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Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments
Jeffrey P Townsend, Daniel L Hartl
Genome Biol. 2002; 3(12): research0071.1–research0071.16. Published online 2002 November 20.
PMCID:
PMC151173
Abstract Full Text PDF–1.2M Supplementary Material
 Is Cited by the Following 27 Articles in this Archive:
Transcriptome Profiling of Sexual Maturation and Mating in the Mediterranean Fruit Fly, Ceratitis capitata
Ludvik M. Gomulski, George Dimopoulos, Zhiyong Xi, Francesca Scolari, Paolo Gabrieli, Paolo Siciliano, Anthony R. Clarke, Anna R. Malacrida, Giuliano Gasperi
PLoS One. 2012; 7(1): e30857. Published online 2012 January 27. doi: 10.1371/journal.pone.0030857
PMCID:
PMC3267753
Abstract Full Text PDF–307K Supplementary Material
Identification of the CRE-1 Cellulolytic Regulon in Neurospora crassa
Jianping Sun, N. Louise Glass
PLoS One. 2011; 6(9): e25654. Published online 2011 September 29. doi: 10.1371/journal.pone.0025654
PMCID:
PMC3183063
Abstract Full Text PDF–1.2M Supplementary Material
Ribosomal DNA Deletions Modulate Genome-Wide Gene Expression: “rDNA–Sensitive” Genes and Natural Variation
Silvana Paredes, Alan T. Branco, Daniel L. Hartl, Keith A. Maggert, Bernardo Lemos
PLoS Genet. 2011 April; 7(4): e1001376. Published online 2011 April 21. doi: 10.1371/journal.pgen.1001376
PMCID:
PMC3080856
Abstract Full Text PDF–472K Supplementary Material
CSP and Takeout Genes Modulate the Switch between Attraction and Repulsion during Behavioral Phase Change in the Migratory Locust
Wei Guo, Xianhui Wang, Zongyuan Ma, Liang Xue, Jingyao Han, Dan Yu, Le Kang
PLoS Genet. 2011 February; 7(2): e1001291. Published online 2011 February 3. doi: 10.1371/journal.pgen.1001291
PMCID:
PMC3033386
Abstract Full Text PDF–1.4M Supplementary Material
Population transcriptomics of Drosophila melanogaster females
Lena Müller, Stephan Hutter, Rayna Stamboliyska, Sarah S Saminadin-Peter, Wolfgang Stephan, John Parsch
BMC Genomics. 2011; 12: 81. Published online 2011 January 28. doi: 10.1186/1471-2164-12-81
PMCID:
PMC3040150
Abstract Full Text PDF–580K Supplementary Material
Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict
Bernardo Lemos, Alan T. Branco, Daniel L. Hartl
Proc Natl Acad Sci U S A. 2010 September 7; 107(36): 15826–15831. Published online 2010 August 23. doi: 10.1073/pnas.1010383107
PMCID:
PMC2936610
Abstract Full Text PDF–536K Supplementary Material
Multi-targeted priming for genome-wide gene expression assays
Aleksandra B Adomas, Francesc Lopez-Giraldez, Travis A Clark, Zheng Wang, Jeffrey P Townsend
BMC Genomics. 2010; 11: 477. Published online 2010 August 17. doi: 10.1186/1471-2164-11-477
PMCID:
PMC3091673
Abstract Full Text PDF–1.1M Supplementary Material
Meiotic Regulators Ndt80 and Ime2 Have Different Roles in Saccharomyces and Neurospora
Elizabeth A. Hutchison, N. Louise Glass
Genetics. 2010 August; 185(4): 1271–1282. doi: 10.1534/genetics.110.117184
PMCID:
PMC2927755
Abstract Full Text PDF–2.4M
Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture
Shuwei Li, Ching-Hua Shih, Michael H Kohn
BMC Genomics. 2010; 11: 322. Published online 2010 May 24. doi: 10.1186/1471-2164-11-322
PMCID:
PMC2891614
Abstract Full Text PDF–1.4M Supplementary Material
Effects of temperature on gene expression in embryos of the coral Montastraea faveolata
Christian R Voolstra, Julia Schnetzer, Leonid Peshkin, Carly J Randall, Alina M Szmant, Mónica Medina
BMC Genomics. 2009; 10: 627. Published online 2009 December 23. doi: 10.1186/1471-2164-10-627
PMCID:
PMC2807443
Abstract Full Text PDF–298K Supplementary Material
The Filamentous Fungal Gene Expression Database (FFGED)
Zhang Zhang, Jeffrey P. Townsend
Fungal Genet Biol. Author manuscript; available in PMC 2011 March 1.
Published in final edited form as: Fungal Genet Biol. 2010 March; 47(3): 199. Published online 2009 December 16. doi: 10.1016/j.fgb.2009.12.001
PMCID:
PMC2822089
Abstract Full Text PDF–1.9M
Transcriptional analysis of the response of Neurospora crassa to phytosphingosine reveals links to mitochondrial function
Arnaldo Videira, Takao Kasuga, Chaoguang Tian, Catarina Lemos, Ana Castro, N. Louise Glass
Microbiology. 2009 September; 155(Pt 9): 3134–3141. doi: 10.1099/mic.0.029710-0
PMCID:
PMC2888170
Abstract Full Text PDF–396K Supplementary Material
A Bayesian model for cross-study differential gene expression
Robert B. Scharpf, Håkon Tjelmeland, Giovanni Parmigiani, Andrew B. Nobel
J Am Stat Assoc. Author manuscript; available in PMC 2010 November 30.
Published in final edited form as: J Am Stat Assoc. 2009; 104(488): 1295–1310. doi: 10.1198/jasa.2009.ap07611
PMCID:
PMC2994029
Abstract Full Text PDF–1.4M Supplementary Material
Dissecting Colony Development of Neurospora crassa Using mRNA Profiling and Comparative Genomics Approaches
Takao Kasuga, N. Louise Glass
Eukaryot Cell. 2008 September; 7(9): 1549–1564. Published online 2008 August 1. doi: 10.1128/EC.00195-08
PMCID:
PMC2547062
Abstract Full Text PDF–496K Supplementary Material
Gene expression variation in African and European populations of Drosophila melanogaster
Stephan Hutter, Sarah S Saminadin-Peter, Wolfgang Stephan, John Parsch
Genome Biol. 2008; 9(1): R12. Published online 2008 January 21. doi: 10.1186/gb-2008-9-1-r12
PMCID:
PMC2395247
Abstract Full Text PDF–658K Supplementary Material
Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA – a Bayesian approach
Carmen Pin, Mark Reuter
BMC Bioinformatics. 2007; 8: 455. Published online 2007 November 19. doi: 10.1186/1471-2105-8-455
PMCID:
PMC2228326
Abstract Full Text PDF–1.1M
Bayesian meta-analysis models for microarray data: a comparative study
Erin M Conlon, Joon J Song, Anna Liu
BMC Bioinformatics. 2007; 8: 80. Published online 2007 March 7. doi: 10.1186/1471-2105-8-80
PMCID:
PMC1851021
Abstract Full Text PDF–581K Supplementary Material
Bayesian models for pooling microarray studies with multiple sources of replications
Erin M Conlon, Joon J Song, Jun S Liu
BMC Bioinformatics. 2006; 7: 247. Published online 2006 May 5. doi: 10.1186/1471-2105-7-247
PMCID:
PMC1534062
Abstract Full Text PDF–497K
A two-sample Bayesian t-test for microarray data
Richard J Fox, Matthew W Dimmic
BMC Bioinformatics. 2006; 7: 126. Published online 2006 March 10. doi: 10.1186/1471-2105-7-126
PMCID:
PMC1431571
Abstract Full Text PDF–348K
Profile and Analysis of Gene Expression Changes during Early Development in Germinating Spores of Ceratopteris richardii
Mari L. Salmi, Thomas J. Bushart, Stephen C. Stout, Stanley J. Roux
Plant Physiol. 2005 July; 138(3): 1734–1745. doi: 10.1104/pp.105.062851
PMCID:
PMC1176442
Abstract Full Text PDF–316K Supplementary Material
Tests for finding complex patterns of differential expression in cancers: towards individualized medicine
James Lyons-Weiler, Satish Patel, Michael J Becich, Tony E Godfrey
BMC Bioinformatics. 2004; 5: 110. Published online 2004 August 12. doi: 10.1186/1471-2105-5-110
PMCID:
PMC514539
Abstract Full Text PDF–446K
Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells
Bin Yao, Sanjay N Rakhade, Qunfang Li, Sharlin Ahmed, Raul Krauss, Sorin Draghici, Jeffrey A Loeb
BMC Bioinformatics. 2004; 5: 99. Published online 2004 July 23. doi: 10.1186/1471-2105-5-99
PMCID:
PMC509237
Abstract Full Text PDF–1.5M
Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays
Jeffrey P Townsend
BMC Bioinformatics. 2004; 5: 54. Published online 2004 May 5. doi: 10.1186/1471-2105-5-54
PMCID:
PMC420235
Abstract Full Text PDF–471K
Anomalies in the Expression Profile of Interspecific Hybrids of Drosophila melanogaster and Drosophila simulans
José M. Ranz, Kalsang Namgyal, Greg Gibson, Daniel L. Hartl
Genome Res. 2004 March; 14(3): 373–379. doi: 10.1101/gr.2019804
PMCID:
PMC353219
Abstract Full Text PDF–395K
Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays
Jeffrey P Townsend
BMC Genomics. 2003; 4: 41. Published online 2003 October 2. doi: 10.1186/1471-2164-4-41
PMCID:
PMC239860
Abstract Full Text PDF–310K Supplementary Material
Rapid evolution of male-biased gene expression in Drosophila
Colin D. Meiklejohn, John Parsch, José M. Ranz, Daniel L. Hartl
Proc Natl Acad Sci U S A. 2003 August 19; 100(17): 9894–9899. Published online 2003 August 7. doi: 10.1073/pnas.1630690100
PMCID:
PMC188344
Abstract Full Text PDF–323K Supplementary Material
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