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Kannan, N., Haste, N., Taylor, S. S., Neuwald, A. F. (January 2007) The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module. Proc Natl Acad Sci U S A, 104 (4). pp. 1272-7.

Neuwald, A. F. (July 2006) Bayesian shadows of molecular mechanisms cast in the light of evolution. Trends Biochem Sci, 31 (7). pp. 374-82. ISSN 0968-0004 (Print)

Neuwald, A. F. (July 2006) Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine. Nucleic Acids Res, 34 (18). pp. 5280-90. ISSN 1362-4962 (Electronic)

Kannan, N., Neuwald, A. F. (September 2005) Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? J Mol Biol, 351 (5). pp. 956-72. ISSN 0022-2836 (Print)

Andersen, J. N., Del Vecchio, R. L., Kannan, N., Gergel, J., Neuwald, A. F., Tonks, N.K. (January 2005) Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources. Methods, 35 (1). pp. 90-114. ISSN 1046-2023 (Print)

Neuwald, Andrew F. (2005) Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases. Nucleic Acids Res, 33 (11). pp. 3614-28. ISSN 1362-4962 (Electronic)

Neuwald, A. F., Liu, J. S. (October 2004) Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. BMC Bioinformatics, 5. p. 157. ISSN 1471-2105 (Electronic)

Kannan, N., Neuwald, A. F. (August 2004) Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha. Protein Sci, 13 (8). pp. 2059-77. ISSN 0961-8368 (Print)

Saitoh, N., Spahr, C. S., Patterson, S. D., Bubulya, P., Neuwald, A. F., Spector, D. L. (August 2004) Proteomic analysis of interchromatin granule clusters. Mol Biol Cell, 15 (8). pp. 3876-90. ISSN 1059-1524 (Print)

Kannan, N., Neuwald, A. F. (May 2004) Evolutionary clues to protein kinase structural mechanisms. Faseb Journal, 18 (8). C189-C189. ISSN 0892-6638

Ono, T., Losada, A., Hirano, M., Myers, M. P., Neuwald, A. F., Hirano, T. (October 2003) Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. Cell, 115 (1). pp. 109-121. ISSN 0092-8674

Neuwald, A. F. (August 2003) Evolutionary clues to DNA polymerase III beta clamp structural mechanisms. Nucleic Acids Research, 31 (15). pp. 4503-4516. ISSN 0305-1048

Neuwald, A. F., Kannan, N., Poleksic, A., Hata, N., Liu, J. S. (April 2003) Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases. Genome Research, 13 (4). pp. 673-692. ISSN 1088-9051

Saitoh, N., Patterson, S. D., Spahr, C. S., Howard, T., Neuwald, A. F., Spector, D. L. (December 2000) Development of an in vitro system to recapitulate interchromatin granule cluster dynamics. Molecular Biology of the Cell, 11. 19A-19A. ISSN 1059-1524

Neuwald, A. F., Hirano, T. (October 2000) HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions. Genome Research, 10 (10). pp. 1445-1452. ISSN 1088-9051

Neuwald, A. F., Poleksic, A. (September 2000) PSI-BLAST searches using hidden Markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. Nucleic Acids Research, 28 (18). pp. 3570-3580. ISSN 0305-1048

Wilbur, W. J., Neuwald, A. F. (January 2000) A theory of information with special application to search problems. Computers & Chemistry, 24 (1). pp. 33-42. ISSN 0097-8485

Neuwald, A. F. (February 1999) The hexamerization domain of N-ethylmaleimide-sensitive factor: structural clues to chaperone function. Structure, 7 (2). R19-23. ISSN 0969-2126 (Print)

Neuwald, A. F., Aravind, L., Spouge, J. L., Koonin, E. V. (January 1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Research, 9 (1). pp. 27-43. ISSN 1088-9051 (Print)

Mintz, P. J., Patterson, S. D., Neuwald, A. F., Spahr, C. S., Spector, D. L. (1999) Purification and biochemical characterization of interchromatin granule clusters. Embo Journal, 18 (15). pp. 4308-4320. ISSN 0261-4189