Zhiping Weng

The paper annotates 18 chromatin states in 66 mouse epigenomes across twelve tissues during development using ChromHMM, identifying bivalent states with evolutionary conservation and gene silencing functions.

This study introduces liquid chromatin Hi-C to analyze chromatin interaction dynamics and finds that compartmentalization stability varies with chromatin domain type and fragment size.

This study identifies a conserved piRNA locus, pi6, essential for male mouse fertility and embryo viability by regulating sperm function through mRNA cleavage.

The paper identifies a network involving Cuff, TRF2, and CtBP that balances canonical and non-canonical piRNA precursor transcription in Drosophila.

The paper benchmarks enhancer-gene prediction methods using a curated dataset, finding TargetFinder performs best but has limited cross-cell-type effectiveness.

The paper develops a fully automated method to annotate 164 human cell types using 1,615 genomics datasets, creating a unified encyclopedia of functional DNA elements with a new importance measure.

This study identifies Armitage as a protein linking piRNA amplification in nuage to phased piRNA production on mitochondria in Drosophila.

The paper analyzes the piRNA response to retroviral invasion in koalas, finding that KoRV piRNAs are sense-biased and derived from unspliced transcripts, suggesting a conserved innate immune mechanism.

The paper shows Maelstrom represses canonical transcription in piRNA clusters, enabling Rhi to initiate piRNA precursor transcription.

The paper develops methods to eliminate PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers, showing improved data reproducibility and reduced bias.

The paper improves protein-protein docking by integrating cross-linking data, enhancing prediction accuracy and reducing false positives.

This study introduces spliceosome profiling to map intron excision sites with high resolution, revealing new introns and correcting misannotations in S. pombe.

This study identifies NHL-2 as a co-factor in C. elegans germline 22G-RNA pathways and shows it regulates gene expression through RNA binding and stability.

The paper identifies piRNA binding sites in C. elegans germline mRNAs and shows piRNA targeting follows microRNA-like rules, with binding energy more important than piRNA abundance.

The paper reports the genome of Trichoplusia ni, identifies small RNA pathways, and establishes genome editing protocols for Hi5 cells.

This study identifies early-firing human replication origins in HeLa cells using Optical Replication Mapping, revealing that initiation occurs across broad zones rather than confined to efficient origins.

The paper develops LR-DNase, a logistic regression model that predicts TF binding sites using DNase-seq and genomic sequence features, outperforming existing methods.