I. Dunham

发表

An SNP map of human chromosome 22

G. D. Wilson, J. Sulston, N. Carter, 2000, Nature.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

Initial sequencing and analysis of the human genome.

J. V. Moran, V. J. Pollara, D. Haussler, 2001, Nature.

The Human Cell Atlas

Fabian J Theis, Jay W. Shin, D. Pe’er, 2017, bioRxiv.

Ensembl regulation resources

Daniel R. Zerbino, Ewan Birney, Michael Nuhn, 2016, Database J. Biol. Databases Curation.

Integrative annotation of chromatin elements from ENCODE data

William Stafford Noble, Maxwell W. Libbrecht, Robert S. Harris, 2012, Nucleic acids research.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

The ENCODE (ENCyclopedia Of DNA Elements) Project

Paul T. Groth, William Stafford Noble, Colin N. Dewey, 2004, Science.

eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data

Andrew E. Teschendorff, Shane J. Neph, John A. Stamatoyannopoulos, 2019, Bioinform..

The DNA sequence of human chromosome 22

Melanie E. Goward, Antony V. Cox, R. Durbin, 1999, Nature.

A Gene Map of the Human Genome

P. Deloukas, E. Lander, M. Adams, 1996, Science.

Defining functional DNA elements in the human genome

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

The landscape of histone modifications across 1% of the human genome in five human cell lines.

Shane C. Dillon, E. Birney, Z. Weng, 2007, Genome research.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2011, PLoS biology.

RPS6KA2, a putative tumour suppressor gene at 6q27 in sporadic epithelial ovarian cancer

S Beck, I. Dunham, A. Mungall, 2007, Oncogene.

Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.

Nuno A. Fonseca, Miguel Pignatelli, Julio Saez-Rodriguez, 2018, Cancer research.

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

Sander W. Timmer, R. Durbin, E. Birney, 2014, PLoS genetics.

The portability of tagSNPs across populations: a worldwide survey.

P. Deloukas, S. Hunt, H. Cann, 2006, Genome research.

Open Targets Platform: supporting systematic drug–target identification and prioritisation

E. McDonagh, I. Dunham, M. Pignatelli, 2020, Nucleic Acids Res..

The DNA sequence and analysis of human chromosome 6

I. Dunham, J. L. Ashurst, D. R. Bentley, 2003, Nature.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Mark Gerstein, Kevin Struhl, Zhiping Weng, 2008, Genome research.

Evidence for widespread reticulate evolution within human duplicons.

M. Hurles, S. Humphray, M. Rocchi, 2005, American journal of human genetics.

YAC Library Storage and Transport

I. Dunham, J. Collins, S. Hassock, 1996 .

The ORFeome Collaboration: a genome-scale human ORF-clone resource

M. Diekhans, T. Moore, M. Vidal, 2016, Nature Methods.

hORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes

J. Rogers, M. Vidal, K. Venkatesan, 2007, Genomics.

The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers

C. Cole, I. Dunham, S. Forbes, 2018, Nature Reviews Cancer.

Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921))

Ronald W. Davis, J. V. Moran, V. J. Pollara, 2001 .

The UK10K project identifies rare variants in health and disease

Tom R. Gaunt, Hashem A. Shihab, Gail P. Clement, 2016 .

Functional annotation of non-coding sequence variants

E. Zeggini, G. Ritchie, I. Dunham, 2014, Nature Methods.

Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians

L. Matthews, J. Rogers, I. Dunham, 2008, Nature Genetics.

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

E. Birney, W. Ouwehand, K. Downes, 2016, Cell reports.

TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images

Yanhui Hu, Lukas Wagner, David E Hill, 2017 .

Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution

Peter Saffrey, Ian Dunham, Cordelia Langford, 2010, PloS one.

Organization of the human immunoglobulin lambda light-chain locus on chromosome 22q11.2.

J E Collins, D. Le Paslier, D. Paslier, 1995, Human molecular genetics.

A first-generation linkage disequilibrium map of human chromosome 22

Lon R. Cardon, Andres Metspalu, David Beare, 2002, Nature.

The Human Cell Atlas

Roland Eils, Alexander van Oudenaarden, Hans Clevers, 2017, bioRxiv.

Evidence That Replication-Associated Mutation Alone Does Not Explain Between-Chromosome Differences In Substitution Rates

Catherine J. Pink, J. Rogers, I. Dunham, 2009, Genome biology and evolution.

Genetic fine-mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

Christian Gieger, Jason Carey, Steven Wiltshire, 2016 .

A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence.

P Sham, S Minoshima, B. Roe, 2001, Genome research.

The DNA sequence and biological annotation of human chromosome 1

I. Dunham, C. Clee, D. R. Bentley, 2006, Nature.

Hes6 is required for actin cytoskeletal organization in differentiating C2C12 myoblasts.

I. Dunham, P. Jones, K. Murai, 2011, Experimental cell research.

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

Matthew E. Ritchie, P. Deloukas, S. Tavaré, 2010, BMC Genetics.

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

Miguel Correa Marrero, Robyn M. Kaake, Gwendolyn M. Jang, 2020, Science.

GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals

E. Birney, Klaudia Walter, G. Ritchie, 2019, Nature Genetics.

A linkage disequilibrium map of chromosome 22

R. Mägi, P. Deloukas, G. Abecasis, 2002 .

Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

Tom R. Gaunt, Thomas M. Keane, Hashem A. Shihab, 2017, Scientific Reports.

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene

John A. Stamatoyannopoulos, Ian Dunham, Job Dekker, 2010, Nucleic acids research.

Universitet Low-frequency variation in TP 53 has large effects on head circumference and intracranial

Tom R. Gaunt, Thomas M. Keane, Hashem A. Shihab, 2019 .

Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Tom R. Gaunt, Hashem A. Shihab, Gail P. Clement, 2018, bioRxiv.

Immune disease variants modulate gene expression in regulatory CD4+ T cells

I. Dunham, N. Soranzo, D. Smyth, 2019, bioRxiv.

Author response: The Human Cell Atlas

Fabian J Theis, Jay W. Shin, D. Pe’er, 2017 .

Isolation of cDNA clones mapping around DXS178: a search for human X-linked agammaglobulinaemia gene using yeast artificial chromosomes, cosmids and direct cDNA selection.

D. Bentley, I. Dunham, D. Vetrie, 1993, Immunodeficiency.

Data disclosure in the human genome project.

I. Dunham, 1998, Molecular medicine today.

Human genome sequences: enigmatic variations.

I. Dunham, 2002, Mutagenesis.

Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites

J. Danesh, Klaudia Walter, W. Ouwehand, 2022, American journal of human genetics.

Faculty Opinions recommendation of Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.

I. Dunham, 2008 .

Where Next for Genetics and Genomics?

P. Donnelly, G. McVean, C. Tyler-Smith, 2015, PLoS biology.

Identification and characterization of NF1-related loci on human chromosomes 22, 14 and 2

I. Dunham, P. Riegman, T. Hulsebos, 1996, Human Genetics.

Genome analysis of the platypus reveals unique signatures of evolution

I. Dunham, 2008, Nature.

Correction: Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

Sander W. Timmer, R. Durbin, E. Birney, 2015, PLoS genetics.

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

Sander W. Timmer, R. Durbin, E. Birney, 2014, PLoS genetics.

Multi-ancestry Mendelian randomization of omics traits revealing drug targets of COVID-19 severity

I. Dunham, M. Ghoussaini, J. Schwartzentruber, 2022, eBioMedicine.

7 – Sequence Ready Clone Maps

I. Dunham, S. Gregory, C. Soderlund, 1998 .

articleHigh-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

Matthew E. Ritchie, P. Deloukas, S. Tavaré, 2019 .

Human genes: Time to follow the roads less traveled?

I. Dunham, 2018, PLoS biology.

Direct observation of the gene organization of the complement C4 and 21- hydroxylase loci by pulsed field gel electrophoresis

I. Dunham, R. Campbell, C. Sargent, 1989, The Journal of experimental medicine.

Mapping of the Human Major Histocompatibility Complex by Pulsed Field Gel Electrophoresis

I. Dunham, J. Trowsdale, R. Campbell, 1989 .

YAC Library Screening

C. Cole, I. Dunham, J. Collins, 1996 .

Localisation of a gene for transient neonatal diabetes mellitus to an 18.72 cR3000 (approximately 5.4 Mb) interval on chromosome 6q.

I. Dunham, J. Barber, A. Mungall, 1999, Journal of medical genetics.

Localisation of a gene for transient neonatal diabetes mellitus to an 18.72 cR3000 (∼5.4 Mb) interval on chromosome 6q

I. Dunham, J. Barber, A. Mungall, 1999 .

Molecular mapping of the human major histocompatibility complex by pulsed-field gel electrophoresis.

I. Dunham, J. Trowsdale, R. Campbell, 1987, Proceedings of the National Academy of Sciences of the United States of America.

An integrated map of human 6q22.3-q24 including a 3-Mb high-resolution BAC/PAC contig encompassing a QTL for fetal hemoglobin.

P. Sanseau, J. Riley, C. G. See, 2000, Genomics.

Molecular analysis of the human MHC class I region in hereditary haemochromatosis

I. Dunham, R. Campbell, T. Strachan, 1990, Human Genetics.

A panel of human chromosome 22-specific sequence tagged sites.

D. Bentley, I. Dunham, J. Collins, 1992, Genomics.

Mapping and complex expression pattern of the human NPAP60L nucleoporin gene

I. Dunham, D. Beare, D. Shkolny, 1999, Cytogenetic and Genome Research.

Steroid receptor coactivator-1 modulates the function of Pomc neurons and energy homeostasis

Tom R. Gaunt, Thomas M. Keane, Hashem A. Shihab, 2019, Nature Communications.

A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans

Gail Clement, Jie Huang, Antonio Ciampi, 2014, Nature Communications.

The DNA sequence and biological annotation of human chromosome 1 (vol 441, pg 315, 2006)

R. Durbin, G. McVean, A. Coulson, 2006 .

The Chromosome 6 database at the Sanger Centre.

S. Hunt, C. Rice, I. Dunham, 1997, DNA sequence : the journal of DNA sequencing and mapping.

Epigenomics at the tipping point. Foreword.

J. Stamatoyannopoulos, I. Dunham, 2008, Pharmacogenomics.

Identification of the primary gene defect at the cytochrome P450 CYP2D

I. Dunham, T. Strachan, A. Bomford, 1991 .

Fine-mapping, genomic organization, and transcript analysis of the human ubiquitin-conjugating enzyme gene UBE2L3.

C. Cole, I. Dunham, A. Markham, 1998, Genomics.

Molecular characterization of the HLA‐linked steroid 21‐hydroxylase B gene from an individual with congenital adrenal hyperplasia.

I. Dunham, R. Campbell, C. Y. Yu, 1987, The EMBO journal.

Mechanism of spreading of the highly related neurofibromatosis type 1 (NF1) pseudogenes on chromosomes 2, 14 and 22

B. Roe, I. Dunham, L. Smink, 2000, European Journal of Human Genetics.

Polymorphism of the human complement component C4.

I. Dunham, R. Campbell, E. Kendall, 1990, Experimental and clinical immunogenetics.

Characterization of a new member of the human beta-adaptin gene family from chromosome 22q12, a candidate meningioma gene.

V. P. Collins, I. Dunham, J. Dumanski, 1994, Human molecular genetics.

Integrative analysis of GWAS and co-localisation data suggests novel genes associated with age-related multimorbidity

Clare E. West, Maria J. Falaguera, I. Dunham, 2022, medRxiv.

The next-generation Open Targets Platform: reimagined, redesigned, rebuilt

Konstantinos D. Tsirigos, E. McDonagh, I. Dunham, 2022, Nucleic Acids Res..

Faculty Opinions recommendation of Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease.

I. Dunham, 2005 .

FORGEdb: systematic analysis of candidate causal variants to uncover target genes and mechanisms in complex traits

E. Haugen, I. Dunham, A. Teschendorff, 2022, bioRxiv.

Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Tom R. Gaunt, Thomas M. Keane, Chin Yang Shapland, 2018, bioRxiv.

Rapid generation of chromosome-specific alphoid DNA probes using the polymerase chain reaction

I. Dunham, T. Cremer, C. Lengauer, 2004, Human Genetics.

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis

Anton J. Enright, Ian Dunham, Andrew G Fraser, 2010, BMC Genomics.

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Tom R. Gaunt, Klaudia Walter, Nicholas J Timpson, 2015, Nature Communications.

Investigating chromosome organization with genomic microarrays

N. Carter, H. Fiegler, I. Dunham, 2005, Chromosome Research.

Molecular mapping of the HLA class II region in HLA-DR3 associated idiopathic membranous nephropathy.

I. Dunham, R. Campbell, S. Sacks, 1993, Kidney international. Supplement.

ATR-X Syndrome Protein Targets Tandem Repeats and Influences Allele-Specific Expression in a Size-Dependent Manner

Steven J. M. Jones, J. Ragoussis, I. Dunham, 2010, Cell.

Psoriasis upregulated phorbolin-1 shares structural but not functional similarity to the mRNA-editing protein apobec-1.

I. Dunham, N. Tommerup, J. Dumanski, 1999, The Journal of investigative dermatology.

Uncovering novel repositioning opportunities using the Open Targets platform.

Gautier Koscielny, Pankaj Agarwal, Philippe Sanseau, 2017, Drug discovery today.

β-1,3-Glucuronyltransferase-1 gene implicated as a candidate for a schizophrenia-like psychosis through molecular analysis of a balanced translocation

R. Murray, E. Dawson, C. Langford, 2003, Molecular Psychiatry.

The human LARGE gene from 22q12.3-q13.1 is a new, distinct member of the glycosyltransferase gene family.

I. Dunham, J. Dumanski, J. Collins, 1999, Proceedings of the National Academy of Sciences of the United States of America.

An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22.

I. Dunham, N. Navaratnam, A. Jarmuz, 2002, Genomics.

Bmc Evolutionary Biology the Evolution of Imprinting: Chromosomal Mapping of Orthologues of Mammalian Imprinted Domains in Monotreme and Marsupial Mammals

J. Graves, I. Dunham, A. Mungall, 2007 .

The Evolution of the DLK1-DIO3 Imprinted Domain in Mammals

L. Matthews, J. Rogers, J. Graves, 2008, PLoS biology.

Systematic evaluation of variability in ChIP-chip experiments using data

Jun S. Song, Xiaoqin, Xiao-qin, 2008 .

MiR-25 Regulates Wwp2 and Fbxw7 and Promotes Reprogramming of Mouse Fibroblast Cells to iPSCs

Anton J. Enright, Lia S. Campos, A. Enright, 2012, PloS one.

Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines

Anton J. Enright, A. Enright, I. Dunham, 2012, PloS one.

GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals

E. Birney, Klaudia Walter, G. Ritchie, 2019, Nature Genetics.

Open Targets Platform: new developments and updates two years on

Gautier Koscielny, Jeffrey Barrett, Miguel Pignatelli, 2018, Nucleic Acids Res..

Open Targets: a platform for therapeutic target identification and validation

Gautier Koscielny, Robert Petryszak, Maria Keays, 2016, Nucleic Acids Res..

Network expansion of genetic associations defines a pleiotropy map of human cell biology

I. Dunham, H. Hermjakob, S. Orchard, 2021, bioRxiv.

Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations

Alex P. Reynolds, E. Haugen, I. Dunham, 2022, Genome biology.

Applications of machine learning in drug discovery and development

Parantu K. Shah, I. Dunham, A. Madabhushi, 2019, Nature Reviews Drug Discovery.

Ensembl 2012

Gautier Koscielny, Laurent Gil, Ewan Birney, 2011, Nucleic Acids Res..

Small regions of overlapping deletions on 6q26 in human astrocytic tumours identified using chromosome 6 tile path array-CGH

N. Carter, H. Fiegler, I. Dunham, 2006, Oncogene.

A User ’ s Guide to the Encyclopedia of DNA Elements ( ENCODE ) The ENCODE Project Consortium

Timothy E. Reddy, E. Birney, K. Roskin, 2011 .

The development and application of automated gridding for efficient screening of yeast and bacterial ordered libraries.

D. Bentley, I. Dunham, J. Collins, 1992, Genomics.

Characterization of a second human clathrin heavy chain polypeptide gene (CLH-22) from chromosome 22q11.

J E Collins, B. Roe, I. Dunham, 1996, Human molecular genetics.

Mutations in a gene encoding a novel protein tyrosine phosphatase cause progressive myoclonus epilepsy

S. Scherer, L. Tsui, I. Dunham, 1998, Nature Genetics.

The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X

P. Deloukas, R. Durbin, J. Sulston, 2001, Nature.

Chromosome 22: Sequencing

I. Dunham, 2005 .

Lessons from the sequence of human chromosome 22.

I. Dunham, 2002, Ernst Schering Research Foundation workshop.

A re-examination of proximodistal patterning during vertebrate limb development

Lon R. Cardon, Andres Metspalu, Jaak Vilo, 2022 .

A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome

Alex E. Lash, Thomas Ried, Ian Dunham, 2000, Nature Genetics.

A sequence-based integrated map of chromosome 22.

N. Morton, I. Dunham, W. Tapper, 2001, Genome research.

Molecular definition of the 22q11 deletions in velo-cardio-facial syndrome.

I. Dunham, R. Shprintzen, B. Morrow, 1995, American journal of human genetics.

Complete MHC haplotype sequencing for common disease gene mapping.

Sophie Palmer, Stephan Beck, Ian Dunham, 2004, Genome research.

Third single chromosome 6 workshop: meeting report.

J. Ragoussis, H. Cann, I. Dunham, 1997, DNA sequence : the journal of DNA sequencing and mapping.

Comparative analyses of the Dominant megacolon-SOX10 genomic interval in mouse and human

Kimberly J. Smith, W. Pavan, E. Green, 1999, Mammalian Genome.

Mapping human chromosomes.

I. Dunham, D. R. Bently, 1995, Current opinion in genetics & development.

The Gene Guessing Game

Ian Dunham, I. Dunham, 2000, Yeast.

between-chromosome differences in substitution rates

Catherine J. Pink, J. Rogers, I. Dunham, 2009 .

Comparative analysis of neutrophil and monocyte epigenomes

Thomas Lengauer, A. Valencia, R. Guigó, 2017, bioRxiv.

The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers

C. Cole, I. Dunham, S. Forbes, 2018, Nature Reviews Cancer.

Open Targets Genetics: An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

Ellen M. Schmidt, J. Todd, J. Barrett, 2020, bioRxiv.

Human genetics evidence supports two-thirds of the 2021 FDA-approved drugs

E. McDonagh, I. Dunham, M. Ghoussaini, 2022, Nature Reviews Drug Discovery.

Mapping the human genetic architecture of COVID-19

Mattia G. Bergomi, Christopher M. DeBoever, Matthew A. Wiles, 2021, Nature.

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.

Paul Flicek, Ian Dunham, Shane C. Dillon, 2009, Genome research.

In silico prediction of novel therapeutic targets using gene–disease association data

P. Sanseau, I. Dunham, E. Ferrero, 2017, Journal of Translational Medicine.

In silico prediction of novel therapeutic targets using gene–disease association data

P. Sanseau, I. Dunham, Enrico Ferrero, 2017, Journal of Translational Medicine.

Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.

Shane C. Dillon, P. Campbell, I. Dunham, 2006, Genome research.

The extent of linkage disequilibrium in four populations with distinct demographic histories.

E Lai, Chun-Fang Xu, B. Ponder, 2000, American journal of human genetics.

Ensembl 2013

Laurent Gil, Paul Flicek, Fiona Cunningham, 2012, Nucleic Acids Res..

Finishing the finished human chromosome 22 sequence

Fengtang Yang, D. Willey, C. Cole, 2008, Genome Biology.

Replication Timing of Human Chromosome 6

Ian Dunham, Andrew J Mungall, Koichi Ichimura, 2005, Cell cycle.

DNA sequence and analysis of human chromosome 9

I. Dunham, J. L. Ashurst, D. R. Bentley, 2003, Nature.

An analysis of variation in the long-range genomic organization of the human major histocompatibility complex class II region by pulsed-field gel electrophoresis.

I. Dunham, R. Campbell, C. Sargent, 1989, Genomics.

The DNA sequence and analysis of human chromosome 13

I. Dunham, J. L. Ashurst, D. R. Bentley, 2004, Nature.

Epigenetic Marking Prepares the Human HOXA Cluster for Activation During Differentiation of Pluripotent Cells

I. Dunham, Christoph M. Koch, Gayle K. Clelland, 2008, Stem cells.

Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.

I. Dunham, Christoph M. Koch, J. Hughes, 2007, Blood.

Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

Tom R. Gaunt, Thomas M. Keane, Hashem A. Shihab, 2017, Scientific Reports.

A high resolution integrated yeast artificial chromosome clone map of human chromosome 22.

R. Durbin, N. Carter, J. Collins, 1995 .

Cloning of a novel, anonymous gene from a megabase-range YAC and cosmid contig in the neurofibromatosis type 2/meningioma region on human chromosome 22q12.

P. Dejong, I. Dunham, J. Dumanski, 1993, Human molecular genetics.

Erratum: Replication timing of the human genome (Human Molecular Genetics) (2004) vol. 13 (191-202))

David Beare, Ian Dunham, Nigel P. Carter, 2004 .

Replication timing of the human genome.

Owen T McCann, Ian Dunham, Richard Mott, 2004, Human molecular genetics.

Genome-wide meta-analysis identifies new susceptibility loci for migraine

Thomas Meitinger, Dorret I. Boomsma, M. Arfan Ikram, 2013, Nature Genetics.

SAM: a system for iteratively building marker maps

Carol Soderlund, I. Dunham, I. Dunham, 1995, Comput. Appl. Biosci..

UK 10 K Consortium

Tom R. Gaunt, Hashem A. Shihab, Gail P. Clement, 2019 .

Faculty Opinions recommendation of Sequencing and comparison of yeast species to identify genes and regulatory elements.

I. Dunham, 2003 .

A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications.

D. Pinkel, D. Albertson, I. Dunham, 2002, Human molecular genetics.

The organization of the gamma-glutamyl transferase genes and other low copy repeats in human chromosome 22q11.

I. Dunham, A. Mungall, J. Collins, 1997, Genome research.

Chromosomes 21 and 22: Comparisons

I. Dunham, 2005 .

The open targets post-GWAS analysis pipeline

William Jones, Gareth Peat, Michael Nuhn, 2020, Bioinform..

The PROTACtable genome

Kristin K. Brown, A. Leach, I. Dunham, 2021, Nature Reviews Drug Discovery.

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics

Gautier Koscielny, Simon Jupp, Zoe May Pendlington, 2020, Nucleic Acids Res..

Mosaic 22q13 deletions: evidence for concurrent mosaic segmental isodisomy and gene conversion

P. Deloukas, R. Gwilliam, I. Dunham, 2009, European Journal of Human Genetics.

Physical and transcript map of the region between D6S264 and D6S149 on chromosome 6q27, the minimal region of allele loss in sporadic epithelial ovarian cancer

I. Dunham, A. Shelling, A. Mungall, 2002, Oncogene.

Multi-omics study revealing putative drug targets of COVID-19 severity and other viral infection diseases

I. Dunham, M. Ghoussaini, G. Smith, 2020 .

Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element‐binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection

I. Dunham, J. Komorowski, Christoph M. Koch, 2009, The FEBS journal.

Characterization of the human synaptogyrin gene family

B. Roe, I. Dunham, H. Pan, 1998, Human Genetics.

Reevaluating human gene annotation: a second-generation analysis of chromosome 22.

Ian Dunham, Melanie E. Goward, C. Cole, 2003, Genome research.

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

H. Parkinson, I. Dunham, Gary Saunders, 2016, J. Biomed. Semant..

Ensembl 2011

Daniel Rios, Yuan Chen, Paul Flicek, 2010, Nucleic Acids Res..

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays.

Jan Komorowski, Ian Dunham, Kenneth Wester, 2005, Human molecular genetics.

High-resolution analysis of cis-acting regulatory networks at the α-globin locus

J. Ragoussis, I. Dunham, J. Hughes, 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

The role of the polycomb complex in silencing alpha-globin gene expression in nonerythroid cells.

I. Dunham, Christoph M. Koch, D. Higgs, 2008, Blood.

Sequencing and association analysis of the type 1 diabetes – linked region on chromosome 10p12-q11

J. Rogers, J. Todd, S. Nutland, 2007, BMC Genetics.

FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions

Ewan Birney, Valentina Iotchkova, Eugene Kulesha, 2014, bioRxiv.

Identification of multiple HTF‐island associated genes in the human major histocompatibility complex class III region.

I. Dunham, R. Campbell, C. Sargent, 1989, The EMBO journal.

Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands

P. Sanseau, I. Dunham, D. Rajpal, 2018, BMC Bioinformatics.

The Characteristics of Human Genes: Analysis of Human Chromosome 22

I. Dunham, D. Beare, J. Collins, 2003, Comparative and functional genomics.

DNA methylation-histone modification relationships across the desmin locus in human primary cells

I. Dunham, Christoph M. Koch, Gayle K. Clelland, 2009, BMC Molecular Biology.

Human major histocompatibility complex contains genes for the major heat shock protein HSP70.

I. Dunham, J. Trowsdale, R. Campbell, 1989, Proceedings of the National Academy of Sciences of the United States of America.

Characterization of the class III region in different MHC haplotypes by pulsed-field gel electrophoresis

I. Dunham, E. Kendall, C. Sargent, 2005, Immunogenetics.

Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish

Ewan Birney, Joachim Wittbrodt, Ravindra Peravali, 2014, G3: Genes, Genomes, Genetics.

A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance

Tom R. Gaunt, V. Gudnason, V. Emilsson, 2021, medRxiv.

Genomic and phenotypic characterisation of a wild Medaka population: Establishing an isogenic population genetic resource in fish

E. Birney, I. Dunham, A. Fujiyama, 2013, 1304.4515.

Ensembl’s 10th year

Gautier Koscielny, Andrew M. Jenkinson, Damian Smedley, 2009, Nucleic Acids Res..

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes.

C. Langford, I. Dunham, J. Komorowski, 2007, Genome research.

The PROTACtable genome

Kristin K. Brown, I. Dunham, G. Hessler, 2021, Nature Reviews Drug Discovery.

Rapid assessment of S. cerevisiae mating type by PCR.

I. Dunham, C. Huxley, E. Green, 1990, Trends in genetics : TIG.

A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae

Ian Dunham, Jim Stalker, Tony Cox, 2008, Nature Methods.

Genomics - the new rock and roll?

I. Dunham, Ian Dunham, 2000, Trends in genetics : TIG.

Isolation of a putative transcriptional regulator from the region of 22q11 deleted in DiGeorge syndrome, Shprintzen syndrome and familial congenital heart disease.

I. Dunham, C. Roberts, A. Baldini, 1993, Human molecular genetics.

Assignment of the beta B1 crystallin gene (CRYBB1) to human chromosome 22 and mouse chromosome 5.

I. Dunham, G. Thomas, O. Delattre, 1995, Genomics.

A random STS strategy for construction of YAC contigs spanning defined chromosomal regions.

D. Bentley, C. Cole, M. Ross, 1992, Genomics.

Integrative annotation of chromatin elements from ENCODE data

William Stafford Noble, Maxwell W. Libbrecht, Robert S. Harris, 2012, Nucleic Acids Research.

Identification of region-specific yeast artificial chromosomes using pools of Alu element-mediated polymerase chain reaction probes labeled via linear amplification.

D. Bentley, C. Cole, I. Dunham, 1992, Genomics.

The DNA sequence and biological annotation of human chromosome 1

I. Dunham, C. Clee, D. R. Bentley, 2006, Nature.

GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

Ewan Birney, Klaudia Walter, Nicole Soranzo, 2016, bioRxiv.

A bacterial artificial chromosome-based framework contig map of human chromosome 22q.

B. Birren, M. Simon, I. Dunham, 1996, Proceedings of the National Academy of Sciences of the United States of America.

A Molecular Cytogenetic Clone Resource for Chromosome 22

N. Carter, I. Dunham, M. Leversha, 2004, Chromosome Research.

Genetic mapping of 14 short tandem repeat polymorphisms on human chromosome 22

R. Murray, D. Collier, E. Dawson, 1994, Human Genetics.

The human homologue of unc-93 maps to chromosome 6q27 – characterisation and analysis in sporadic epithelial ovarian cancer

I. Dunham, A. Mungall, S. Beck, 2002, BMC Genetics.

Designing an intuitive web application for drug discovery scientists

Gautier Koscielny, Miguel Pignatelli, Nikiforos Karamanis, 2017, bioRxiv.

Why Clinical Trials Stop: The Role of Genetics

I. Dunham, D. Ochoa, I. Lopez, 2023, medRxiv.

correction: The DNA sequence of human chromosome 22

B. Roe, I. Dunham, S. Chissoe, 2000, Nature.

Future prospects for human genetics and genomics in drug discovery

M. Nelson, I. Dunham, M. Ghoussaini, 2023, Current opinion in structural biology.

Systematic disease-agnostic identification of therapeutically actionable targets using the genetics of human plasma proteins

E. McDonagh, I. Dunham, M. Ghoussaini, 2023, medRxiv.

Genome mapping and sequencing

I. Dunham, 2003 .

Literature evidence in open targets - a target validation platform

I. Dunham, J. Mcentyre, Ş. Kafkas, 2017, J. Biomed. Semant..

Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars

Leyla Jael García-Castro, Ian Dunham, Cath Brooksbank, 2018, PLoS Comput. Biol..

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Tudor I. Oprea, Rommie E. Amaro, Yoshua Bengio, 2021, Nature Reviews Chemistry.

FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases

E. Haugen, I. Dunham, A. Teschendorff, 2023, bioRxiv.

The UK10K project identifies rare variants in health and disease

Tom R. Gaunt, Thomas M. Keane, Hashem A. Shihab, 2015, Nature.

A genome annotation-driven approach to cloning the human ORFeome

Younes Mokrab, Ian Dunham, James A. Grinham, 2004, Genome Biology.

Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.

I. Dunham, Christoph M. Koch, J. Hughes, 2007, Blood.

The Human Cell Atlas

Fabian J Theis, Jay W. Shin, Michael J. T. Stubbington, 2017, bioRxiv.

An integrated encyclopedia of DNA elements in the human genome

Melissa C. Greven, E. Birney, Z. Weng, 2014 .

Sex difference contributes to phenotypic diversity in individuals with neurodevelopmental disorders

I. Dunham, A. Droit, F. Bolduc, 2023, Frontiers in Pediatrics.

Escholarship@umms Program in Gene Function and Expression Publications and Presentations Molecular, Cell and Cancer Biology Cell-type-specific Long-range Looping Interactions Identify Distant Regulatory Elements of the Cftr Gene Repository Citation Cell-type-specific Long-range Looping Interactions

J. Stamatoyannopoulos, I. Dunham, Christoph M. Koch, 2022 .

Literature evidence in open targets - a target validation platform

Senay Kafkas, Johanna McEntyre, Ian Dunham, 2017, Journal of Biomedical Semantics.

Genetic fine-mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

Tanya M. Teslovich, Kyle J. Gaulton, Sara M. Willems, 2015, Nature Genetics.

Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands

Philippe Sanseau, Ian Dunham, Deepak K Rajpal, 2018, BMC Bioinformatics.

Mapping the human genetic architecture of COVID-19

Mattia G. Bergomi, Christopher M. DeBoever, Matthew A. Wiles, 2021, Nature.

Phase I Solicitation

E. Lander, B. Wold, J. Sanes, 2020 .

A YAC contig spanning the ataxia-telangiectasia locus (groups A and C) at 11q22-q23.

D. Bentley, C. Cole, F. Collins, 1994, Genomics.

Faculty Opinions recommendation of The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote.

I. Dunham, 2004 .

DNA rescue by the vectorette method.

I. Dunham, A. Coffey, M. A. McAleer, 2003, Methods in molecular biology.

Novel microsatellite markers and single nucleotide polymorphisms refine the tylosis with oesophageal cancer (TOC) minimal region on 17q25 to 42.5 kb: sequencing does not identify the causative gene

J. E. Langan, C. Cole, I. Dunham, 2004, Human Genetics.

Using human genetics to make new medicines

E. Birney, J. Barrett, I. Dunham, 2015, Nature reviews genetics.

YAC library screening. I. Preparation of hybridization filters and PCRpools.

C. Cole, I. Dunham, J. Collins, 1996, Methods in molecular biology.

In silico prediction of novel therapeutic targets using gene–disease association data

Philippe Sanseau, Ian Dunham, Enrico Ferrero, 2017, Journal of Translational Medicine.

Replication timing of the human genome.

N. Carter, H. Fiegler, R. Mott, 2004, Human molecular genetics.

Applications of machine learning in drug discovery and development

Bin Li, Anant Madabhushi, Dominic Clark, 2019, Nature Reviews Drug Discovery.

From long range mapping to sequence-ready contigs on human chromosome 6.

C. Soderlund, A. Butler, C. Clee, 1997, DNA Sequence.

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Tom R. Gaunt, Thomas M. Keane, Hashem A. Shihab, 2015, Nature Communications.

Ensembl regulation resources

E. Birney, P. Flicek, D. Zerbino, 2016, Database J. Biol. Databases Curation.

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

Matthew E. Ritchie, P. Deloukas, S. Tavaré, 2010, BMC Genetics.

Defining functional DNA elements in the human genome

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

Designing an intuitive web application for drug discovery scientists.

Miguel Pignatelli, Nikiforos Karamanis, Ian Dunham, 2018, Drug discovery today.

The role of the polycomb complex in silencing alpha-globin gene expression in nonerythroid cells.

I. Dunham, Christoph M. Koch, D. Higgs, 2008, Blood.

An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

J. Todd, J. Barrett, I. Dunham, 2021, Nature Genetics.