-
1
-
-
57749183063
-
Biological clustering method for logistic place decision making
-
Lovrek, I. et al (eds). Springer, Berlin Heidelberg
-
Bakar, R. B. A. and Watada, J. (2008) Biological clustering method for logistic place decision making. In: Lovrek, I. et al (eds). Knowledge-Based Intelligent Information and Engineering Systems. Springer, Berlin Heidelberg, pp. 136-143.
-
(2008)
Knowledge-Based Intelligent Information and Engineering Systems
, pp. 136-143
-
-
Bakar, R.B.A.1
Watada, J.2
-
2
-
-
44949110144
-
Chlorophyll fluorescence: A probe of photosynthesis in vivo
-
Baker, N. R. (2008) Chlorophyll fluorescence: A probe of photosynthesis in vivo. Annu. Rev. Plant Biol., 59, 89-113.
-
(2008)
Annu. Rev. Plant Biol.
, vol.59
, pp. 89-113
-
-
Baker, N.R.1
-
3
-
-
0041346457
-
Continuous representations of time-series gene expression data
-
Bar-Joseph, Z. et al. (2003) Continuous representations of time-series gene expression data. J. Comput. Biol., 10, 341-356.
-
(2003)
J. Comput. Biol.
, vol.10
, pp. 341-356
-
-
Bar-Joseph, Z.1
-
4
-
-
8844277626
-
Analyzing time series gene expression data
-
Bar-Joseph, Z. (2004) Analyzing time series gene expression data. Bioinformatics, 20, 2493-2503.
-
(2004)
Bioinformatics
, vol.20
, pp. 2493-2503
-
-
Bar-Joseph, Z.1
-
5
-
-
0032728081
-
Clustering gene expression patterns
-
Ben-Dor, A. et al. (1999) Clustering gene expression patterns. J. Comput. Biol., 6, 281-297.
-
(1999)
J. Comput. Biol.
, vol.6
, pp. 281-297
-
-
Ben-Dor, A.1
-
6
-
-
70349578234
-
Cognitive ontologies for neuropsychiatric phenomics research
-
Bilder, R. M. et al. (2009) Cognitive ontologies for neuropsychiatric phenomics research. Cogn. Neuropsychiatry, 14, 419-450.
-
(2009)
Cogn. Neuropsychiatry
, vol.14
, pp. 419-450
-
-
Bilder, R.M.1
-
7
-
-
30544439504
-
Creation and implications of a phenomegenome network
-
Butte, A. J. and Kohane, I. S. (2006) Creation and implications of a phenomegenome network. Nat. Biotech., 24, 55-62.
-
(2006)
Nat. Biotech.
, vol.24
, pp. 55-62
-
-
Butte, A.J.1
Kohane, I.S.2
-
9
-
-
84875426911
-
Next-generation phenotyping: Requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement
-
Cobb, J. N. et al. (2013) Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. Theor. Appl. Genet., 126, 867-887.
-
(2013)
Theor. Appl. Genet.
, vol.126
, pp. 867-887
-
-
Cobb, J.N.1
-
10
-
-
84864312283
-
Protein function prediction by clustering of protein-protein interaction network
-
Springer, Berlin Heidelberg
-
Cingovska, I. et al. (2012) Protein Function Prediction by Clustering of Protein-Protein Interaction Network. ICT Innovations 2011, Springer, Berlin Heidelberg, pp. 39-49.
-
(2012)
ICT Innovations 2011
, pp. 39-49
-
-
Cingovska, I.1
-
12
-
-
0024297354
-
Multiple sequence alignment with hierarchical clustering
-
Corpet, F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881-10890.
-
(1988)
Nucleic Acids Res.
, vol.16
, pp. 10881-10890
-
-
Corpet, F.1
-
13
-
-
11344295027
-
Comparative analysis of clustering methods for gene expression time course data
-
Costa, I. G. (2004) Comparative analysis of clustering methods for gene expression time course data. Genet. Mol. Biol., 27, 623-631.
-
(2004)
Genet. Mol. Biol.
, vol.27
, pp. 623-631
-
-
Costa, I.G.1
-
14
-
-
84959884682
-
Dynamic environmental photosynthetic imaging (DEPI) reveals emergent phenotypes related to the environmental responses of photosynthesis
-
Cruz, J. A. et al. (2015) Dynamic environmental photosynthetic imaging (DEPI) reveals emergent phenotypes related to the environmental responses of photosynthesis. Nat. Biotech., in press.
-
(2015)
Nat. Biotech., in Press
-
-
Cruz, J.A.1
-
15
-
-
0036999722
-
Structure, dynamics, and energetics of the primary photochemistry of photosystem II of oxygenic photosynthesis
-
Diner, B. A. and Rappaport, F. (2002) Structure, dynamics, and energetics of the primary photochemistry of photosystem II of oxygenic photosynthesis. Annu. Rev. Plant Biol., 53, 551-580.
-
(2002)
Annu. Rev. Plant Biol.
, vol.53
, pp. 551-580
-
-
Diner, B.A.1
Rappaport, F.2
-
16
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen, M. B. et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl. Acad. Sci., 95, 14863-14868.
-
(1998)
Proc Natl. Acad. Sci.
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
-
17
-
-
0033944826
-
GeneRAGE: A robust algorithm for sequence clustering and domain detection
-
Enright, A. J. and Ouzounis, C. A. (2000) GeneRAGE: A robust algorithm for sequence clustering and domain detection. Bioinformatics, 16, 451-457.
-
(2000)
Bioinformatics
, vol.16
, pp. 451-457
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
19
-
-
33846036091
-
PhenomicDB: A new cross-species genotype/phenotype resource
-
Groth, P. et al. (2007) PhenomicDB: A new cross-species genotype/phenotype resource. Nucleic Acids Res., 35(Suppl. 1), D696-D699.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D696-D699
-
-
Groth, P.1
-
20
-
-
77955032112
-
Phenoclustering: Online mining of cross-species phenotypes
-
Groth, P. et al. (2010) Phenoclustering: Online mining of cross-species phenotypes. Bioinformatics, 26, 1924-1925.
-
(2010)
Bioinformatics
, vol.26
, pp. 1924-1925
-
-
Groth, P.1
-
21
-
-
79960909630
-
Phenotype mining for functional genomics and gene discovery
-
Springer, New York
-
Groth, P. et al. (2011) Phenotype mining for functional genomics and gene discovery. Silico Tools for Gene Discovery. Springer, New York, pp. 159-173.
-
(2011)
Silico Tools for Gene Discovery
, pp. 159-173
-
-
Groth, P.1
-
22
-
-
85011844710
-
Photosynthetic measurements with the idea spec: An integrated diode emitter array spectrophotometer/fluorometer
-
Springer, Berlin Heidelberg
-
Hall, C. C. et al. (2013) Photosynthetic measurements with the idea spec: An integrated diode emitter array spectrophotometer/fluorometer. In: Photosynthesis Research for Food, Fuel and the Future. Springer, Berlin Heidelberg, pp. 184-188.
-
(2013)
Photosynthesis Research for Food, Fuel and the Future
, pp. 184-188
-
-
Hall, C.C.1
-
23
-
-
32644439684
-
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons
-
Harr, B. and Schlötterer, C. (2006) Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons. Nucleic Acids Res., 34, e8.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. e8
-
-
Harr, B.1
Schlötterer, C.2
-
24
-
-
0345580221
-
Large-scale clustering of cDNA-fingerprinting data
-
Herwig, R. et al. (1999) Large-scale clustering of cDNA-fingerprinting data. Genome Res., 9, 1093-1105.
-
(1999)
Genome Res.
, vol.9
, pp. 1093-1105
-
-
Herwig, R.1
-
25
-
-
34547852209
-
Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics
-
Jaqaman, K. et al. (2007) Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics. Bioinformatics, 23, 1666-1673.
-
(2007)
Bioinformatics
, vol.23
, pp. 1666-1673
-
-
Jaqaman, K.1
-
26
-
-
0014129195
-
Hierarchical clustering schemes
-
Johnson, S. C. (1967) Hierarchical clustering schemes. Psychometrika, 32, 241-254.
-
(1967)
Psychometrika
, vol.32
, pp. 241-254
-
-
Johnson, S.C.1
-
28
-
-
78650985721
-
The importance of energy balance in improving photosynthetic productivity
-
Kramer, D. M. and Evans, J. R. (2011) The importance of energy balance in improving photosynthetic productivity. Plant Physiol., 155, 70-78.
-
(2011)
Plant Physiol.
, vol.155
, pp. 70
-
-
Kramer, D.M.1
Evans, J.R.2
-
29
-
-
3042804076
-
Dynamic flexibility in the light reactions of photosynthesis governed by both electron and proton transfer reactions
-
Kramer, D. M. et al. (2004) Dynamic flexibility in the light reactions of photosynthesis governed by both electron and proton transfer reactions. Trends Plant Sci., 9, 349-357.
-
(2004)
Trends Plant Sci.
, vol.9
, pp. 349-357
-
-
Kramer, D.M.1
-
30
-
-
84862234802
-
The arabidopsis information resource (tair): Improved gene annotation and new tools
-
Lamesch, P. et al. (2012) The arabidopsis information resource (tair): improved gene annotation and new tools. Nucleic Acids Res., 40, D1202-D1210.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D1202-D1210
-
-
Lamesch, P.1
-
31
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li, W. and Godzik, A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
32
-
-
34547967202
-
Regulatory motif discovery using a population clustering evolutionary algorithm
-
Lones, M. A. and Tyrrell, A. M. (2007) Regulatory motif discovery using a population clustering evolutionary algorithm. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 4, 403-414.
-
(2007)
IEEE/ACM Trans. Comput. Biol. Bioinformatics
, vol.4
, pp. 403-414
-
-
Lones, M.A.1
Tyrrell, A.M.2
-
33
-
-
79953719673
-
Chloroplast 2010: A database for large-scale phenotypic screening of Arabidopsis mutants
-
Lu, Y. et al. (2011) Chloroplast 2010: A database for large-scale phenotypic screening of Arabidopsis mutants. Plant Physiol., 155, 1589-1600.
-
(2011)
Plant Physiol.
, vol.155
, pp. 1589-1600
-
-
Lu, Y.1
-
37
-
-
77958504829
-
Model-based clustering of microarray expression data via latent Gaussian mixture models
-
McNicholas, P. D. and Murphy, T. B. (2010) Model-based clustering of microarray expression data via latent Gaussian mixture models. Bioinformatics, 26, 2705-2712.
-
(2010)
Bioinformatics
, vol.26
, pp. 2705-2712
-
-
McNicholas, P.D.1
Murphy, T.B.2
-
38
-
-
0000570384
-
On non-parametric estimates of density functions and regression curves
-
Nadaraya, E. A. (1965) On non-parametric estimates of density functions and regression curves. Theor. Probab. Appl., 10, 186-190.
-
(1965)
Theor. Probab. Appl.
, vol.10
, pp. 186-190
-
-
Nadaraya, E.A.1
-
39
-
-
84865141182
-
Bayesian model-based clustering of temporal gene expression using autoregressive panel data approach
-
Nascimento, M. et al. (2012) Bayesian model-based clustering of temporal gene expression using autoregressive panel data approach. Bioinformatics, 28, 2004-2007.
-
(2012)
Bioinformatics
, vol.28
, pp. 2004-2007
-
-
Nascimento, M.1
-
40
-
-
79951562208
-
ATTED-II updates: Condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
-
Obayashi, T. et al. (2011) ATTED-II updates: Condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell. Physiol., 52, 213-219.
-
(2011)
Plant Cell. Physiol.
, vol.52
, pp. 213-219
-
-
Obayashi, T.1
-
41
-
-
0001473437
-
On estimation of a probability density function and mode
-
Parzen, E. (1962) On estimation of a probability density function and mode. Ann. Math. Stat., 33, 1065-1076.
-
(1962)
Ann. Math. Stat.
, vol.33
, pp. 1065-1076
-
-
Parzen, E.1
-
42
-
-
15244355067
-
Kolmogorov-smirnov test
-
2nd edn, Cambridge University Press, Cambridge, England, New York
-
Press, W. H. et al. (1992) Kolmogorov-Smirnov Test. In: Numerical Recipes in FORTRAN: The Art of Scientific Computing, 2nd edn, Cambridge University Press, Cambridge, England, New York, pp. 617-620.
-
(1992)
Numerical Recipes in FORTRAN: The Art of Scientific Computing
, pp. 617-620
-
-
Press, W.H.1
-
43
-
-
34247875975
-
Evaluation of gene-expression clustering via mutual information distance measure
-
Priness, I. et al. (2007) Evaluation of gene-expression clustering via mutual information distance measure. BMC Bioinformatics, 8, 111.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 111
-
-
Priness, I.1
-
44
-
-
0035861975
-
Beyond synexpression relationships: Local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions
-
Qian, J. et al. (2001) Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J. Mol. Biol., 314, 1053-1066.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 1053-1066
-
-
Qian, J.1
-
45
-
-
0037047161
-
Cluster analysis of gene expression dynamics
-
Ramoni, M. F. et al. (2002) Cluster analysis of gene expression dynamics. Proc. Natl. Acad. Sci. USA, 99, 9121-9126.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 9121-9126
-
-
Ramoni, M.F.1
-
46
-
-
0031061864
-
Parametric and non-parametric unsupervised cluster analysis
-
Roberts, S. J. (1997) Parametric and non-parametric unsupervised cluster analysis. Pattern Recogn., 30, 261-272.
-
(1997)
Pattern Recogn.
, vol.30
, pp. 261-272
-
-
Roberts, S.J.1
-
47
-
-
0001529784
-
Remarks on some nonparametric estimates of a density function
-
Rosenblatt, M. (1956) Remarks on some nonparametric estimates of a density function. Ann. Math. Stat., 27, 832-837.
-
(1956)
Ann. Math. Stat.
, vol.27
, pp. 832-837
-
-
Rosenblatt, M.1
-
48
-
-
4944252468
-
Using hidden Markov models to analyze gene expression time course data
-
Schliep, A. et al. (2003) Using hidden Markov models to analyze gene expression time course data. Bioinformatics, 19(Suppl 1), i255-i263.
-
(2003)
Bioinformatics
, vol.19
, pp. i255-i263
-
-
Schliep, A.1
-
49
-
-
33646307647
-
Maximum likelihood estimation
-
Kotz, S. et al, (eds.), 2nd edn. Wiley, Hobokenm NJ
-
Scholz, F. W. (1985) Maximum likelihood estimation. In: Kotz, S. et al, (eds.) Encyclopedia of Statistical Sciences, 2nd edn. Wiley, Hobokenm NJ, pp. 4629-4639.
-
(1985)
Encyclopedia of Statistical Sciences
, pp. 4629-4639
-
-
Scholz, F.W.1
-
50
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure, J. and Ji, H. (2008) Next-generation DNA sequencing. Nat Biotech., 26, 1135-1145.
-
(2008)
Nat Biotech.
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
51
-
-
79959422007
-
An integrative clustering and modeling algorithm for dynamical gene expression data
-
Sivriver, J. et al. (2011) An integrative clustering and modeling algorithm for dynamical gene expression data. Bioinformatics, 27, i392-i400.
-
(2011)
Bioinformatics
, vol.27
, pp. i392-i400
-
-
Sivriver, J.1
-
52
-
-
0001942153
-
Model selection for probabilistic clustering using cross-validated likelihood
-
Smyth, P. (2000) Model selection for probabilistic clustering using cross-validated likelihood. Stat. Comput., 10, 63-72.
-
(2000)
Stat. Comput.
, vol.10
, pp. 63-72
-
-
Smyth, P.1
-
53
-
-
0001297207
-
A law of the logarithm for kernel density estimators
-
Stute, W. (1982) A law of the logarithm for kernel density estimators. Ann. Probab., 10, 414-422.
-
(1982)
Ann. Probab.
, vol.10
, pp. 414-422
-
-
Stute, W.1
-
54
-
-
0033027794
-
Interpreting patterns of gene expression with selforganizing maps: Methods and application to hematopoietic differentiation
-
Tamayo, P. et al. (1999) Interpreting patterns of gene expression with selforganizing maps: Methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA, 96, 2907-2912.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 2907-2912
-
-
Tamayo, P.1
-
55
-
-
34848863975
-
The thylakoid proton motive force in vivo. Quantitative, non-invasive probes, energetics, and regulatory consequences of light-induced pmf
-
Takizawa, K. et al. (2007). The thylakoid proton motive force in vivo. Quantitative, non-invasive probes, energetics, and regulatory consequences of light-induced pmf. BBA-Bioenergetics, 1767, 1233-1244.
-
(2007)
BBA-Bioenergetics
, vol.1767
, pp. 1233-1244
-
-
Takizawa, K.1
-
56
-
-
84903637193
-
Functional approach to high-throughput plant growth analysis
-
Tessmer, O. L. et al. (2013) Functional Approach to High-throughput Plant Growth Analysis. BMC Syst. Biol., 7(Suppl. 6), S17.
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. S17
-
-
Tessmer, O.L.1
-
57
-
-
34548583274
-
A tutorial on spectral clustering
-
Von Luxburg, U. (2007) A tutorial on spectral clustering. Stat. Comput., 17, 395-416.
-
(2007)
Stat. Comput.
, vol.17
, pp. 395-416
-
-
Von Luxburg, U.1
-
58
-
-
79951799418
-
The pleiotropic structure of the genotype-phenotype map: The evolvability of complex organisms
-
Wagner, G. P. and Zhang, J. (2013) The pleiotropic structure of the genotype-phenotype map: The evolvability of complex organisms. Nat. Rev. Gen., 12, 204-213.
-
(2013)
Nat. Rev. Gen.
, vol.12
, pp. 204-213
-
-
Wagner, G.P.1
Zhang, J.2
-
59
-
-
84876235775
-
Function-function correlated multi-label protein function prediction over interaction networks
-
Wang, H. et al. (2013) Function-function correlated multi-label protein function prediction over interaction networks. J. Comput. Biol., 20, 322-343.
-
(2013)
J. Comput. Biol.
, vol.20
, pp. 322-343
-
-
Wang, H.1
-
60
-
-
0025573210
-
A new approach to clustering
-
Wilson, R. and Spann, M. (1990) A new approach to clustering. Pattern Recogn., 23, 1413-1425.
-
(1990)
Pattern Recogn.
, vol.23
, pp. 1413-1425
-
-
Wilson, R.1
Spann, M.2
-
61
-
-
0036649020
-
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
-
Wu, L. F. et al. (2002) Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet., 31, 255-265.
-
(2002)
Nat. Genet.
, vol.31
, pp. 255-265
-
-
Wu, L.F.1
-
62
-
-
37549058830
-
A point mutation in atpC1 raises the redox potential of the Arabidopsis chloroplast ATP synthase c-subunit regulatory disulfide above the range of thioredoxin modulation
-
Wu, G. et al. (2007) A point mutation in atpC1 raises the redox potential of the Arabidopsis chloroplast ATP synthase c-subunit regulatory disulfide above the range of thioredoxin modulation. J. Biol. Chem., 282, 36782-36789.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 36782-36789
-
-
Wu, G.1
-
63
-
-
84941649661
-
Plant photosynthesis phenomics data quality control
-
Xu, L. et al. (2015) Plant photosynthesis phenomics data quality control. Bioinformatics, 31, 1796-1804.
-
(2015)
Bioinformatics
, vol.31
, pp. 1796-1804
-
-
Xu, L.1
-
64
-
-
84922203325
-
Combining high-throughput phenotyping and genomewide association studies to reveal natural genetic variation in rice
-
Yang, W. et al. (2014) Combining high-throughput phenotyping and genomewide association studies to reveal natural genetic variation in rice. Nat. Commun., 5, 5087.
-
(2014)
Nat. Commun.
, vol.5
, pp. 5087
-
-
Yang, W.1
-
65
-
-
77955695587
-
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants
-
Zhang, P. et al. (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol., 153, 1479-1491.
-
(2010)
Plant Physiol.
, vol.153
, pp. 1479-1491
-
-
Zhang, P.1
|