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A new non-linear normalization method for reducing variability in DNA microarray experiments
Christopher Workman, Lars Juhl Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Bjørn Nielser, Hans-Henrik Saxild, Claus Nielsen, Søren Brunak, Steen Knudsen
Genome Biol. 2002; 3(9): research0048.1–research0048.16. Published online 2002 August 30.
PMCID:
PMC126873
Abstract Full Text PDF–2.2M Supplementary Material
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 Is Cited by the Following 68 Articles in this Archive:
Os-GIGANTEA Confers Robust Diurnal Rhythms on the Global Transcriptome of Rice in the Field
Takeshi Izawa, Motohiro Mihara, Yuji Suzuki, Meenu Gupta, Hironori Itoh, Atsushi J. Nagano, Ritsuko Motoyama, Yuji Sawada, Masahiro Yano, Masami Yokota Hirai, Amane Makino, Yoshiaki Nagamura
Plant Cell. 2011 May; 23(5): 1741–1755. Published online 2011 May 13. doi: 10.1105/tpc.111.083238
PMCID:
PMC3123946
Abstract Full Text PDF–1.4M
Whole blood transcriptional profiling in ankylosing spondylitis identifies novel candidate genes that might contribute to the inflammatory and tissue-destructive disease aspects
Fernando M Pimentel-Santos, Dário Ligeiro, Mafalda Matos, Ana F Mourão, José Costa, Helena Santos, Anabela Barcelos, Fátima Godinho, Patricia Pinto, Margarida Cruz, João E Fonseca, Henrique Guedes-Pinto, Jaime C Branco, Matthew A Brown, Gethin P Thomas
Arthritis Res Ther. 2011; 13(2): R57. Published online 2011 April 7. doi: 10.1186/ar3309
PMCID:
PMC3132052
Abstract Full Text PDF–326K 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
Equitoxic Doses of 5-Azacytidine and 5-Aza-2′Deoxycytidine Induce Diverse Immediate and Overlapping Heritable Changes in the Transcriptome
Xiangning Qiu, Christoffer Hother, Ulrik M. Ralfkiær, Alexandra Søgaard, Qianjin Lu, Christopher T. Workman, Gangning Liang, Peter A. Jones, Kirsten Grønbæk
PLoS One. 2010; 5(9): e12994. Published online 2010 September 29. doi: 10.1371/journal.pone.0012994
PMCID:
PMC2947512
Abstract Full Text PDF–1.8M Supplementary Material
Ethylene Suppression of Sugar-Induced Anthocyanin Pigmentation in Arabidopsis
Seok-Won Jeong, Prasanta Kumar Das, Sae Chae Jeoung, Ji-Young Song, Hyun Kyoung Lee, Yeon-Ki Kim, Woo Jung Kim, Yong Il Park, Sang-Dong Yoo, Sang-Bong Choi, Giltsu Choi, Youn-Il Park
Plant Physiol. 2010 November; 154(3): 1514–1531. Published online 2010 September 27. doi: 10.1104/pp.110.161869
Correction in:
Plant Physiol. 2011 February; 155(2): 1047.
PMCID:
PMC2971625
Abstract Full Text PDF–1.3M Supplementary Material Correction
Melanoma sentinel node biopsy and prediction models for relapse and overall survival
A Mitra, C Conway, C Walker, M Cook, B Powell, S Lobo, M Chan, M Kissin, G Layer, J Smallwood, C Ottensmeier, P Stanley, H Peach, H Chong, F Elliott, M M Iles, J Nsengimana, J H Barrett, D T Bishop, J A Newton-Bishop
Br J Cancer. 2010 October 12; 103(8): 1229–1236. Published online 2010 September 21. doi: 10.1038/sj.bjc.6605849
PMCID:
PMC2967048
Abstract Full Text PDF–434K
Molecular Signature of Mineralocorticoid Receptor Signaling in Cardiomyocytes: From Cultured Cells to Mouse Heart
Celine Latouche, Yannis Sainte-Marie, Marja Steenman, Paulo Castro Chaves, Aniko Naray-Fejes-Toth, Geza Fejes-Toth, Nicolette Farman, Frederic Jaisser
Endocrinology. 2010 September; 151(9): 4467–4476. Published online 2010 June 30. doi: 10.1210/en.2010-0237
PMCID:
PMC2940498
Abstract Full Text Supplementary Material
Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays
High Seng Chai, Terry M Therneau, Kent R Bailey, Jean-Pierre A Kocher
BMC Bioinformatics. 2010; 11: 356. Published online 2010 June 29. doi: 10.1186/1471-2105-11-356
PMCID:
PMC2910027
Abstract Full Text PDF–1.2M Supplementary Material
Bifidobacterium bifidum Actively Changes the Gene Expression Profile Induced by Lactobacillus acidophilus in Murine Dendritic Cells
Gudrun Weiss, Simon Rasmussen, Lisbeth Nielsen Fink, Hanne Jarmer, Birgit Nøhr Nielsen, Hanne Frøkiær
PLoS One. 2010; 5(6): e11065. Published online 2010 June 10. doi: 10.1371/journal.pone.0011065
PMCID:
PMC2883554
Abstract Full Text PDF–455K
Bayesian integrated modeling of expression data: a case study on RhoG
Rashi Gupta, Dario Greco, Petri Auvinen, Elja Arjas
BMC Bioinformatics. 2010; 11: 295. Published online 2010 June 1. doi: 10.1186/1471-2105-11-295
PMCID:
PMC2894040
Abstract Full Text PDF–834K Supplementary Material
Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain
J. Raphael Gibbs, Marcel P. van der Brug, Dena G. Hernandez, Bryan J. Traynor, Michael A. Nalls, Shiao-Lin Lai, Sampath Arepalli, Allissa Dillman, Ian P. Rafferty, Juan Troncoso, Robert Johnson, H. Ronald Zielke, Luigi Ferrucci, Dan L. Longo, Mark R. Cookson, Andrew B. Singleton
PLoS Genet. 2010 May; 6(5): e1000952. Published online 2010 May 13. doi: 10.1371/journal.pgen.1000952
PMCID:
PMC2869317
Abstract Full Text PDF–1.3M Supplementary Material
Chromosomal and miRNA Expression Patterns Reveal Biologically Distinct Subgroups of 11q− Neuroblastoma
Patrick G Buckley, Leah Alcock, Kenneth Bryan, Isabella Bray, Johannes H Schulte, Alexander Schramm, Angelika Eggert, Pieter Mestdagh, Katleen De Preter, Jo Vandesompele, Frank Speleman, Raymond L Stallings
Clin Cancer Res. Author manuscript; available in PMC 2011 June 1.
Published in final edited form as: Clin Cancer Res. 2010 June 1; 16(11): 2971–2978. Published online 2010 April 20. doi: 10.1158/1078-0432.CCR-09-3215
PMCID:
PMC2880207
Abstract Full Text PDF–558K Supplementary Material
Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution
Martin Völker, Niclas Backström, Benjamin M. Skinner, Elizabeth J. Langley, Sydney K. Bunzey, Hans Ellegren, Darren K. Griffin
Genome Res. 2010 April; 20(4): 503–511. doi: 10.1101/gr.103663.109
PMCID:
PMC2847753
Abstract Full Text PDF–412K
Genetic Variability in CLU and Its Association with Alzheimer's Disease
Rita J. Guerreiro, John Beck, J. Raphael Gibbs, Isabel Santana, Martin N. Rossor, Jonathan M. Schott, Michael A. Nalls, Helena Ribeiro, Beatriz Santiago, Nick C. Fox, Catarina Oliveira, John Collinge, Simon Mead, Andrew Singleton, John Hardy
PLoS One. 2010; 5(3): e9510. Published online 2010 March 3. doi: 10.1371/journal.pone.0009510
PMCID:
PMC2831070
Abstract Full Text PDF–270K
Structure, Function, and Evolution of the Thiomonas spp. Genome
Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy, Céline Brochier-Armanet, Mohamed Barakat, Valérie Barbe, Fabienne Battaglia-Brunet, Odile Bruneel, Christopher G. Bryan, Jessica Cleiss-Arnold, Stéphane Cruveiller, Mathieu Erhardt, Audrey Heinrich-Salmeron, Florence Hommais, Catherine Joulian, Evelyne Krin, Aurélie Lieutaud, Didier Lièvremont, Caroline Michel, Daniel Muller, Philippe Ortet, Caroline Proux, Patricia Siguier, David Roche, Zoé Rouy, Grégory Salvignol, Djamila Slyemi, Emmanuel Talla, Stéphanie Weiss, Jean Weissenbach, Claudine Médigue, Philippe N. Bertin
PLoS Genet. 2010 February; 6(2): e1000859. Published online 2010 February 26. doi: 10.1371/journal.pgen.1000859
PMCID:
PMC2829063
Abstract Full Text PDF–924K Supplementary Material
Hybridization thermodynamics of NimbleGen Microarrays
Ulrike Mueckstein, Germán G Leparc, Alexandra Posekany, Ivo Hofacker, David P Kreil
BMC Bioinformatics. 2010; 11: 35. Published online 2010 January 19. doi: 10.1186/1471-2105-11-35
PMCID:
PMC2823707
Abstract Full Text PDF–343K Supplementary Material
T-helper 1 and T-helper 2 adjuvants induce distinct differences in the magnitude, quality and kinetics of the early inflammatory response at the site of injection
Karen Smith Korsholm, Rune V Petersen, Else Marie Agger, Peter Andersen
Immunology. 2010 January; 129(1): 75–86. doi: 10.1111/j.1365-2567.2009.03164.x
PMCID:
PMC2807488
Abstract Full Text PDF–465K
Genome-Wide Characterization of the SloR Metalloregulome in Streptococcus mutans
Kevin P. O'Rourke, Jeremy D. Shaw, Mitchell W. Pesesky, Brian T. Cook, Susanne M. Roberts, Jeffrey P. Bond, Grace A. Spatafora
J Bacteriol. 2010 March; 192(5): 1433–1443. Published online 2009 November 13. doi: 10.1128/JB.01161-09
PMCID:
PMC2820837
Abstract Full Text PDF–956K
New insights into molecular pathways associated with flatfish ovarian development and atresia revealed by transcriptional analysis
Angèle Tingaud-Sequeira, François Chauvigné, Juanjo Lozano, María J Agulleiro, Esther Asensio, Joan Cerdà
BMC Genomics. 2009; 10: 434. Published online 2009 September 15. doi: 10.1186/1471-2164-10-434
PMCID:
PMC2751788
Abstract Full Text PDF–5.3M Supplementary Material
Impaired Uptake and/or Utilization of Leucine by Saccharomyces cerevisiae Is Suppressed by the SPT15-300 Allele of the TATA-Binding Protein Gene
Richard J. S. Baerends, Jin-Long Qiu, Simon Rasmussen, Henrik Bjørn Nielsen, Anders Brandt
Appl Environ Microbiol. 2009 October; 75(19): 6055–6061. Published online 2009 August 7. doi: 10.1128/AEM.00989-09
PMCID:
PMC2753098
Abstract Full Text PDF–996K
Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis
Benjamin M Skinner, Lindsay BW Robertson, Helen G Tempest, Elizabeth J Langley, Dimitris Ioannou, Katie E Fowler, Richard PMA Crooijmans, Anthony D Hall, Darren K Griffin, Martin Völker
BMC Genomics. 2009; 10: 357. Published online 2009 August 5. doi: 10.1186/1471-2164-10-357
PMCID:
PMC2907691
Abstract Full Text PDF–1.0M Supplementary Material
Genome-wide screen of promoter methylation identifies novel markers in melanoma
Yasuo Koga, Mattia Pelizzola, Elaine Cheng, Michael Krauthammer, Mario Sznol, Stephan Ariyan, Deepak Narayan, Annette M. Molinaro, Ruth Halaban, Sherman M. Weissman
Genome Res. 2009 August; 19(8): 1462–1470. doi: 10.1101/gr.091447.109
PMCID:
PMC2720187
Abstract Full Text PDF–1.0M
A Large X-Chromosomal Deletion is Associated with Microphthalmia with Linear Skin Defects (MLS) and Amelogenesis Imperfecta (XAI)
Grace M. Hobson, Carolyn W. Gibson, Melissa Aragon, Zhi-an Yuan, Angelique Davis-Williams, Linda Banser, Jennifer Kirkham, Alan H. Brook
Am J Med Genet A. Author manuscript; available in PMC 2010 August 1.
Published in final edited form as: Am J Med Genet A. 2009 August; 149A(8): 1698–1705. doi: 10.1002/ajmg.a.32968
PMCID:
PMC2760392
Abstract Full Text PDF–787K Supplementary Material
The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies
Jan O. Korbel, Tal Tirosh-Wagner, Alexander Eckehart Urban, Xiao-Ning Chen, Maya Kasowski, Li Dai, Fabian Grubert, Chandra Erdman, Michael C. Gao, Ken Lange, Eric M. Sobel, Gillian M. Barlow, Arthur S. Aylsworth, Nancy J. Carpenter, Robin Dawn Clark, Monika Y. Cohen, Eric Doran, Tzipora Falik-Zaccai, Susan O. Lewin, Ira T. Lott, Barbara C. McGillivray, John B. Moeschler, Mark J. Pettenati, Siegfried M. Pueschel, Kathleen W. Rao, Lisa G. Shaffer, Mordechai Shohat, Alexander J. Van Riper, Dorothy Warburton, Sherman Weissman, Mark B. Gerstein, Michael Snyder, Julie R. Korenberg
Proc Natl Acad Sci U S A. 2009 July 21; 106(29): 12031–12036. Published online 2009 July 13. doi: 10.1073/pnas.0813248106
PMCID:
PMC2709665
Abstract Full Text PDF–1.2M Supplementary Material
Overexpression of the Transcription Factor AP37 in Rice Improves Grain Yield under Drought Conditions
Se-Jun Oh, Youn Shic Kim, Chang-Woo Kwon, Hye Kyong Park, Jin Seo Jeong, Ju-Kon Kim
Plant Physiol. 2009 July; 150(3): 1368–1379. doi: 10.1104/pp.109.137554
PMCID:
PMC2705040
Abstract Full Text PDF–1.1M Supplementary Material
A novel and universal method for microRNA RT-qPCR data normalization
Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele
Genome Biol. 2009; 10(6): R64. Published online 2009 June 16. doi: 10.1186/gb-2009-10-6-r64
PMCID:
PMC2718498
Abstract Full Text PDF–292K Supplementary Material
Improved ChIP-chip analysis by a mixture model approach
Wei Sun, Michael J Buck, Mukund Patel, Ian J Davis
BMC Bioinformatics. 2009; 10: 173. Published online 2009 June 7. doi: 10.1186/1471-2105-10-173
PMCID:
PMC2700807
Abstract Full Text PDF–995K Supplementary Material
Urinary Protein Profiles in a Rat Model for Diabetic Complications
Daniela M. Schlatzer, Jean-Eudes Dazard, Moyez Dharsee, Rob M. Ewing, Serguei Ilchenko, Ian Stewart, George Christ, Mark R. Chance
Mol Cell Proteomics. 2009 September; 8(9): 2145–2158. Published online 2009 June 4. doi: 10.1074/mcp.M800558-MCP200
PMCID:
PMC2742441
Abstract Full Text Supplementary Material
Methyl Jasmonate Reduces Grain Yield by Mediating Stress Signals to Alter Spikelet Development in Rice
Eun Hye Kim, Youn Shic Kim, Su-Hyun Park, Yeon Jong Koo, Yang Do Choi, Yong-Yoon Chung, In-Jung Lee, Ju-Kon Kim
Plant Physiol. 2009 April; 149(4): 1751–1760. doi: 10.1104/pp.108.134684
PMCID:
PMC2663756
Abstract Full Text PDF–736K Supplementary Material
A comparison on effects of normalisations in the detection of differentially expressed genes
Monica Chiogna, Maria Sofia Massa, Davide Risso, Chiara Romualdi
BMC Bioinformatics. 2009; 10: 61. Published online 2009 February 13. doi: 10.1186/1471-2105-10-61
PMCID:
PMC2680204
Abstract Full Text PDF–483K Supplementary Material
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