-
1
-
-
61749093225
-
A novel methodology for finding the regulation on gene expression data
-
Liu W, Wang B, Glassey J, Martin E, Zhao J. A novel methodology for finding the regulation on gene expression data. Proc Natl Acad Sci U S A 2009, 19:267-272.
-
(2009)
Proc Natl Acad Sci U S A
, vol.19
, pp. 267-272
-
-
Liu, W.1
Wang, B.2
Glassey, J.3
Martin, E.4
Zhao, J.5
-
2
-
-
0035845501
-
Correspondence analysis applied to microarray data
-
10.1073/pnas.181597298, 58552, 11535808
-
Fellenberg K, Hauser NC, Brors B, Neutzner A, Hoheisel JD, Vingron M. Correspondence analysis applied to microarray data. Proc Natl Acad Sci 2001, 98:10781. 10.1073/pnas.181597298, 58552, 11535808.
-
(2001)
Proc Natl Acad Sci
, vol.98
, pp. 10781
-
-
Fellenberg, K.1
Hauser, N.C.2
Brors, B.3
Neutzner, A.4
Hoheisel, J.D.5
Vingron, M.6
-
3
-
-
84864054608
-
Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data
-
Kim MH, Seo HJ, Joung JG, Kim JH. Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data. BMC bioinformatics 2011, 12(Suppl 1):S8.
-
(2011)
BMC bioinformatics
, vol.12
, Issue.SUPPL 1
-
-
Kim, M.H.1
Seo, H.J.2
Joung, J.G.3
Kim, J.H.4
-
4
-
-
0035375137
-
Computational analysis of microarray data: nature reviews
-
Quackenbush J. Computational analysis of microarray data: nature reviews. Genetics 2001, 2:418-427.
-
(2001)
Genetics
, vol.2
, pp. 418-427
-
-
Quackenbush, J.1
-
5
-
-
84855238658
-
Archetypal analysis for machine learning and data mining
-
Mørup M, Hansen LK. Archetypal analysis for machine learning and data mining. Neurocomputing 2012, 80:54-63.
-
(2012)
Neurocomputing
, vol.80
, pp. 54-63
-
-
Mørup, M.1
Hansen, L.K.2
-
7
-
-
33846015059
-
Archetypes and principal components of an IR image sequence
-
Marinetti S, Finesso L, Marsilio E. Archetypes and principal components of an IR image sequence. Infrared Phys Technol 2007, 49:272-276.
-
(2007)
Infrared Phys Technol
, vol.49
, pp. 272-276
-
-
Marinetti, S.1
Finesso, L.2
Marsilio, E.3
-
9
-
-
35649024854
-
Toward the human genotope
-
10.1007/s11538-007-9244-7, 17874271
-
Huggins P, Pachter L, Sturmfels B. Toward the human genotope. Bull Math Biol 2007, 69:2723-2735. 10.1007/s11538-007-9244-7, 17874271.
-
(2007)
Bull Math Biol
, vol.69
, pp. 2723-2735
-
-
Huggins, P.1
Pachter, L.2
Sturmfels, B.3
-
10
-
-
76949086352
-
Applying unmixing to gene expression data for tumor phylogeny inference
-
Schwartz R, Shackney SE. Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinforma 2010, 11:42.
-
(2010)
BMC Bioinforma
, vol.11
, pp. 42
-
-
Schwartz, R.1
Shackney, S.E.2
-
11
-
-
84861663597
-
Evolutionary trade-offs, pareto optimality, and the geometry of phenotype space
-
Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O, Mayo A, Dekel E, Kavanagh K, Alon U. Evolutionary trade-offs, pareto optimality, and the geometry of phenotype space. Science 2012, 1157:1157-1160.
-
(2012)
Science
, vol.1157
, pp. 1157-1160
-
-
Shoval, O.1
Sheftel, H.2
Shinar, G.3
Hart, Y.4
Ramote, O.5
Mayo, A.6
Dekel, E.7
Kavanagh, K.8
Alon, U.9
-
12
-
-
84861671055
-
Efficiency in evolutionary trade-offs
-
10.1126/science.1223193, 22654045
-
Noor E, Milo R. Efficiency in evolutionary trade-offs. Science 2012, 336:1114-1115. 10.1126/science.1223193, 22654045.
-
(2012)
Science
, vol.336
, pp. 1114-1115
-
-
Noor, E.1
Milo, R.2
-
13
-
-
1342288026
-
Affy-analysis of affymetrix genechip data at the probe level
-
Gautier L, Cope L, Bolstad BM, Irizarry RA. Affy-analysis of affymetrix genechip data at the probe level. Bioinformatics (Oxford, England) 2004, 20:307-315.
-
(2004)
Bioinformatics (Oxford, England)
, vol.20
, pp. 307-315
-
-
Gautier, L.1
Cope, L.2
Bolstad, B.M.3
Irizarry, R.A.4
-
14
-
-
0037200201
-
A new non-linear normalization method for reducing variability in DNA microarray experiments
-
Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielsen HB, Saxild H, Brunak S, Knudsen S. A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 2002, 3:1-16.
-
(2002)
Genome Biol
, vol.3
, pp. 1-16
-
-
Workman, C.1
Jensen, L.J.2
Jarmer, H.3
Berka, R.4
Gautier, L.5
Nielsen, H.B.6
Saxild, H.7
Brunak, S.8
Knudsen, S.9
-
15
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (Oxford, England) 2003, 4:249-264.
-
(2003)
Biostatistics (Oxford, England)
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
Speed, T.P.7
-
16
-
-
78751522378
-
Parallel evolution in pseudomonas aeruginosa over 39,000 generations in vivo
-
Huse H, Kwon T, Zlosnik J, Speert D. Parallel evolution in pseudomonas aeruginosa over 39,000 generations in vivo. MBio 2010, 1:0-8.
-
(2010)
MBio
, vol.1
, pp. 0-8
-
-
Huse, H.1
Kwon, T.2
Zlosnik, J.3
Speert, D.4
-
17
-
-
80051785694
-
Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data
-
10.1186/1471-2180-11-184, 3224102, 21851621
-
Yang L, Rau MH, Yang L, Hoiby N, Molin S, Jelsbak L. Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data. BMC Microbiol 2011, 11:184. 10.1186/1471-2180-11-184, 3224102, 21851621.
-
(2011)
BMC Microbiol
, vol.11
, pp. 184
-
-
Yang, L.1
Rau, M.H.2
Yang, L.3
Hoiby, N.4
Molin, S.5
Jelsbak, L.6
-
18
-
-
67650685860
-
Dynamics of adaptive microevolution of hypermutable pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis
-
10.1086/599360, 19459782
-
Hoboth C, Hoffmann R, Eichner A, Henke C, Schmoldt S, Imhof A, Heesemann J, Hogardt M. Dynamics of adaptive microevolution of hypermutable pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis. J Infect Dis 2009, 200:118-130. 10.1086/599360, 19459782.
-
(2009)
J Infect Dis
, vol.200
, pp. 118-130
-
-
Hoboth, C.1
Hoffmann, R.2
Eichner, A.3
Henke, C.4
Schmoldt, S.5
Imhof, A.6
Heesemann, J.7
Hogardt, M.8
-
19
-
-
79954716359
-
Mucoid pseudomonas aeruginosa isolates maintain the biofilm formation capacity and the gene expression profiles during the chronic lung infection of CF patients
-
10.1111/j.1600-0463.2011.02726.x, 21492226
-
Lee B, Schjerling CK, Kirkby N, Hoffmann N, Borup R, Molin S, Høiby N, Ciofu O. Mucoid pseudomonas aeruginosa isolates maintain the biofilm formation capacity and the gene expression profiles during the chronic lung infection of CF patients. APMIS 2011, 119:263-274. 10.1111/j.1600-0463.2011.02726.x, 21492226.
-
(2011)
APMIS
, vol.119
, pp. 263-274
-
-
Lee, B.1
Schjerling, C.K.2
Kirkby, N.3
Hoffmann, N.4
Borup, R.5
Molin, S.6
Høiby, N.7
Ciofu, O.8
-
20
-
-
0018391742
-
Chromosomal genetics of pseudomonas
-
281463, 111024
-
Holloway BW, Krishnapillai V, Morgan AF. Chromosomal genetics of pseudomonas. Microbiol Rev 1979, 43:73-102. 281463, 111024.
-
(1979)
Microbiol Rev
, vol.43
, pp. 73-102
-
-
Holloway, B.W.1
Krishnapillai, V.2
Morgan, A.F.3
-
21
-
-
0029035765
-
Common virulence factors for bacterial pathogenicity in plants and animals
-
Rahme LG, Stevens EJ, Wolfort SF, Shao J, Tompkins RG, Ausubel FM. Common virulence factors for bacterial pathogenicity in plants and animals. Science (New York, N.Y.) 1995, 268:1899-1902.
-
(1995)
Science (New York, N.Y.)
, vol.268
, pp. 1899-1902
-
-
Rahme, L.G.1
Stevens, E.J.2
Wolfort, S.F.3
Shao, J.4
Tompkins, R.G.5
Ausubel, F.M.6
-
22
-
-
34249946313
-
Population structure of pseudomonas aeruginosa
-
10.1073/pnas.0609213104, 1876578, 17468398
-
Wiehlmann L, Wagner G, Cramer N, Siebert B, Gudowius P, Morales G, Köhler T, Van Delden C, Weinel C, Slickers P, Tümmler B. Population structure of pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2007, 104:8101-8106. 10.1073/pnas.0609213104, 1876578, 17468398.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 8101-8106
-
-
Wiehlmann, L.1
Wagner, G.2
Cramer, N.3
Siebert, B.4
Gudowius, P.5
Morales, G.6
Köhler, T.7
Van Delden, C.8
Weinel, C.9
Slickers, P.10
Tümmler, B.11
-
23
-
-
79956307094
-
Evolutionary dynamics of bacteria in a human host environment
-
10.1073/pnas.1018249108, 3088582, 21518885
-
Yang L, Jelsbak L, Marvig RL, Damkiær S, Workman CT, Rau MH, Hansen SK, Folkesson A, Johansen HK, Ciofu O, Høiby N, Sommer MOA, Molin S. Evolutionary dynamics of bacteria in a human host environment. Proc Natl Acad Sci U S A 2011, 108:7481-7486. 10.1073/pnas.1018249108, 3088582, 21518885.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 7481-7486
-
-
Yang, L.1
Jelsbak, L.2
Marvig, R.L.3
Damkiær, S.4
Workman, C.T.5
Rau, M.H.6
Hansen, S.K.7
Folkesson, A.8
Johansen, H.K.9
Ciofu, O.10
Høiby, N.11
Sommer, M.O.A.12
Molin, S.13
-
24
-
-
77954645140
-
Early adaptive developments of pseudomonas aeruginosa after the transition from life in the environment to persistent colonization in the airways of human cystic fibrosis hosts
-
Rau MH, Hansen SK, Johansen HK, Thomsen LE, Workman CT, Nielsen KF, Jelsbak L, Høiby N, Yang L, Molin S. Early adaptive developments of pseudomonas aeruginosa after the transition from life in the environment to persistent colonization in the airways of human cystic fibrosis hosts. Environ Microbiol 2010, 12:1643-1658.
-
(2010)
Environ Microbiol
, vol.12
, pp. 1643-1658
-
-
Rau, M.H.1
Hansen, S.K.2
Johansen, H.K.3
Thomsen, L.E.4
Workman, C.T.5
Nielsen, K.F.6
Jelsbak, L.7
Høiby, N.8
Yang, L.9
Molin, S.10
-
25
-
-
78651267246
-
Pseudomonas genome database: improved comparative analysis and population genomics capability for pseudomonas genomes
-
10.1093/nar/gkq869, 3013766, 20929876
-
Winsor GL, Lam DKW, Fleming L, Lo R, Whiteside MD, Yu NY, Hancock REW, Brinkman FSL. Pseudomonas genome database: improved comparative analysis and population genomics capability for pseudomonas genomes. Nucleic Acids Res 2011, 39:D596-D600. 10.1093/nar/gkq869, 3013766, 20929876.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Winsor, G.L.1
Lam, D.K.W.2
Fleming, L.3
Lo, R.4
Whiteside, M.D.5
Yu, N.Y.6
Hancock, R.E.W.7
Brinkman, F.S.L.8
-
26
-
-
33847264343
-
Enrichment or depletion of a GO category within a class of genes: which test?
-
10.1093/bioinformatics/btl633, 17182697
-
Rivals I, Personnaz L, Taing L, Potier M. Enrichment or depletion of a GO category within a class of genes: which test?. Bioinformatics 2007, 23:401-407. 10.1093/bioinformatics/btl633, 17182697.
-
(2007)
Bioinformatics
, vol.23
, pp. 401-407
-
-
Rivals, I.1
Personnaz, L.2
Taing, L.3
Potier, M.4
-
27
-
-
84864390974
-
Deletion and acquisition of genomic content during early stage adaptation of pseudomonas aeruginosa to a human host environment
-
10.1111/j.1462-2920.2012.02795.x, 22672046
-
Rau MH, Marvig RL, Ehrlich GD, Molin S, Jelsbak L. Deletion and acquisition of genomic content during early stage adaptation of pseudomonas aeruginosa to a human host environment. Environ Microbiol 2012, 14:2200-2211. 10.1111/j.1462-2920.2012.02795.x, 22672046.
-
(2012)
Environ Microbiol
, vol.14
, pp. 2200-2211
-
-
Rau, M.H.1
Marvig, R.L.2
Ehrlich, G.D.3
Molin, S.4
Jelsbak, L.5
-
28
-
-
0029814366
-
Microbial pathogenesis in cystic fibrosis: mucoid pseudomonas aeruginosa and burkholderia cepacia
-
239456, 8840786
-
Govan JR, Deretic V. Microbial pathogenesis in cystic fibrosis: mucoid pseudomonas aeruginosa and burkholderia cepacia. Microbiological reviews 1996, 60:539-574. 239456, 8840786.
-
(1996)
Microbiological reviews
, vol.60
, pp. 539-574
-
-
Govan, J.R.1
Deretic, V.2
-
29
-
-
34248402460
-
Molecular epidemiology and dynamics of pseudomonas aeruginosa populations in lungs of cystic fibrosis patients
-
10.1128/IAI.01282-06, 1865789, 17261614
-
Jelsbak L, Johansen HK, Frost AL, Thøgersen R, Thomsen LE, Ciofu O, Yang L, Haagensen JAJ, Høiby N, Molin S. Molecular epidemiology and dynamics of pseudomonas aeruginosa populations in lungs of cystic fibrosis patients. Infect Immun 2007, 75:2214-2224. 10.1128/IAI.01282-06, 1865789, 17261614.
-
(2007)
Infect Immun
, vol.75
, pp. 2214-2224
-
-
Jelsbak, L.1
Johansen, H.K.2
Frost, A.L.3
Thøgersen, R.4
Thomsen, L.E.5
Ciofu, O.6
Yang, L.7
Haagensen, J.A.J.8
Høiby, N.9
Molin, S.10
-
30
-
-
35748957770
-
The microbiology of mutability
-
10.1111/j.1574-6968.2007.00901.x, 17714481
-
Sundin GW, Weigand MR. The microbiology of mutability. FEMS Microbiol Lett 2007, 277:11-20. 10.1111/j.1574-6968.2007.00901.x, 17714481.
-
(2007)
FEMS Microbiol Lett
, vol.277
, pp. 11-20
-
-
Sundin, G.W.1
Weigand, M.R.2
-
31
-
-
57349088170
-
Genetic adaptation of pseudomonas aeruginosa to the airways of cystic fibrosis patients is catalyzed by hypermutation
-
10.1128/JB.01147-08, 2593214, 18849421
-
Mena A, Smith EE, Burns JL, Speert DP, Moskowitz SM, Perez JL, Oliver A. Genetic adaptation of pseudomonas aeruginosa to the airways of cystic fibrosis patients is catalyzed by hypermutation. J Bacteriol 2008, 190:7910-7917. 10.1128/JB.01147-08, 2593214, 18849421.
-
(2008)
J Bacteriol
, vol.190
, pp. 7910-7917
-
-
Mena, A.1
Smith, E.E.2
Burns, J.L.3
Speert, D.P.4
Moskowitz, S.M.5
Perez, J.L.6
Oliver, A.7
-
32
-
-
77954644239
-
Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance
-
10.1111/j.1469-0691.2010.03250.x, 20880409
-
Oliver A, Mena A. Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance. Clin Microbiol Infect 2010, 16:798-808. 10.1111/j.1469-0691.2010.03250.x, 20880409.
-
(2010)
Clin Microbiol Infect
, vol.16
, pp. 798-808
-
-
Oliver, A.1
Mena, A.2
-
33
-
-
79955723729
-
Inactivation of the DNA repair genes mutS, mutL or the anti-recombination gene mutS2 leads to activation of vitamin B1 biosynthesis genes
-
10.1371/journal.pone.0019053, 3084264, 21552516
-
Fukui K, Wakamatsu T, Agari Y, Masui R, Kuramitsu S. Inactivation of the DNA repair genes mutS, mutL or the anti-recombination gene mutS2 leads to activation of vitamin B1 biosynthesis genes. PloS one 2011, 6:e19053. 10.1371/journal.pone.0019053, 3084264, 21552516.
-
(2011)
PloS one
, vol.6
-
-
Fukui, K.1
Wakamatsu, T.2
Agari, Y.3
Masui, R.4
Kuramitsu, S.5
-
34
-
-
77949515264
-
Simple sequence repeats and mucoid conversion: biased mucA mutagenesis in mismatch repair-deficient pseudomonas aeruginosa
-
10.1371/journal.pone.0008203, 2781719, 19997602
-
Moyano AJ, Smania AM. Simple sequence repeats and mucoid conversion: biased mucA mutagenesis in mismatch repair-deficient pseudomonas aeruginosa. PloS one 2009, 4:e8203. 10.1371/journal.pone.0008203, 2781719, 19997602.
-
(2009)
PloS one
, vol.4
-
-
Moyano, A.J.1
Smania, A.M.2
|