Shotgun sequencing:

1. An optimal procedure for gap closing in whole genome shotgun sequences.

R. Beigel, N. Alon, M.S. Apaydin, L. Fortnow and S. Kasif.

The Fifth Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2001.

Roadmaps for Molecular motion:

1. Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics: folding rates and phi-values.

TH Chiang, M.S. Apaydin, DL Brutlag, D Hsu, JC Latombe.

J Comput Biol. 2007 Jun;14(5):578-93.

2. Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation (pdf)

T. H. Chiang, M.S. Apaydin, D. L. Brutlag, D. Hsu, and J.-C. Latombe

The Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2006.

3. Stochastic Roadmap Simulation: An efficient Representation and Algorithm for Analyzing Molecular Motion.

Ph.D. thesis, Stanford University, August 2004

4. Stochastic Roadmap Simulation: An efficient Representation and Algorithm for Analyzing Molecular Motion

M. S. Apaydin, D. L. Brutlag, C. Guestrin, D. Hsu, J.-C. Latombe and C. Varma

Journal of Computational Biology 2003, 10 (3-4):257-281.

5. Stochastic Conformational Roadmaps for Computing Ensemble Properties of Molecular Motion.

M. S. Apaydin, D. L. Brutlag, C. Guestrin, D. Hsu and J.-C. Latombe.

Fifth International Workshop on Algorithmic Foundations of Robotics (WAFR), Dec. 2002, Nice, France.

6. Studying Protein-Ligand Interactions with Stochastic Roadmap Simulation

M.S. Apaydin, C. Guestrin, C. Varma, D.L. Brutlag, and J.-C. Latombe.

Proc. European Conf. on Computational Biology (ECCB), Oct. 2002, Saarbruecken, Germany.

7. Using robotics to fold proteins and dock ligands

D. L. Brutlag, M.S. Apaydin, C. Guestrin, D. Hsu, C. Varma, A. Singh and J.-C. Latombe

Proc. European Conf. on Computational Biology (ECCB), Oct. 2002, Saarbruecken, Germany.

8. Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion.

M.S. Apaydin, D.L. Brutlag, C. Guestrin, D. Hsu. and J.-C. Latombe.

RECOMB 2002.

9. Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps.

M.S. Apaydin, A. P. Singh, D. L. Brutlag, and J.-C. Latombe.

International Conference on Robotics and Automation (ICRA), 2001.

NMR Structure-Based Assignments:

1. Incorporating HADAMAC experiment into NVR for NMR Structure-Based Assignments

H. Erdogan and M. S. Apaydin

6th International Symposium on Health Informatics and Bioinformatics (HIBIT 2011), USA: IEEE (Institute of Electrical and Electronics Engineers) (forthcoming).

2. Developing a scoring function for NMR structure-based assignments using machine learning

MC Calpur and H. Erdogan and B. Catay and B. R. Donald and M. S. Apaydin

25th international symposium on computer and information sciences (ISCIS 2010), London: Oxford University Press.

3. Using amino acid typing to improve the accuracy of NMR structure based assignments

H. Erdogan and M. S. Apaydin

5th International Symposium on Health Informatics and Bioinformatics (HIBIT 2010), USA: IEEE (Institute of Electrical and Electronics Engineers), April 2010, 206-210

4. NVR-BIP: nuclear vector replacement using binary integer programming for NMR structure-based assignments.

M. S. Apaydin and B. Catay and N. Patrick and B. R. Donald

The Computer Journal, Advance Access doi:10.1093/comjnl/bxp120.

An earlier version appeared in the 24th International Symposium on Computer and Information Sciences (ISCIS09), USA: IEEE (Institute of Electrical and Electronics Engineers), September 2009, 177-182

5. Structure-Based Protein NMR Assignments using Native Structural Ensembles

M.S. Apaydin, V. Conitzer, B.R. Donald.

Journal of Biomolecular NMR 2008; 40(4):263-276. PMID: 18365752