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Orthologous gene-expression profiling in multi-species models: search for candidate genes
Dmitry N Grigoryev, Shwu-Fan Ma, Rafael A Irizarry, Shui Qing Ye, John Quackenbush, Joe GN Garcia
Genome Biol. 2004; 5(5): R34. Published online 2004 April 27.
PMCID:
PMC416470
Abstract Full Text PDF–287K Supplementary Material
 Is Cited by the Following 28 Articles in this Archive:
Activation of the Wnt/β-Catenin Signaling Pathway by Mechanical Ventilation Is Associated with Ventilator-Induced Pulmonary Fibrosis in Healthy Lungs
Jesús Villar, Nuria E. Cabrera, Francisco Valladares, Milena Casula, Carlos Flores, Lluís Blanch, María Elisa Quilez, Norberto Santana-Rodríguez, Robert M. Kacmarek, Arthur S. Slutsky
PLoS One. 2011; 6(9): e23914. Published online 2011 September 15. doi: 10.1371/journal.pone.0023914
PMCID:
PMC3174135
Abstract Full Text PDF–710K Supplementary Material
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns
Daniel Baron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péréon, Reiner Veitia, Frédérique Savagner, Gérard Ramstein, Rémi Houlgatte
BMC Genomics. 2011; 12: 113. Published online 2011 February 16. doi: 10.1186/1471-2164-12-113
PMCID:
PMC3049149
Abstract Full Text PDF–3.5M Supplementary Material
Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data
Ilya Kupershmidt, Qiaojuan Jane Su, Anoop Grewal, Suman Sundaresh, Inbal Halperin, James Flynn, Mamatha Shekar, Helen Wang, Jenny Park, Wenwu Cui, Gregory D. Wall, Robert Wisotzkey, Satnam Alag, Saeid Akhtari, Mostafa Ronaghi
PLoS One. 2010; 5(9): e13066. Published online 2010 September 29. doi: 10.1371/journal.pone.0013066
PMCID:
PMC2947508
Abstract Full Text PDF–1021K Supplementary Material
Highly conserved transcriptional responses to mechanical ventilation of the lung
Kenneth S. Kompass, Gaetan Deslee, Carla Moore, Donald McCurnin, Richard A. Pierce
Physiol Genomics. 2010 August; 42(3): 384–396. Published online 2010 May 11. doi: 10.1152/physiolgenomics.00117.2009
PMCID:
PMC2929881
Abstract Full Text
Cyclic Stretch Magnitude and Duration Affect Rat Alveolar Epithelial Gene Expression
Adi Yerrapureddy, John Tobias, Susan S. Margulies
Cell Physiol Biochem. 2010; 25(1): 113–122.
PMCID:
PMC3025888
Abstract Full Text PDF–478K
Recent Advances and New Opportunities in Lung Mechanobiology
Daniel J. Tschumperlin, Francis Boudreault, Fei Liu
J Biomech. Author manuscript; available in PMC 2011 January 5.
Published in final edited form as: J Biomech. 2010 January 5; 43(1): 99. Published online 2009 October 4. doi: 10.1016/j.jbiomech.2009.09.015
PMCID:
PMC2813412
Abstract Full Text PDF–2.5M
Genetic polymorphisms associated with acute lung injury
Anita J Reddy, Steven R Kleeberger
Pharmacogenomics. Author manuscript; available in PMC 2010 July 1.
Published in final edited form as: Pharmacogenomics. 2009 September; 10(9): 1527–1539. doi: 10.2217/pgs.09.89
PMCID:
PMC2801141
Abstract Full Text PDF–519K
GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling
Nuala J. Meyer, Yong Huang, Patrick A. Singleton, Saad Sammani, Jaideep Moitra, Carrie L. Evenoski, Aliya N. Husain, Sumegha Mitra, Liliana Moreno-Vinasco, Jeffrey R. Jacobson, Yves A. Lussier, Joe G. N. Garcia
FASEB J. 2009 May; 23(5): 1325–1337. doi: 10.1096/fj.08-119073
PMCID:
PMC2669422
Abstract Full Text Supplementary Material
Kidney ischemia-reperfusion injury induces caspase-dependent pulmonary apoptosis
Heitham T. Hassoun, Mihaela L. Lie, Dmitry N. Grigoryev, Manchang Liu, Rubin M. Tuder, Hamid Rabb
Am J Physiol Renal Physiol. 2009 July; 297(1): F125–F137. Published online 2009 April 29. doi: 10.1152/ajprenal.90666.2008
PMCID:
PMC2711715
Abstract Full Text
Activated protein C protects against ventilator-induced pulmonary capillary leak
James H. Finigan, Adel Boueiz, Emily Wilkinson, Rachel Damico, Jarrett Skirball, Hyun Hae Pae, Mahendra Damarla, Emile Hasan, David B. Pearse, Sekhar P. Reddy, Dmitry N. Grigoryev, Christopher Cheadle, Charles T. Esmon, Joe G. N. Garcia, Paul M. Hassoun
Am J Physiol Lung Cell Mol Physiol. 2009 June; 296(6): L1002–L1011. Published online 2009 April 10. doi: 10.1152/ajplung.90555.2008
PMCID:
PMC2692806
Abstract Full Text
A quality assessment of genetic association studies supporting susceptibility and outcome in acute lung injury
Carlos Flores, Maria del Mar Pino-Yanes, Jesús Villar
Crit Care. 2008; 12(5): R130. Published online 2008 October 25. doi: 10.1186/cc7098
PMCID:
PMC2592769
Abstract Full Text PDF–418K
Cross-species comparison of biological themes and underlying genes on a global gene expression scale in a mouse model of colorectal liver metastasis and in clinical specimens
Obul Reddy Bandapalli, Christoph Kahlert, Victoria Hellstern, Luis Galindo, Peter Schirmacher, Jürgen Weitz, Karsten Brand
BMC Genomics. 2008; 9: 448. Published online 2008 September 29. doi: 10.1186/1471-2164-9-448
PMCID:
PMC2573898
Abstract Full Text PDF–983K
Murine Lung Responses to Ambient Particulate Matter: Genomic Analysis and Influence on Airway Hyperresponsiveness
Ting Wang, Liliana Moreno-Vinasco, Yong Huang, Gabriel D. Lang, Jered D. Linares, Sascha N. Goonewardena, Alayna Grabavoy, Jonathan M. Samet, Alison S. Geyh, Patrick N. Breysse, Yves A. Lussier, Viswanathan Natarajan, Joe G.N. Garcia
Environ Health Perspect. 2008 November; 116(11): 1500–1508. Published online 2008 June 20. doi: 10.1289/ehp.11229
PMCID:
PMC2592270
Abstract Full Text PDF–475K
Genome-wide screen for temperature-regulated genes of the obligate intracellular bacterium, Rickettsia typhi
Sheila M Dreher-Lesnick, Shane M Ceraul, M Sayeedur Rahman, Abdu F Azad
BMC Microbiol. 2008; 8: 61. Published online 2008 April 15. doi: 10.1186/1471-2180-8-61
PMCID:
PMC2335108
Abstract Full Text PDF–417K Supplementary Material
Making Genomics Functional: Deciphering the Genetics of Acute Lung Injury
Ryan Kamp, Xiaoguang Sun, Joe G. N. Garcia
Proc Am Thorac Soc. 2008 April 15; 5(3): 348–353. doi: 10.1513/pats.200709-152DR
PMCID:
PMC2645247
Abstract Full Text PDF–376K
Development of a Cross-Disciplinary Investigative Model for the Introduction of Microarray Techniques at Non-R1 Undergraduate Institutions
David E. Walker, Gary P. Lutz, Consuelo J. Alvarez
CBE Life Sci Educ. 2008 Spring; 7(1): 118–131. doi: 10.1187/cbe.07-01-0006
PMCID:
PMC2262120
Abstract Full Text PDF–1.2M
The Local and Systemic Inflammatory Transcriptome after Acute Kidney Injury
Dmitry N. Grigoryev, Manchang Liu, Heitham T. Hassoun, Chris Cheadle, Kathleen C. Barnes, Hamid Rabb
J Am Soc Nephrol. 2008 March; 19(3): 547–558. doi: 10.1681/ASN.2007040469
PMCID:
PMC2391061
Abstract Full Text Supplementary Material
Mitogen-Activated Protein Kinases Regulate Susceptibility to Ventilator-Induced Lung Injury
Tamás Dolinay, Wei Wu, Naftali Kaminski, Emeka Ifedigbo, A. Murat Kaynar, Mária Szilasi, Simon C. Watkins, Stefan W. Ryter, Alexander Hoetzel, Augustine M. K. Choi
PLoS ONE. 2008; 3(2): e1601. Published online 2008 February 13. doi: 10.1371/journal.pone.0001601
PMCID:
PMC2223071
Abstract Full Text PDF–619K Supplementary Material
Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'
Alexandre Kuhn, Ruth Luthi-Carter, Mauro Delorenzi
BMC Bioinformatics. 2008; 9: 26. Published online 2008 January 17. doi: 10.1186/1471-2105-9-26
PMCID:
PMC2267709
Abstract Full Text PDF–511K
Genetic and Pharmacologic Evidence Links Oxidative Stress to Ventilator-induced Lung Injury in Mice
Srinivas Papaiahgari, Adi Yerrapureddy, Swetha R. Reddy, Narsa M. Reddy, Jeffery M. Dodd-O, Michael T. Crow, Dimitry N. Grigoryev, Kathleen Barnes, Rubin M. Tuder, Masayuki Yamamoto, Thomas W. Kensler, Shyam Biswal, Wayne Mitzner, Paul M. Hassoun, Sekhar P. Reddy
Am J Respir Crit Care Med. 2007 December 15; 176(12): 1222–1235. Published online 2007 September 27. doi: 10.1164/rccm.200701-060OC
PMCID:
PMC2176106
Abstract Full Text PDF–690K Supplementary Material
Differential analysis for high density tiling microarray data
Srinka Ghosh, Heather A Hirsch, Edward A Sekinger, Philipp Kapranov, Kevin Struhl, Thomas R Gingeras
BMC Bioinformatics. 2007; 8: 359. Published online 2007 September 24. doi: 10.1186/1471-2105-8-359
PMCID:
PMC2231405
Abstract Full Text PDF–1.8M Supplementary Material
Microarray-based Analysis of Ventilator-induced Lung Injury
Mark M. Wurfel
Proc Am Thorac Soc. 2007 January; 4(1): 77–84. doi: 10.1513/pats.200608-149JG
PMCID:
PMC2647617
Abstract Full Text PDF–846K
Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results
Carmiya Bar-Or, Meira Bar-Eyal, Tali Z Gal, Yoram Kapulnik, Henryk Czosnek, Hinanit Koltai
BMC Genomics. 2006; 7: 110. Published online 2006 May 8. doi: 10.1186/1471-2164-7-110
PMCID:
PMC1482311
Abstract Full Text PDF–655K Supplementary Material
Molecular evidence for arterial repair in atherosclerosis
Ravi Karra, Sreekanth Vemullapalli, Chunming Dong, Edward E. Herderick, Xiaohua Song, Kathy Slosek, Joseph R. Nevins, Mike West, Pascal J. Goldschmidt-Clermont, David Seo
Proc Natl Acad Sci U S A. 2005 November 15; 102(46): 16789–16794. Published online 2005 November 7. doi: 10.1073/pnas.0507718102
PMCID:
PMC1277970
Abstract Full Text PDF–744K Supplementary Material
Genetic Determinants and Ethnic Disparities in Sepsis-associated Acute Lung Injury
Kathleen C. Barnes
Proc Am Thorac Soc. 2005 October; 2(3): 195–201. doi: 10.1513/pats.200502-013AC
PMCID:
PMC2713318
Abstract Full Text PDF–96K
In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip® technology
Dmitry N Grigoryev, Shwu-Fan Ma, Brett A Simon, Rafael A Irizarry, Shui Q Ye, Joe GN Garcia
BMC Genomics. 2005; 6: 62. Published online 2005 May 4. doi: 10.1186/1471-2164-6-62
PMCID:
PMC1156887
Abstract Full Text PDF–706K
Searching for Candidate Genes in Acute Lung Injury: SNPS, CHIPS and PBEF
Joe G. N Garcia
Trans Am Clin Climatol Assoc. 2005; 116: 205–220.
PMCID:
PMC1473142
Abstract Full Text PDF–1.0M
Science review: Searching for gene candidates in acute lung injury
Dmitry N Grigoryev, James H Finigan, Paul Hassoun, Joe GN Garcia
Crit Care. 2004; 8(6): 440–447. Published online 2004 June 30. doi: 10.1186/cc2901
PMCID:
PMC1065043
Abstract Full Text PDF–99K Supplementary Material
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