Reflections on the quest to obtain biological information from genomic data

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References

[1] Brownlee, C. (2004) Biography of Phil Green. Proc. Natl. Acad. Sci. USA., 101, 13991–13993.

[2] Lipman, D. J. and Pearson, W. R. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435–1441.

[3] Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–410.

[4] Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F. and Wootton, J. C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208–214.

[5] Neuwald, A. F. (1997) Barth syndrome may be due to an acyltransferase deficiency. Curr. Biol., 7, R462–R466.

[6] Ono, T., Losada, A., Hirano, M., Myers, M. P., Neuwald, A. F. and Hirano, T. (2003) Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. Cell, 115, 109–121.

[7] Neuwald, A. F., Aravind, L., Spouge, J. L. and Koonin, E. V. (1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res, 9, 27–43

[8] Gabrielsen, P. (2017) Profile of Eugene V. Koonin. Proc. Natl. Acad. Sci. USA, 114, 793–796.

[9] Koonin, E. V., Altschul, S. F. and Bork, P. (1996) ... Functional motifs.... Nat. Genet., 13, 266–268.

[10] Tatusov, R. L., Altschul, S. F. and Koonin, E. V. (1994) Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl. Acad. Sci. USA, 91, 12091–12095.

[11] Neuwald, A. F., Liu, J. S., Lipman, D. J. and Lawrence, C. E. (1997) Extracting protein alignment models from the sequence database. Nucleic Acids Res., 25, 1665–1677.

[12] Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402.

[13] Marshall, E. (1996) Hot property: biologists who compute. Science, 272, 1730–1732.

[14] Karlin, S. and Altschul, S. F. (1993) Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA, 90, 5873–5877.

[15] Alberts, B. (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell, 92, 291–294.

[16] Arndt, M., Nairz, O., Vos-Andreae, J., Keller, C., van der Zouw, G. and Zeilinger, A. (1999) Wave-particle duality of C₆₀ molecules. Nature, 401, 680–682.

[17] Tondnevis, F., Dudenhausen, E. E., Miller, A. M., McKenna, R., Altschul, S. F., Bloom, L. B. and Neuwald, A. F. (2020) Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity. Sci. Rep., 10, 1691

[18] AlQuraishi, M. (2019) AlphaFold at CASP13. Bioinformatics, 35, 4862–4865.

[19] Hornik, K. (1991) Approximation capabilities of multilayer feedforward networks. Neural Netw., 4, 251–257.

ACKNOWLEDGEMENTS

This work was supported by National Institute of General Medical Sciences grant R01 GM125878.

COMPLIANCE WITH ETHICS GUIDELINES

The author Andrew F. Neuwald declare that he has no competing interests.

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