-
1
-
-
0032509302
-
Genome sequence of the nematode C. elegans: A platform for investigating biology
-
The primary publication of the Genome Sequencing Consortium describing the approach to obtaining the complete sequence and associated caveats. It also discusses the strategies used to discover how genes annotate the large proteome and makes some observations regarding the striking features that can be inferred from the proteome
-
Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 282:1998;2012-2018. The primary publication of the Genome Sequencing Consortium describing the approach to obtaining the complete sequence and associated caveats. It also discusses the strategies used to discover how genes annotate the large proteome and makes some observations regarding the striking features that can be inferred from the proteome.
-
(1998)
Science
, vol.282
, pp. 2012-2018
-
-
-
2
-
-
0005324072
-
Arabidopsis thaliana: A model plant for genome analysis
-
679-682. A report on the progress of the Arabidopsis genome sequencing projects with respect to generation of primary sequence, its assembly and annotation
-
Meinke, D.W., Cherry, J.M., Dean, C., Rounsley, S.D., Koornneef, M.: Arabidopsis thaliana: a model plant for genome analysis. Science 1998, 282:662,679-682. A report on the progress of the Arabidopsis genome sequencing projects with respect to generation of primary sequence, its assembly and annotation.
-
(1998)
Science
, vol.282
, pp. 662
-
-
Meinke, D.W.1
Cherry, J.M.2
Dean, C.3
Rounsley, S.D.4
Koornneef, M.5
-
5
-
-
0030023247
-
Determining divergence times of the major kingdoms of living organisms with a protein clock
-
[see comments]
-
Doolittle R.F., Feng D.F., Tsang S., Cho G., Little E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science. 271:1996;470-477. [see comments].
-
(1996)
Science
, vol.271
, pp. 470-477
-
-
Doolittle, R.F.1
Feng, D.F.2
Tsang, S.3
Cho, G.4
Little, E.5
-
7
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
8
-
-
0031743421
-
Profile hidden Markov models
-
Provides a very useful review of the use of HMM in biological sequence analysis. The methods described here are implemented in the 'easy to use' HMMER program that can be downloaded from the World Wide Web at:
-
Eddy S.R. Profile hidden Markov models. Bioinformatics. 14:1998;755-763. Provides a very useful review of the use of HMM in biological sequence analysis. The methods described here are implemented in the 'easy to use' HMMER program that can be downloaded from the World Wide Web at: http://hmmer.wustl.edu/.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
9
-
-
0032919370
-
SMART: Identification and annotation of domains from signalling and extracellular protein sequences
-
Excellent system for the annotation of signaling domains in proteins based on HMMs derived from high-quality alignments. Can be accessed on the World Wide Web at:
-
Ponting C.P., Schultz J., Milpetz F., Bork P. SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res. 27:1999;229-232. Excellent system for the annotation of signaling domains in proteins based on HMMs derived from high-quality alignments. Can be accessed on the World Wide Web at: http://coot.embl-heidelberg.de/SMART/.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 229-232
-
-
Ponting, C.P.1
Schultz, J.2
Milpetz, F.3
Bork, P.4
-
10
-
-
0032509179
-
Comparison of the complete protein sets of worm and yeast: Orthology and divergence
-
The first comparison of the complete proteomes of two eukaryotes. The authors describe the lineage-specific domain expansions, conservation of the core functions and the use of PSI-BLAST sequence profiles in establishing counts for proteins containing particular domains
-
Chervitz S.A., Aravind L., Sherlock G., Ball C.A., Koonin E.V., Dwight S.S., Harris M.A., Dolinski K., Mohr S., Smith T.et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 282:1998;2022-2028. The first comparison of the complete proteomes of two eukaryotes. The authors describe the lineage-specific domain expansions, conservation of the core functions and the use of PSI-BLAST sequence profiles in establishing counts for proteins containing particular domains.
-
(1998)
Science
, vol.282
, pp. 2022-2028
-
-
Chervitz, S.A.1
Aravind, L.2
Sherlock, G.3
Ball, C.A.4
Koonin, E.V.5
Dwight, S.S.6
Harris, M.A.7
Dolinski, K.8
Mohr, S.9
Smith, T.10
-
11
-
-
0033053181
-
The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes
-
Detailed analysis of the largest transcription factor family - the nuclear hormone receptors in the C. elegans proteome. The analysis identifies the ancient families as well as the nematode-specific expansion that has occurred within this superfamily
-
Sluder A.E., Mathews S.W., Hough D., Yin V.P., Maina C.V. The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. Genome Res. 9:1999;103-120. Detailed analysis of the largest transcription factor family - the nuclear hormone receptors in the C. elegans proteome. The analysis identifies the ancient families as well as the nematode-specific expansion that has occurred within this superfamily.
-
(1999)
Genome Res
, vol.9
, pp. 103-120
-
-
Sluder, A.E.1
Mathews, S.W.2
Hough, D.3
Yin, V.P.4
Maina, C.V.5
-
12
-
-
0031914530
-
The T-box gene family
-
Describes the diversity of the T-Box transcription factors in the animals
-
Papaioannou V.E., Silver L.M. The T-box gene family. Bioessays. 20:19989-19;. Describes the diversity of the T-Box transcription factors in the animals.
-
(1998)
Bioessays
, vol.20
, pp. 9-19
-
-
Papaioannou, V.E.1
Silver, L.M.2
-
13
-
-
0033153141
-
Pax genes in Caenorhabditis elegans: A new twist
-
Describes the interesting case of the alternative domain organizations of two HTH domains comprising the Paired Box. The carboxy- and amino-terminal HTH domains have been shown to occur independently of each other as well as in the form of fusions as in the classic Paired domains
-
Hobert O., Ruvkun G. Pax genes in Caenorhabditis elegans: a new twist. Trends Genet. 15:1999;214-216. Describes the interesting case of the alternative domain organizations of two HTH domains comprising the Paired Box. The carboxy- and amino-terminal HTH domains have been shown to occur independently of each other as well as in the form of fusions as in the classic Paired domains.
-
(1999)
Trends Genet
, vol.15
, pp. 214-216
-
-
Hobert, O.1
Ruvkun, G.2
-
14
-
-
0032509303
-
The taxonomy of developmental control in Caenorhabditis elegans
-
Provides a detailed summary of the conservation of developmental pathways in the nematode. Some of the conclusions reported here need to be reconsidered due to use of an outdated sequence set
-
Ruvkun G., Hobert O. The taxonomy of developmental control in Caenorhabditis elegans. Science. 282:1998;2033-2041. Provides a detailed summary of the conservation of developmental pathways in the nematode. Some of the conclusions reported here need to be reconsidered due to use of an outdated sequence set.
-
(1998)
Science
, vol.282
, pp. 2033-2041
-
-
Ruvkun, G.1
Hobert, O.2
-
15
-
-
0033613909
-
Fold prediction and evolutionary analysis of the POZ domain: Structural and evolutionary relationship with the potassium channel tetramerization domain
-
This paper describes the provenance of the 'eukaryotic' signaling domains. The intracellular occurrence of von Willebrand factor A domains in the TFIIH p44 subunit is reported for the first time and enumeration of these domains in complete genomes is provided
-
Aravind L., Koonin E.V. Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain. J Mol Biol. 285:1999;1353-1361. This paper describes the provenance of the 'eukaryotic' signaling domains. The intracellular occurrence of von Willebrand factor A domains in the TFIIH p44 subunit is reported for the first time and enumeration of these domains in complete genomes is provided.
-
(1999)
J Mol Biol
, vol.285
, pp. 1353-1361
-
-
Aravind, L.1
Koonin, E.V.2
-
16
-
-
0033057517
-
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer
-
Describes the intracellular occurrence of von Willebrand factor A domains in the TFIIH subunit p44 subunit
-
Ponting C.P., Aravind L., Schultz J., Bork P., Koonin E.V. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J Mol Biol. 289:1999;729-745. Describes the intracellular occurrence of von Willebrand factor A domains in the TFIIH subunit p44 subunit.
-
(1999)
J Mol Biol
, vol.289
, pp. 729-745
-
-
Ponting, C.P.1
Aravind, L.2
Schultz, J.3
Bork, P.4
Koonin, E.V.5
-
17
-
-
0030477366
-
Fibronectin type III domains in yeast detected by a hidden Markov model
-
Bateman A., Chothia C. Fibronectin type III domains in yeast detected by a hidden Markov model. Curr Biol. 6:1996;1544-1547.
-
(1996)
Curr Biol
, vol.6
, pp. 1544-1547
-
-
Bateman, A.1
Chothia, C.2
-
18
-
-
0031457622
-
Signaling through scaffold, anchoring, and adaptor proteins
-
Pawson T., Scott J.D. Signaling through scaffold, anchoring, and adaptor proteins. Science. 278:1997;2075-2080.
-
(1997)
Science
, vol.278
, pp. 2075-2080
-
-
Pawson, T.1
Scott, J.D.2
-
19
-
-
0031197193
-
SH2 and PTB domain interactions in tyrosine kinase signal transduction
-
Shoelson S.E. SH2 and PTB domain interactions in tyrosine kinase signal transduction. Curr Opin Chem Biol. 1:1997;227-234.
-
(1997)
Curr Opin Chem Biol
, vol.1
, pp. 227-234
-
-
Shoelson, S.E.1
-
20
-
-
0032425454
-
The adenylyl and guanylyl cyclase superfamily
-
Provides an introduction to the recent developments regarding the cyclic nucleotide generating enzymes
-
Hurley J.H. The adenylyl and guanylyl cyclase superfamily. Curr Opin Struct Biol. 8:1998;770-777. Provides an introduction to the recent developments regarding the cyclic nucleotide generating enzymes.
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 770-777
-
-
Hurley, J.H.1
-
21
-
-
0031460029
-
PDZ domain proteins: Scaffolds for signaling complexes
-
Reviews the role of PDZ domains in acting as the sub-membrane scaffolds in animal signaling systems
-
Ranganathan R., Ross E.M. PDZ domain proteins: scaffolds for signaling complexes. Curr Biol. 7:1997;R770-R773. Reviews the role of PDZ domains in acting as the sub-membrane scaffolds in animal signaling systems.
-
(1997)
Curr Biol
, vol.7
-
-
Ranganathan, R.1
Ross, E.M.2
-
22
-
-
0030032040
-
Calcium binding and conformational response in EF-hand proteins
-
Ikura M. Calcium binding and conformational response in EF-hand proteins. Trends Biochem Sci. 21:1996;14-17.
-
(1996)
Trends Biochem Sci
, vol.21
, pp. 14-17
-
-
Ikura, M.1
-
23
-
-
0031831274
-
Combinatorial control in ubiquitin dependent proteolysis: Don't Skp the F-box hypothesis
-
Provides a good introduction to the significance of the F-Box in ubiquitin-dependent signaling. The role of the F-box modules in targeting the ubiquitin-conjugating system is described
-
Patton E.E., Willems A.R., Tyers M. Combinatorial control in ubiquitin dependent proteolysis: don't Skp the F-box hypothesis. Trends Genet. 14:1998;236-243. Provides a good introduction to the significance of the F-Box in ubiquitin-dependent signaling. The role of the F-box modules in targeting the ubiquitin-conjugating system is described.
-
(1998)
Trends Genet
, vol.14
, pp. 236-243
-
-
Patton, E.E.1
Willems, A.R.2
Tyers, M.3
-
24
-
-
0029803121
-
Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators
-
Schjerling P., Holmberg S. Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators. Nucleic Acids Res. 24:1996;4599-4607.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4599-4607
-
-
Schjerling, P.1
Holmberg, S.2
-
25
-
-
0033582917
-
Structural and functional analysis of the ARF1 ARFGAP complex reveals a role for coatomer in GTP hydrolysis
-
A primary paper describing the molecular mechanism of the ARF-like GTPase-activating proteins. These GAPs have a structure similar to the GATA zinc fingers and unlike other GAPs contribute no residues to the GTPase active site
-
Goldberg J. Structural and functional analysis of the ARF1 ARFGAP complex reveals a role for coatomer in GTP hydrolysis. Cell. 96:1999;893-902. A primary paper describing the molecular mechanism of the ARF-like GTPase-activating proteins. These GAPs have a structure similar to the GATA zinc fingers and unlike other GAPs contribute no residues to the GTPase active site.
-
(1999)
Cell
, vol.96
, pp. 893-902
-
-
Goldberg, J.1
-
26
-
-
0028137615
-
Activators and effectors of ras p21 proteins
-
McCormick F. Activators and effectors of ras p21 proteins. Curr Opin Genet Dev. 4:1994;71-76.
-
(1994)
Curr Opin Genet Dev
, vol.4
, pp. 71-76
-
-
McCormick, F.1
-
27
-
-
0030968580
-
Rho GTPases and signaling networks
-
Van Aelst L. Rho GTPases and signaling networks. Genes Dev. 11:1997;2295-2322.
-
(1997)
Genes Dev
, vol.11
, pp. 2295-2322
-
-
Van Aelst, L.1
-
28
-
-
0032509320
-
Zinc fingers in Caenorhabditis elegans: Finding families and probing pathways
-
Describes the elaboration of different zinc chelating domains in C. elegans
-
Clarke N.D., Berg J.M. Zinc fingers in Caenorhabditis elegans: finding families and probing pathways. Science. 282:1998;2018-2022. Describes the elaboration of different zinc chelating domains in C. elegans.
-
(1998)
Science
, vol.282
, pp. 2018-2022
-
-
Clarke, N.D.1
Berg, J.M.2
-
29
-
-
0032447692
-
Asymmetric cell division: From A to Z
-
Reviews the role of asymmetric divisions in patterning and differentiation
-
Hawkins N., Garriga G. Asymmetric cell division: from A to Z. Genes Dev. 12:1998;3625-3638. Reviews the role of asymmetric divisions in patterning and differentiation.
-
(1998)
Genes Dev
, vol.12
, pp. 3625-3638
-
-
Hawkins, N.1
Garriga, G.2
-
30
-
-
0033617522
-
Notch signaling: Cell fate control and signal integration in development
-
An update review of the animal-specific Notch signaling pathway describing the role of the recently uncovered components of this pathway
-
Artavanis-Tsakonas S., Rand M.D., Lake R.J. Notch signaling: cell fate control and signal integration in development. Science. 284:1999;770-776. An update review of the animal-specific Notch signaling pathway describing the role of the recently uncovered components of this pathway.
-
(1999)
Science
, vol.284
, pp. 770-776
-
-
Artavanis-Tsakonas, S.1
Rand, M.D.2
Lake, R.J.3
-
31
-
-
0031561502
-
Secreted fringe-like signaling molecules may be glycosyltransferases
-
Yuan Y.P., Schultz J., Mlodzik M., Bork P. Secreted fringe-like signaling molecules may be glycosyltransferases. Cell. 88:1997;9-11.
-
(1997)
Cell
, vol.88
, pp. 9-11
-
-
Yuan, Y.P.1
Schultz, J.2
Mlodzik, M.3
Bork, P.4
-
32
-
-
0028226218
-
Mobile Minos elements from Drosophila hydei encode a two-exon transposase with similarity to the paired DNA-binding domain
-
Franz G., Loukeris T.G., Dialektaki G., Thompson C.R., Savakis C. Mobile Minos elements from Drosophila hydei encode a two-exon transposase with similarity to the paired DNA-binding domain. Proc Natl Acad Sci USA. 91:1994;4746-4750.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 4746-4750
-
-
Franz, G.1
Loukeris, T.G.2
Dialektaki, G.3
Thompson, C.R.4
Savakis, C.5
-
33
-
-
0342813091
-
Crystal structure of a Hedgehog autoprocessing domain: Homology between Hedgehog and self-splicing proteins
-
Hall T.M., Porter J.A., Young K.E., Koonin E.V., Beachy P.A., Leahy D.J. Crystal structure of a Hedgehog autoprocessing domain: homology between Hedgehog and self-splicing proteins. Cell. 91:1997;85-97.
-
(1997)
Cell
, vol.91
, pp. 85-97
-
-
Hall, T.M.1
Porter, J.A.2
Young, K.E.3
Koonin, E.V.4
Beachy, P.A.5
Leahy, D.J.6
-
34
-
-
0028155096
-
Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP
-
Perez-Alvarado G.C., Miles C., Michelsen J.W., Louis H.A., Winge D.R., Beckerle M.C., Summers M.F. Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP. Nat Struct Biol. 1:1994;388-398.
-
(1994)
Nat Struct Biol
, vol.1
, pp. 388-398
-
-
Perez-Alvarado, G.C.1
Miles, C.2
Michelsen, J.W.3
Louis, H.A.4
Winge, D.R.5
Beckerle, M.C.6
Summers, M.F.7
-
35
-
-
0029157378
-
Evolution of the SNF2 family of proteins: Subfamilies with distinct sequences and functions
-
Eisen J.A., Sweder K.S., Hanawalt P.C. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23:1995;2715-2723.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 2715-2723
-
-
Eisen, J.A.1
Sweder, K.S.2
Hanawalt, P.C.3
-
36
-
-
0032982976
-
The functions of breast cancer susceptibility gene 1 (BRCA1) product and its associated proteins
-
A summing up of the present understanding of the role the BRCA proteins in the regulation of cellular proliferation
-
Irminger-Finger I., Siegel B.D., Leung W.C. The functions of breast cancer susceptibility gene 1 (BRCA1) product and its associated proteins. Biol Chem. 380:1999;117-128. A summing up of the present understanding of the role the BRCA proteins in the regulation of cellular proliferation.
-
(1999)
Biol Chem
, vol.380
, pp. 117-128
-
-
Irminger-Finger, I.1
Siegel, B.D.2
Leung, W.C.3
-
37
-
-
0033040967
-
PRb and E2f-1 in mouse development and tumorigenesis
-
A discussion of the role of the E2F/Rb system in regulating cell proliferation in animals
-
Macleod K. pRb and E2f-1 in mouse development and tumorigenesis. Curr Opin Genet Dev. 9:1999;31-39. A discussion of the role of the E2F/Rb system in regulating cell proliferation in animals.
-
(1999)
Curr Opin Genet Dev
, vol.9
, pp. 31-39
-
-
Macleod, K.1
-
38
-
-
2642713363
-
The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity
-
Suzuki M., Kao C.Y., McCarty D.R. The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. Plant Cell. 9:1997;799-807.
-
(1997)
Plant Cell
, vol.9
, pp. 799-807
-
-
Suzuki, M.1
Kao, C.Y.2
McCarty, D.R.3
-
39
-
-
0031845074
-
The AP2/EREBP family of plant transcription factors
-
Riechmann J.L., Meyerowitz E.M. The AP2/EREBP family of plant transcription factors. Biol Chem. 379:1998;633-646.
-
(1998)
Biol Chem
, vol.379
, pp. 633-646
-
-
Riechmann, J.L.1
Meyerowitz, E.M.2
-
40
-
-
0032506138
-
Eukaryotic phytochromes: Light-regulated serine/threonine protein kinases with histidine kinase ancestry
-
Yeh K.C., Lagarias J.C. Eukaryotic phytochromes: light-regulated serine/threonine protein kinases with histidine kinase ancestry. Proc Natl Acad Sci USA. 95:1998;13976-13981.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 13976-13981
-
-
Yeh, K.C.1
Lagarias, J.C.2
|