D. Odom

发表

Transcriptional Regulatory Networks in Saccharomyces cerevisiae

Nicola J. Rinaldi, John J. Wyrick, I. Simon, 2002, Science.

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth

Adam A. Margolin, R. Young, D. Odom, 2006, Proceedings of the National Academy of Sciences.

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

Michael D. Wilson, Petra C. Schwalie, D. Odom, 2010, Science.

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

D. Gifford, E. Fraenkel, D. Odom, 2007, Nature Genetics.

Nuclear transcription factors in mammalian mitochondria

D. Odom, Sarah Leigh-Brown, J. Enríquez, 2010, Genome Biology.

Integrative detection and analysis of structural variation in cancer genomes

William Stafford Noble, Jesse R. Dixon, Royden A. Clark, 2018, Nature Genetics.

Control of Pancreas and Liver Gene Expression by HNF Transcription Factors

Nicola J. Rinaldi, T. Volkert, D. Gifford, 2004, Science.

Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues.

Richard G. Jenner, R. Young, D. Odom, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells

Megan F. Cole, Richard G. Jenner, Sarah E. Johnstone, 2006, Cell.

Species-Specific Transcription in Mice Carrying Human Chromosome 21

Michael D. Wilson, Victor L. J. Tybulewicz, Elizabeth M. C. Fisher, 2008, Science.

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

Chris P. Ponting, Michael D. Wilson, Klara Stefflova, 2012, PLoS genetics.

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

Michael D. Wilson, Andre J. Faure, W. McLaren, 2014, eLife.

Enhancer Evolution across 20 Mammalian Species

J. T. Erichsen, Tim F. Rayner, D. Odom, 2015, Cell.

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

Bianca M. Schmitt, D. Odom, P. Flicek, 2015, Genome research.

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

D. Odom, A. Tanay, S. Henderson, 2015, Cell reports.

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface

Nuno A. Fonseca, Bianca M. Schmitt, D. Odom, 2014, Genome research.

Pol Iii Binding in Six Mammalian Genomes Shows High Conservation among Amino Acid Isotypes, despite Divergence in Trna Gene Usage Ukpmc Funders Group Author Manuscript Introduction

Alvis Brazma, Michael D. Wilson, Stephen Watt, 2022 .

Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation.

Hiroshi Kimura, Rory Stark, Michael D. Wilson, 2012, Molecular cell.

regulatory modules cis occupied Cohesin regulates tissue-specific expression by stabilising highly

Paul Flicek, Michael D. Wilson, Stephen Watt, 2012 .

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

D. Odom, P. Flicek, D. Villar, 2014, Nature Reviews Genetics.

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Michael D. Wilson, Philip M. Kim, B. Frey, 2012, Science.

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

Petra C. Schwalie, Andre J. Faure, D. Odom, 2013, Genome Biology.

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

Michael D. Wilson, D. Odom, J. Marioni, 2013, Cell.

A CTCF-independent role for cohesin in tissue-specific transcription.

Petra C. Schwalie, D. Odom, P. Flicek, 2010, Genome research.

ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.

Michael D. Wilson, D. Odom, J. Hadfield, 2009, Methods.

Insights into hominid evolution from the gorilla genome sequence

Albert J. Vilella, Gregory E. Jordan, Petra C. Schwalie, 2012, Nature.

Gibbon genome and the fast karyotype evolution of small apes

August E. Woerner, Matthew W. Hahn, Miriam K. Konkel, 2014 .

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

D. Odom, M. Merkenschlager, 2013, Cell.

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

Michael D. Wilson, Petra C. Schwalie, D. Odom, 2012, Cell.

LINE elements are a reservoir of regulatory potential in mammalian genomes

Osagie G. Izuogu, Fergal J. Martin, D. Odom, 2020, bioRxiv.

Charting the transcriptional regulatory changes in mouse liver during fasting

D. Odom, Elodie Thierion, 2018, Hepatology.

Core transcriptional regulatory circuitry in human hepatocytes

Ernest Fraenkel, Robin D Dowell, Richard A Young, 2006, Molecular systems biology.

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation.

Arun K. Ramani, A. Fraser, B. Blencowe, 2011, Genome research.

alternative splicing regulation Global impact of RNA polymerase II elongation inhibition on Material Supplemental

Arun K. Ramani, A. Fraser, B. Blencowe, 2011 .

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

Jernej Ule, Michaela Frye, Duncan T. Odom, 2013, Cell reports.

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

D. Odom, T. Fioretos, R. Jafari, 2019, Nature Communications.

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

D. Odom, T. Fioretos, R. Jafari, 2019, Nature Communications.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Mark Gerstein, Benedict Paten, Paul Flicek, 2017, bioRxiv.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Son K. Pham, Ian T. Fiddes, Bronwen L. Aken, 2017, bioRxiv.

Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis

Tim F. Rayner, D. Odom, C. Kutter, 2016, eLife.

The Evolutionary Fates of a Large Segmental Duplication in Mouse

John P. Didion, T. A. Bell, L. McMillan, 2016, Genetics.

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

D. Odom, P. Flicek, J. Horvath, 2017, bioRxiv.

A feedback loop between the liver-enriched transcription factor network and miR-122 controls hepatocyte differentiation.

Michael D. Wilson, D. Odom, Dominic Schmidt, 2012, Gastroenterology.

Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

Thomas M. Keane, Ian T. Fiddes, M. Gerstein, 2018, bioRxiv.

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation

Daniel J. Gaffney, Tim F. Rayner, D. Odom, 2013, Genome Biology.

Pervasive lesion segregation shapes cancer genome evolution

Martin S. Taylor, Andrew D. Yates, Tim F. Rayner, 2019, bioRxiv.

Pervasive lesion segregation shapes cancer genome evolution

Martin S. Taylor, Andrew D. Yates, Tim F. Rayner, 2019, Nature.

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

Aaron T. L. Lun, C. Bakal, D. Odom, 2020, Nature Communications.

Functional signatures of evolutionarily young CTCF binding sites

Jonathan M. Mudge, D. Odom, P. Flicek, 2020, bioRxiv.

Transcriptional activity and strain-specific history of mouse pseudogenes

Ian T. Fiddes, M. Gerstein, J. Harrow, 2020, Nature Communications.

Strand-resolved mutagenicity of DNA damage and repair

Martin S. Taylor, Michael D. Nicholson, D. Odom, 2022, bioRxiv.

organization and CTCF binding in multiple mammalian lineages.

Michael D. Wilson, Petra C. Schwalie, D. Odom, 2022 .

The Evolutionary Fates of a Large Segmental Duplication in Mouse

John P. Didion, T. A. Bell, L. McMillan, 2016, Genetics.

The opposing transcriptional functions of Sin3A and c-Myc are required to maintain tissue homeostasis

D. Odom, J. Nichols, M. Trotter, 2011, Nature Cell Biology.

Synthesis and characterization of magnesium and zinc complexes of 1,4,7-triazacyclononane- N -acetate. Potential models for the active site of RuBisCo

D. Odom, S. Hilderbrand, V. Young, 2000 .

Latent Regulatory Potential of Human-Specific Repetitive Elements

Paul Flicek, Rory Stark, Michael D. Wilson, 2013, Molecular cell.

DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts

D. Odom, P. Flicek, J. Taipale, 2022, bioRxiv.

Long-range oxidative damage in DNA/RNA duplexes.

D. Odom, J. Barton, 2001, Biochemistry.

Chromosome assembly of large and complex genomes using multiple references

Son K. Pham, Thomas M. Keane, Fengtang Yang, 2016, bioRxiv.

Erratum: NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth (Proceedings of the National Academy of Sciences of the United States of America (2006) 103, 48, (18261-18266) DOI: 10.1073/pnas.0606108103)

Andrew P. Weng, Jon C. Aster, Andrea Califano, 2007 .

Genome-Scale Validation of Deep-Sequencing Libraries

Rory Stark, Michael D. Wilson, Duncan T. Odom, 2008, PloS one.

Edinburgh Research Explorer Pervasive lesion segregation shapes cancer genome evolution

Martin S. Taylor, Andrew D. Yates, Lana, 2020 .

The evolution of mammalian transcription factor binding

Michael D. Wilson, Petra C. Schwalie, P. Flicek, 2010 .

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

D. Odom, P. Flicek, Klara Stefflova, 2019, Genome Biology.

Recognition and reaction of metallointercalators with DNA.

D. Odom, J. Barton, J K Barton, 1999, Chemical reviews.

Variations in DNA Charge Transport with Nucleotide Composition and Sequence

Jacqueline K. Barton, Duncan T. Odom, Tashica T. Williams, 2000 .

Oxidative Repair of a Thymine Dimer in DNA from a Distance by a Covalently Linked Organic Intercalator

D. Odom, J. Barton, D. Gianolio, 2000 .

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders

Jernej Ule, Michaela Frye, Wolfgang Wurst, 2014, The EMBO journal.

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

Petra C. Schwalie, Andre J. Faure, D. Odom, 2013, Genome Biology.

Evolution of transcriptional control in mammals.

Michael D. Wilson, D. Odom, M. Wilson, 2009, Current opinion in genetics & development.

The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity

D. Odom, C. Kutter, Christina Ernst, 2017, Nature Communications.

Transducin-like enhancer protein 1 mediates estrogen receptor binding and transcriptional activity in breast cancer cells

James Hadfield, Jason S. Carroll, Duncan T. Odom, 2011, Proceedings of the National Academy of Sciences.

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

Osagie G. Izuogu, Fergal J. Martin, D. Odom, 2021, Genome biology.

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

John C Marioni, Duncan T Odom, Nils Eling, 2018, Nature Communications.

Transcriptional role of cyclin D1 in development revealed by a genetic–proteomic screen

Clifford A. Meyer, Joshua E. Elias, Megan F. Cole, 2010, Nature.

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

Aaron T. L. Lun, Chris Bakal, John C Marioni, 2017, bioRxiv.

Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

J. Rinn, D. Odom, Yoko Ito, 2016, Nature Communications.

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

Tim F. Rayner, Bianca M. Schmitt, D. Odom, 2016, Nature Communications.

Interplay of cis and trans mechanisms driving transcription factor binding, chromatin, and gene expression evolution

Bianca M. Schmitt, D. Odom, J. Marioni, 2016 .

Sequence analysis A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data

Ernest Fraenkel, Richard A. Young, David K. Gifford, 2006 .

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

D. Odom, R. Klose, Hamish W. King, 2016, Nucleic acids research.

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

Andreas Heger, Frank Grützner, Roger Patient, 2013, eLife.

A transcriptional and regulatory map of mouse somitogenesis

Gi Fay Mok, D. Odom, J. Marioni, 2023, bioRxiv.

Aging increases cell-to-cell transcriptional variability upon immune stimulation

Sarah A. Teichmann, Catalina A. Vallejos, John C. Marioni, 2017, Science.

Genome-Wide Analysis of Menin Binding Provides Insights into MEN1 Tumorigenesis

Sean Davis, Francis S Collins, Peter C Scacheri, 2006, PLoS genetics.

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data

D. Odom, P. Flicek, J. Horvath, 2016, Genome Biology.

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

Michael D. Wilson, Petra C. Schwalie, Andre J. Faure, 2012, Genome research.

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States

Bianca M. Schmitt, D. Odom, J. Marioni, 2016, PLoS genetics.

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Michael D. Wilson, Philip M. Kim, B. Frey, 2013 .

acute lymphoblastic leukemia Transcriptional regulatory networks downstream of TAL1/SCL in t-cell

Adam A. Margolin, D. Odom, A. Ferrando, 2013 .

Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia.

Adam A. Margolin, Richard A Young, Teresa Palomero, 2005, Blood.

The mechanisms shaping the single-cell transcriptional landscape.

Duncan T Odom, D. Odom, C. Martinez-Jimenez, 2016, Current opinion in genetics & development.

Zebrafish promoter microarrays identify actively transcribed embryonic genes

Richard A Young, Bingbing Yuan, Duncan T Odom, 2006, Genome Biology.

Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse.

Michael D. Wilson, Tyrone Ryba, Duncan T Odom, 2012, Human molecular genetics.

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

D. Odom, J. Marioni, Nils Eling, 2018, bioRxiv.

NSUN 2-mediated cytosine-5 RNA methylation

J. Ule, H. Fuchs, D. Odom, 2014 .

Integrative detection and analysis of structural variation in cancer genomes

William Stafford Noble, Jesse R. Dixon, Royden A. Clark, 2018, Nature Genetics.

An Integrative Framework for Detecting Structural Variations in Cancer Genomes

William Stafford Noble, Feng Yue, Jesse R. Dixon, 2017, bioRxiv.

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

Aaron T. L. Lun, C. Bakal, D. Odom, 2019, bioRxiv.

Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Mark Gerstein, Jane Loveland, Dent Earl, 2018, Nature Genetics.

Mutational landscape of a chemically-induced mouse model of liver cancer

Tim F. Rayner, D. Odom, Javier Santoyo-Lopez, 2018, bioRxiv.

Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Son K. Pham, Thomas M. Keane, Ian T. Fiddes, 2018, Nature Genetics.

Identification of Transcription Factor-DNA Interactions In Vivo.

Duncan T Odom, D. Odom, 2011, Sub-cellular biochemistry.

Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor

Michael D. Wilson, Simon Tavaré, Nuno L. Barbosa-Morais, 2007, PloS one.

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System

D. Odom, J. Marioni, A. Brazma, 2015, PloS one.

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Mark Gerstein, Jane Loveland, Dent Earl, 2018, bioRxiv.

CTCF maintains regulatory homeostasis of cancer pathways

D. Odom, J. Marioni, P. Flicek, 2018, Genome Biology.

Unwinding Limb Development

D. Odom, D. Villar, 2016, Cell.

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

Paul Flicek, Alvis Brazma, Klara Stefflova, 2012, Genome research.

Global Gene Expression Profiling Reveals SPINK1 as a Potential Hepatocellular Carcinoma Marker

Margus Lukk, Duncan T. Odom, D. Odom, 2013, PloS one.

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

D. Odom, T. Fioretos, R. Jafari, 2019, Nature Communications.

IL‐7‐dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti‐tumour response

D. Odom, J. Marioni, Nils Eling, 2019, EMBO reports.

Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth

D. Odom, J. Marioni, Nils Eling, 2018, bioRxiv.

Bookmarking by Non-pioneer Transcription Factors during Liver Development Establishes Competence for Future Gene Activation

D. Odom, P. Moulos, Dominic Schmidt, 2019, Cell reports.

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

Michael D. Wilson, Petra C. Schwalie, D. Odom, 2012, Cell.

Robust charge transport in DNA double crossover assemblies.

D. Odom, J. Barton, E. Dill, 2000, Chemistry & biology.

One for all

D. Odom, 2016, eLife.

Using a common analysis pipeline to compare data from three major lineages of complex eukaryotes reveals that transcription seems to evolve at a common rate.

D. Odom, 2016 .

Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species

D. Odom, C. Mellersh, S. Rossiter, 2018, Genome Biology.

A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden.

Michael D. Wilson, D. Odom, P. Flicek, 2013, American journal of human genetics.

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

John C Marioni, Duncan T Odom, Nils Eling, 2018, bioRxiv.

Epigenetic predictors of maximum lifespan and other life history traits in mammals

S. Horvath, J. Gaillard, D. Blumstein, 2021, bioRxiv.

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

Bianca M. Schmitt, D. Odom, J. Marioni, 2017, bioRxiv.

Supporting online material for : Transcriptional Regulatory Networks in Saccharomyces cerevisiae

Nicola J. Rinaldi, John J. Wyrick, I. Simon, 2002 .

A transcriptional and regulatory map of mouse somite maturation

Gi Fay Mok, D. Odom, J. Marioni, 2023, Developmental cell.

Sequence analysis A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data

D. Gifford, R. Young, E. Fraenkel, 2006 .

DNA methylation networks underlying mammalian traits

Joseph A. Cook, S. Horvath, A. Lu, 2023, Science.

Universal DNA methylation age across mammalian tissues

R. Williams, J. Gaillard, D. Blumstein, 2023, Nature Aging.

Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation

Margus Lukk, Adrien Ls Jacquin, Duncan T Odom, 2019, Bioinform..

Cohesin's role as an active chromatin domain anchorage revealed

D. Odom, C. Feig, 2013, EMBO Journal.

Comparative HiC Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture Graphical

D. Odom, A. Tanay, S. Henderson, 2015 .

Species-Specific Transcription in Mice Carrying Human Chromosome 21

S. Tavaré, D. Odom, N. Barbosa-Morais, 2008, Science.

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Philip M. Kim, B. Frey, Leo J. Lee, 2012, Science.

Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage

D. Odom, A. Brazma, C. Kutter, 2011, Nature Genetics.

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data

D. Odom, J. Horvath, D. Villar, 2016, Genome Biology.

Bioinformatics Original Paper a Hypothesis-based Approach for Identifying the Binding Specificity of Regulatory Proteins from Chromatin Immunoprecipitation Data

D. Gifford, D. B. Gordon, E. Fraenkel, 2022 .

CTCF maintains regulatory homeostasis of cancer pathways

D. Odom, J. Marioni, Ximena Ibarra-Soria, 2018, Genome Biology.

When the Snake Lost Its Limbs, What Did the Mouse and Lizard Say?

D. Odom, D. Villar, 2015, Developmental cell.

Gibbon genome and the fast karyotype evolution of small apes

August E. Woerner, Matthew W. Hahn, Miriam K. Konkel, 2014, Nature.

Opus: University of Bath Online Publication Store Aberrant Methylation of Trnas Links Cellular Stress to Neuro-developmental Disorders

J. Ule, D. Odom, C. Kutter, 2022 .