Rhodopsin


Center For Biological Language Modeling
@
Carnegie Mellon University | University of Pittsburgh | Massachusetts Institute of Technology
Boston University Medical School | National Research Council Canada


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Publications

Peer-reviewed journal publications

  1. Miao, J., Klein-Seetharaman, J. and Meirovitch, H. (2005) The optimal fraction of hydrophobic residues required to ensure protein collapse. J. Mol. Biol., in press.

  2. Miao, J., J. Klein-Seetharaman, and H. Meirovitch, What is the Optimal Fraction of Hydrophobic Residues Required to Ensure Protein Collapse? J. Mol. Biol., 2004: p. submitted.

  3. Ganapathiraju, M., Manoharan, V. and Klein-Seetharaman, J. (2004) BLMT. Statistical Sequence Analysis Using N-Grams. Appl. Bioinformatics, in press.

  4. Getmanova, E., Patel, A.B., Klein-Seetharaman, J., Loewen, M.C., Reeves, P.J., Friedman, N., Sheves, M., Smith, S.O. and Khorana, H.G. (2004) NMR spectroscopy of phosphorylated wild-type rhodopsin: mobility of the phosphorylated C-terminus of rhodopsin in the dark and upon light-activation. Biochemistry 43, 1126-1133.

  5. Klein-Seetharaman, J., Yanamala, N.V.K., Javeed, F., Reeves, P.J., Getmanova, E.V., Loewen, M.C., Schwalbe, H. and Khorana, H.G. (2004) Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR. Proc. Natl. Acad. Sci. 101, 3409-3413.

  6. Rader, A.J., Anderson, G., Isin, B., Khorana, H.G., Bahar, I. and Klein-Seetharaman, J. (2004) Identification of core amino acids stabilizing rhodopsin. Proc. Natl. Acad. Sci. USA 101(19), 7246­7251.

  7. Cai, Y., Snel, I., Cheng, B.Y.M., Bharathi, B.S., Klein, C. and Klein-Seetharaman, J. (2004) BioSim ­ A Biomedical Character-Based Problem Solving Environment, Future Generation Computer Systems. In press.

  8. Wirmer, J., Schloerb, C., Hirano, R., Ueda, T., Klein-Seetharaman, J., Imoto, T. and Schwalbe, H. (2004) Modulation of Compactness and Long-range Interactions of Unfolded Lysozyme by Single Point Mutations. Angew. Chemie, in press.

  9. Vries, J., Munshi, R., Tobi, D., Klein-Seetharaman, J., Benos, P.V. and Bahar, I. (2004) A Sequence Alignment-Independent Method for Protein Classification. Appl. Bioinformatics, inn press.

  10. Hoberman, R., Klein-Seetharaman, J. and Rosenfeld, R. (2004) Inferring property selection pressure from positional residue conservation. Appl. Bioinformatics, in press.

  11. Liu, Y., Carbonell, J., Klein-Seetharaman, J. and Gopalakrishnan, V. (2004) Comparison of probabilistic combination methods for protein secondary structure prediction. Bioinformatics, in press.   

  12. Cheng BY, Carbonell JG, Klein-Seetharaman J (2004). Protein Classification based on Text Document Classification Techniques.Proteins: Structure, Function and Bioinformatics, accepted.

  13. Marni Brisson, Theresa Nguyen, Andreas Vogt, Jack Yalowich, Angela Giorgianni, Dror Tobi, Ivet Bahar. Corey R. J. Stephenson, Peter Wipf, and John S. Lazo (2004) Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase, Mol Pharmacology, in press.  

  14. NA Temiz, E Meirovitch, I Bahar. (2004) E. coli Adenylate Kinase Dynamics: Comparison of Elastic Network Model Modes with Mode-Coupling 15N-NMR Relaxation Data., Proteins: Structure, Function and Bioinformatics, in press.

  15. Nicolas Sluis-Cremer, N. Alpay Temiz and Ivet Bahar. (2004) Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding. Current Research in HIV, in press.

  16.  Wang, Y. Rader, AJ, Bahar, I. and Jernigan, RL. (2004) "Global Ribosome Motions Revealed with Elastic Network Model", J. Struct Biol, in press.   

  17. AJ Rader and Ivet Bahar (2004) "Folding Core Predictions  from Network Models of Proteins" , Polymer 45, 659-668.

  18. Yoram Vodovotz, Peter Kim, E. Zerrin Bagci, G. Bard Ermentrout, Carson C. Chow, Ivet Bahar, Timothy R. Billiar. (2004) "Inflammatory Modulation of Hepatocyte Apoptosis by Nitric Oxide: In Vivo, In Vitro, and In Silico Studies." Current Molecular Medicine 4, 753-762.

  19. Weigele, P.R., E. Scanlon, and J. King, Homotrimeric, beta-stranded viral adhesins and tail proteins. J. Bacteriology, 2003. 185(14): p. 4022-4030.

  20. Ganapathiraju, M., Klein-Seetharaman, J., Balakrishnan, B. and Reddy, R. (2003) Characterization of Protein Secondary Structure using Latent Semantic Analysis. IEEE Signal Processing Magazine. 21(3), 78-87.

  21. Chunyan Xu, Dror Tobi and Ivet Bahar (2003) "Allosteric Changes in Protein Structure Computed by a Simple Mechanical Model: Hemoglobin T -- R2 Transition" J. Mol. Biol. 333, 153-168.

  22. Zerrin Bagci, Andrzej Kloczkowski, Robert L. Jernigan and Ivet Bahar (2003) "The Origin and Extent of Coarse-Grained Regularities in Protein Internal Packing" Proteins: Structure, Function and Genetics 53.   

  23. Ozkan BS, Meirovitch H. (2003) Efficient conformational search method for peptides and proteins: Monte Carlo minimization with an Adaptive bias. J. Phys. Chem. B 107; 9128-9131.

  24. Ozkan S.B., Dill K.A., Bahar I (2003). Computing the Transition State Populations in Simple Protein Models  Biopolymers 68, 35-46.

  25. Klein-Seetharaman, J., Oikawa, M., Wirmer, J., Duchardt, E., Ueda, T., Imoto, T., Smith, L.J., Dobson, C. and Schwalbe, H. (2002) Long-Range Interactions within a Nonnative Protein. Science 295, 1719-1722.

  26. Kim, J., J. Hwa, P. Garriga, P.J. Reeves, U.L. RajBhandary, and H.G. Khorana, Light-driven activation of 2-adrenergic receptor signaling by replacing the cytoplasmic loops of rhodopsin by the 2-adrenergic receptor. in preparation, 2004.

 

Reviews, invited published papers, monographs, books and book chapters

  1. Klein-Seetharaman, J. (2005) Impact of stability and conformational changes of membrane receptors for their signaling function. Trends in Pharmacological Sciences. Under preparation (Invited).

  2. Klein-Seetharaman, J., Reddy, R., N. Balakrishnan and Ganapathiraju, M. (2005) Biological Language Modeling. In: Lecture Notes in Computer Science, in preparation.

  3. Klein-Seetharaman, J. (2004) The Use of Analogies for Interdisciplinary Research in the Convergence of Nano-, Bio- and Information Technology. In: NSF Report on Societal Implications of Nanoscience and Nanotechnology. In press.

  4. Klein-Seetharaman, J. (2004) Interactive, Entertaining, Virtual Learning Environments. In: NSF Report on Societal Implications of Nanoscience and Nanotechnology. In press.

  5. Klein-Seetharaman, J. and Loewen, M. (2004) Structure and dynamics of G protein coupled receptors. In: G protein coupled receptors. In press.

  6. Klein-Seetharaman, J. and Reddy, R. (2002) Biological Language Modeling: Convergence of Computational Linguistics and Biological Chemistry. In: Converging Technology  for Improving Human Performance ­ Nanotechnology, Biotechnology, Information Technology and Cognitive Science. Eds. Roco, M.C. and Bainbridge, W.S., National Science Foundation, 378-385.

  7. Klein-Seetharaman, J. (2002) Dynamics in Rhodopsin. ChemBioChem 3, 981-986.

 

Published proceedings of conferences and symposia 

  1. Qi, Y., Klein-Seetharaman, J. and Bar-Joseph, Z. (2005) Random forest similarity for protein-protein interaction prediction from multiple sources. Pacific Symposium on Biocomputing 10, in press.

  2. Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon and Roni Rosenfeld, "Deconvolving Cell-Cycle Expression Data with Complementary Information", ISMB'04.

  3. Francis Y.L. Chin, Henry C.M. Leung, S.M. Yiu, T.W. Lam, Roni Rosenfeld, W.W. Tsang, David K. Smith, Y.Jiang, "Finding Motifs for Insufficient Number of Sequences with Strong Binding to Transcription Factor", RECOMB 2004.

  4. Chen, S.-C. and I. Bahar  "Mining frequent patterns in proteins: A study of serine proteinases" Bioinformatics, Volume 20, Suppl. 1 2004: i77-i85.   

  5. Weisser, D. and Klein-Seetharaman, J. (2004) Automatic identification of segment boundaries in protein sequences using mutual information. ACM SAC 2004, 154-161.

  6. Liu, Y., Carbonell, J., Klein-Seetharaman, J. and Gopalakrishnan, V. Context Sensitive Vocabulary And its Application in Protein Secondary Structure Prediction. ACM SIGIR 2004. In press.

  7. Ganapathiraju, M., D. Weisser, and J. Klein-Seetharaman, Yule Value Tables from Protein Datasets. Proc. SCI-2004, 2004.

  8. John Lafferty, Xiaojin Zhu, Yan Liu. Kernel Conditional Random Fields: Representation and Clique Selection. ICML'04.

  9. Cai, Y., Snel, I., Bharathi, B.S., Klein, C. and Klein-Seetharaman, J. (2003) Towards Biomedical Problem Solving in a Game Environment. Lecture Notes in Computer Science 2659, 1005-1014.

  10. Liu, Y., Carbonell, J., Klein-Seetharaman, J. and Gopalakrishnan, V. (2003) Prediction of parallel and antiparallel beta-sheets using conditional random fields. Proc. Biological Language Conference 1, 35-43.

  11. Li, F., Yang, Y., Jitender, V., Anderson, G., Gopalakrishnan, V. and Klein-Seetharaman, J. (2003) Constructing Gene Networks Using Microarray Data. Proc. Biological Language Conference 1, 74-83.

  12. Balakrishnan, S., Ganapathiraju, M., Klein-Seetharaman, J., Balakrishnan, N. And Reddy, R. (2003) Extensions to the Biological Language Modeling Toolkit (BLMT). Proc. Biological Language Conference 1, 353-365.

  13. Manoharan, V., Lam, D. and Klein-Seetharaman, J. (2003) Biological Language Modeling Toolkit Web-Interface. Proc. Biological Language Conference 1, 366-373.

  14. Ganpathiraju, M., Weisser, D., Rosenfeld, R., Carbonell, J. Reddy, R. and Klein-Seetharaman, J. (2002) Comparative n-gram analysis of whole-genome protein sequences. In: Proceedings of the Human Language Technologies Conference, San Diego 2002.

  15. Li, F., Yang, Y. (2004) Learning linear bayesian network with large number of variables. In ACM Sigir 2004 bioinformatics workshop.

  16. Cheng BY, Carbonell JG, Klein-Seetharaman J (2005). A Machine Text-Inspired Machine Learning Approach for Identification of Transmembrane Helix Boundaries. 15th International Symposium on Methodologies for Intelligent Systems, Saratoga Springs, New York, USA. Accepted

  17. Li, F., Y. Yang, and J. Zhang, An analysis of recursive feature elimination methods for statistical classification. Proc. BLC2003, 2003: p. 84-90.

 

 

 

 

 


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Last updated June 08, 2005


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