2023
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
Ben Guebila M, Wang T, Lopes-Ramos C, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson J, Altenbuchinger M, Shutta K, Sonawane A, Lim J, Calderer G, van IJzendoorn D, Morgan D, Marin A, Chen C, Song Q, Saha E, DeMeo D, Padi M, Platig J, Kuijjer M, Glass K, Quackenbush J. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology 2023, 24: 45. PMID: 36894939, PMCID: PMC9999668, DOI: 10.1186/s13059-023-02877-1.Peer-Reviewed Original Research
2017
Regulatory network changes between cell lines and their tissues of origin
Lopes-Ramos C, Paulson J, Chen C, Kuijjer M, Fagny M, Platig J, Sonawane A, DeMeo D, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics 2017, 18: 723. PMID: 28899340, PMCID: PMC5596945, DOI: 10.1186/s12864-017-4111-x.Peer-Reviewed Original ResearchConceptsLymphoblastoid cell linesCell linesTranscription factor (TFChIP-seq dataRegulatory network changesRNA-seq dataTissue of originRegulatory network analysisCell cycle genesPrimary tissuesGene expression analysisEpstein-Barr virus-transformed lymphoblastoid cell linesChIP-seqVirus-transformed lymphoblastoid cell linesTF-targetRNA-seqGTEx projectTF regulationCycle genesTranscriptomic differencesBackgroundCell linesTranscript levelsExpression analysisFibroblast cell lineNetwork analysis