Associate Professor

Education and Training

Ph.D. UCSD
Postdoctoral Training, UCSF

Contact

E-mail: bystrc@rpi.edu
Website: http://www.bioinfo.rpi.edu/~bystrc
Tel: (518) 276-3185
Fax: (518) 276-2344

Office: Science Center Rm. 3C07

Rensselaer Polytechnic Institute
110 8th Street
Troy, NY 12180

Research Interests

Bioinformatics, protein folding, and design; computational biology

My lab studies the folding of proteins via database modeling and simulation. Proteins contain in their primary sequence all of the information necessary to fold spontaneously into their respective three-dimensional structures. How is that information encoded? Knowledge of the protein folding pathway will lead to improved predictionof structure and function of unknown genes, and to better and more accurate approaches to computational protein design, a field with enormous potential application and impact.

Other research interests involve sequence alignment, evolutionary models, and the modeling of evolving ecosystems.  See my homepage for details.

Selected Publications

Ramakrishnan V, Salem SM, Zaki MJ & Bystroff C. (2007) Developing a detailed mechanistic model for protein unfolding. Proteins (submitted)

Xia K, Manning M, Hesham H, Lin Q, Bystroff C & Colon W. (2007) Identifying the Subproteome of Kinetically Stable Proteins Via Diagonal 2D SDS-PAGE. Proc Nat Acad Sci (submitted)

Shentu, Z., al Hasan, M., Bystroff, C., Zaki, MJ. (2007) Context Shapes: Efficient Complementary Shape Matching for Protein-Protein Docking. Proteins: Structure, Function and Bioinformatics, 2007 Sep 10; [Epub ahead of print]

Bystroff C & Krogh A. (2007). Hidden Markov Models for Predicting Protein Features, in Protein Structure Prediction: Methods and Protocols (C Bystroff, MJ Zaki, eds.)

Yuan X & Bystroff C. (2006). Protein Contact Map Prediction, in Computational Methods for Protein Structure Prediction and Modeling (Ying Xu, Dong Xu, eds.)

Huang Y-M & Bystroff C. (2006). Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions. Bioinformatics 22(4):413-420

Yuan X & Bystroff C. (2005). Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins. Bioinformatics 21(7):1010-1019

Bystroff C, Shao Y & Yuan X. (2004). Five heirarchical levels of sequence-structure correlation in proteins. Applied Bioinformatics 3 (2):97-104

Zaki MJ, Nadimpally V, Bardhan D, & Bystroff C. (2004). Predicting Protein Folding Pathways. Bioinformatics 20 Suppl. 1, i387-i393.

Hou Y, Hsu W, Lee ML & Bystroff C. (2004). Remote Homology Detection Using Local Sequence-structure Correlations. Proteins 57(3):518-30.