Cole B & Bystroff C. (2009) Alpha helical crossovers favor right-handed supersecondary structures by a kinetic trapping mechanism. The phone cord effect in protein folding. Protein Science, Jun 8. [Epub ahead of print]
Lee A. Newberg (2009) Error statistics of hidden Markov model and hidden Boltzmann model results. BMC Bioinformatics, 10, article 212. doi: 10.1186/1471-2105-10-212.
Lee A. Newberg and Charles E. Lawrence (2009) Exact calculation of distributions on integers, with application to sequence alignment. J Comput Biol, 16(1), 1-18. doi: 10.1089/cmb.2008.0137.
Salem S, Zaki MJ, Bystroff C (2009) Iterative non-sequential protein structural alignment. J Bioinform Comput Biol 7(3):571-96
Buck P. & Bystroff C. (2008) Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field Proteins, Structure, Function and Bioinformatics, 76(2):331-342.
Bystroff C. & Webb-Robertson, B.J. (2008) Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure BMC Bioinformatics 9:429
Ian C. Jacobi, Heidi J. Newberg, Darren Broder, Rose A. Finn, Anthony J. Milano, Lee A. Newberg, Allan T. Weatherwax, and Douglas C. B. Whittet (2008) Effect of night laboratories on learning objectives for a nonmajor astronomy class. Astronomy Education Review, 7(2), article 301.
Lee A. Newberg (2008) Significance of gapped sequence alignments. J Comput Biol, 15(9), 1187-1194. doi: 10.1089/cmb.2008.0125.
Lee A. Newberg (2008) Memory-efficient dynamic programming backtrace and pairwise local sequence alignment. Bioinformatics, 24(16), 1772-1778. doi: 10.1093/bioinformatics/btn308.
Benjarath Phoophakdee and Mohammed J. Zaki "TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences using Suffix Trees" 13th Pacific Symposium on Biocomputing (PSB), Hawaii January 2008.
Shentu, Z., al Hasan, M., Bystroff, C., Zaki, MJ. (2008) Context Shapes: Efficient Complementary Shape Matching for Protein-Protein Docking. Proteins: Structure, Function and Bioinformatics 70(3):1056-1073
E. Acar, C. Aykut-Bingol, H. Bingol, R. Bro, B. Yener. "Multiway Analysis of Epilepsy Tensors." Bioinformatics 23: i10-i18 (February 2007)
E. Acar, C. Aykut-Bingol, H. Bingol. R. Bro, B. Yener. "Seizure Recognition on Epilepsy Feature Tensor." To Appear in IEEE EMBC 2007.
C. Bilgin, C. Demir, C. Nagi. "Cell-Graph Mining for Breast Tissue Modeling and Analysis." To Appear in IEEE EMBC 2007.
Bystroff C & Krogh A. "Hidden Markov Models for Predicting Protein Features" Protein Structure Prediction: Methods and Protocols (2007)
C. Steven Carmack, Lee Ann McCue, Lee A. Newberg, and Charles E. Lawrence (2007) PhyloScan: Identification of transcription factor binding sites using cross-species evidence. Algorithms for Molecular Biology, 2(1), article 1. doi: 10.1186/1748-7188-2-1.
Sanmay Das, Milton H. Saier, Jr. and Charles Elkan. "Finding Transport Proteins in a General Protein Database" Principles and Practice of Knowledge Discovery in Databases (Proc. PKDD 2007) September 2007.
Lee A. Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee Ann McCue, and Charles E. Lawrence (2007) A phylogenetic Gibbs sampler that yields centroid solutions for cis regulatory site prediction. Bioinformatics, 23(14), 1718-1727. doi: 10.1093/bioinformatics/btm241.
Lee A. Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee Ann McCue, and Charles E. Lawrence "A phylogenetic Gibbs sampler that yields centroid solutions for cis regulatory site prediction." Bioinformatics, 23(14), 1718-1727. (2007)
Benjarath Phoophakdee and Mohammed J. Zaki "Genome-scale Disk-based Suffix Tree Indexing" ACM SIGMOD International Conference on Management of Data, Beijing, China June 2007.
Shentu, Z., al Hasan, M., Bystroff, C., Zaki, MJ. "Context Shapes: Efficient Complementary Shape Matching for Protein-Protein Docking." Proteins: Structure, Function and Bioinformatics (2007 Sep 10)
William A. Thompson, Lee A. Newberg, Sean Conlan, Lee Ann McCue, and Charles E. Lawrence "The Gibbs centroid sampler" Nucleic Acids Research 35(Web Server Issue), W232-W237 (2007)
2006 E. Acar, C. Bingol, H. Bingol, B. Yener. "Computational Analysis of Epileptic Focus Localization." Proceedings of The Fourth IASTED International Conference on Biomedical Engineering - BioMED2006, 15-17 (February 2006)
Bouchra Bouqata, Christopher D. Carothers, Boleslaw K. Szymanski and Mohammed J. Zaki "VOGUE: A Novel Variable Order-Gap State Machine for Modeling Sequences" 10th European Conference on Principles and Practice of Knowledge Discovery (PKDD), Berlin, Germany September 2006.
Huang Y-M & Bystroff C. "Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions." Bioinformatics 22(4):413-420 (2006)
Mahoney, M.W, M. Maggioni, and P. Drineas. "Tensor-CUR decompositions for tensor-based data" manuscript (2006)
Yongqiang Zhang, Mohammed J. Zaki. "sMOTIF: Efficient structured pattern and profile motif search" Algorithms for Molecular Biology, Vol. 1, 22, November 2006.
Yongqiang Zhang, Mohammed J. Zaki. "ExMOTIF: Efficient Structured Motif Extraction" Algorithms for Molecular Biology, Vol. 1, 21 November 2006.
Yuan X & Bystroff C. "Protein Contact Map Prediction" Computational Methods for Protein Structure Prediction and Modeling (2006)
Yuan X & Bystroff C. "Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins." Bioinformatics 21(7):1010-1019 (2005)