SCOPUS 정보 검색 플랫폼

Volumn 1, Issue 1, 2016, Pages

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

(4) Tan, Jie a Hammond, John H a Hogan, Deborah A a Greenea, Casey S b

a DARTMOUTH MEDICAL SCHOOL (United States)

b UNIVERSITY OF PENNSYLVANIA (United States)

Author keywords

Bioinformatics; Data integration; Denoising autoencoders; Gene expression; Genomics

Indexed keywords

EID: 84991259184 PISSN: None EISSN: 23795077 Source Type: Journal
DOI: 10.1128/mSystems.00025-15 Document Type: Article

Times cited : (103)

References (68)

1
- 37749031255
- Next-generation sequencing transforms today’s biology
- Schuster SC. 2008. Next-generation sequencing transforms today’s biology. Nat Methods 5:16–18. http://dx.doi.org/10.1038/nmeth1156.
- (2008) Nat Methods , vol.5 , pp. 16-18
- Schuster, S.C.¹

2
- 53649106195
- Next-generation DNA sequencing
- Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145. http://dx.doi.org/10.1038/nbt1486.
- (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
- Shendure, J.¹ Ji, H.²

3
- 85028165246
- Ten years of next-generation sequencing technology
- Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. 2014. Ten years of next-generation sequencing technology. Trends Genet 30:418–426. http://dx.doi.org/10.1016/j.tig.2014.07.001.
- (2014) Trends Genet , vol.30 , pp. 418-426
- Van Dijk, E.L.¹ Auger, H.² Jaszczyszyn, Y.³ Thermes, C.⁴

4
- 41149167170
- Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
- Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17:1636 –1647. http://dx.doi.org/10.1111/j.1365-294X.2008.03666.x.
- (2008) Mol Ecol , vol.17 , pp. 1636-1647
- Vera, J.C.¹ Wheat, C.W.² Fescemyer, H.W.³ Frilander, M.J.⁴ Crawford, D.L.⁵ Hanski, I.⁶ Marden, J.H.⁷

5
- 78649294100
- Optimization of de novo transcriptome assembly from next-generation sequencing data
- Surget-Groba Y, Montoya-Burgos JI. 2010. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 20:1432–1440. http://dx.doi.org/10.1101/gr.103846.109.
- (2010) Genome Res , vol.20 , pp. 1432-1440
- Surget-Groba, Y.¹ Montoya-Burgos, J.I.²

6
- 79959300621
- Applications of next generation sequencing in molecular ecology of non-model organisms
- Ekblom R, Galindo J. 2011. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) 107: 1–15. http://dx.doi.org/10.1038/hdy.2010.152.
- (2011) Heredity (Edinb) , vol.107 , pp. 1-15
- Ekblom, R.¹ Galindo, J.²

7
- 84865300368
- Reference-free transcriptome assembly in non-model animals from next-generation sequencing data
- Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert L, Chiari Y, Belkhir K, Ranwez V, Galtier N. 2012. Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Mol Ecol Resour 12:834–845. http://dx.doi.org/10.1111/j.1755-0998.2012.03148.x.
- (2012) Mol Ecol Resour , vol.12 , pp. 834-845
- Cahais, V.¹ Gayral, P.² Tsagkogeorga, G.³ Melo-Ferreira, J.⁴ Ballenghien, M.⁵ Weinert, L.⁶ Chiari, Y.⁷ Belkhir, K.⁸ Ranwez, V.⁹ Galtier, N.¹⁰

8
- 0035375137
- Computational analysis of microarray data
- Quackenbush J. 2001. Computational analysis of microarray data. Nat Rev Genet 2:418–427. http://dx.doi.org/10.1038/35076576.
- (2001) Nat Rev Genet , vol.2 , pp. 418-427
- Quackenbush, J.¹

9
- 55349134919
- Atlas of gene expression in the developing kidney at microanatomic resolution
- Brunskill EW, Aronow BJ, Georgas K, Rumballe B, Valerius MT, Aronow J, Kaimal V, Jegga AG, Yu J, Grimmond S, McMahon AP, Patterson LT, Little MH, Potter SS. 2008. Atlas of gene expression in the developing kidney at microanatomic resolution. Dev Cell 15: 781–791. http://dx.doi.org/10.1016/j.devcel.2008.09.007.
- (2008) Dev Cell , vol.15 , pp. 781-791
- Brunskill, E.W.¹ Aronow, B.J.² Georgas, K.³ Rumballe, B.⁴ Valerius, M.T.⁵ Aronow, J.⁶ Kaimal, V.⁷ Jegga, A.G.⁸ Yu, J.⁹ Grimmond, S.¹⁰ McMahon, A.P.¹¹ Patterson, L.T.¹² Little, M.H.¹³ Potter, S.S.¹⁴

10
- 84875448616
- Transcriptional insights into the CD8() T cell response to infection and memory T cell formation
- Immunological Genome Project Consortium
- Best JA, Blair DA, Knell J, Yang E, Mayya V, Doedens A, Dustin ML, Goldrath AW, Immunological Genome Project Consortium. 2013. Transcriptional insights into the CD8() T cell response to infection and memory T cell formation. Nat Immunol 14:404–412. http://dx.doi.org/10.1038/ni.2536.
- (2013) Nat Immunol , vol.14 , pp. 404-412
- Best, J.A.¹ Blair, D.A.² Knell, J.³ Yang, E.⁴ Mayya, V.⁵ Doedens, A.⁶ Dustin, M.L.⁷ Goldrath, A.W.⁸

11
- 0035942271
- Significance analysis of microarrays applied to the ionizing radiation response
- Tusher VG, Tibshirani R, Chu G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98:5116–5121. http://dx.doi.org/10.1073/pnas.091062498.
- (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 5116-5121
- Tusher, V.G.¹ Tibshirani, R.² Chu, G.³

12
- 77954269901
- The Gene-MANIA prediction server: Biological network integration for gene prioritization and predicting gene function
- Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q. 2010. The Gene-MANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38: W214–W220. http://dx.doi.org/10.1093/nar/gkq537.
- (2010) Nucleic Acids Res , vol.38 , pp. W214-W220
- Warde-Farley, D.¹ Donaldson, S.L.² Comes, O.³ Zuberi, K.⁴ Badrawi, R.⁵ Chao, P.⁶ Franz, M.⁷ Grouios, C.⁸ Kazi, F.⁹ Lopes, C.T.¹⁰ Maitland, A.¹¹ Mostafavi, S.¹² Montojo, J.¹³ Shao, Q.¹⁴ Wright, G.¹⁵ Bader, G.D.¹⁶ Morris, Q.¹⁷

13
- 79959981751
- PILGRM: An interactive data-driven discovery platform for expert biologists
- Greene CS, Troyanskaya OG. 2011. PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res 39: W368–W374. http://dx.doi.org/10.1093/nar/gkr440.
- (2011) Nucleic Acids Res , vol.39 , pp. W368-W374
- Greene, C.S.¹ Troyanskaya, O.G.²

14
- 84930083700
- Understanding multicellular function and disease with human tissue-specific networks
- Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmel-stein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. 2015. Understanding multicellular function and disease with human tissue-specific networks. Nat Genet 47:569–576. http://dx.doi.org/10.1038/ng.3259.
- (2015) Nat Genet , vol.47 , pp. 569-576
- Greene, C.S.¹ Krishnan, A.² Wong, A.K.³ Ricciotti, E.⁴ Zelaya, R.A.⁵ Himmel-Stein, D.S.⁶ Zhang, R.⁷ Hartmann, B.M.⁸ Zaslavsky, E.⁹ Sealfon, S.C.¹⁰ Chasman, D.I.¹¹ FitzGerald, G.A.¹² Dolinski, K.¹³ Grosser, T.¹⁴ Troyanskaya, O.G.¹⁵

15
- 84904691723
- Genomic data integration for ecological and evolutionary traits in non-model organisms
- Tagu D, Colbourne JK, Nègre N. 2014. Genomic data integration for ecological and evolutionary traits in non-model organisms. BMC Genomics 15:490. http://dx.doi.org/10.1186/1471-2164-15-490.
- (2014) BMC Genomics , vol.15 , pp. 490
- Tagu, D.¹ Colbourne, J.K.² Nègre, N.³

16
- 84893437280
- Extracting data from the muck: Deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing
- Solomon KV, Haitjema CH, Thompson DA, O’Malley MA. 2014. Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing. Curr Opin Biotechnol 28:103–110. http://dx.doi.org/10.1016/j.copbio.2014.01.007.
- (2014) Curr Opin Biotechnol , vol.28 , pp. 103-110
- Solomon, K.V.¹ Haitjema, C.H.² Thompson, D.A.³ O’Malley, M.A.⁴

17
- 84867135575
- Building high-level features using large scale unsupervised learning
- International Machine Learning Society, Princeton, NJ
- Ranzato M, Monga R, Devin M, Chen K, Corrado G, Dean J, Le QV, Ng AY. 2012. Building high-level features using large scale unsupervised learning, p 81– 88. Proc 29th Int Conf Machine Learn (ICML-12). International Machine Learning Society, Princeton, NJ.
- (2012) Proc 29th Int Conf Machine Learn (ICML-12) , pp. 81-88
- Ranzato, M.¹ Monga, R.² Devin, M.³ Chen, K.⁴ Corrado, G.⁵ Dean, J.⁶ Le, Q.V.⁷ Ng, A.Y.⁸

18
- 56449089103
- Extracting and composing robust features with denoising autoencoders, p 1096–1103
- ACM Press, New York, New York, USA
- Vincent P, Larochelle H, Bengio Y, Manzagol P-A. 2008. Extracting and composing robust features with denoising autoencoders, p 1096–1103. Proc 25th Int Conf Machine Learn (ICML-08). ACM Press, New York, New York, USA.
- (2008) Proc 25th Int Conf Machine Learn (ICML-08)
- Vincent, P.¹ Larochelle, H.² Bengio, Y.³ Manzagol, P.-A.⁴

19
- 84906237188
- Reverberant speech recognition based on denoising autoencoder
- In
- Ishii T, Komiyama H, Shinozaki T, Horiuchi Y, Kuroiwa S. 2013. Reverberant speech recognition based on denoising autoencoder, p 3512–3516. In Interspeech.
- (2013) Interspeech , pp. 3512-3516
- Ishii, T.¹ Komiyama, H.² Shinozaki, T.³ Horiuchi, Y.⁴ Kuroiwa, S.⁵

20
- 80053443013
- Domain adaptation for large-scale sentiment classification: A deep learning approach
- International Machine Learning Society, Princeton, NJ
- Glorot X, Bordes A, Bengio Y. 2011. Domain adaptation for large-scale sentiment classification: a deep learning approach, p 513–520. Proc 28th Int Conf Mach Learn (ICML-11). International Machine Learning Society, Princeton, NJ.
- (2011) Proc 28th Int Conf Mach Learn (ICML-11) , pp. 513-520
- Glorot, X.¹ Bordes, A.² Bengio, Y.³

21
- 84876097557
- ArrayExpress update—trends in database growth and links to data analysis tools
- Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U. 2013. ArrayExpress update—trends in database growth and links to data analysis tools. Nucleic Acids Res 41:D987–D990. http://dx.doi.org/10.1093/nar/gks1174.
- (2013) Nucleic Acids Res , vol.41 , pp. D987-D990
- Rustici, G.¹ Kolesnikov, N.² Brandizi, M.³ Burdett, T.⁴ Dylag, M.⁵ Emam, I.⁶ Farne, A.⁷ Hastings, E.⁸ Ison, J.⁹ Keays, M.¹⁰ Kurbatova, N.¹¹ Malone, J.¹² Mani, R.¹³ Mupo, A.¹⁴ Pedro Pereira, R.¹⁵ Pilicheva, E.¹⁶ Rung, J.¹⁷ Sharma, A.¹⁸ Tang, Y.A.¹⁹ Ternent, T.²⁰ more..

22
- 56449089103
- Extracting and composing robust features with denoising autoencoders, p 1096–1103
- ACM Press, New York, NY
- Vincent P, Larochelle H, Bengio Y, Manzagol P-A. 2008. Extracting and composing robust features with denoising autoencoders, p 1096–1103. Proc 25th Int Conf Mach Learn (ICML-08). ACM Press, New York, NY.
- (2008) Proc 25th Int Conf Mach Learn (ICML-08)
- Vincent, P.¹ Larochelle, H.² Bengio, Y.³ Manzagol, P.-A.⁴

23
- 79551480483
- Stacked denoising autoencoders: Learning useful representations in a deep network with a local denoising criterion
- Vincent P, Larochelle H, Lajoie I, Bengio Y, Manzagol P-A. 2010. Stacked denoising autoencoders: learning useful representations in a deep network with a local denoising criterion. J Mach Learn Res 11: 3371–3408.
- (2010) J Mach Learn Res , vol.11 , pp. 3371-3408
- Vincent, P.¹ Larochelle, H.² Lajoie, I.³ Bengio, Y.⁴ Manzagol, P.-A.⁵

24
- 84891765377
- DOer 2.0: Presenting operons and their functions through dynamic and integrated views
- Mao X, Ma Q, Zhou C, Chen X, Zhang H, Yang J, Mao F, Lai W, Xu Y. 2014. DOer 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Res 42:D654–D659. http://dx.doi.org/10.1093/nar/gkt1048.
- (2014) Nucleic Acids Res , vol.42 , pp. D654-D659
- Mao, X.¹ Ma, Q.² Zhou, C.³ Chen, X.⁴ Zhang, H.⁵ Yang, J.⁶ Mao, F.⁷ Lai, W.⁸ Xu, Y.⁹

25
- 0033982936
- KEGG: Kyoto encyclopedia of genes and genomes
- Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30. http://dx.doi.org/10.1093/nar/28.1.27.
- (2000) Nucleic Acids Res , vol.28 , pp. 27-30
- Kanehisa, M.¹ Goto, S.²

26
- 33750924336
- Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial
- Lee DG, Urbach JM, Wu G, Liberati NT, Feinbaum RL, Miyata S, Diggins LT, He J, Saucier M, Déziel E, Friedman L, Li L, Grills G, Montgomery K, Kucherlapati R, Rahme LG, Ausubel FM. 2006. Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial. Genome Biol 7:R90. http://dx.doi.org/10.1186/gb-2006-7-10-r90.
- (2006) Genome Biol , vol.7 , pp. R90
- Lee, D.G.¹ Urbach, J.M.² Wu, G.³ Liberati, N.T.⁴ Feinbaum, R.L.⁵ Miyata, S.⁶ Diggins, L.T.⁷ He, J.⁸ Saucier, M.⁹ Déziel, E.¹⁰ Friedman, L.¹¹ Li, L.¹² Grills, G.¹³ Montgomery, K.¹⁴ Kucherlapati, R.¹⁵ Rahme, L.G.¹⁶ Ausubel, F.M.¹⁷

27
- 0017250449
- Suppressor mutations in Pseudomonas aeruginosa
- Watson JM, Holloway BW. 1976. Suppressor mutations in Pseudomonas aeruginosa. J Bacteriol 125:780 –786.
- (1976) J Bacteriol , vol.125 , pp. 780-786
- Watson, J.M.¹ Holloway, B.W.²

28
- 0029035765
- Common virulence factors for bacterial pathogenicity in plants and animals
- Rahme LG, Stevens EJ, Wolfort SF, Shao J, Tompkins RG, Ausubel FM. 1995. Common virulence factors for bacterial pathogenicity in plants and animals. Science 268:1899–1902. http://dx.doi.org/10.1126/science.7604262.
- (1995) Science , 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

29
- 0346801873
- The Gene Ontology (GO) database and informatics resource
- Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Stern-berg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R. 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258–D261. http://dx.doi.org/10.1093/nar/gkh036.
- (2004) Nucleic Acids Res , vol.32 , pp. D258-D261
- Harris, M.A.¹ Clark, J.² Ireland, A.³ Lomax, J.⁴ Ashburner, M.⁵ Foulger, R.⁶ Eilbeck, K.⁷ Lewis, S.⁸ Marshall, B.⁹ Mungall, C.¹⁰ Richter, J.¹¹ Rubin, G.M.¹² Blake, J.A.¹³ Bult, C.¹⁴ Dolan, M.¹⁵ Drabkin, H.¹⁶ Eppig, J.T.¹⁷ Hill, D.P.¹⁸ Ni, L.¹⁹ Ringwald, M.²⁰ more..

30
- 34250745704
- Characterization of the integrated filamentous phage Pf5 and its involvement in small-colony formation
- Mooij MJ, Drenkard E, Llamas MA, Vandenbroucke-Grauls CM, Savelkoul PH, Ausubel FM, Bitter W. 2007. Characterization of the integrated filamentous phage Pf5 and its involvement in small-colony formation. Microbiology 153:1790–1798. http://dx.doi.org/10.1099/mic.0.2006/003533-0.
- (2007) Microbiology , vol.153 , pp. 1790-1798
- Mooij, M.J.¹ Drenkard, E.² Llamas, M.A.³ Vandenbroucke-Grauls, C.M.⁴ Savelkoul, P.H.⁵ Ausubel, F.M.⁶ Bitter, W.⁷

31
- 77949741786
- Lipopolysaccharide as shield and receptor for R-pyocin-mediated killing in Pseudomonas aeruginosa
- Köhler T, Donner V, van Delden C. 2010. Lipopolysaccharide as shield and receptor for R-pyocin-mediated killing in Pseudomonas aeruginosa. J Bacteriol 192:1921–1928. http://dx.doi.org/10.1128/JB.01459-09.
- (2010) J Bacteriol , vol.192 , pp. 1921-1928
- Köhler, T.¹ Donner, V.² Van Delden, C.³

32
- 35648949942
- In vivo evidence of Pseudomonas aeruginosa nutrient acquisition and pathogenesis in the lungs of cystic fibrosis patients
- Son MS, Matthews WJ, Kang Y, Nguyen DT, Hoang TT. 2007. In vivo evidence of Pseudomonas aeruginosa nutrient acquisition and pathogenesis in the lungs of cystic fibrosis patients. Infect Immun 75: 5313–5324. http://dx.doi.org/10.1128/IAI.01807-06.
- (2007) Infect Immun , vol.75 , pp. 5313-5324
- Son, M.S.¹ Matthews, W.J.² Kang, Y.³ Nguyen, D.T.⁴ Hoang, T.T.⁵

33
- 34948905258
- Transcriptomic analysis of the sulfate starvation response of Pseudomonas aeruginosa
- Tralau T, Vuilleumier S, Thibault C, Campbell BJ, Hart CA, Kertesz MA. 2007. Transcriptomic analysis of the sulfate starvation response of Pseudomonas aeruginosa. J Bacteriol 189:6743–6750. http://dx.doi.org/10.1128/JB.00889-07.
- (2007) J Bacteriol , vol.189 , pp. 6743-6750
- Tralau, T.¹ Vuilleumier, S.² Thibault, C.³ Campbell, B.J.⁴ Hart, C.A.⁵ Kertesz, M.A.⁶

34
- 48449106179
- The Pseudomonas aeruginosa PsrA responds to long-chain fatty acid signals to regulate the fadBA5 beta-oxidation operon
- Kang Y, Nguyen DT, Son MS, Hoang TT. 2008. The Pseudomonas aeruginosa PsrA responds to long-chain fatty acid signals to regulate the fadBA5 beta-oxidation operon. Microbiology 154:1584 –1598. http://dx.doi.org/10.1099/mic.0.2008/018135-0.
- (2008) Microbiology , vol.154 , pp. 1584-1598
- Kang, Y.¹ Nguyen, D.T.² Son, M.S.³ Hoang, T.T.⁴

35
- 0025873743
- Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depend on anr, a regulatory gene homologous with fnr of Escherichia coli
- Zimmermann A, Reimmann C, Galimand M, Haas D. 1991. Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depend on anr, a regulatory gene homologous with fnr of Escherichia coli. Mol Microbiol 5:1483–1490. http://dx.doi.org/10.1111/j.1365-2958.1991.tb00794.x.
- (1991) Mol Microbiol , vol.5 , pp. 1483-1490
- Zimmermann, A.¹ Reimmann, C.² Galimand, M.³ Haas, D.⁴

36
- 84880018817
- Anr and its activation by PlcH activity in Pseudomonas aeruginosa host colonization and virulence
- Jackson AA, Gross MJ, Daniels EF, Hampton TH, Hammond JH, Vallet-Gely I, Dove SL, Stanton BA, Hogan DA. 2013. Anr and its activation by PlcH activity in Pseudomonas aeruginosa host colonization and virulence. J Bacteriol 195:3093–3104. http://dx.doi.org/10.1128/JB.02169-12.
- (2013) J Bacteriol , vol.195 , pp. 3093-3104
- Jackson, A.A.¹ Gross, M.J.² Daniels, E.F.³ Hampton, T.H.⁴ Hammond, J.H.⁵ Vallet-Gely, I.⁶ Dove, S.L.⁷ Stanton, B.A.⁸ Hogan, D.A.⁹

37
- 77957950357
- Anaerobic adaptation in Pseudomonas aeruginosa: Definition of the Anr and Dnr regulons
- Trunk K, Benkert B, Quäck N, Münch R, Scheer M, Garbe J, Jänsch L, Trost M, Wehland J, Buer J, Jahn M, Schobert M, Jahn D. 2010. Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons. Environ Microbiol 12:1719–1733. http://dx.doi.org/10.1111/j.1462-2920.2010.02252.x.
- (2010) Environ Microbiol , vol.12 , pp. 1719-1733
- Trunk, K.¹ Benkert, B.² Quäck, N.³ Münch, R.⁴ Scheer, M.⁵ Garbe, J.⁶ Jänsch, L.⁷ Trost, M.⁸ Wehland, J.⁹ Buer, J.¹⁰ Jahn, M.¹¹ Schobert, M.¹² Jahn, D.¹³

38
- 77957935610
- Differential expression of multiple terminal oxidases for aerobic respiration in Pseudomonas aeruginosa
- Kawakami T, Kuroki M, Ishii M, Igarashi Y, Arai H. 2010. Differential expression of multiple terminal oxidases for aerobic respiration in Pseudomonas aeruginosa. Environ Microbiol 12:1399 –1412. http://dx.doi.org/10.1111/j.1462-2920.2009.02109.x.
- (2010) Environ Microbiol , vol.12 , pp. 1399-1412
- Kawakami, T.¹ Kuroki, M.² Ishii, M.³ Igarashi, Y.⁴ Arai, H.⁵

39
- 84881498162
- Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions
- Tielen P, Rosin N, Meyer A-K, Dohnt K, Haddad I, Jänsch L, Klein J, Narten M, Pommerenke C, Scheer M, Schobert M, Schomburg D, Thielen B, Jahn D. 2013. Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions. PLoS One 8:e71845. http://dx.doi.org/10.1371/ journal.pone.0071845.
- (2013) PLoS One , vol.8 , pp. e71845
- Tielen, P.¹ Rosin, N.² Meyer, A.-K.³ Dohnt, K.⁴ Haddad, I.⁵ Jänsch, L.⁶ Klein, J.⁷ Narten, M.⁸ Pommerenke, C.⁹ Scheer, M.¹⁰ Schobert, M.¹¹ Schomburg, D.¹² Thielen, B.¹³ Jahn, D.¹⁴

40
- 84893193594
- 2-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions
- 2-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions. Integr Biol (Camb) 6:215–223. http://dx.doi.org/10.1039/c3ib40180d.
- (2014) Integr Biol (Camb) , vol.6 , pp. 215-223
- He, F.Q.¹ Wang, W.² Zheng, P.³ Sudhakar, P.⁴ Sun, J.⁵ Zeng, A.-P.⁶

41
- 84938824620
- Links between Anr and quorum sensing in Pseudomonas aeruginosa biofilms
- Hammond JH, Dolben EF, Smith TJ, Bhuju S, Hogan DA. 2015. Links between Anr and quorum sensing in Pseudomonas aeruginosa biofilms. J Bacteriol 197:2810–2820. http://dx.doi.org/10.1128/JB.00182-15.
- (2015) J Bacteriol , vol.197 , pp. 2810-2820
- Hammond, J.H.¹ Dolben, E.F.² Smith, T.J.³ Bhuju, S.⁴ Hogan, D.A.⁵

42
- 85041897127
- Cross-platform normalization of microarray and RNA-seq data for machine learning applications
- Thompson JA, Tan J, Greene CS. 2015. Cross-platform normalization of microarray and RNA-seq data for machine learning applications. PeerJ preprint archive. https://peerj.com/preprints/1460/.
- (2015) PeerJ Preprint Archive
- Thompson, J.A.¹ Tan, J.² Greene, C.S.³

43
- 42149086134
- In vitro analysis of tobramycin-treated Pseudomonas aeruginosa biofilms on cystic fibrosis-derived airway epithelial cells
- Anderson GG, Moreau-Marquis S, Stanton BA, O’Toole GA. 2008. In vitro analysis of tobramycin-treated Pseudomonas aeruginosa biofilms on cystic fibrosis-derived airway epithelial cells. Infect Immun 76: 1423-1433. http://dx.doi.org/10.1128/IAI.01373-07.
- (2008) Infect Immun , vol.76 , pp. 1423-1433
- Anderson, G.G.¹ Moreau-Marquis, S.² Stanton, B.A.³ O’Toole, G.A.⁴

44
- 84926507971
- Limma powers differential expression analyses for RNA-sequencing and microarray studies
- Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. 2015. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43:e47. http://dx.doi.org/10.1093/nar/gkv007.
- (2015) Nucleic Acids Res , vol.43 , pp. e47
- Ritchie, M.E.¹ Phipson, B.² Wu, D.³ Hu, Y.⁴ Law, C.W.⁵ Shi, W.⁶ Smyth, G.K.⁷

45
- 77349109267
- The Pseudomonas aeruginosa magnesium transporter MgtE inhibits transcription of the type III secretion system
- Anderson GG, Yahr TL, Lovewell RR, O’Toole GA. 2010. The Pseudomonas aeruginosa magnesium transporter MgtE inhibits transcription of the type III secretion system. Infect Immun 78:1239 -1249. http://dx.doi.org/10.1128/IAI.00865-09.
- (2010) Infect Immun , vol.78 , pp. 1239-1249
- Anderson, G.G.¹ Yahr, T.L.² Lovewell, R.R.³ O’Toole, G.A.⁴

46
- 27344435774
- Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
- Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102:15545-15550. http://dx.doi.org/10.1073/pnas.0506580102.
- (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 15545-15550
- Subramanian, A.¹ Tamayo, P.² Mootha, V.K.³ Mukherjee, S.⁴ Ebert, B.L.⁵ Gillette, M.A.⁶ Paulovich, A.⁷ Pomeroy, S.L.⁸ Golub, T.R.⁹ Lander, E.S.¹⁰ Mesirov, J.P.¹¹

47
- 0036069214
- Interactive exploration of microarray gene expression patterns in a reduced dimensional space
- Misra J, Schmitt W, Hwang D, Hsiao L-L, Gullans S, Stephanopoulos G, Stephanopoulos G. 2002. Interactive exploration of microarray gene expression patterns in a reduced dimensional space. Genome Res 12: 1112-1120. http://dx.doi.org/10.1101/gr.225302.
- (2002) Genome Res , vol.12 , pp. 1112-1120
- Misra, J.¹ Schmitt, W.² Hwang, D.³ Hsiao, L.-L.⁴ Gullans, S.⁵ Stephanopoulos, G.⁶ Stephanopoulos, G.⁷

48
- 84964308876
- Gene expression analysis identifies global gene dosage sensitivity in cancer
- Fehrmann RS, Karjalainen JM, Krajewska M, Westra H-J, Maloney D, Simeonov A, Pers TH, Hirschhorn JN, Jansen RC, Schultes EA, van Haagen HH, de Vries EG, Te Meerman GJ, Wijmenga C, van Vugt MA, Franke L. 2015. Gene expression analysis identifies global gene dosage sensitivity in cancer. Nat Genet 47:115-125. http://dx.doi.org/10.1038/ng.3173.
- (2015) Nat Genet , vol.47 , pp. 115-125
- Fehrmann, R.S.¹ Karjalainen, J.M.² Krajewska, M.³ Westra, H.-J.⁴ Maloney, D.⁵ Simeonov, A.⁶ Pers, T.H.⁷ Hirschhorn, J.N.⁸ Jansen, R.C.⁹ Schultes, E.A.¹⁰ Van Haagen, H.H.¹¹ De Vries, E.G.¹² Te Meerman, G.J.¹³ Wijmenga, C.¹⁴ Van Vugt, M.A.¹⁵ Franke, L.¹⁶

49
- 1542473171
- Application of independent component analysis to microarrays
- Lee S-I, Batzoglou S. 2003. Application of independent component analysis to microarrays. Genome Biol 4:R76. http://dx.doi.org/10.1186/gb-2003-4-11-r76.
- (2003) Genome Biol , vol.4 , pp. R76
- Lee, S.-I.¹ Batzoglou, S.²

50
- 78649334862
- Independent component analysis: Mining microarray data for fundamental human gene expression modules
- Engreitz JM, Daigle BJ, Marshall JJ, Altman RB. 2010. Independent component analysis: mining microarray data for fundamental human gene expression modules. J Biomed Inform 43:932-944. http://dx.doi.org/10.1016/j.jbi.2010.07.001.
- (2010) J Biomed Inform , vol.43 , pp. 932-944
- Engreitz, J.M.¹ Daigle, B.J.² Marshall, J.J.³ Altman, R.B.⁴

51
- 34548444625
- Elucidating the altered transcriptional programs in breast cancer using independent component analysis
- Teschendorff AE, Journée M, Absil PA, Sepulchre R, Caldas C. 2007. Elucidating the altered transcriptional programs in breast cancer using independent component analysis. PLoS Comput Biol 3:e161. http://dx.doi.org/10.1371/journal.pcbi.0030161.
- (2007) PLoS Comput Biol , vol.3 , pp. e161
- Teschendorff, A.E.¹ Journée, M.² Absil, P.A.³ Sepulchre, R.⁴ Caldas, C.⁵

52
- 0036167851
- Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients
- Worlitzsch D, Tarran R, Ulrich M, Schwab U, Cekici A, Meyer KC, Birrer P, Bellon G, Berger J, Weiss T, Botzenhart K, Yankaskas JR, Randell S, Boucher RC, Döring G. 2002. Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J Clin Invest 109:317-325. http://dx.doi.org/10.1172/JCI13870.
- (2002) J Clin Invest , vol.109 , pp. 317-325
- Worlitzsch, D.¹ Tarran, R.² Ulrich, M.³ Schwab, U.⁴ Cekici, A.⁵ Meyer, K.C.⁶ Birrer, P.⁷ Bellon, G.⁸ Berger, J.⁹ Weiss, T.¹⁰ Botzenhart, K.¹¹ Yankaskas, J.R.¹² Randell, S.¹³ Boucher, R.C.¹⁴ Döring, G.¹⁵

53
- 84877028141
- Comprehensive molecular portraits of human breast tumours
- Cancer Genome Atlas Network
- Cancer Genome Atlas Network. 2012. Comprehensive molecular portraits of human breast tumours. Nature 490:61-70. http://dx.doi.org/ 10.1038/nature11412.
- (2012) Nature , vol.490 , pp. 61-70

54
- 79959838081
- Integrated genomic analyses of ovarian carcinoma
- Cancer Genome Atlas Network
- Cancer Genome Atlas Network. 2011. Integrated genomic analyses of ovarian carcinoma. Nature 474:609-615. http://dx.doi.org/10.1038/nature10166.
- (2011) Nature , vol.474 , pp. 609-615

55
- 84875968177
- Functional knowledge transfer for high-accuracy prediction of under-studied biological processes
- Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. 2013. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol 9: e1002957. http://dx .doi.org/10.1371/journal.pcbi.1002957.
- (2013) PLoS Comput Biol , vol.9 , pp. e1002957
- Park, C.Y.¹ Wong, A.K.² Greene, C.S.³ Rowland, J.⁴ Guan, Y.⁵ Bongo, L.A.⁶ Burdine, R.D.⁷ Troyanskaya, O.G.⁸

56
- 33746067911
- Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
- Reiss DJ, Baliga NS, Bonneau R. 2006. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics 7:280. http://dx.doi.org/10.1186/1471-2105-7-280.
- (2006) BMC Bioinformatics , vol.7 , pp. 280
- Reiss, D.J.¹ Baliga, N.S.² Bonneau, R.³

57
- 84930630277
- Deep learning
- LeCun Y, Bengio Y, Hinton G. 2015. Deep learning. Nature 521: 436–444. http://dx.doi.org/10.1038/nature14539.
- (2015) Nature , vol.521 , pp. 436-444
- LeCun, Y.¹ Bengio, Y.² Hinton, G.³

58
- 1342288026
- Affy—analysis of Affymetrix GeneChip data at the probe level
- Gautier L, Cope L, Bolstad BM, Irizarry RA. 2004. Affy—analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20:307–315. http://dx.doi.org/10.1093/bioinformatics/btg405.
- (2004) Bioinformatics , vol.20 , pp. 307-315
- Gautier, L.¹ Cope, L.² Bolstad, B.M.³ Irizarry, R.A.⁴

59
- 84857819132
- Theano: A CPU and GPU math expression compiler, p 3–10
- 30 June to 3 July, Austin, TX
- Bergstra J, Breuleux O, Bastien F, Lamblin P, Pascanu R, Desjardins G, Turian J, Warde-Farley D, Bengio Y. 2010. Theano: a CPU and GPU math expression compiler, p 3–10. Proc Python Sci Comput Conf (SciPy) 2010, 30 June to 3 July, Austin, TX.
- (2010) Proc Python Sci Comput Conf (SciPy) 2010
- Bergstra, J.¹ Breuleux, O.² Bastien, F.³ Lamblin, P.⁴ Pascanu, R.⁵ Desjardins, G.⁶ Turian, J.⁷ Warde-Farley, D.⁸ Bengio, Y.⁹

60
- 84971231452
- Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders
- Tan J, Ung M, Cheng C, Greene CS. 2015. Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Pac Symp Biocomput 20:132–143.
- (2015) Pac Symp Biocomput , vol.20 , pp. 132-143
- Tan, J.¹ Ung, M.² Cheng, C.³ Greene, C.S.⁴

61
- 0026724465
- Characterization of immortal cystic fibrosis tracheo-bronchial gland epithelial cells
- Cozens AL, Yezzi MJ, Chin L, Simon EM, Finkbeiner WE, Wagner JA, Gruenert DC. 1992. Characterization of immortal cystic fibrosis tracheo-bronchial gland epithelial cells. Proc Natl Acad Sci U S A 89:5171–5175. http://dx.doi.org/10.1073/pnas.89.11.5171.
- (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 5171-5175
- Cozens, A.L.¹ Yezzi, M.J.² Chin, L.³ Simon, E.M.⁴ Finkbeiner, W.E.⁵ Wagner, J.A.⁶ Gruenert, D.C.⁷

62
- 49049089612
- The ?F508-CFTR mutation results in increased biofilm formation by Pseudomonas aeruginosa by increasing iron availability
- Moreau-Marquis S, Bomberger JM, Anderson GG, Swiatecka-Urban A, Ye S, O’Toole GA, Stanton BA. 2008. The ?F508-CFTR mutation results in increased biofilm formation by Pseudomonas aeruginosa by increasing iron availability. Am J Physiol Lung Cell Mol Physiol 295: L25–L37. http://dx.doi.org/10.1152/ajplung.00391.2007.
- (2008) Am J Physiol Lung Cell Mol Physiol , vol.295 , pp. L25-L37
- Moreau-Marquis, S.¹ Bomberger, J.M.² Anderson, G.G.³ Swiatecka-Urban, A.⁴ Ye, S.⁵ O’Toole, G.A.⁶ Stanton, B.A.⁷

63
- 0034069495
- Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25–29. http://dx.doi.org/10.1038/75556.
- (2000) Nat Genet , vol.25 , pp. 25-29
- Ashburner, M.¹ Ball, C.A.² Blake, J.A.³ Botstein, D.⁴ Butler, H.⁵ Cherry, J.M.⁶ Davis, A.P.⁷ Dolinski, K.⁸ Dwight, S.S.⁹ Eppig, J.T.¹⁰ Harris, M.A.¹¹ Hill, D.P.¹² Issel-Tarver, L.¹³ Kasarskis, A.¹⁴ Lewis, S.¹⁵ Matese, J.C.¹⁶ Richardson, J.E.¹⁷ Ringwald, M.¹⁸ Rubin, G.M.¹⁹ Sherlock, G.²⁰ more..

64
- 78651267246
- Pseudomonas Genome Database: Improved comparative analysis and population genomics capability for Pseudomonas genomes
- Winsor GL, Lam DK, Fleming L, Lo R, Whiteside MD, Yu NY, Hancock RE, Brinkman FS. 2011. Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 39:D596 –D600. http://dx.doi.org/10.1093/nar/gkq869.
- (2011) Nucleic Acids Res , vol.39 , pp. D596-D600
- Winsor, G.L.¹ Lam, D.K.² Fleming, L.³ Lo, R.⁴ Whiteside, M.D.⁵ Yu, N.Y.⁶ Hancock, R.E.⁷ Brinkman, F.S.⁸

65
- 80054078476
- Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. http://dx.doi.org/10.1038/msb.2011.75.
- (2011) Mol Syst Biol , vol.7 , pp. 539
- Sievers, F.¹ Wilm, A.² Dineen, D.³ Gibson, T.J.⁴ Karplus, K.⁵ Li, W.⁶ Lopez, R.⁷ McWilliam, H.⁸ Remmert, M.⁹ Söding, J.¹⁰ Thompson, J.D.¹¹ Higgins, D.G.¹²

66
- 84883577718
- Analysis Tool Web services from the EMBL-EBI
- McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R. 2013. Analysis Tool Web services from the EMBL-EBI. Nucleic Acids Res 41:W597–W600. http://dx.doi.org/10.1093/nar/gkt376.
- (2013) Nucleic Acids Res , vol.41 , pp. W597-W600
- McWilliam, H.¹ Li, W.² Uludag, M.³ Squizzato, S.⁴ Park, Y.M.⁵ Buso, N.⁶ Cowley, A.P.⁷ Lopez, R.⁸

67
- 75149150388
- TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
- Stöver BC, Müller KF. 2010. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7. http://dx.doi.org/10.1186/1471-2105-11-7.
- (2010) BMC Bioinformatics , vol.11 , pp. 7
- Stöver, B.C.¹ Müller, K.F.²

68
- 62749177074
- Marchini JL, Heaton C, Ripley BD. 2013. FastICA algorithms to perform ICA and projection pursuit (R package). http://cran.r-project.org/web/packages/fastICA/fastICA.pdf.
- (2013) FastICA Algorithms to Perform ICA and Projection Pursuit (R Package)
- Marchini, J.L.¹ Heaton, C.² Ripley, B.D.³

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.