Zhiping Weng

A data model for longitudinal multi-modal biomedical cohorts

The paper introduces a data model for longitudinal multimodal biomedical cohorts, demonstrating its ability to manage heterogeneous data across multiple modalities and study visits.

Inferring binding specificities of human transcription factors with the wisdom of crowds

The paper benchmarks methods for inferring transcription factor binding specificities using a large community challenge and finds deep learning models outperform traditional methods, though positional weight matrices are competitive.

A linguistics-based algorithm for RBP motif and context discovery

This paper introduces a linguistics-based algorithm for discovering RNA-binding protein motifs and their sequence contexts, showing improved accuracy over existing methods.

A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions

This paper introduces an NLP-based method to predict RBP binding motifs, contexts, and interactions, identifying novel motifs and RBP-RBP interactions in HepG2 and K562 cells.

Natural language-based representation and modeling of RBP binding

The paper introduces a natural language-based approach to model RBP binding by decomposing RNA sequences into linguistic regions and using iterative relabeling for prediction.

Rapid disassembly and Piwi-independent reassembly of Drosophila piRNA cluster heterochromatin following acute heat shock

This study shows that acute heat shock rapidly disassembles and reassembles Drosophila piRNA cluster heterochromatin, with RDC re-localization independent of maternal piRNAs.

An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome

The paper constructs a bovine epigenomic atlas to annotate regulatory elements and decode the regulatory syntax of the cattle genome, aiding in fine-mapping GWAS loci for complex traits.

Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR

This study benchmarks the OTTR protocol for characterizing tRNAs and tRNA fragments in yeast and mouse, showing its accuracy and revealing new insights into sperm small RNA content.

LOCATE: using Long-read to Characterize All Transposable Elements

LOCATE uses long-read sequencing to detect transposon insertions, outperforming existing tools and revealing new insights into transposon insertion hotspots and mechanisms.

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

A consensus variant-to-function score to functionally prioritize variants for disease

This paper introduces a consensus variant-to-function score to prioritize disease-causing variants, showing improved performance in heritability enrichment and fine-mapping.

Single-cell genomics and regulatory networks for 388 human brains

The paper processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

An encyclopedia of enhancer-gene regulatory interactions in the human genome

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

Single-cell transcriptomic and genomic changes in the aging human brain

The paper identifies transcriptomic and genomic changes in the aging human brain using single-nucleus RNA-sequencing and single-cell whole-genome sequencing, revealing age-related gene expression patterns and somatic mutation dynamics.

Aub, Vasa and Armi localization to phase separated nuage is dispensable for piRNA biogenesis and transposon silencing in Drosophila

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

Evolutionary constraint and innovation across hundreds of placental mammals

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain

The paper constructs a cross-ancestry, cell-type-informed gene regulatory atlas of the developing human brain, identifying genetic regulation and linking it to neuropsychiatric disorders.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome

FAVOR provides an online resource and tool for functional annotation of variants from whole genome sequencing studies to aid in disease gene prioritization.

Flnc: Machine Learning Improves the Identification of Novel Full-length Long Noncoding RNAs from RNA Sequencing Data Without Transcriptional Initiation Profiles

Flnc improves lncRNA identification from RNA-seq data by using machine learning, achieving over 85% accuracy without requiring H3K4me3 profiles.

MafB, WDR77, and ss-catenin interact with each other and have similar genome association profiles

The paper identifies interactions between MafB, WDR77, and β-catenin and shows they share similar genomic binding profiles near paused RNA polymerase at promoter-proximal regions.

A catalog of transcription start sites across 115 human tissue and cell types

The paper generates a catalog of experimentally validated transcription start sites (TSSs) across 115 human tissues and cell types, updating TSS annotations for 20% of GENCODE genes and identifying new GWAS candidate genes.

Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites

The paper updates Factorbook, a TF-centric database, by expanding its motif catalog and integrating it with ENCODE data to annotate candidate regulatory sites and provide tools for variant and disease analysis.

YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation

This study identifies YAP and TAZ as transcriptional co-activators of AP-1 and STAT3 in breast cancer, showing their role in gene regulation and poor patient survival.

Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication

This study uses Optical Replication Mapping to map human DNA replication initiation sites and finds that replication initiation is stochastic and not confined to specific origins.

Genetic and Epigenetic Features of Promoters with Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription of Cell-essential Genes

The paper identifies ubiquitously open chromatin regions in human and mouse genomes that support the transcription of cell-essential genes.

The testis-specific transcription factor TCFL5 responds to A MYBto elaborate the male meiotic program in placental mammals

The paper shows that A-MYB activates TCFL5, which is essential for meiosis and spermiogenesis in placental mammals, and its loss causes sterility.

Somatic piRNAs and Transposons are Differentially Regulated During Skeletal Muscle Atrophy and Programmed Cell Death

The paper shows piRNAs are expressed in somatic muscles of Manduca sexta and regulate transposons during muscle atrophy and programmed cell death.