Peer-reviewed
journal publications
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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.
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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.
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Ganapathiraju,
M., Manoharan, V. and Klein-Seetharaman, J. (2004) BLMT.
Statistical Sequence Analysis Using N-Grams. Appl.
Bioinformatics, in press.
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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.
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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.
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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.
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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.
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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.
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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.
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Hoberman,
R., Klein-Seetharaman, J. and Rosenfeld, R. (2004)
Inferring property selection pressure from positional
residue conservation.
Appl. Bioinformatics, in press.
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Liu,
Y., Carbonell, J., Klein-Seetharaman, J. and Gopalakrishnan,
V. (2004) Comparison of probabilistic combination
methods for
protein secondary structure prediction.
Bioinformatics, in press.
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Cheng BY, Carbonell JG, Klein-Seetharaman J (2004).
Protein Classification based on Text Document Classification
Techniques.Proteins: Structure, Function and Bioinformatics, accepted.
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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.
-
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.
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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.
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Wang,
Y. Rader, AJ, Bahar, I. and Jernigan, RL. (2004) "Global
Ribosome Motions Revealed with Elastic Network Model",
J. Struct Biol, in
press.
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AJ
Rader and Ivet Bahar (2004) "Folding Core
Predictions from
Network Models of Proteins" , Polymer 45,
659-668.
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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.
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Weigele,
P.R., E. Scanlon, and J. King, Homotrimeric, beta-stranded viral adhesins and tail
proteins. J. Bacteriology, 2003. 185(14): p.
4022-4030.
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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.
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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.
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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.
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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.
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Ozkan
S.B., Dill K.A., Bahar I (2003). Computing
the Transition State
Populations in Simple Protein Models
Biopolymers 68,
35-46.
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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.
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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
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Klein-Seetharaman,
J. (2005) Impact of stability and conformational
changes of membrane receptors for their signaling
function. Trends in
Pharmacological Sciences. Under preparation
(Invited).
-
Klein-Seetharaman,
J., Reddy, R., N. Balakrishnan and Ganapathiraju,
M. (2005) Biological Language Modeling. In: Lecture
Notes in
Computer Science, in preparation.
-
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.
-
Klein-Seetharaman,
J. (2004) Interactive, Entertaining,
Virtual Learning Environments. In: NSF Report on
Societal Implications
of Nanoscience and Nanotechnology. In press.
-
Klein-Seetharaman,
J. and Loewen, M. (2004) Structure and
dynamics of G protein coupled receptors. In: G
protein coupled receptors.
In press.
-
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.
-
Klein-Seetharaman,
J. (2002) Dynamics in Rhodopsin. ChemBioChem 3,
981-986.
Published
proceedings of conferences and symposia
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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.
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Ziv
Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar
Simon and Roni Rosenfeld, "Deconvolving
Cell-Cycle Expression Data with
Complementary Information", ISMB'04.
-
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.
-
Chen,
S.-C. and I. Bahar
"Mining frequent patterns in
proteins: A study of serine proteinases"
Bioinformatics, Volume 20, Suppl.
1 2004: i77-i85.
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Weisser,
D. and Klein-Seetharaman, J. (2004) Automatic
identification of segment
boundaries in protein sequences using mutual information.
ACM SAC 2004, 154-161.
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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.
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Ganapathiraju, M., D. Weisser, and J. Klein-Seetharaman,
Yule Value
Tables from Protein Datasets. Proc. SCI-2004, 2004.
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John
Lafferty, Xiaojin Zhu, Yan Liu. Kernel Conditional
Random Fields:
Representation and Clique Selection. ICML'04.
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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.
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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.
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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.
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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.
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Manoharan,
V., Lam, D. and Klein-Seetharaman, J. (2003)
Biological Language Modeling Toolkit Web-Interface.
Proc. Biological
Language Conference 1, 366-373.
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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.
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Li,
F., Yang, Y. (2004) Learning linear bayesian network with large number of variables.
In ACM Sigir 2004 bioinformatics workshop.
-
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
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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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