Featured Publications
Differential richness inference for 16S rRNA marker gene surveys
Kumar M, Slud E, Hehnly C, Zhang L, Broach J, Irizarry R, Schiff S, Paulson J. Differential richness inference for 16S rRNA marker gene surveys. Genome Biology 2022, 23: 166. PMID: 35915508, PMCID: PMC9344657, DOI: 10.1186/s13059-022-02722-x.Peer-Reviewed Original ResearchConceptsMarker gene surveysRRNA marker gene surveysGene surveysMicrobial assemblagesSpecies discoveryMicrobial taxaMicrobial communitiesMicrobiome surveysRichness estimationSequencing readsDiversity measuresTaxaGenus abundanceMicrobiome dataR packageAbundanceRichnessDiscoveryDiversityReadsAssemblagesObserved numberExperimental evidenceAccumulationInference
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