journal article Jun 01, 2000

Who's your neighbor? New computational approaches for functional genomics

Topics

No keywords indexed for this article. Browse by subject →

References
43
[1]
Beyond complete genomes: from sequence to structure and function

Eugene V Koonin, Roman L Tatusov, Michael Y Galperin

Current Opinion in Structural Biology 1998 10.1016/s0959-440x(98)80070-5
[2]
Predicting function: from genes to genomes and back 1 1Edited by P. E. Wright

Peer Bork, Thomas Dandekar, Yolande Diaz-Lazcoz et al.

Journal of Molecular Biology 1998 10.1006/jmbi.1998.2144
[3]
Predicting functions from protein sequences—where are the bottlenecks?

Peer Bork, Eugene V. Koonin

Nature Genetics 1998 10.1038/ng0498-313
[4]
http://www.ncbi.nlm.nih.gov/Entrez/Genome/org.html .
[5]
http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/bact.html .
[6]
http://www-fp.mcs.anl.gov/~gaasterland/genomes.html .
[7]
Huynen, M.J. & Snel, B. Gene and context: integrative approaches to genome analysis. Adv. Prot. Chem. 54, 345–380 (2000).
[8]
Distinguishing Homologous from Analogous Proteins

Walter M. Fitch

Systematic Zoology 1970 10.2307/2412448
[9]
Henikoff, S. et al. Gene families: the taxonomy of protein paralogs and chimeras. Science 278, 609–614 (1997). 10.1126/science.278.5338.609
[10]
A Genomic Perspective on Protein Families

Roman L. Tatusov, Eugene V. Koonin, David J. Lipman

Science 1997 10.1126/science.278.5338.631
[11]
The COG database: a tool for genome-scale analysis of protein functions and evolution

R. L. Tatusov

Nucleic Acids Research 2000 10.1093/nar/28.1.33
[12]
http://www.ncbi.nlm.nih.gov/COG .
[13]
Microbial Genescapes: Phyletic and Functional Patterns of ORF Distribution among Prokaryotes

Terry Gaasterland, Mark A. Ragan

Microbial & Comparative Genomics 1998 10.1089/omi.1.1998.3.199
[14]
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

Matteo Pellegrini, Edward M. Marcotte, Michael J. Thompson et al.

Proceedings of the National Academy of Sciences 1999 10.1073/pnas.96.8.4285
[15]
Brown, J.R. & Doolittle, W.F. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61, 456–502 (1997). 10.1128/.61.4.456-502.1997
[16]
Makarova, K.S. et al. Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9, 608–628 (1999). 10.1101/gr.9.7.608
[17]
Dandekar, T., Schuster, S., Snel, B., Huynen, M. & Bork, P. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343, 115–124 (1999). 10.1042/bj3430115
[18]
Huynen, M.A., Dandekar, T. & Bork, P. Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol. 7, 281–291 (1999). 10.1016/s0966-842x(99)01539-5
[19]
Ibba, M. et al. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278, 1119–1122 (1997). 10.1126/science.278.5340.1119
[20]
Ibba, M., Bono, J.L., Rosa, P.A. & Soll, D. Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA 94, 14383–14388 (1997). 10.1073/pnas.94.26.14383
[21]
Wolf, Y.I., Aravind, L., Grishin, N.V. & Koonin, E.V. Evolution of aminoacyl-tRNA synthetases—analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9, 689–710 (1999). 10.1101/gr.9.8.689
[22]
Galperin, M.Y., Aravind, L. & Koonin, E.V. Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea. FEMS Microbiol. Lett. 183, 269–264 (2000). 10.1111/j.1574-6968.2000.tb08968.x
[23]
Thomson, G.J., Howlett, G.J., Ashcroft, A.E. & Berry, A. The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem. J. 331, 437–445 (1998). 10.1042/bj3310437
[24]
Dynes, J.L. & Firtel, R.A. Molecular complementation of a genetic marker in Dictyostelium using a genomic DNA library. Proc. Natl. Acad. Sci. USA. 86, 7966–7970 (1989). 10.1073/pnas.86.20.7966
[25]
Detecting Protein Function and Protein-Protein Interactions from Genome Sequences

Edward M. Marcotte, Matteo Pellegrini, Ho-Leung Ng et al.

Science 1999 10.1126/science.285.5428.751
[26]
Enright, A.J., Ilipoulos, I., Kyrpides, N.C. & Ouzounis, C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86–90 (1999). 10.1038/47056
[27]
Snel, B., Bork, P. & Huynen, M. Genome evolution: Gene fusion versus gene fission. Trends Genet. 16, 9–11 (2000). 10.1016/s0168-9525(99)01924-1
[28]
Aravind, L. & Ponting, C.P. The GAF domain: an evolutionary link between diverse phototransducing proteins. Trends Biochem. Sci. 22, 458–459 (1997). 10.1016/s0968-0004(97)01148-1
[29]
Galperin, M.Y., Natale, D.A., Aravind, L. & Koonin, E.V. A specialized version of the HD hydrolase domain implicated in signal transduction. J. Mol. Microbiol. Biotechnol. 1, 303–305 (1999).
[30]
Doolittle, R.F. Do you dig my groove? Nat. Genet. 23, 6–8 (1999). 10.1038/12597
[31]
Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D. & Maltsev, N. Use of contiguity on the chromosome to predict functional coupling. In Silico Biol. http://www.bioinfo.de/isb/1998/01/0009/ (1998).
[32]
Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D. & Maltsev, N. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96, 2896–2901 (1999). 10.1073/pnas.96.6.2896
[33]
Conservation of gene order: a fingerprint of proteins that physically interact

T Dandekar

Trends in Biochemical Sciences 1998 10.1016/s0968-0004(98)01274-2
[34]
Schiott, T., Throne-Holst, M. & Hederstedt, L. Bacillus subtilis CcdA-defective mutants are blocked in a late step of cytochrome c biogenesis. J. Bacteriol. 179, 4523–4529 (1997). 10.1128/jb.179.14.4523-4529.1997
[35]
Mironov, A.A., Koonin, E.V., Roytberg, M.A. & Gelfand, M.S. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 27, 2981–2989 (1999). 10.1093/nar/27.14.2981
[36]
Gelfand, M.S., Koonin, E.V. & Mironov, A.A. Prediction of transcription regulatory sites in Archaea by a comparative-genomic approach. Nucleic Acids Res. 28, 695–705 (2000). 10.1093/nar/28.3.695
[37]
Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development

Albertha J. M. Walhout, Raffaella Sordella, Xiaowei Lu et al.

Science 2000 10.1126/science.287.5450.116
[38]
Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O. & Eisenberg, D. A combined algorithm for genome-wide prediction of protein function. Nature 402, 83–86 (1999). 10.1038/47048
[39]
Mewes, H.W., Hani, J., Pfeiffer, F. & Frishman, D. MIPS: a database for protein sequences and complete genomes. Nucleic Acids Res. 26, 33–37 (1998). 10.1093/nar/26.1.33
[40]
Doolittle, W.F. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 14, 307–311 (1998). 10.1016/s0168-9525(98)01494-2
[41]
Doolittle, W.F. Phylogenetic classification and the universal tree. Science 284, 2124–2129 (1999). 10.1126/science.284.5423.2124
[42]
Mushegian, A.R. & Koonin, E.V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 93, 10268–10273 (1996). 10.1073/pnas.93.19.10268
[43]
Aravind, L., Tatusov, R.L., Wolf, Y.I., Walker, D.R. & Koonin, E.V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14, 442–444 (1998). 10.1016/s0168-9525(98)01553-4
Cited By
247
New Phytologist
Proceedings of the National Academy...
Bacterial Interactomes: From Interactions to Networks

Emmanuelle Bouveret, Christine Brun · 2011

Methods in Molecular Biology™
Journal of The Royal Society Interf...
Zinc through the Three Domains of Life

Claudia Andreini, Lucia Banci · 2006

Journal of Proteome Research
Protein interaction networks from yeast to human

Peer Bork, Lars Juhl Jensen · 2004

Current Opinion in Structural Biolo...
BMC Bioinformatics
Novel domains of the prokaryotic two-component signal transduction systems

Michael Y. Galperin, Anastasia N. Nikolskaya · 2001

FEMS Microbiology Letters
Metrics
247
Citations
43
References
Details
Published
Jun 01, 2000
Vol/Issue
18(6)
Pages
609-613
License
View
Cite This Article
Michael Y. Galperin, Eugene V. Koonin (2000). Who's your neighbor? New computational approaches for functional genomics. Nature Biotechnology, 18(6), 609-613. https://doi.org/10.1038/76443