinform., 2023)

GRAF: Graph Attention-aware Fusion Networks. - Ziynet Nesibe Kesimoglu; Serdar Bozdag (CoRR, 2023)

Pvtad: Alzheimer's Disease Diagnosis Using Pyramid Vision Transformer Applied to White Matter of T1-Weighted Structural Mri Data. - Maryam Akhavan Aghdam; Serdar Bozdag; Fahad Saeed (ISBI, 2024)

TA-RNN: an attention-based time-aware recurrent neural network architecture for electronic health records. - Mohammad Al Olaimat; Serdar Bozdag (Bioinform., 2024)

TA-RNN: an Attention-based Time-aware Recurrent Neural Network Architecture for Electronic Health Records. - Mohammad Al Olaimat; Serdar Bozdag; Alzheimer's Disease Neuroimaging Initiative (CoRR, 2024)

IGCN: Integrative Graph Convolutional Networks for Multi-modal Data. - Cagri Ozdemir; Mohammad Al Olaimat; Yashu Vashishath; Serdar Bozdag; Alzheimer's Disease Neuroimaging Initiative (CoRR, 2024)

Longitudinal Ensemble Integration for sequential classification with multimodal data. - Aviad Susman; Rupak Krishnamurthy; Yan Chak Li; Mohammad Al Olaimat; Serdar Bozdag; Bino A. Varghese; Nasim Sheikh-Bahaei; Gaurav Pandey (CoRR, 2024)

CAAT-EHR: Cross-Attentional Autoregressive Transformer for Multimodal Electronic Health Record Embeddings. - Mohammad Al Olaimat; Serdar Bozdag (CoRR, 2025)

DyGSSM: Multi-view Dynamic Graph Embeddings with State Space Model Gradient Update. - Bizhan Alipour Pijani; Serdar Bozdag (CoRR, 2025)

Machine-learning models for Alzheimer's disease diagnosis using neuroimaging data: survey, reproducibility, and generalizability evaluation. - Maryam Akhavan Aghdam; Serdar Bozdag; Fahad Saeed (Brain Informatics, 2025)