Shotgun sequencing:
1. An optimal procedure for gap closing in whole genome shotgun sequences.
R. Beigel, N. Alon, M.S. Apaydın, 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. Apaydın, 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. Apaydın, 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. (pdf)
Ph.D. thesis, Stanford University, August 2004 (slides)
4. Stochastic Roadmap Simulation: An efficient Representation and Algorithm for Analyzing Molecular Motion
M. S. Apaydın, 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. Apaydın, 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. Apaydın, 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. Apaydın, 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. Apaydın, D.L. Brutlag, C. Guestrin, D. Hsu. and J.-C. Latombe.
RECOMB 2002.
9. Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps.
M.S. Apaydın, A. P. Singh, D. L. Brutlag, and J.-C. Latombe.
International Conference on Robotics and Automation (ICRA), 2001.
NMR Structure-Based Assignments:
1. Structure-Based Protein NMR Assignments using Native Structural Ensembles
M.S. Apaydın, V. Conitzer, B.R. Donald.
Journal of Biomolecular NMR 2008; 40(4):263-276. PMID: 18365752