Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: puma
https://packages.ecosyste.ms/registries/bioconductor.org/packages/puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
1 version
Latest release: about 1 year ago
1 dependent package
44,269 downloads total
Papers Mentioning puma 14
10.1186/1748-7188-4-7
Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificityCited by: 71
Author(s): Koji Kadota, Yuji Nakai, Kentaro Shimizu
Software Mentions: 13
Published: over 15 years ago
10.1186/1471-2105-10-211
puma: a Bioconductor package for propagating uncertainty in microarray analysisCited by: 67
Author(s): Richard D. Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D. Lawrence, Magnus Rattray
Software Mentions: 9
Published: over 15 years ago
10.1186/1471-2105-14-263
Ontology based molecular signatures for immune cell types via gene expression analysisCited by: 12
Author(s): Terrence F. Meehan, Nicole Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl
Software Mentions: 5
Published: about 11 years ago
10.1186/1471-2164-14-930
RETRACTED ARTICLE: Gene expression analysis indicates CB1 receptor upregulation in the hippocampus and neurotoxic effects in the frontal cortex 3 weeks after single-dose MDMA administration in Dark Agouti ratsCited by: 9
Author(s): Péter Petschner, Viola Tamási, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, György Bagdy
Software Mentions: 5
Published: almost 11 years ago
10.1371/journal.pone.0081167
Cytokeratin 15 Marks Basal Epithelia in Developing Ureters and Is Upregulated in a Subset of Urothelial Cell CarcinomasCited by: 21
Author(s): Guihua Tai, Parisa Ranjzad, Fiona Marriage, Samrina Rehman, Helen Denley, Jill Dixon, Karen S. Mitchell, Philip J. Day, Adrian S. Woolf
Software Mentions: 5
Published: about 11 years ago
10.1186/s12864-018-4929-x
Gene expression analysis indicates reduced memory and cognitive functions in the hippocampus and increase in synaptic reorganization in the frontal cortex 3 weeks after MDMA administration in Dark Agouti ratsCited by: 12
Author(s): Péter Petschner, Viola Tamási, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, György Bagdy
Software Mentions: 5
Published: over 6 years ago
10.1186/s12864-016-2851-7
The application of transcriptomic data in the authentication of beef derived from contrasting production systemsCited by: 6
Author(s): T. Sweeney, Alexandre Lejeune, A.P. Moloney, Frank J. Monahan, Paul M Gettigan, Gérard Downey, Stephen D. E. Park, M. F. Ryan
Software Mentions: 5
Published: about 8 years ago
10.1371/journal.pone.0113662
Transcriptional Evidence for the Role of Chronic Venlafaxine Treatment in Neurotrophic Signaling and Neuroplasticity Including also Glutatmatergic- and Insulin-Mediated Neuronal ProcessesCited by: 52
Author(s): Viola Tamási, Péter Petschner, Csaba Ádori, Eszter Kirilly, Rómeó D. Andó, László Tóthfalusi, Gabriella Juhász, György Bagdy
Software Mentions: 4
Published: almost 10 years ago
10.1186/1471-2105-10-389
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variabilityCited by: 18
Author(s): Herman M. J. Sontrop, Perry D. Moerland, René van den Ham, Marcel J. T. Reinders, Wim Verhaegh
Software Mentions: 4
Published: almost 15 years ago
10.1186/1471-2105-14-39
puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysisCited by: 7
Author(s): Xuejun Liu, Zhenzhu Gao, Lili Zhang, Magnus Rattray
Software Mentions: 3
Published: almost 12 years ago
10.1371/journal.pone.0242584
Correction: The challenge of monitoring elusive large carnivores: An accurate and cost-effective tool to identify and sex pumas (Puma concolor) from footprintsCited by: 1
Author(s): Sky K. Alibhai, Zoë C. Jewell, Jeffrey S. Evans
Software Mentions: 3
Published: about 4 years ago
10.1093/ibd/izz311
Differential Expression of Soluble Receptor for Advanced Glycation End-products in Mice Susceptible or Resistant to Chronic ColitisCited by: 8
Author(s): Michael Bramhall, Kevin Rich, Ajanta Chakraborty, Larisa Logunova, Namshik Han, James L. Wilson, John McLaughlin, Andy Brass, Sheena M. Cruickshank
Software Mentions: 2
Published: almost 5 years ago
10.1186/1471-2164-14-453
Transcriptome analysis of porcine M. semimembranosus divergent in intramuscular fat as a consequence of dietary protein restrictionCited by: 43
Author(s): Ruth M. Hamill, Ozlem Aslan, Anne Maria Mullen, John V. O’Doherty, Jean McBryan, Deborah Morris, T. Sweeney
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0007144
Genomic Analysis of the Function of the Transcription Factor gata3 during Development of the Mammalian Inner EarCited by: 21
Author(s): Marta Milo, Daniela I. Cacciabue-Rivolta, Adam Kneebone, Hikke van Doorninck, Claire M. Johnson, Grace Lawoko‐Kerali, Mahesan Niranjan, Marcelo N. Rivolta, Matthew C. Holley
Software Mentions: 2
Published: about 15 years ago