List of works - Shaun Mahony

A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis

scientific article published on 7 November 2013

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

scientific article

A high-resolution protein architecture of the budding yeast genome

scientific article published on 10 March 2021

A multi-parametric flow cytometric assay to analyze DNA-protein interactions.

scientific article published on 11 November 2012

An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding

scientific article published on 27 March 2014

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

scientific article published on 04 March 2020

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

scientific article published on 07 January 2021

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

scientific article published on 01 March 2019

Combined analysis reveals a core set of cycling genes

scientific article published on January 2007

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies

scientific article

Deconvolving sequence features that discriminate between overlapping regulatory annotations.

scientific article published on 19 October 2017

Direct prediction of regulatory elements from partial data without imputation

scientific article published on 04 November 2019

Discovering homotypic binding events at high spatial resolution.

scientific article

Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast

scientific article

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

scientific journal article

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

scientific article

Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution

scientific article published on 26 October 2015

Global control of motor neuron topography mediated by the repressive actions of a single hox gene.

scientific article published on September 2010

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

scientific article

Improved detection of DNA motifs using a self-organized clustering of familial binding profiles

scientific article published in June 2005

Inferring protein-DNA dependencies using motif alignments and mutual information.

scientific article published on July 2007

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

scientific article published on 08 October 2019

Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque

scientific article

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

scientific article

ORegAnno: an open-access community-driven resource for regulatory annotation

scientific article

Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes

scientific article published on 13 May 2019

Protein-DNA binding in high-resolution

scientific article

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex

scientific article published in March 2006

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

scientific article

Reprogrammed Stomach Tissue as a Renewable Source of Functional β Cells for Blood Glucose Regulation

scientific article published on 16 February 2016

STAMP: a web tool for exploring DNA-binding motif similarities

scientific article published on 3 May 2007

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals.

scientific article published on 18 August 2013

Self-organizing neural networks to support the discovery of DNA-binding motifs.

scientific article published on 12 July 2006

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity.

scientific article published on 21 July 2013

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

scientific article

Transcription factor binding site identification using the self-organizing map.

scientific article published on 12 January 2005

Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock

scientific article published on 14 February 2018

miniMDS: 3D structural inference from high-resolution Hi-C data

scientific article published on July 2017

List of works by Shaun Mahony

A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

A high-resolution protein architecture of the budding yeast genome

A multi-parametric flow cytometric assay to analyze DNA-protein interactions.

An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding

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

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

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

Combined analysis reveals a core set of cycling genes

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies

Deconvolving sequence features that discriminate between overlapping regulatory annotations.

Direct prediction of regulatory elements from partial data without imputation

Discovering homotypic binding events at high spatial resolution.

Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution

Global control of motor neuron topography mediated by the repressive actions of a single hox gene.

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

Improved detection of DNA motifs using a self-organized clustering of familial binding profiles

Inferring protein-DNA dependencies using motif alignments and mutual information.

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

Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

ORegAnno: an open-access community-driven resource for regulatory annotation

Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes

Protein-DNA binding in high-resolution

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

Reprogrammed Stomach Tissue as a Renewable Source of Functional β Cells for Blood Glucose Regulation

STAMP: a web tool for exploring DNA-binding motif similarities

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals.

Self-organizing neural networks to support the discovery of DNA-binding motifs.

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity.

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

Transcription factor binding site identification using the self-organizing map.

Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock

miniMDS: 3D structural inference from high-resolution Hi-C data