Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps. - Mehmet Serkan Apaydin; Amit Pal Singh; Douglas L. Brutlag; Jean-Claude Latombe (ICRA, 2001)

An optimal procedure for gap closing in whole genome shotgun sequencing. - Richard Beigel; Noga Alon; Simon Kasif; Mehmet Serkan Apaydin; Lance Fortnow (RECOMB, 2001)

Stochastic roadmap simulation for the study of ligand-protein interactions. - Mehmet Serkan Apaydin; Carlos Guestrin; Chris Varma; Douglas L. Brutlag; Jean-Claude Latombe (ECCB, 2002)

Using robotics to fold proteins and dock ligands. - Douglas L. Brutlag; Mehmet Serkan Apaydin; Carlos Guestrin; David Hsu; Chris Varma; Amit Pal Singh; Jean-Claude Latombe (ECCB, 2002)

Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. - Mehmet Serkan Apaydin; Douglas L. Brutlag; Carlos Guestrin; David Hsu; Jean-Claude Latombe (RECOMB, 2002)

Stochastic Conformational Roadmaps for Computing Ensemble Properties of Molecular Motion. - Mehmet Serkan Apaydin; Douglas L. Brutlag; Carlos Guestrin; David Hsu; Jean-Claude Latombe (WAFR, 2002)

Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion. - Mehmet Serkan Apaydin; Douglas L. Brutlag; Carlos Guestrin; David Hsu; Jean-Claude Latombe; Chris Varma (J. Comput. Biol., 2003)

Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation. - Tsung-Han Chiang 001; Mehmet Serkan Apaydin; Douglas L. Brutlag; David Hsu; Jean-Claude Latombe (RECOMB, 2006)

Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values. - Tsung-Han Chiang 001; Mehmet Serkan Apaydin; Douglas L. Brutlag; David Hsu; Jean-Claude Latombe (J. Comput. Biol., 2007)

Developing a Scoring Function for NMR Structure-based Assignments using Machine Learning. - Mehmet Çagri Çalpur; Hakan Erdogan; Bülent Çatay; Bruce Randall Donald; Mehmet Serkan Apaydin (ISCIS, 2010)

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments. - Mehmet Serkan Apaydin; Bülent Çatay; Nicholas Patrick; Bruce Randall Donald (Comput. J., 2011)

A Tabu Search Approach for the NMR Protein Structure-Based Assignment Problem. - Gizem Çavuslar; Bülent Çatay; Mehmet Serkan Apaydin (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

An ant colony optimization approach for solving the nuclear magnetic resonance structure based assignment problem. - Jeyhun Aslanov; Bülent Çatay; Mehmet Serkan Apaydin (GECCO (Companion), 2013)

Distinguishing the type of NOE for NMR protein Structure-Based Assignments. - Murodzhon Akhmedov; Bülent Çatay; Mehmet Serkan Apaydin (SIU, 2013)

Incorporating triple resonance experiment data into NVR for NMR protein structure-based assignments. - Seyma Nur Ekren; Mehmet Serkan Apaydin (SIU, 2014)

Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments. - Murodzhon Akhmedov; Bülent Çatay; Mehmet Serkan Apaydin (J. Bioinform. Comput. Biol., 2015)

Progress in Nuclear Vector Replacement for NMR Protein Structure-Based Assignments. - SeymaÇetnIkaya; Seyma Nur Ekren; Mehmet Serkan Apaydin (RAIRO Oper. Res., 2016)

Traffic Speed Prediction with Neural Networks. - Umut Can Çakmak; Mehmet Serkan Apaydin; Bülent Çatay (OR, 2017)

A neural network approach for predicting speeds on road networks. - Umut Can Çakmak; Bülent Çatay; Mehmet Serkan Apaydin (SIU, 2018)

Classification of Turkish and Balkan House Architectures Using Transfer Learning and Deep Learning. - Veli Mustafa Yönder; Emre Ipek; Tarik Çetin; Hasan Burak Çavka; Mehmet Serkan Apaydin; Fehmi Dogan (ICIAP Workshops (2), 2023)