Blog

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).

Ploid AI is working with La Canastita’s genetics teams at Berryum Varieties and Remo Varieties to bring genomic analysis into their breeding programs. What we are doing together, and the results we are seeing.

Ploid AI is certified against ISO/IEC 27001, ISO 42001 and ISO 9001 by OCA Global. What each standard covers, why we did the work, and what it means for the security of the data you trust us with.

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.

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.

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.

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.

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.

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.

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.

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.

We evaluated Ploid AI on BixBench, the most realistic benchmark for bioinformatics agents. Here are our results across 20 bioinformatics domains, compared to leading general-purpose and domain-specific agents.