List of works - Mark J. Cowley

A De Novo Mutation in the Sodium-Activated Potassium Channel KCNT2 Alters Ion Selectivity and Causes Epileptic Encephalopathy

scientific article published in October 2017

A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures

scientific article published in February 2018

A Novel Orthotopic Patient-Derived Xenograft Model of Radiation-Induced Glioma Following Medulloblastoma

scientific article published on 12 October 2020

A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations

scientific article

A SLC39A8 variant causes manganese deficiency, and glycosylation and mitochondrial disorders.

scientific article

A preexistent hypoxic gene signature predicts impaired islet graft function and glucose homeostasis

scientific article

A sustained dietary change increases epigenetic variation in isogenic mice

scientific article

Analysis of clinically relevant somatic mutations in high-risk head and neck cutaneous squamous cell carcinoma.

scientific article published on 6 October 2017

Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases

scientific article published on 20 April 2021

Asparagine Synthetase Deficiency causes reduced proliferation of cells under conditions of limited asparagine.

scientific article published on 14 August 2015

BCL-2 hypermethylation is a potential biomarker of sensitivity to antimitotic chemotherapy in endocrine-resistant breast cancer

scientific article published on 16 July 2013

Beyond the panel: preconception screening in consanguineous couples using the TruSight One "clinical exome"

scientific article published on 02 July 2018

Biparental inheritance of mitochondrial DNA in humans is not a common phenomenon

scientific article published on 07 June 2019

Brief Report: Potent clinical and radiological response to larotrectinib in TRK fusion-driven high-grade glioma

scientific article published on 17 September 2018

Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression

scientific article

Cell and molecular determinants of in vivo efficacy of the BH3 mimetic ABT-263 against pediatric acute lymphoblastic leukemia xenografts

scientific article

Clinical Spectrum and Functional Consequences Associated with Bi-Allelic Pathogenic PNPT1 Variants

scientific article published on 19 November 2019

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

Clonal expansions of cytotoxic T cells exist in the blood of patients with Waldenstrom macroglobulinemia but exhibit anergic properties and are eliminated by nucleoside analogue therapy

scientific article published on 26 February 2010

Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomics

scientific article published in October 2010

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

scientific article

Cryptic intronic NBAS variant reveals the genetic basis of recurrent liver failure in a child

scientific article published on 11 December 2018

Deep multi-region whole-genome sequencing reveals heterogeneity and gene-by-environment interactions in treatment-naive, metastatic lung cancer

article

Defining the genetic basis of early onset hereditary spastic paraplegia using whole genome sequencing

scientific article published on 28 September 2016

Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity

scientific article published on 18 September 2019

Detection of growth hormone doping by gene expression profiling of peripheral blood.

scientific article

Differential regulation of the Let-7 family of microRNAs in CD4+ T cells alters IL-10 expression.

scientific article published on 14 May 2012

ELF5 suppresses estrogen sensitivity and underpins the acquisition of antiestrogen resistance in luminal breast cancer.

scientific article

EPG5-Related Vici Syndrome: A Primary Defect of Autophagic Regulation with an Emerging Phenotype Overlapping with Mitochondrial Disorders

scientific article published on 21 November 2017

Evaluation of Streck BCT and PAXgene Stabilised Blood Collection Tubes for Cell-Free Circulating DNA Studies in Plasma.

scientific article published on 19 June 2017

Expanding the spectrum of PEX16 mutations and novel insights into disease mechanisms

scientific article published on 20 July 2018

Expression of pro- and antiapoptotic molecules of the Bcl-2 family in human islets postisolation

scientific article

Extracellular matrix composition significantly influences pancreatic stellate cell gene expression pattern: role of transgelin in PSC function

scientific article published on 18 July 2013

Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus

scientific article published on 09 July 2020

Gene-expression profiling of gram-positive and gram-negative sepsis in critically ill patients.

scientific article

Genetic dissection of gene regulation in multiple mouse tissues.

scientific article published on 12 June 2006

Genome sequencing as a first-line genetic test in familial dilated cardiomyopathy

scientific article published on 02 July 2018

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

Genomic analyses identify molecular subtypes of pancreatic cancer

scientific article published on 24 February 2016

Germline variants in familial pituitary tumour syndrome genes are common in young patients and families with additional endocrine tumours

scientific article published on 20 February 2017

Glutamine addiction promotes glucose oxidation in triple-negative breast cancer

scientific article published on 18 July 2022

Gonadal mosaicism of a novel IQSEC2 variant causing female limited intellectual disability and epilepsy.

scientific article

High Degree of Genetic Heterogeneity for Hereditary Cerebellar Ataxias in Australia

scientific article published on 01 February 2019

Histomolecular phenotypes and outcome in adenocarcinoma of the ampulla of vater

scientific article published on 25 February 2013

Human islets express a marked proinflammatory molecular signature prior to transplantation.

scientific article published on 8 March 2012

Hypermutation In Pancreatic Cancer

scientific article

Identification of Novel GH-Regulated Pathway of Lipid Metabolism in Adipose Tissue: A Gene Expression Study in Hypopituitary Men

article

Impaired B cell development in the absence of Krüppel-like factor 3.

scientific article

Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework

scientific article published in January 2017

Infant high grade gliomas comprise multiple subgroups characterized by novel targetable gene fusions and favorable outcomes

scientific article published on 01 April 2020

Influence of atrial fibrillation on microRNA expression profiles in left and right atria from patients with valvular heart disease.

scientific article published on 6 December 2011

Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome

scientific article published on 9 February 2012

Integrating exome sequencing into a diagnostic pathway for epileptic encephalopathy: Evidence of clinical utility and cost effectiveness.

scientific article

Integration of genomics, high throughput drug screening, and personalized xenograft models as a novel precision medicine paradigm for high risk pediatric cancer

scientific article published on 09 October 2018

Intra- and inter-individual genetic differences in gene expression

scientific article published on 08 May 2009

JRK is a positive regulator of β-catenin transcriptional activity commonly overexpressed in colon, breast and ovarian cancer

scientific article published on 12 October 2015

MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer

scientific article published on 01 June 2020

Maternal obesity and diabetes induces latent metabolic defects and widespread epigenetic changes in isogenic mice

scientific article published on 26 April 2013

MicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene

scientific article published on 13 June 2015

Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance.

scientific article

Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents

scientific article published on 24 February 2016

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

scientific article published on 20 May 2013

Next-Generation Sequencing and Emerging Technologies

scientific article published on 16 May 2019

Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling

scientific article

Normalization procedures and detection of linkage signal in genetical-genomics experiments

scientific article published on 01 August 2006

Oral malignant gastrointestinal neuroectodermal tumour with junctional component mimicking mucosal melanoma

scientific article published on 31 August 2018

PINA v2.0: mining interactome modules.

scientific article published on 8 November 2011

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

scientific article

Population data improves variant interpretation in autosomal dominant polycystic kidney disease

scientific article published on 29 October 2018

Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry.

scientific article published on 02 August 2011

RON is not a prognostic marker for resectable pancreatic cancer ⬇️

scientific article published on September 7, 2012

Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection

scientific article published on 31 January 2019

Recurrent SPECC1L-NTRK fusions in paediatric sarcoma and brain tumours

scientific article published on 03 November 2020

Response to Brodehl et al

scientific article published on 28 September 2018

Reversible Suppression of Lymphoproliferation and Thrombocytopenia with Rapamycin in a Patient with Common Variable Immunodeficiency

scientific article

SOX9 regulates ERBB signalling in pancreatic cancer development.

scientific article published on 21 October 2014

Seave: a comprehensive web platform for storing and interrogating human genomic variation

scientific article published on 01 January 2019

SerpinB2 regulates stromal remodelling and local invasion in pancreatic cancer.

scientific article published on 27 March 2017

Sirtuin-1 regulates acinar-to-ductal metaplasia and supports cancer cell viability in pancreatic cancer

scientific article published on 31 January 2013

Somatic mutations in salivary duct carcinoma and potential therapeutic targets.

scientific article published on 25 May 2017

Somatic point mutation calling in low cellularity tumors.

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

Targeted therapy of TERT-rearranged neuroblastoma with BET bromodomain inhibitor and proteasome inhibitor combination therapy

scientific article published on 11 December 2020

The pseudokinase SgK223 promotes invasion of pancreatic ductal epithelial cells through JAK1/Stat3 signaling

scientific article published on 29 July 2015

Understanding pancreatic cancer genomes

scientific article published on August 2013

Unique presentation of cutis laxa with Leigh-like syndrome due to ECHS1 deficiency

scientific article published on 13 April 2017

Unscrambling cancer genomes via integrated analysis of structural variation and copy number

scientific article published in 2022

Whole Genome Sequencing Improves Outcomes of Genetic Testing in Patients With Hypertrophic Cardiomyopathy

scientific article published on 01 July 2018

Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing

scientific article published on 09 April 2018

Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer

scientific article published on 05 October 2020

Whole genomes redefine the mutational landscape of pancreatic cancer

scientific article published in February 2015

Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders

scientific article published on 29 March 2018

Whole-genome landscape of pancreatic neuroendocrine tumours.

scientific article published on 15 February 2017

Whole-genome sequencing overcomes pseudogene homology to diagnose autosomal dominant polycystic kidney disease

scientific article

c-Myc and Her2 cooperate to drive a stem-like phenotype with poor prognosis in breast cancer.

scientific article published on 23 September 2013

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

scientific article

List of works by Mark J. Cowley

A De Novo Mutation in the Sodium-Activated Potassium Channel KCNT2 Alters Ion Selectivity and Causes Epileptic Encephalopathy

A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures

A Novel Orthotopic Patient-Derived Xenograft Model of Radiation-Induced Glioma Following Medulloblastoma

A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations

A SLC39A8 variant causes manganese deficiency, and glycosylation and mitochondrial disorders.

A preexistent hypoxic gene signature predicts impaired islet graft function and glucose homeostasis

A sustained dietary change increases epigenetic variation in isogenic mice

Analysis of clinically relevant somatic mutations in high-risk head and neck cutaneous squamous cell carcinoma.

Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases

Asparagine Synthetase Deficiency causes reduced proliferation of cells under conditions of limited asparagine.

BCL-2 hypermethylation is a potential biomarker of sensitivity to antimitotic chemotherapy in endocrine-resistant breast cancer

Beyond the panel: preconception screening in consanguineous couples using the TruSight One "clinical exome"

Biparental inheritance of mitochondrial DNA in humans is not a common phenomenon

Brief Report: Potent clinical and radiological response to larotrectinib in TRK fusion-driven high-grade glioma

Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression

Cell and molecular determinants of in vivo efficacy of the BH3 mimetic ABT-263 against pediatric acute lymphoblastic leukemia xenografts

Clinical Spectrum and Functional Consequences Associated with Bi-Allelic Pathogenic PNPT1 Variants

Clinical and molecular characterization of HER2 amplified-pancreatic cancer.

Clinical and pathologic features of familial pancreatic cancer

Clonal expansions of cytotoxic T cells exist in the blood of patients with Waldenstrom macroglobulinemia but exhibit anergic properties and are eliminated by nucleoside analogue therapy

Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomics

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

Cryptic intronic NBAS variant reveals the genetic basis of recurrent liver failure in a child

Deep multi-region whole-genome sequencing reveals heterogeneity and gene-by-environment interactions in treatment-naive, metastatic lung cancer

Defining the genetic basis of early onset hereditary spastic paraplegia using whole genome sequencing

Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity

Detection of growth hormone doping by gene expression profiling of peripheral blood.

Differential regulation of the Let-7 family of microRNAs in CD4+ T cells alters IL-10 expression.

ELF5 suppresses estrogen sensitivity and underpins the acquisition of antiestrogen resistance in luminal breast cancer.

EPG5-Related Vici Syndrome: A Primary Defect of Autophagic Regulation with an Emerging Phenotype Overlapping with Mitochondrial Disorders

Evaluation of Streck BCT and PAXgene Stabilised Blood Collection Tubes for Cell-Free Circulating DNA Studies in Plasma.

Expanding the spectrum of PEX16 mutations and novel insights into disease mechanisms

Expression of pro- and antiapoptotic molecules of the Bcl-2 family in human islets postisolation

Extracellular matrix composition significantly influences pancreatic stellate cell gene expression pattern: role of transgelin in PSC function

Fatal perinatal mitochondrial cardiac failure caused by recurrent <i>de novo</i> duplications in the <i>ATAD3</i> locus

Gene-expression profiling of gram-positive and gram-negative sepsis in critically ill patients.

Genetic dissection of gene regulation in multiple mouse tissues.

Genome sequencing as a first-line genetic test in familial dilated cardiomyopathy

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

Genomic analyses identify molecular subtypes of pancreatic cancer

Germline variants in familial pituitary tumour syndrome genes are common in young patients and families with additional endocrine tumours

Glutamine addiction promotes glucose oxidation in triple-negative breast cancer

Gonadal mosaicism of a novel IQSEC2 variant causing female limited intellectual disability and epilepsy.

High Degree of Genetic Heterogeneity for Hereditary Cerebellar Ataxias in Australia

Histomolecular phenotypes and outcome in adenocarcinoma of the ampulla of vater

Human islets express a marked proinflammatory molecular signature prior to transplantation.

Hypermutation In Pancreatic Cancer

Identification of Novel GH-Regulated Pathway of Lipid Metabolism in Adipose Tissue: A Gene Expression Study in Hypopituitary Men

Impaired B cell development in the absence of Krüppel-like factor 3.

Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework

Infant high grade gliomas comprise multiple subgroups characterized by novel targetable gene fusions and favorable outcomes

Influence of atrial fibrillation on microRNA expression profiles in left and right atria from patients with valvular heart disease.

Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome

Integrating exome sequencing into a diagnostic pathway for epileptic encephalopathy: Evidence of clinical utility and cost effectiveness.

Integration of genomics, high throughput drug screening, and personalized xenograft models as a novel precision medicine paradigm for high risk pediatric cancer

Intra- and inter-individual genetic differences in gene expression

JRK is a positive regulator of β-catenin transcriptional activity commonly overexpressed in colon, breast and ovarian cancer

MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer

Maternal obesity and diabetes induces latent metabolic defects and widespread epigenetic changes in isogenic mice

MicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene

Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance.

Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents

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

Next-Generation Sequencing and Emerging Technologies

Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling

Normalization procedures and detection of linkage signal in genetical-genomics experiments

Oral malignant gastrointestinal neuroectodermal tumour with junctional component mimicking mucosal melanoma

PINA v2.0: mining interactome modules.

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

Population data improves variant interpretation in autosomal dominant polycystic kidney disease

Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry.

RON is not a prognostic marker for resectable pancreatic cancer ⬇️

Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection

Recurrent SPECC1L-NTRK fusions in paediatric sarcoma and brain tumours

Response to Brodehl et al

Reversible Suppression of Lymphoproliferation and Thrombocytopenia with Rapamycin in a Patient with Common Variable Immunodeficiency

SOX9 regulates ERBB signalling in pancreatic cancer development.

Seave: a comprehensive web platform for storing and interrogating human genomic variation

SerpinB2 regulates stromal remodelling and local invasion in pancreatic cancer.