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: CoGAPS
https://packages.ecosyste.ms/registries/bioconductor.org/packages/CoGAPS
Coordinated Gene Activity in Pattern Sets
1 version
Latest release: 8 months ago
2 dependent packages
25,308 downloads total
Papers Mentioning CoGAPS 14
10.1093/bfgp/elx018
Epigenetic regulation of gene expression in cancer: techniques, resources and analysisCited by: 91
Author(s): Luciane T. Kagohara, Genevieve Stein-O’Brien, Dylan Z. Kelley, Emily Flam, Heather C. Wick, Ludmila Danilova, Hariharan Easwaran, Alexander V. Favorov, Jiang Qian, Daria A. Gaykalova, Elana J. Fertig
Software Mentions: 7
Published: almost 7 years ago
10.1186/s12859-019-3291-6
DeepMF: deciphering the latent patterns in omics profiles with a deep learning methodCited by: 10
Author(s): Lingxi Chen, Jianjun Xu, Shuai Cheng Li
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-020-57542-5
Large-scale Analyses of Disease Biomarkers and Apremilast Pharmacodynamic EffectsCited by: 11
Author(s): И. В. Медведева, Matthew E. Stokes, Dominic Eisinger, Samuel T. LaBrie, Jing Ai, Matthew Trotter, Peter Schäfer, Robert Yang
Software Mentions: 4
Published: over 4 years ago
10.1186/s13073-021-00944-5
Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumorsCited by: 10
Author(s): Emily F. Davis-Marcisak, Allison A. Fitzgerald, Michael Kessler, Ludmila Danilova, Elizabeth M. Jaffee, Neeha Zaidi, Louis M. Weiner, Elana J. Fertig
Software Mentions: 4
Published: almost 3 years ago
10.1016/j.xpro.2021.100561
A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cellsCited by: 1
Author(s): Kevin Chen, Kıvılcım Öztürk, Ted Liefeld, Michael Reich, Jill P. Mesirov, Hannah Carter, Stephanie I. Fraley
Software Mentions: 3
Published: about 3 years ago
10.1186/1751-0473-8-10
The non-negative matrix factorization toolbox for biological data miningCited by: 147
Author(s): Yifeng Li, Alioune Ngom
Software Mentions: 2
Published: about 11 years ago
10.1186/1471-2164-13-160
Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinomaCited by: 32
Author(s): Elana J. Fertig, Qing Ren, Haixia Cheng, Hyōe Hatakeyama, Adam P. Dicker, Ulrich Rodeck, Michael Considine, Michael F. Ochs, Christine H. Chung
Software Mentions: 2
Published: over 12 years ago
10.18632/oncotarget.12075
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR networkCited by: 18
Author(s): Elana J. Fertig, Hiroyuki Ozawa, Manjusha Thakar, Jason D. Howard, Luciane T. Kagohara, Gabriel Krigsfeld, Ruchira S. Ranaweera, Robert M. Hughes, Jimena Pérez, Siân Jones, Alexander V. Favorov, Jacob Carey, Genevieve Stein-O’Brien, Daria A. Gaykalova, Michael F. Ochs, Christine H. Chung
Software Mentions: 1
Published: over 7 years ago
10.1186/s12859-020-03796-9
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structuresCited by: 20
Author(s): Thomas D. Sherman, Tiger Gao, Elana J. Fertig
Software Mentions: 1
Published: over 3 years ago
10.1186/1741-7015-10-43
A new analysis approach of epidermal growth factor receptor pathway activation patterns provides insights into cetuximab resistance mechanisms in head and neck cancerCited by: 1
Author(s): Silvia von der Heyde, Tim Beißbarth
Software Mentions: 1
Published: about 12 years ago
10.1371/journal.pone.0078127
Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway AnalysisCited by: 39
Author(s): Elana J. Fertig, Ana Marković, Ludmila Danilova, Daria A. Gaykalova, Leslie Cope, Christine H. Chung, Michael F. Ochs, Joseph A. Califano
Software Mentions: 1
Published: over 10 years ago
10.3389/fcell.2020.00698
Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient CellsCited by: 17
Author(s): Tatiana Lopatina, Enrica Favaro, Ludmila Danilova, Elana J. Fertig, Alexander V. Favorov, Luciane T. Kagohara, Tiziana Martone, Benedetta Bussolati, Renato Romagnoli, Roberto Albera, Giancarlo Pecorari, Maria Felice Brizzi, Giovanni Camussi, Daria A. Gaykalova
Software Mentions: 1
Published: over 3 years ago
10.1186/s13073-018-0545-2
Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistanceCited by: 24
Author(s): Genevieve Stein-O’Brien, Luciane T. Kagohara, Sijia Li, Manjusha Thakar, Ruchira S. Ranaweera, Hiroyuki Ozawa, Haixia Cheng, Michael Considine, Sandra Schmitz, Alexander V. Favorov, Ludmila Danilova, Joseph A. Califano, Evgeny Izumchenko, Daria A. Gaykalova, Christine H. Chung, Elana J. Fertig
Software Mentions: 1
Published: about 6 years ago
10.1016/j.tig.2018.07.003
Enter the Matrix: Factorization Uncovers Knowledge from OmicsCited by: 177
Author(s): Genevieve Stein-O’Brien, Raman Arora, Aedín C. Culhane, Alexander V. Favorov, Lana X. Garmire, Casey S. Greene, Loyal A. Goff, Yifeng Li, Aloune Ngom, Michael F. Ochs, Yanxun Xu, Elana J. Fertig
Software Mentions: 1
Published: over 5 years ago