#17 · Epigenomics

Auditing and correcting technical distortions in long-read, probe, and ATAC-seq data

The dominant thread is auditing or calibrating a representation before biological inference is drawn from it. Hyper3D-lite compares an all-pair projection of long-read multi-contact genome data against a count-preserving reference, making representation choices explicit. TraceBind fits Tn5 cleavage bias to each sample using mtDNA reads before calling transcription factor and nucleosome footprints in bulk and single-cell ATAC-seq. The probe-design preprint applies a related logic to specificity: it proposes topology-aware thermodynamic scores (retained paired boxes, Nbox, Zbox,NN) and reanalyzes published mismatch-probe datasets under fixed stringency, linking mismatch placement to nearest-neighbor stability. What is new is the emphasis on sample-specific calibration and explicit reference comparison before downstream interpretation.