Apollo: a community resource for genome annotation editing

By Eduardo Lee, N. Harris, Mark Gibson, Raymond Chetty, Suzanna Lewis. Bioinform., 2009

1,484 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/7e648eb043ca6154d1e4c36c21e548f4d1486d57

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Citations in the corpus

PINA v2.0: mining interactome modules (2011, methodology): “The output files of each tool were parsed using custom R scripts and the functional enrichment analyses were performed on an SGE cluster using GOstats (29) and a custom extension to the Category package from the Bioconductor project v2.”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, methodology): “(E) Graphical schematic of putative stable, soluble multiprotein complexes, drawn using the GenePRO Cytoscape plugin [104] (see Table S7 for listing).”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, methodology): “…tool BIOCHAM using Boolean, differential, stochastic models and providing among others bifurcation diagrams (http://contraintes.inria.fr/biocham; Calzone et al., 2006); • the random walk-based ITM-Probe, also available as a Cytoscape plug-in (http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/mn/itm_…”
Robust Satisfaction of Temporal Logic over Real-Valued Signals (2010, methodology): “Their approach has been integrated into the BIOCHAM tool [6] and has been applied to numerous biological examples.”
A long noncoding RNA induced by TLRs mediates both activation and repression of immune response genes (2013, methodology): “Using the GOstats package (32), the top 800 up-regulated genes (using log2FC between base mean counts) were analyzed to detect biological processes with over-represented genes.”
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing (2015, methodology): “3, [105]), and genes included in phylogenetic analyses were manually checked against transcript information generated by Cufflinks to correct for 1) missing genes, 2) partial genes, and 3) separated genes.”
A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. (2011, methodology): “Gene ontology analysis was assisted by the GOstats package (Falcon and Gentleman, 2007).”
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources (2020, methodology): “, all analytes measured, or all analytes in a pathway database) used for each pathway [205,206].”
Detecting subnetwork-level dynamic correlations (2017, methodology): “…each X, as well as their main biological functions as defined by over-represented gene ontology (GO) biological process terms found by the GOstats package (Falcon and Gentleman, 2007) are listed in the supplementary file at http://web1.sph.emory.edu/users/tyu8/LANDD%20Supplements/ Spt_2_all_W.xls.”