Reflections on the quest to obtain biological information from genomic data

Graphical abstract

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.

RIGHTS & PERMISSIONS

The Author(s) 2021. Published by Higher Education Press