Shaun Mahony

Oncofetal RNA-binding proteins of IGF2BP family suppress IRF-3 and NF-kB dependent transcription downstream of cytosolic RNA sensors

This study shows that IGF2BP family proteins suppress RNA-sensing pathways by binding TNFAIP3 mRNA, reducing innate immune signaling in AML cells.

TPCAV: Interpreting deep learning genomics models via concept attribution

This paper introduces TPCAV, a method to interpret genomics deep learning models by adapting concept attribution, showing it can analyze both motif features and general genomic concepts.

Widespread Regulatory Turnover Across Human Segmental Duplications

This study investigates regulatory turnover in human segmental duplications using T2T genome assembly and ChIP-seq data, finding that regulatory elements are rarely conserved but gene expression and spatial proximity are preserved.

Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements

The paper shows that the human CCR4-NOT complex suppresses pervasive transcription and retrotransposable elements by repressing transcription and stabilizing their RNAs.

Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle

This study examines chromatin state dynamics and TF binding in Plasmodium falciparum during its intraerythrocytic development cycle, revealing stable and dynamic chromatin states linked to gene regulation.

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

This paper introduces an optimized ChIP-exo protocol for mammalian cells, improving efficiency and compatibility with modern sequencing platforms.

Human CCR4-NOT globally regulates gene expression and is a novel silencer of retrotransposon activation

The paper shows that CCR4-NOT regulates gene expression and suppresses retrotransposon activation by modulating RNA decay and KZNF gene expression.

SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes

SEM identifies nucleosome subtypes from MNase-seq data by modeling fragment length distributions, revealing three nucleosome types including accessible short-fragment nucleosomes.

Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1

The paper uses ChIP-ISO to analyze sequence features affecting FOXA1 binding and finds that AP-1 influences FOXA1 binding specificity and context-dependent binding.

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

This study identifies conserved and species-specific cis-regulatory elements in human and mouse blood cells using integrative epigenomic analysis and clustering.

DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite, Plasmodium falciparum

The paper investigates how DNA sequence and chromatin context influence transcription factor binding in Plasmodium falciparum, showing that both factors contribute to differential binding site selection.

Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)

The paper investigates parent-of-origin gene expression differences in honey bee caste determination, finding patrigenes favor queen fate and linking these to histone modifications.

Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats

Allo improves regulatory element analysis in repetitive regions by accurately allocating multi-mapped reads, leading to the discovery of new peaks and interactions in ChIP-seq data.

Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin

The paper investigates how sequence preferences and chromatin environments influence Fox TF binding using neural networks and mouse stem cells.

The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles

The paper evaluates 23 imputation models for cross-cell type epigenomic data, finding quality assessment challenging due to distributional shifts, data availability, and redundant metrics.

PEGR: a flexible management platform for reproducible epigenomic and genomic research

PEGR is a web-based platform that manages epigenomic and genomic research projects, ensuring reproducibility across experimental and computational workflows.

Domain adaptive neural networks improvecross-species prediction of transcription factor binding

This study improves cross-species prediction of transcription factor binding by addressing domain shifts caused by species-specific repeats using domain adaptive neural networks.

Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation

The paper uses synthetic genomic reconstitution to study Hox cluster regulation, finding that distal enhancers are required for full transcriptional output while chromatin remodeling can occur without them.

S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types

S3V2-IDEAS normalizes, denoises, and integrates epigenomic data across cell types to identify epigenetic states and signal intensity patterns.

An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced TF binding

The paper develops Bichrom, a bimodal neural network that models sequence and preexisting chromatin data to predict TF-DNA binding and shows preexisting chromatin improves binding specificity prediction for some TFs.

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II atpro-differentiation genes

A CRISPR screen identifies ZBTB11 and ZFP131 as factors maintaining pluripotency by pausing POL II at pro-differentiation genes.

Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes

The paper presents a computational framework to align and quantify ChIP-exo crosslinking patterns, enabling inference of spatial organization within protein-DNA complexes.

Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map

The paper introduces a SOM-based method to visualize and analyze relationships between chromatin interactions and regulatory genomic activities using Hi-C data.

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

The paper integrates epigenomic and transcriptomic data from mouse hematopoiesis to identify regulatory elements and their dynamics across cell types.

Hox binding specificity is directed by DNA sequence preferences and differential abilities to engage inaccessible chromatin.

The paper investigates how posterior HOX TFs differ in their ability to bind inaccessible chromatin, leading to distinct gene expression patterns during motor neuron differentiation.

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells

The paper integrates GATA transcription factors and epigenomes in mouse hematopoietic cells using IDEAS to map regulatory landscapes and identify candidate cis-regulatory elements.

Direct prediction of regulatory elements from partial data without imputation

The paper introduces a genome segmentation method that works with incomplete regulatory data without imputation, showing improved results over imputation-based approaches and applying it to human cell types.

Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types

The paper develops MultiMDS to compare 3D chromosomal structures across Hi-C datasets, revealing compartment-independent relocalizations of loci.

Characterizing protein-DNA binding event subtypes in ChIP-exo data

The paper introduces ChExMix, a method to detect and classify distinct protein-DNA binding subtypes in ChIP-exo data using probabilistic modeling of tag distributions and DNA motifs.

Deconvolving sequence features that discriminate between overlapping regulatory annotations

The paper introduces SeqUnwinder, a method to identify sequence features specific to overlapping regulatory annotations, demonstrating its application on TF binding and chromatin state data.