Novel Approaches to Biomolecular Sequence Indexing. - Emre Karakoç; Z. Meral Özsoyoglu; Süleyman Cenk Sahinalp; Murat Tasan; Xiang Zhang 001 (IEEE Data Eng. Bull., 2004)

Distance based algorithms for small biomolecule classification and structural similarity search. - Emre Karakoç; Artem Cherkasov; Süleyman Cenk Sahinalp (ISMB (Supplement of Bioinformatics), 2006)

RNA Secondary Structure Prediction Via Energy Density Minimization. - Can Alkan; Emre Karakoç; Süleyman Cenk Sahinalp; Peter J. Unrau; H. Alexander Ebhardt; Kaizhong Zhang; Jeremy Buhler (RECOMB, 2006)

RNA-RNA Interaction Prediction and Antisense RNA Target Search. - Can Alkan; Emre Karakoç; Joseph H. Nadeau; Süleyman Cenk Sahinalp; Kaizhong Zhang (J. Comput. Biol., 2006)

Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds. - Emre Karakoç; Süleyman Cenk Sahinalp; Artem Cherkasov (J. Chem. Inf. Model., 2006)

Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. - Emre Karakoç; Süleyman Cenk Sahinalp; Artem Cherkasov (Pacific Symposium on Biocomputing, 2007)

taveRNA: a web suite for RNA algorithms and applications. - Cagri Aksay; Raheleh Salari; Emre Karakoç; Can Alkan; Süleyman Cenk Sahinalp (Nucleic Acids Res., 2007)

Novel approaches for small biomolecule classification and structural similarity search. - Emre Karakoç; Artem Cherkasov; Süleyman Cenk Sahinalp (SIGKDD Explor., 2007)

PICKY: a novel SVD-based NMR spectra peak picking method. - Babak Alipanahi; Xin Gao 001; Emre Karakoç; Logan Donaldson; Ming Li 001 (Bioinform., 2009)

Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation. - Babak Alipanahi; Xin Gao 001; Emre Karakoç; Shuai Cheng Li 001; Frank J. Balbach; Guangyu Feng; Logan Donaldson; Ming Li 001 (J. Bioinform. Comput. Biol., 2011)

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. - Phuong Dao; Ibrahim Numanagic; Yen-Yi Lin; Faraz Hach; Emre Karakoç; Nilgun Donmez; Colin C. Collins; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2014)

Black hole attack prevention scheme using a blockchain-block approach in SDN-enabled WSN. - Emre Karakoç; Celal Çeken (Int. J. Ad Hoc Ubiquitous Comput., 2021)

Blokzincir ve akıllı sözleşmelerkullanılarak yeni bir güvenliktasarımının ıot için uygulanması (Implementing a new security design for iot usingblockchain and smart contracts) - Emre Karakoç (2021)

Secure SLA Management Using Smart Contracts for SDN-Enabled WSN. - Emre Karakoç; Celal Çeken (KSII Trans. Internet Inf. Syst., 2023)

Identification of protein-protein interaction bridges for multiple sclerosis. - Gözde Yazici; Burcu Kurt Vatandaslar; Ilknur Aydin Canturk; Fatmagul I Aydinli; Ozge Arici Duz; Emre Karakoç; Bilal Ersen Kerman; Can Alkan (Bioinform., 2023)