S. Schoenfelder

发表

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

Cameron S. Osborne, Jennifer A. Mitchell, N. Luscombe, 2015, Genome research.

Single cell Hi-C reveals cell-to-cell variability in chromosome structure

A. Tanay, P. Fraser, S. Schoenfelder, 2013, Nature.

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

Jennifer A. Mitchell, Chia-Lin Wei, Y. Ruan, 2010, Nature Genetics.

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

Philip A. Ewels, Cameron S. Osborne, N. Luscombe, 2015, Nature Genetics.

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

R. Houlston, O. Fletcher, P. Fraser, 2015, Nature Communications.

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

Jonathan M. Cairns, Cameron S. Osborne, P. Freire-Pritchett, 2017, eLife.

HiCUP: pipeline for mapping and processing Hi-C data

Philip A. Ewels, P. Fraser, S. Schoenfelder, 2015, F1000Research.

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

Jonathan M. Cairns, Cameron S. Osborne, D. Zerbino, 2015, Genome Biology.

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins

J. Ellenberg, J. Peters, J. Zuber, 2017, The EMBO journal.

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C

A. Ashworth, N. Orr, O. Fletcher, 2014, Genome research.

Nuclear RNA Sequencing of the Mouse Erythroid Cell Transcriptome

Ieuan Clay, Stefan Schoenfelder, Peter Fraser, 2012, PloS one.

Long-range enhancer–promoter contacts in gene expression control

Stefan Schoenfelder, Peter Fraser, P. Fraser, 2019, Nature Reviews Genetics.

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

Stefan Schoenfelder, Peter Fraser, Chris Wallace, 2015, Nature Communications.

Comparison of Hi-C results using in-solution versus in-nucleus ligation

P. Fraser, S. Schoenfelder, B. Javierre, 2015, Genome Biology.

Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence

Yoko Ito, K. Shirahige, G. Slater, 2020, Nature Communications.

Transcription-driven cohesin repositioning rewires chromatin loops in cellular senescence

K. Shirahige, G. Slater, P. Fraser, 2019, bioRxiv.

Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages

C. Senner, S. Schoenfelder, Borbala Mifsud, 2018, Nature Communications.

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Steven W. Wingett, Stefan Schoenfelder, Peter Fraser, 2018, Journal of visualized experiments : JoVE.

CTCF, WAPL and PDS5 proteins control the formation of TADs and loops by cohesin

J. Ellenberg, J. Peters, J. Zuber, 2017, bioRxiv.

The transcriptional interactome: gene expression in 3D.

Ieuan Clay, Stefan Schoenfelder, Peter Fraser, 2010, Current opinion in genetics & development.

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model.

B. Göttgens, N. Wilson, Victoria Moignard, 2016, Blood.

CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

Jonathan M. Cairns, D. Zerbino, P. Freire-Pritchett, 2015, bioRxiv.

Network analysis of promoter interactions reveals the hierarchical differences in genome organisation between human pluripotent states

S. Schoenfelder, C. Várnai, C. Krueger, 2019, bioRxiv.

Long-Range Enhancer Inte ractions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition Graphical

Jonathan M. Cairns, P. Freire-Pritchett, P. Fraser, 2018 .

Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters

L. Hurst, S. Schoenfelder, A. Murrell, 2022, bioRxiv.

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

J. Peters, K. Mechtler, Erez Lieberman-Aiden, 2020, eLife.

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

J. Peters, J. Zuber, P. Fraser, 2020, Cell reports.

Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers

J. Peters, J. Zuber, P. Fraser, 2020, bioRxiv.

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

Erez Lieberman Aiden, J. Peters, K. Mechtler, 2019, bioRxiv.

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

Louise S. Matheson, P. Freire-Pritchett, P. Fraser, 2018, Genome Biology.

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

A. Green, P. Fraser, S. Schoenfelder, 2017, bioRxiv.

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

A. Green, P. Fraser, S. Schoenfelder, 2017, bioRxiv.

Loss of Cell Cycle Checkpoint Control in Drosophila Rfc4 Mutants

Sue A. Krause, S. Schoenfelder, Margarete M S Heck, 2001, Molecular and Cellular Biology.

Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters

L. Hurst, S. Schoenfelder, A. Murrell, 2022, bioRxiv.

Drosophila Su(Hw) regulates an evolutionarily conserved silencer from the mouse H19 imprinting control region.

R. Paro, S. Schoenfelder, 2004, Cold Spring Harbor symposia on quantitative biology.

3D genome organization links non-coding disease-associated variants to genes

P. Fraser, S. Schoenfelder, G. Orozco, 2022, Frontiers in Cell and Developmental Biology.

Locus-specific induction of gene expression from heterochromatin loci during cellular senescence

Yoko Ito, G. Slater, P. Fraser, 2020, Nature Aging.

High-resolution promoter interaction analysis in Type 3 Innate Lymphoid Cells implicates Batten Disease gene CLN3 in Crohn’s Disease aetiology

M. Weirauch, C. Wallace, P. Fraser, 2022, bioRxiv.

High-resolution promoter interaction analysis in Type 3 Innate Lymphoid Cells implicates Batten Disease gene CLN3 in Crohn’s Disease aetiology

M. Weirauch, C. Wallace, P. Fraser, 2022, bioRxiv.

Heterogeneous chromatin mobility derived from chromatin states is a determinant of genome organisation in S. cerevisiae

Otávio J. B. Brustolini, S. Oliver, P. Fraser, 2017, bioRxiv.

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis

Anton J. Enright, A. Enright, G. Bussotti, 2021, PLoS pathogens.

Three-dimensional interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis

Anton J. Enright, A. Enright, G. Bussotti, 2021, bioRxiv.

Cis-Regulatory Control of Mammalian Sex Determination

S. Schoenfelder, N. Gonen, Meshi Ridnik, 2021, Sexual Development.

Long-range enhancer–promoter contacts in gene expression control

P. Fraser, S. Schoenfelder, 2019, Nature Reviews Genetics.

Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

Stefan Schoenfelder, Peter Fraser, Kamal Kishore, 2017, Genome Biology.

Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

A. Barton, S. Eyre, Jane Worthington, 2016, Genome Biology.

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

Jonathan M. Cairns, P. Freire-Pritchett, P. Fraser, 2018, Cell reports.

Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C

A. Barton, S. Eyre, Jane Worthington, 2016, PloS one.

Global Reorganization of the Nuclear Landscape in Senescent Cells

Philip A. Ewels, Simon Andrews, Stefan Schoenfelder, 2015, Cell reports.

Non‐coding transcripts in the H19 imprinting control region mediate gene silencing in transgenic Drosophila

R. Paro, W. Reik, P. Fraser, 2007, EMBO reports.

susceptibility loci by Capture HiC Unbiased analysis of potential targets of breast cancer

A. Ashworth, N. Orr, O. Fletcher, 2014 .

HiCUP: pipeline for mapping and processing Hi-C data

Philip A. Ewels, Stefan Schoenfelder, Peter Fraser, 2015, F1000Research.

Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification

W. Reik, S. Schoenfelder, S. Wingett, 2023, bioRxiv.

Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states

S. Schoenfelder, C. Várnai, C. Krueger, 2021, Nature Communications.

High‐resolution three‐dimensional chromatin profiling of the Chinese hamster ovary cell genome

P. Fraser, S. Schoenfelder, S. Andrews, 2020, Biotechnology and bioengineering.

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

Jonathan M. Cairns, D. Zerbino, P. Freire-Pritchett, 2016, Genome Biology.

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

Louise S. Matheson, Cameron S. Osborne, N. Luscombe, 2015, Nature Genetics.

GOTHiC, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C data

Nicholas M. Luscombe, Borbala Mifsud, Inigo Martincorena, 2015, bioRxiv.

Comparison of Hi-C results using in-solution versus in-nucleus ligation

P. Fraser, S. Schoenfelder, B. Javierre, 2015, Genome Biology.

Transcription factories and nuclear organization of the genome.

I. Clay, P. Fraser, S. Schoenfelder, 2010, Cold Spring Harbor symposia on quantitative biology.

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data

Borbala Mifsud, Inigo Martincorena, Peter Fraser, 2017, PloS one.

Genome-wide analysis of promoter contacts identifies novel regulators of late-stage adipogenesis

S. O’Rahilly, I. Sandovici, P. Fraser, 2023, bioRxiv.

Additional File 3 : The CHiCAGO R package vignette

Jonathan M. Cairns, Plagnol, D. Zerbino, 2016 .

Interchromosomal Huddle Kickstarts Antiviral Defense

P. Fraser, S. Schoenfelder, 2008, Cell.

Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes

S. Schoenfelder, B. Javierre, S. Wingett, 2023, Cell reports.

Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

S. Eyre, Jane Worthington, P. Fraser, 2016, Genome Biology.

The transcriptional interactome: gene expression in 3D.

I. Clay, P. Fraser, S. Schoenfelder, 2010, Current opinion in genetics & development.

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model.

Nicola K. Wilson, B. Göttgens, N. Wilson, 2016, Blood.

Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

P. Fraser, S. Schoenfelder, S. Wingett, 2017, Genome Biology.

Heterogeneous

Ralph Matthes, Benedikt Ahrens, S. Schoenfelder, 2009, Encyclopedia of Biometrics.

Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR

S. Schoenfelder, D. Tannahill, Sean M. Flynn, 2024, Genome biology.

Non asymptotic minimax rates of testing in signal detection with heterogeneous variances

B. Laurent, Jean-Michel Loubes, C. Marteau, 2009, Electronic Journal of Statistics.

University of Birmingham CHiCAGO

Jonathan M. Cairns, D. Zerbino, P. Freire-Pritchett, 2016 .