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List of works by Sean Grimmond

A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae

scientific article

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

scientific article

A continuum of cell states spans pluripotency and lineage commitment in human embryonic stem cells

scientific article

A de novo mutation in the β-tubulin gene TUBB4A results in the leukoencephalopathy hypomyelination with atrophy of the basal ganglia and cerebellum

scientific article

A global role for EKLF in definitive and primitive erythropoiesis

scientific article

A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells

scientific article published on 27 May 2010

A global role for zebrafish klf4 in embryonic erythropoiesis

scientific article published on 23 June 2007

A high-throughput platform for lentiviral overexpression screening of the human ORFeome

scientific article

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

scientific article

A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing.

scientific article published in July 2014

Alternate transcription of the Toll-like receptor signaling cascade

scientific article published on 17 February 2006

Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation.

scientific article published on 19 January 2016

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator

scientific article

Analysis of Brca1-deficient mouse mammary glands reveals reciprocal regulation of Brca1 and c-kit

scientific article published on 6 December 2010

Analysis of early nephron patterning reveals a role for distal RV proliferation in fusion to the ureteric tip via a cap mesenchyme-derived connecting segment

scientific article published on 6 June 2009

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Analysis of the mouse transcriptome for genes involved in the function of the nervous system.

scientific article

Anlaysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1.

scientific article published on April 2004

Ascorbate promotes epigenetic activation of CD30 in human embryonic stem cells

scientific article published on October 2010

Atlas of Gene Expression in the Developing Kidney at Microanatomic Resolution

article

Atlas of gene expression in the developing kidney at microanatomic resolution

scientific article

BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression

scientific article

Can we move towards personalised pancreatic cancer therapy?

Carriage of an ACME II variant may have contributed to methicillin-resistant Staphylococcus aureus sequence type 239-like strain replacement in Liverpool Hospital, Sydney, Australia.

scientific article published on 5 March 2012

Caveolin-1 is necessary for hepatic oxidative lipid metabolism: evidence for crosstalk between caveolin-1 and bile acid signaling

scientific article published on 11 July 2013

Characterisation and trophic functions of murine embryonic macrophages based upon the use of a Csf1r-EGFP transgene reporter

scientific article published on 25 May 2007

Characterisation of a new human and murine member of the DnaJ family of proteins

scientific article

Characterization of RasGRP2, a plasma membrane-targeted, dual specificity Ras/Rap exchange factor

scientific article

Characterization of an ntrX mutant of Neisseria gonorrhoeae reveals a response regulator that controls expression of respiratory enzymes in oxidase-positive proteobacteria

scientific article published on 5 April 2013

Characterization of the OxyR regulon of Neisseria gonorrhoeae

scientific article

Characterization of the breast cancer associated ATM 7271T>G (V2424G) mutation by gene expression profiling

scientific article published on December 2006

Characterization of the mouse Men1 gene and its expression during development

scientific journal article

Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection

scientific article

Clinical and molecular characterization of HER2 amplified-pancreatic cancer.

scientific article published on 31 August 2013

Clinical and pathologic features of familial pancreatic cancer

scientific article published on 14 October 2014

Comparative gene expression analysis of genital tubercle development reveals a putative appendicular Wnt7 network for the epidermal differentiation

scientific article

Comprehensive transcriptome and immunophenotype analysis of renal and cardiac MSC-like populations supports strong congruence with bone marrow MSC despite maintenance of distinct identities

article

Confirmation of a susceptibility locus on chromosome 13 in Australian breast cancer families

article

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

scientific article

Correction: Transcriptome-Wide Prediction of miRNA Targets in Human and Mouse Using FASTH.

scientific article published on 16 July 2009

Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution

scholarly article published in Nature Genetics

Corrigendum: Tiny RNAs associated with transcription start sites in animals

scholarly article published in Nature Genetics

DRES-05. MOLECULAR EVOLUTION OF DIFFUSE GLIOMAS AND THE GLIOMA LONGITUDINAL ANALYSIS CONSORTIUM

scientific article published on 5 November 2018

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells

scientific article

Definition and spatial annotation of the dynamic secretome during early kidney development

scientific article published on June 2006

Detection of a rare point mutation in Ki-ras of a human bladder cancer xenograft by polymerase chain reaction and direct sequencing

scientific article published on 01 January 1992

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

scientific article published on January 2006

Differential gene expression in the developing mouse ureter

scientific article published on 3 February 2006

Divergent reprogramming routes lead to alternative stem-cell states

scientific article

Dual targeting of p53 and c-MYC selectively eliminates leukaemic stem cells

scientific article

Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture

scientific article

EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas

scientific article published on 23 June 2017

Effects of A1 adenosine receptor overexpression on normoxic and post-ischemic gene expression

scientific article published in March 2003

Erratum: Corrigendum: Divergent reprogramming routes lead to alternative stem-cell states

scientific article published in Nature

Erratum: Corrigendum: Genome-wide characterization of the routes to pluripotency

scientific article published in Nature

Erratum: Corrigendum: Signatures of mutational processes in human cancer

scientific article published in Nature

Erratum: Corrigendum: The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

scientific article published in Nature

Erratum: Corrigendum: Whole–genome characterization of chemoresistant ovarian cancer

scientific article published in Nature

Exclusion of the 13-kDa rapamycin binding protein gene (FKBP2) as a candidate gene for multiple endocrine neoplasia type 1

Exclusion of the phosphoinositide-specific phospholipase C?3 ( PLCB3 ) gene as a candidate for multiple endocrine neoplasia type 1

scientific article published on 3 December 1996

Exome-Wide Association Study of Pancreatic Cancer Risk

scientific article published on 23 October 2017

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

scientific article

Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set.

scientific article

Expression Profiling with cDNA Microarrays: A User’s Perspective and Guide

Expression of a novel mammalian epidermal growth factor-related gene during mouse neural development

scientific article published on 01 April 2001

Expression of the VEGF-related factor gene in pre- and postnatal mouse

scientific article published in March 1996

Ferrets exclusively synthesize Neu5Ac and express naturally humanized influenza A virus receptors

scientific article

G Protein Mutations in Tumors of the Pituitary, Parathyroid and Endocrine Pancreas

scientific article published on 01 June 1995

GUDMAP – An Online GenitoUrinary Resource

GUDMAP – An Online GenitoUrinary Resource

GUDMAP: the genitourinary developmental molecular anatomy project

scientific article published on 20 February 2008

Gemcitabine and CHK1 inhibition potentiate EGFR-directed radioimmunotherapy against pancreatic ductal adenocarcinoma

scientific article published on 16 May 2014

Gene expression profile of the fibrotic response in the peritoneal cavity

article

Generation of diversity in the innate immune system: macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes

scientific article

Genome sequencing approaches and successes

scientific article published on January 2009

Genome-Wide Identification of Long Noncoding RNAs in CD8+ T Cells

scientific article published on 01 June 2009

Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling.

scientific article published on 9 May 2014

Genome-wide analysis of mammalian promoter architecture and evolution

scientific article (publication date: June 2006)

Genome-wide characterization of the routes to pluripotency.

scientific article published on December 2014

Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases.

scientific article

Genomic analyses identify molecular subtypes of pancreatic cancer

scientific article published on 24 February 2016

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis.

scientific article

Genomic organization and complete cDNA sequence of the human phosphoinositide-specific phospholipase C beta 3 gene (PLCB3)

scientific article published on 10 April 1995

Glioma Through the Looking GLASS: Molecular Evolution of Diffuse Gliomas and the Glioma Longitudinal AnalySiS Consortium.

scientific article published on 8 February 2018

Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer.

scientific article

Hypermutation In Pancreatic Cancer

scientific article

Identification of a novel de novo p.Phe932Ile KCNT1 mutation in a patient with leukoencephalopathy and severe epilepsy

scientific article

Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways

scientific article

Identification of human embryonic stem cell surface markers by combined membrane-polysome translation state array analysis and immunotranscriptional profiling

scientific article

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney ⬇️

scientific article

Identification of novel markers of mouse fetal ovary development

scientific article

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma

scientific article published on 10 February 2016

Identification of three gene candidates for multicellular resistance in colon carcinoma

scientific article published on September 2004

Identification of unsafe human induced pluripotent stem cell lines using a robust surrogate assay for pluripotency

scientific article published on August 2013

Identifying the Molecular Phenotype of Renal Progenitor Cells

scientific article published on 01 September 2004

Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs

scientific article

In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

scientific article published on 18 September 2013

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites

scientific article

Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance

scientific article published on 14 July 2015

Integration-free induced pluripotent stem cells model genetic and neural developmental features of down syndrome etiology

scientific article published in March 2013

Interaction of c-Myb with p300 is required for the induction of acute myeloid leukemia (AML) by human AML oncogenes.

scientific article published on 4 March 2014

Kidney transcriptome reveals altered steroid homeostasis in NaS1 sulfate transporter null mice

scientific article

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

scientific article

Lost in translation: returning germline genetic results in genome-scale cancer research

scientific article

Manganese regulation of virulence factors and oxidative stress resistance in Neisseria gonorrhoeae

scientific article

Mice lacking the vascular endothelial growth factor-B gene (Vegfb) have smaller hearts, dysfunctional coronary vasculature, and impaired recovery from cardiac ischemia

scientific journal article

MicroRNA-182-5p targets a network of genes involved in DNA repair

scientific article

MicroRNAs and their isomiRs function cooperatively to target common biological pathways

scientific article

MicroRNAs-140-5p/140-3p modulate Leydig cell numbers in the developing mouse testis

scientific article published on 6 June 2013

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

scientific article

Mining the genomes of exceptional responders

scientific article published in May 2014

Minor class splicing shapes the zebrafish transcriptome during development

scientific article published on 10 February 2014

Mitochondrial mutations and metabolic adaptation in pancreatic cancer.

scientific article published on 30 January 2017

Molecular biology of urological tumours.

scientific article published on February 1990

Molecular diagnostics in pancreatic cancer

Molecular tools for presymptomatic testing in multiple endocrine neoplasia type 1

scientific article published on 01 September 1995

Mouse proteome analysis

scientific article

Multiple endocrine neoplasia type 1 (MEN1) in two Asian families

article

Multiple endocrine neoplasia type I: clinical syndrome to molecular genetics

scientific article published on October 1995

Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor β signaling

scientific article published on April 2014

Mutation analysis of the MEN1 gene in multiple endocrine neoplasia type 1, familial acromegaly and familial isolated hyperparathyroidism

article

Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity.

scientific article

Mutations in the voltage-gated potassium channel gene KCNH1 cause Temple-Baraitser syndrome and epilepsy

scientific article published on 24 November 2014

NRED: a database of long noncoding RNA expression

scientific article

Neuropilin-2 promotes extravasation and metastasis by interacting with endothelial α5 integrin

scientific article published on 20 May 2013

New RAS-mutant pancreatic adenocarcinoma with combined BRAF and MEK inhibition for metastatic melanoma

scientific article published on 12 May 2014

Novel cancer drivers: mining the kinome ⬇️

scientific article published on February 28, 2013

Novel genes regulated by Sonic Hedgehog in pluripotent mesenchymal cells

scientific article

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization

scientific article

PINA v2.0: mining interactome modules.

scientific article published on 8 November 2011

PRMT2 and RORγ expression are associated with breast cancer survival outcomes

scientific article

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

scientific article

Pancreatic cancer genomics

scientific article published on 28 January 2014

Pancreatic cancer genomics: where can the science take us?

scientific article

Pax9 and Jagged1 act downstream of Gli3 in vertebrate limb development

scientific article published on August 2005

PerR controls Mn-dependent resistance to oxidative stress in Neisseria gonorrhoeae

scientific article published on April 2006

Phasevarion mediated epigenetic gene regulation in Helicobacter pylori

scientific article

Phasevarions mediate random switching of gene expression in pathogenic Neisseria

scientific article

PhosphoregDB: the tissue and sub-cellular distribution of mammalian protein kinases and phosphatases

scientific article

Phosphoregulators: protein kinases and protein phosphatases of mouse.

scientific article

Platypus Induced Pluripotent Stem Cells: The Unique Pluripotency Signature of a Monotreme

scientific article published on 09 January 2019

Precision Medicine for Advanced Pancreas Cancer: The Individualized Molecular Pancreatic Cancer Therapy (IMPaCT) Trial

scientific article published on May 2015

Predictive diagnosis of multiple endocrine neoplasia (MEN 1) in four Australian kindreds

article

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

scientific article

Profiling gene expression induced by protease-activated receptor 2 (PAR2) activation in human kidney cells

scientific article

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline

scientific article published on 23 July 2013

Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks

scientific article published on 10 December 2014

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

scientific article

RON is not a prognostic marker for resectable pancreatic cancer ⬇️

scientific article published on September 7, 2012

Rapid identification of a novel complex I MT-ND3 m.10134C>A mutation in a Leigh syndrome patient

scientific article

Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.

scientific article

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

scientific article published on 20 July 2018

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma

scientific article published on 8 May 2017

Redirection of renal mesenchyme to stromal and chondrocytic fates in the presence of TGF-beta2.

scientific article

Reduced mucin sulfonation and impaired intestinal barrier function in the hyposulfataemic NaS1 null mouse.

scientific article

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

scientific article

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

scientific article

Report of the Sixth International Workshop on Human Chromosome 11 Mapping 1998. Nice, France, May 2-5, 1998.

scientific article published in January 1999

Returning individual research results for genome sequences of pancreatic cancer

scientific article

SOX9 regulates ERBB signalling in pancreatic cancer development.

scientific article published on 21 October 2014

Sequencing transcriptomes in toto.

scientific article published on 04 February 2011

Setting CAGE Tags in a Genomic Context

Sexually dimorphic expression of protease nexin-1 and vanin-1 in the developing mouse gonad prior to overt differentiation suggests a role in mammalian sexual development.

scientific article published in June 2000

Simplifying complexity

article

Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma

scientific article published on 15 March 2012

Small RNA changes en route to distinct cellular states of induced pluripotency.

scientific article published on 10 December 2014

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample

scientific article

Somatic point mutation calling in low cellularity tumors.

scientific article

Stem cell transcriptome profiling via massive-scale mRNA sequencing

scientific article

Stromal protein Ecm1 regulates ureteric bud patterning and branching

scientific article

Subcellular Localization of Mammalian Type II Membrane Proteins

scientific article published on 01 May 2006

Subfractionation of differentiating human embryonic stem cell populations allows the isolation of a mesodermal population enriched for intermediate mesoderm and putative renal progenitors

scientific article

Subtypes of familial breast tumours revealed by expression and copy number profiling

scientific article

Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome

scientific article

Tailored first-line and second-line CDK4-targeting treatment combinations in mouse models of pancreatic cancer

scientific article published on 28 October 2017

Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia.

scientific article published on 20 June 2019

Targeting mTOR dependency in pancreatic cancer

scientific article

Telomere sequence content can be used to determine ALT activity in tumours

scientific article published on 30 April 2018

The abundance of short proteins in the mammalian proteome

scientific article published on 28 April 2006

The clinical potential and challenges of sequencing cancer genomes for personalized medical genomics.

scientific article

The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

scientific article

The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition

scientific article

The mouse Y chromosome interval necessary for spermatogonial proliferation is gene dense with syntenic homology to the human AZFa region.

scientific article published in October 1998

The mouse secretome: functional classification of the proteins secreted into the extracellular environment

scientific article

The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes

scientific article

The phospholipase C beta 3 gene located in the MEN1 region shows loss of expression in endocrine tumours

scientific article

The regulated retrotransposon transcriptome of mammalian cells

scientific article (publication date: May 2009)

The transcriptional landscape of the mammalian genome

scientific article

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

The uniqueome: a mappability resource for short-tag sequencing

scientific article

Tiny RNAs associated with transcription start sites in animals

scientific article published on 19 April 2009

Tissue-specific gene expression in soybean (Glycine max) detected by cDNA microarray analysis

article

Towards the systematic mapping and engineering of the protein prenylation machinery in Saccharomyces cerevisiae

scientific article

Transcriptional analysis of early lineage commitment in human embryonic stem cells

scientific article

Transcriptional profile reveals altered hepatic lipid and cholesterol metabolism in hyposulfatemic NaS1 null mice

Transcriptional responses to ischemia in A1AR transgenic and wild-type hearts

article

Transcriptional switching in macrophages associated with the peritoneal foreign body response

scientific article published on 18 March 2014

Transcriptome content and dynamics at single-nucleotide resolution

scientific article

Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH.

scientific article

Tumour-induced host stromal-cell transformation: induction of mouse spindle-cell fibrosarcoma not mediated by gene transfer

scientific article published on August 1990

Understanding pancreatic cancer genomes

scientific article published on August 2013

Use of DNA-damaging agents and RNA pooling to assess expression profiles associated with BRCA1 and BRCA2 mutation status in familial breast cancer patients.

scientific article

Use of expression data and the CGEMS genome-wide breast cancer association study to identify genes that may modify risk in BRCA1/2 mutation carriers

scientific article

Using the MCF10A/MCF10CA1a Breast Cancer Progression Cell Line Model to Investigate the Effect of Active, Mutant Forms of EGFR in Breast Cancer Development and Treatment Using Gefitinib

scientific article published on 13 May 2015

Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells

scientific article published on October 2010

Whole exome sequencing in patients with white matter abnormalities.

scientific article published on 09 May 2016

Whole genome sequence analysis of the first Australian OXA-48-producing outbreak-associated Klebsiella pneumoniae isolates: the resistome and in vivo evolution

scientific article

Whole genomes redefine the mutational landscape of pancreatic cancer

scientific article published in February 2015

Whole-genome characterization of chemoresistant ovarian cancer

scientific article published in May 2015

Whole-genome landscape of pancreatic neuroendocrine tumours.

scientific article published on 15 February 2017

Whole-genome landscapes of major melanoma subtypes.

scientific article published on 3 May 2017

X-MATE: a flexible system for mapping short read data

scientific article

miR-139-5p is a regulator of metastatic pathways in breast cancer

scientific article published on 24 October 2013

p53 is required for etoposide-induced apoptosis of human embryonic stem cells

scientific article published on 22 October 2007

qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles

scientific article

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