Erez Lieberman Aiden

The paper identifies widespread readthrough transcription in human cells and shows that depletion of specific factors increases its extent.

The paper shows that locust swarming evolves through diverse molecular pathways rather than shared genes, highlighting flexible regulatory architectures and modular systems.

This study identifies WOX1 mutations as the genetic basis of the prickleless S locus in blackberry and red raspberry, enabling gene editing to create prickleless cultivars.

TwinC predicts trans-chromosomal DNA contacts using DNA sequence and provides insights into their functional mechanisms.

The paper uses chromosome-level genome assembly and historical museum collections to study waterbuck population structure and chromosome evolution, finding genomic differentiation and recombination patterns linked to Robertsonian fusions.

The paper presents chromosome-length genome assemblies for three marten subspecies, revealing genomic features and improving taxonomic understanding.

The paper presents a chromosome-level genome assembly for Uta stansburiana and uses RNA-seq data to identify gene expression differences linked to pace-of-life syndromes across environments.

This study integrates genomic, transcriptomic, and morphological data from the small-spotted catshark to uncover molecular mechanisms underlying sensory organ evolution in jawed vertebrates.

This study uses CRUDO to show that cohesin and 3D contacts influence enhancer-promoter regulation, with distal enhancers showing stronger cohesin dependence.

This paper reports the 3D genome architecture of a 52,000-year-old woolly mammoth using a novel method, revealing conserved epigenetic features across elephantids.

This paper introduces a deep learning model to predict A/B compartments from histone modifications, achieving high accuracy across cell types and showing the importance of specific histone marks.

This paper introduces a low-cost, high-throughput method for SARS-CoV-2 detection using whole genome sequencing, achieving high sensitivity and accuracy comparable to clinical tests.

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.

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The paper presents a chromosome-length genome assembly of the Black Petaltail dragonfly, providing the first such assembly for a non-libelluloid dragonfly.

The paper presents a high-quality chromosome-level genome assembly, DNA methylome, and cranial morphology analysis of an Alpine dingo, supporting its status as an archetype for evolutionary studies.

The paper uses physical simulations to study the 3D genome architecture of Aedes aegypti, revealing liquid crystalline structures and sensitivity to nuclear deformation.

The paper shows that the lncRNA Airn recruits Polycomb Repressive Complexes to silence genes during mouse embryogenesis through chromatin contacts and regulatory elements.

The paper presents a chromosome-length genome assembly and annotation of the blackberry species Rubus argutus, identifying candidate genes for primocane-fruiting.

The paper investigates the effects of MEF2C mutations and chromatin structural variants on transcriptional and functional outcomes in neuronal models, revealing differential impacts based on mutation type and chromatin topology.

The paper generates the first chromosome-length annotated genomes and transcriptomes of black and mute swans, revealing immune system limitations and plumage-related genetic differences.

The paper presents a desert dingo genome assembly and compares it to domestic dog genomes, identifying structural variants and physiological differences linked to ecological roles.

This study investigates how 3D chromatin architecture influences and is influenced by somatic structural variants in cancer, showing an interplay between chromatin structure and SV formation.

The paper presents a chromosome-length assembly of the Hawaiian monk seal, revealing genomic stability and low variation, with implications for conservation and evolutionary studies.

The paper assembles the mule deer genome into chromosome-length contigs using long-read sequencing and Hi-C, and compares demographic histories with white-tail deer.

The paper analyzes synteny patterns across insect genomes, finding that synteny scales with clade age and that some beetle chromosomes maintain gene order over 200 million years.

The paper examines genome architecture changes during medaka gastrulation, finding that CTCF loops form while CTCF binding sites remain fixed, and transcription precedes mature domain formation.

The paper identifies 150 transcriptional activation domains in yeast, shows their binding to Mediator, and develops a neural network to predict ADs across species.

The paper presents two high-quality Basenji genome assemblies and compares structural variations across three dog breeds, highlighting the impact of reference genome choice on variant detection.