Use Cases
Real analyses our users shared with Ploid. Explore them live or download the report.
agriculture
Blackberry thornlessness GWAS & functional annotation
Genome-wide association study in tetraploid blackberry identifying a WOX homeodomain transcription factor as the key regulator of prickle presence using GWASpoly and EggNOG functional annotation.
agriculture
Blueberry fruit ripening RNA-Seq analysis
Transcriptomic reanalysis of ethylene-mediated fruit ripening in blueberry, integrating WGCNA, transcription factor network inference, and factorial interaction modeling to uncover the regulatory architecture of ripening.
pharmaceutical
Hen egg-white lysozyme: epitope mapping and antibody binder retrieval
Integrated structural analysis of 88 antibody-antigen complexes (24 distinct antibodies) on hen egg-white lysozyme (HEWL), yielding a per-residue immunodominance map and five epitope patches. Shows that CDR-loop geometry alone predicts epitope site (within- vs between-group overlap 0.954 vs 0.257) and delivers a retrieval method that recovers same-site antibodies at the top of the ranking (MRR 0.93 to 1.00).
research
Human paleofeces metagenomics
Shotgun metagenomic analysis of two human paleofeces samples using Kraken2 and Kaiju classifiers, revealing high inter-individual microbial dissimilarity, contrasting diversity profiles, and evidence of unsampled rare taxa beyond current sequencing depth.
pharmaceutical
Melanoma MAPK inhibitor response: multi-omic biomarker discovery
Integrated genomic, transcriptomic, and drug-sensitivity analysis of 122 GDSC melanoma cell lines, revealing BRAF V600 as a genomic biomarker of BRAF inhibitor sensitivity and a novel AXL/WNT5A/EGFR signature predicting MEK inhibitor resistance, supporting the rationale for BRAF+MEK combination therapy.
pharmaceutical
Multi-omics integration: RNA-Seq, Methylation and ChIP-Seq
Integrated RNA-seq, spike-in ChIP-seq, and EPIC methylation array analysis of EZH2/DNMT inhibition in multiple myeloma (INA-6), revealing genome-wide H3K27me3 loss and its convergence with DNA methylation on oncogenic programs, supporting combination epigenetic therapy.
pharmaceutical
Ovarian carcinoma microenvironment: spatial immune exclusion mapping
Integrated spatial transcriptomic analysis of 407,124 cells from an ovarian carcinoma FFPE section, revealing an 18-fold vascular deficit and a stroma-restricted CD8 phenotype.
pharmaceutical
Single-cell transcriptomic analysis of human PBMCs
Multi-layered scRNA-seq analysis of 10,000 human PBMCs identifying cell-type specific regulatory networks, druggable targets, and intercellular communication axes across seven immune cell populations.
pharmaceutical
Spatial transcriptomics of human breast cancer
SOPA-based spatial transcriptomics analysis of Xenium human breast cancer FFPE tissue, mapping tumor microenvironment cell types, myoepithelial markers, fibroblast heterogeneity, and immune clusters using a 280-gene biomarker panel.