PUBLICATIONS
Judith Klein-Seetharaman
1.
Nechushtai, R., Eden, A., Cohen, Y. and Klein, J.
(1994) Introduction to Photosystem I Reaction
Center Function, Composition and Structure. In: D. J. Ort and C. F. Yocum. (eds.) Oxygenic Photosynthesis: The Light
Reactions.
2.
Klein,
J., De Las Rivas, J. and Barber, J. (1995) Indirect Reduction of Cytochrome b559 in Isolated Reaction Centers of Photosystem II by Exogenous Flavins.
Bioelectrochem. and Bioenergetics
38, 9-14.
3.
De
Las Rivas, J., Klein, J. and Barber, J. (1995) pH Sensitivity of the Redox State of Cytochrome
b559 May Regulate Its Function As a Protectant Against
Donor and Acceptor Side Photoinhibition. Photosynth. Res. 46, 193-202.
4.
Hwa, J., Reeves, P.J., Klein-Seetharaman,
J., Davidson, F. and Khorana, H.G. (1999)
Structure and Function in Rhodopsin: Further
Elucidation of the Role of the Intradiscal Cysteines, Cys-110, -185, and -187, in Rhodopsin Folding and Function. Proc. Natl. Acad. Sci. USA 96, 1932-1935. [pdf]
5.
Cai, K., Klein-Seetharaman,
J., Farrens, D., Zhang, C., Altenbach,
C., Hubbell, W.L. and Khorana, H.G. (1999)
Single Cysteine Substitution Mutants at Amino
Acid Positions 306-312 in Rhodopsin, the
Sequence between the Cytoplasmic End of Helix
VII and the Palmitoylation Sites: Sulfhydryl Reactivity and Transducin
Activation Reveal a Tertiary Structure. Biochemistry 38,
7925-7930. [pdf]
6.
Klein-Seetharaman, J., Hwa, J., Cai, K., Altenbach, C.,
Hubbell, W.L. and Khorana, H.G. (1999) Single Cysteine Substitution Mutants at Amino Acid Positions
55-75, the Sequence Connecting the Cytoplasmic
Ends of Helix I and II in Rhodopsin: Reactivity
of the Sulfhydryl Groups and their Derivatives
Identifies a Tertiary Structure that Changes Upon Light-Activation. Biochemistry
38, 7938-7944. [pdf]
7.
Altenbach, C., Klein-Seetharaman,
J., Hwa, J., Khorana,
H.G. and Hubbell, W.L. (1999) Structural Features and Light-Dependent
Changes in the Sequence 59-75 Connecting Helices I and II in Rhodopsin: A Site-Directed Spin Labeling Study. Biochemistry
38, 7945-7949. [pdf]
8.
Cai, K., Klein-Seetharaman,
J., Hwa, J., Hubbell, W.L. and Khorana, H.G. (1999) Structure and Function in Rhodopsin. Effects of Disulfide Cross-Links in the Cytoplasmic Face of Rhodopsin
on Transducin Activation and Phosphorylation by Rhodopsin
Kinase. Biochemistry 38,
12893-12898. [pdf]
9.
Klein-Seetharaman, J., Getmanova,
E.V., Loewen, M.C., Reeves, P.J. and Khorana, H.G. (1999) NMR Spectroscopy in Studies of
Light-Induced Structural Changes in Mammalian Rhodopsin:
Applicability of Solution 19F NMR. Proc. Natl. Acad. Sci. USA 96, 13744-13749. [pdf]
10. Reeves,
P.J., Klein-Seetharaman, J., Getmanova, E.V., Eilers,
M., Loewen, M.C., Smith, S.O. and Khorana, H.G. (1999) Expression and Purification of Rhodopsin and Its Mutants from Stable Mammalian Cell
Lines: Application to NMR Studies. Biochem.
Soc. Trans. 27, 950-955.
11. Loewen, M.C., Klein-Seetharaman,
J., Getmanova, E.V., Reeves, P.J., Schwalbe, H. and Khorana,
H.G. (2001) Solution 19F Nuclear Overhauser
Effects in Structural Studies of the Cytoplasmic
Domain of Mammalian Rhodopsin Proc. Natl.
Acad. Sci. USA 98, 4888-4892. [pdf]
12. Hwa, J., Klein-Seetharaman,
J. and Khorana, H.G. (2001) Structure and
Function in Rhodopsin: Mass Spectrometric
Identification of the Abnormal Intradiscal
Disulfide Bond in Misfolded Retinitis Pigmentosa Mutants. Proc. Natl. Acad. Sci. 98: 4872-4876. [pdf]
13. Klein-Seetharaman, J., Hwa, J., Cai, K., Altenbach, C.,
Hubbell, W.L. and Khorana, H.G. (2001) Probing
the Dark State Tertiary Structure in the Cytoplasmic
Domain of Rhodopsin: Proximities Between Amino
Acids Deduced from Spontaneous Disulfide Bond Formation between Cys316
and Engineered Cysteines in Cytoplasmic
Loop 1. Biochemistry 40, 12472-12478. [pdf]
14. Cai, K., Klein-Seetharaman,
J., Altenbach, C., Hubbell, W.L. and Khorana, H.G. (2001) Probing the Dark State Tertiary
Structure in the Cytoplasmic Domain of Rhodopsin: Proximities between Amino Acids
Deduced from Spontaneous Disulfide Bond Formation between Cysteine Pairs Engineered in Cytoplasmic
Loops 1, 3 and 4. Biochemistry 40, 12479-12485. [pdf]
15. Altenbach, C., Klein-Seetharaman,
J., Cai, K., Khorana,
H.G. and Hubbell, W.L. (2001) Structure and Function in Rhodopsin: Mapping Light-Dependent Changes in
Distance between Residue 316 in Helix 8 and Residues in the Sequence
60-75, Covering the Cytoplasmic End of Helices
TM1 and TM2 and their Connection Loop CL1. Biochemistry 40,
15493-15500. [pdf]
16. Altenbach, C., Cai, K.,
Klein-Seetharaman, J., Khorana,
H.G. and Hubbell, W.L. (2001) Structure and Function in Rhodopsin: Mapping Light-Dependent Changes in
Distance between Residue 65 in Helix TM1 and Residues in the Sequence
306-319 at the Cytoplasmic End of Helix TM7 and
Helix H8. Biochemistry 40, 15483-15492. [pdf]
17. Klein-Seetharaman,J., Reeves, P.J., Loewen,
M.C., Getmanova, E.V., Chung, J., Schwalbe, H., Wright, P.E. and Khorana,
H.G. (2002) Solution NMR Spectroscopy of a- 15N-Lysine Labeled
Rhodopsin: The Single Peak Observed in both
Conventional and TROSY-type HSQC Spectra Originates from Lys339 in the
Carboxyl Terminal Peptide Sequence. Proc. Natl. Acad. Sci. USA 99, 3452-3457. [pdf]
18. 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 Non-Native Protein. Science
295, 1719-1722. [pdf]
Also see Perspective Article: Baldwin, R. (2002) Making
a Network of Hydrophobic Clusters. Science 295, 1657-1658.
[pdf]
19. Ganpathiraju, M., Weisser,
D., Rosenfeld, R., Carbonell, J., Reddy, R. and
Klein-Seetharaman, J. (2002) Comparative n-gram
anaylsis of whole-genome protein sequences. In:
Proceedings of the Human Language Technologies Conference, San
Diego 2002.
20. Cai, Y., Snel, I., Bharathi, B.S., Klein, C. and Klein-Seetharaman, J.(2003) Towards Biomedical Problem Solving
in a Game Environment. In: Lecture Notes in Computer Science 2659,
1005-1014.[pdf]
21. Klein-Seetharaman, J. and Reddy, R. (2002) Biological
Language Modeling: Convergence of Computational Linguistics and
Biological Chemistry. In: Report on the NSF Workshop
"Converging Technolgoy (NBIC) for
Improving Human Performance".
22. Klein-Seetharaman, J. (2002)
Dynamics in Rhodopsin. ChemBioChem
3, 981-986. [pdf]
23. Getmanova, E., Patel, A.B., Klein-Seetharaman,
J., Loewen, M.C., Reeves, P.J., 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 [pdf].
24. Ganapathiraju, M., Klein-Seetharaman,
J., Balakrishnan, B. and Reddy, R. (2004)
Characterization of Secondary Structure using Latent Semantic Analysis. IEEE
Signal Processing Magazine. 21(3), 78-87 [pdf].
25. 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(10), 3409–3413. [pdf]
26. 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., 101(19),
7246–7251 [pdf]
27. Weisser, D., and Klein-Seetharaman,
J. (2004) Automatic identification of segment boundaries in protein
sequences using mutual information. ACM Symposium on Applied Computing
(SAC) 2004, 154-161. [pdf]
28. Liu,
Y., Carbonell, J., Klein-Seetharaman,
J. and Gopalakrishnan, V. (2004) Context Sensitive
Vocabulary And its Application in Protein Secondary Structure Prediction.
ACM SIGIR Conference [pdf]
29. Hoberman, R, Klein-Seetharaman,
J and Rosenfeld, R. (2004) Inferring Property Selection Pressure from
Positional Residue Conservation. Appl.
Bioinformatics 3(2-3) 167-180 [pdf].
30. Ganapathiraju, M., Manoharan,
V. and Klein-Seetharaman, J. (2004)
BLMT-Statistical Sequence Analysis Using N-Grams. Appl. Bioinformatics 3(2-3) 193-200
[pdf]
31. Miao, J., Klein-Seetharaman,
J. and Meirovitch, H. (2004) The Optimal
Fraction of Hydrophobic Residues Required to Ensure Protein
Collapse. J. Mol. Biol. 344(3), 797-811. [pdf]
32. Wirmer, J., SchlÖrb, C., Klein-Seetharaman, J., Hirano, R., Ueda, T., Imoto, T. and Schwalbe, H.
(2004) Modulation of Compactness and
Long-Range Interactions of Unfolded Lysozyme by
Single Point Mutations. Angew.
Chem. Int. Ed. 43(143), 5780 –5785. [pdf]
33. 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
3(2-3), 137-148. [pdf]
34. Klein-Seetharaman, J. (2005) 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. 128-133. [pdf]
35. Klein-Seetharaman, J. (2005) Interactive, Entertaining,
Virtual Learning Environments. In: NSF Report on Societal Implications of
Nanoscience and Nanotechnology. 258-262. [pdf]
36. Klein-Seetharaman, J. and Loewen,
M. (2005) Structures and dynamics of G protein coupled receptors. In: G
protein coupled receptors. Editors: Kenneth Lundstrom,
Mark Chiu, pp 230-271. Taylor & Francis Books, Boca Raton, Florida,
USA. [pdf]
37. Ganapathiraju, M., Weisser,
D., and Klein-Seetharaman, J. (2004) Yule Value
Tables from Protein Datasets. In: Eighth World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando,
Florida, USA, July 18-21, 2004. [pdf]
38. Ganapathiraju, M., Balakrishnan, N.,
Reddy, R. and Klein-Seetharaman, J., (2005) Computational Biology and Language. In: Y. Cai (Ed.): Ambient Intelligence for Scientific
Discovery, Lecture Notes in Artificial Intelligence (LNAI) 3345, 25-47. [pdf]
39. Qi, Y., Klein-Seetharaman, J.
and Joseph, Z.(2005) Random
forest similarity for protein-protein interaction prediction from
multiple sources. Pacific Symposium on Biocomputing
10, 531-542. [pdf]
40. Liu,
Y., Carbonell, J., Klein-Seetharaman,
J. and Gopalakrishnan, V. (2004) Comparison of
probabilistic combination methods for protein secondary structure
prediction. Bioinformatics 20(17), 3099–3107. [pdf]
41. Cheng,
B., Carbonell, J. and Klein-Seetharaman,
J. (2004) A Machine Text-Inspired Machine Learning Approach for
Identification of Transmembrane Helix
Boundaries. Proc. ISMIS, 15th International Symposium on Methodologies
for Intelligent Systems, Saratoga Springs, New York, May 25-28, 2005. [pdf]
42. Cheng,
B., Carbonell, J. and Klein-Seetharman,
J. (2005) Protein Classification based on Text Document Classification
Techniques. Proteins - Structure, Function and Bioinformatics 58(4),
955-70. [pdf]
43. Klein-Seetharaman, J. (2005) Dual role of interactions
between membranous and soluble portions of helical membrane receptors for
folding and signaling. Trends in Pharmacological Science 26(4),
183-189 [pdf]
44. Cai, Y., Snel, I., Cheng,
B., Bharathi, S., Klein, C. and Klein-Seetharman, J. (2005) BioSim--a
biomedical character-based problem solving environment. Future Generation
Computer Systems 21(7), 1145-1156 [pdf]
45. Qi, Y., Klein-Seetharaman,
J. and Bar-Joseph, Z. (2005) A mixture of experts approach for
protein-protein interaction predictionIn:
Proceedings of the Neural Information Processing Systems (NIPS) Workshop
on Computational Biology and the Analysis of Heterogeneous Data.
Whistler (B.C.) December 9-10, 2005 [pdf]
46. Batra-Safferling R, Abarca Heidemann K, Korschen HG, Tziatzios C, Stoldt M, Budyak I, Willbold D, Schwalbe H, Klein-Seetharaman
J, Kaupp UB.(2005) Glutamic
acid-rich proteins of rod photoreceptors are natively unfolded. Journal
of Biological Chemistry, in press.[pdf]
47. Qi, Y., Bar-Joseph, Z. and Klein-Seetharaman,
J. (2006) Evaluation of different biological data and computational
classification methods for use in protein interaction prediction. Proteins
- Structure, Function and Bioinformatics, 63, 490-500. [pdf] [Supplement]
48. Ganapathiraju, M., Manoharan,
V. Reddy, R. and Klein-Seetharaman, J. (2006)
Collaborative Discovery Through Biological Language Modeling Interface.
In: Y. Cai and J. Abascal
(Eds.): Ambient Intelligence in Everyday Life, Lecture Notes in
Artificial Intelligence, LNAI 3864, 300-321. [pdf]
49. Isin, B., Rader, A.J., Dhiman,
H., Klein-Seetharaman, J. and Bahar, I. (2006) Predispostion
of the Dark State of Rhodopsin To Functional
Changes in Structure. Proteins - Structure, Function and
Bioinformatics,
65(4),
970-983. [pdf] [Supplement]
50.
Alessandro
Iannaccone, David Man, Naushin
Waseemc, Barbara J.
Jennings, Madhavi Ganapathiraju,
Kevin Gallaher, Elisheva
Reese, Shomi S. Bhattacharya, Judith Klein-Seetharaman. (2006) Retinitis pigmentosa
associated with rhodopsin mutations:
Correlation between phenotypic variability and molecular effects. Vision
Research 46(27),
4556-67.[ pdf]
51.
Haber-Pohlmeier,
S., Körschen, H.G., Abarca-Heidemann, K., Kaur Dhiman, H., Heberle, J.,
Schwalbe, H., Klein-Seetharaman, J., Kaupp, U.B. and Pohlmeier, A.
(2007) Binding of Ca2+ to glutamic acid-rich polypeptides from the rod
outer segment. Biophys. J. 92(9), 3207-14. [pdf]
52.
Budyak, I.,
Pipich, V., Mironova, O., Schlesinger, R., Zaccai, G. &
Klein-Seetharaman, J. (2006) Shape and oligomerization state of the
cytoplasmic domain of the phototaxis transducer II from Natronobacterium
pharaonis.
Proc.
Natl. Acad. Sci. USA
103(42),
15428-33. [pdf]
53. Tastan, O., Yu, E.,
Ganapathiraju, M., Aref, A., Rader, A.J. and Klein-Seetharaman, J.
(2007) Comparison of stability predictions and simulated unfolding of
rhodopsin structures. Photochemistry and Photobiology 83(2),
251-362. [pdf]
54. Karla Werner, Ines Lehner, Harpreet Kaur Dhiman,
Christian Richter, Clemens Glaubitz, Harald Schwalbe, Judith
Klein-Seetharaman and H. Gobind Khorana (2007) Combined solid state and
solution NMR studies of a,e-15N labeled bovine rhodopsin.
J. Biomol. NMR 37(4), 303-312. [pdf]
55.
Ganapathiraju,
M., Balakrishnan, N., Reddy, R. and Klein-Seetharaman, J. (2007)
Transmembrane helix prediction using latent semantic analysis, Incob
Proceedings
http://srs1.bic.nus.edu.sg/ocs/viewabstract.php?id=46
56.
Yanamala, N.,
Tirupula, K. and Klein-Seetharaman, J. (2007) Preferential Binding of
Allosteric Modulators to Active and Inactive Conformational States of
Metabotropic Glutamate Receptors, Incob Proceedings
http://srs1.bic.nus.edu.sg/ocs/viewabstract.php?id=73
57. Qi, Y., Klein-Seetharaman, J. and Bar-Joseph, Z.
(2007) A mixture of experts approach for protein-protein interaction
prediction. BMC Bioinformatics, in press. [pdf]
58. Ganapathiraju, M., Jursa, C.J., Karimi, H.A. &
Klein-Seetharaman, J. (2007) TMpro web server and web service:
Transmembrane helix prediction through amino acid property analysis,
Bioinformatics, in press. [pdf]
59. Poddar, A., Chandra, N., Ganpathiraju, M., Sekar,
K., Klein-Seetharaman, J., Reddy, R. & Balakrishnan, N. (2007)
Evolutionary insights from suffix array based genome sequence analysis.
J. Biosci. 32(5), 871-881. [pdf]
Theses
1. Klein, J. (1995) Studies on a
Functional Role of Cytochrome b559. Diploma
Thesis at the University of Cologne, Cologne, Germany.
2. Klein, J. (2000) Visual Signal
Transduction: Studies of Light-Induced Conformational Changes in the Cytoplasmic Face of Rhodopsin.
Ph.D. Thesis at the Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA.
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