#3 · Genomics
Ancient and phased human genomes test selection and imputation inference methods
The common thread is the use of ancient and haplotype-resolved human genomes to evaluate evolutionary and population-genetic inference. A benchmark of eight local ancestry inference methods on 176 imputed Neolithic genomes recommends Gnomix or RFMix and tests selection signals at FADS1/2. Coalescent theory and simulations assess reference panel design for ancient DNA imputation, where a joint 1000 Genomes–ancient panel modestly improves rare-variant imputation. A study of genomic history and selection in Roman and early medieval Britain extends this framing to a regional historical setting. The HLA preprint is less directly inferential: it maps structural variation across 460 phased assemblies and links structural haplotypes to HLA expression differences. What is new is the pairing of explicit method benchmarking with archival material and haplotype-resolved structural comparison.
Published papers
Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes.
Single-cell tools deconvolve 9p21 transcripts (p16INK4A, p14ARF, p15INK4B) and map cis-regulatory elements, showing independent expression across tissues and…
A theoretical and experimental framework enables low-coverage sequencing for accurate quantification of genome-wide cytosine modification levels.
Framework showing low-coverage sequencing (Sparse-Seq) can quantify genome-wide 5mC and 5hmC with predictable error, plus an online error-calculation tool.
The hidden sources of spurious fusion transcripts in plants.
Rice long-read RNA-seq shows most plant fusion transcripts are artifacts, mainly RT template switching; proposes a validation pipeline.
Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline.
nucDetective pipeline benchmarked on P. falciparum MNase-seq reveals regular phased nucleosome arrays and canonical promoter architecture.
Preprints
Targeted sequencing of expanded tandem repeats: Identifying interruptions and errors
CHARLIE is a pipeline for locating interruptions within expanded repeats from Illumina and PacBio targeted sequencing, and profiles platform-specific…
Sensitive Chromosomal Translocation Quantitation from Amplicon Sequencing Using Primer-Anchored Statistical Translocation Analysis (PASTA)
PASTA, a count-based statistical tool for quantifying and confirming chromosomal translocation junctions from targeted amplicon sequencing, validated against…
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