List of works - Marc Zapatka

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

scientific article published on 27 January 2016

Analysis of Epstein-Barr Virus Genomes and Expression Profiles in Gastric Adenocarcinoma

scientific article published in November 2017

Association of mutation signature effectuating processes with mutation hotspots in driver genes and non-coding regions

scientific article published on 10 January 2022

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes

scientific article

Author Correction: The landscape of genomic alterations across childhood cancers

scientific article published in Nature

BRCA1-associated breast and ovarian cancer risks in Poland: no association with commonly studied polymorphisms

scientific article

Basement membrane component laminin-5 is a target of the tumor suppressor Smad4.

scientific article published on 4 September 2006

Breast cancer: a candidate gene approach across the estrogen metabolic pathway

scientific article

Bronchoalveolar lavage fluid of lung cancer patients: Mapping the uncharted waters using proteomics technology

CCM2 mediates death signaling by the TrkA receptor tyrosine kinase

scientific article published on September 2009

Chromosome 17/17q gain and unaltered profiles in high resolution array-CGH are prognostically informative in neuroblastoma.

scientific article published on 15 April 2014

Chromothripsis in human breast cancer

scientific article published on 24 September 2020

Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states

scientific article published in 2022

Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation

scientific article published on 27 December 2018

Corrigendum: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

scientific article published in Nature

Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies

scientific article

DNA methylation-based classification of central nervous system tumours.

scientific article published on 14 March 2018

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

scientific article

Differential clinical significance of individual NKG2D ligands in melanoma: soluble ULBP2 as an indicator of poor prognosis superior to S100B.

scientific article

Differential proteome analysis of conditioned media to detect Smad4 regulated secreted biomarkers in colon cancer

scientific article

Dissecting the genomic complexity underlying medulloblastoma

scientific article

Divergent mechanisms underlie Smad4-mediated positive regulation of the three genes encoding the basement membrane component laminin-332 (laminin-5).

scientific article

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

scientific article (publication date: 29 January 2012)

EPIG-04THE CHROMATIN LANDSCAPE OF MEDULLOBLASTOMA.

scientific article

ERCC5 p.Asp1104His and ERCC2 p.Lys751Gln Polymorphisms Are Independent Prognostic Factors for the Clinical Course of Melanoma

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

scientific article

GENE-06. DISTINCT MOLECULAR SUBGROUPS OF TUMORS OF THE PINEAL REGION CORRELATE WITH CLINICAL PARAMETERS AND GENETIC ALTERATIONS

scientific article published on 23 April 2019

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

scientific article

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

scientific article

Genome-wide identification of translationally inhibited and degraded miR-155 targets using RNA-interacting protein-IP.

scientific article published on 15 April 2013

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma

scientific article published on 29 March 2019

Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis

scientific article published on 15 February 2017

High-level inducible Smad4-reexpression in the cervical cancer cell line C4-II is associated with a gene expression profile that predicts a preferential role of Smad4 in extracellular matrix composition

scientific article

Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma

scientific article published in October 2012

Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration

scientific article published on 07 November 2019

Impact of the CCR5 gene polymorphism on the survival of metastatic melanoma patients receiving immunotherapy

scientific article published on 2 October 2007

Integrative genomic and transcriptomic analysis of leiomyosarcoma.

scientific article published on 10 January 2018

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks

scientific article published on 22 May 2019

Loss of Smad4 correlates with loss of the invasion suppressor E-cadherin in advanced colorectal carcinomas

scientific article published in April 2004

Low p14ARF expression in neuroblastoma cells is associated with repressed histone mark status, and enforced expression induces growth arrest and apoptosis.

scientific article published on 23 January 2013

Lsd1 as a therapeutic target in Gfi1-activated medulloblastoma

scientific article published in Nature Communications

MED12 mutations and NOTCH signalling in chronic lymphocytic leukaemia.

scientific article published on 2 August 2017

Merkel cell polyomavirus status is not associated with clinical course of Merkel cell carcinoma.

scientific article published on 12 May 2011

MicroRNA miR-885-5p targets CDK2 and MCM5, activates p53 and inhibits proliferation and survival

scientific article

Microphthalmia-associated transcription factor gene amplification in metastatic melanoma is a prognostic marker for patient survival, but not a predictive marker for chemosensitivity and chemotherapy response

scientific article published on 01 November 2007

Molecular subgrouping of primary pineal parenchymal tumors reveals distinct subtypes correlated with clinical parameters and genetic alterations

scientific article published on 25 November 2019

Monitoring CSF proteome alterations in amyotrophic lateral sclerosis: obstacles and perspectives in translating a novel marker panel to the clinic

scientific article

Oligonucleotide array-based comparative genomic hybridization (aCGH) of 90 neuroblastomas reveals aberration patterns closely associated with relapse pattern and outcome

scientific article published on 01 December 2006

Ontological Analysis and Pathway Modelling in Drug Discovery

PCM-15SOMATIC CRISPR/Cas9-MEDIATED TUMOR SUPPRESSOR DISRUPTION ENABLES VERSATILE BRAIN TUMOR MODELING.

scientific article

Pilocytic Astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response

scientific article published on 13 February 2020

Postoperative serum proteomic profiles may predict recurrence-free survival in high-risk primary breast cancer

scientific article

Proteomic analysis of field cancerization in pharynx and oesophagus: a prospective pilot study.

scientific article

Proteomic bronchiolitis obliterans syndrome risk monitoring in lung transplant recipients

scientific article

RNAi screening in glioma stem-like cells identifies PFKFB4 as a key molecule important for cancer cell survival.

scientific article published on 7 November 2011

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

scientific article

Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M mutant pediatric high-grade gliomas

scientific article

Relevance of PTEN loss in brain metastasis formation in breast cancer patients

scientific article

Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays

scientific article published on 14 May 2013

Serum amyloid A as a prognostic marker in melanoma identified by proteomic profiling

scientific article

Serum proteomics and disease-specific biomarkers of patients with advanced gastric cancer

scientific article

Smad4 deficiency in cervical carcinoma cells.

scientific article

Survivin-specific T-cell reactivity correlates with tumor response and patient survival: a phase-II peptide vaccination trial in metastatic melanoma

scientific article

TB-17A COMPREHENSIVE PAN-CANCER ANALYSIS OF CHILDHOOD MALIGNANCIES.

scientific article published on 30 May 2016

Telomere dysfunction and chromothripsis

scientific article published on 9 February 2016

The FRA2C common fragile site maps to the borders of MYCN amplicons in neuroblastoma and is associated with gross chromosomal rearrangements in different cancers.

scientific article published on 21 January 2011

The branched-chain amino acid transaminase 1 sustains growth of antiestrogen-resistant and ERα-negative breast cancer

scientific article published on 20 March 2017

The landscape of chromothripsis across adult cancer types

scientific article published on 08 May 2020

The landscape of genomic alterations across childhood cancers

scientific article published on 28 February 2018

The landscape of viral associations in human cancers

scientific article published on 05 February 2020

The whole-genome landscape of medulloblastoma subtypes

scientific article published in July 2017

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

scientific article published on 20 December 2017

Tumor suppressor Smad4 mediates downregulation of the anti-adhesive invasion-promoting matricellular protein SPARC: Landscaping activity of Smad4 as revealed by a "secretome" analysis.

scientific article

Tumor-derived exosomes modulate PD-L1 expression in monocytes.

scientific article published in July 2017

Tumor-microenvironment interactions studied by zonal transcriptional profiling of squamous cell lung carcinoma

scientific article

Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli

scientific article

confFuse: High-Confidence Fusion Gene Detection across Tumor Entities.

scientific article published on 29 September 2017

qPCR in gastrointestinal stromal tumors: Evaluation of reference genes and expression analysis of KIT and the alternative receptor tyrosine kinases FLT3, CSF1-R, PDGFRB, MET and AXL.

scientific article

List of works by Marc Zapatka

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

Analysis of Epstein-Barr Virus Genomes and Expression Profiles in Gastric Adenocarcinoma

Association of mutation signature effectuating processes with mutation hotspots in driver genes and non-coding regions

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes

Author Correction: The landscape of genomic alterations across childhood cancers

BRCA1-associated breast and ovarian cancer risks in Poland: no association with commonly studied polymorphisms

Basement membrane component laminin-5 is a target of the tumor suppressor Smad4.

Breast cancer: a candidate gene approach across the estrogen metabolic pathway

Bronchoalveolar lavage fluid of lung cancer patients: Mapping the uncharted waters using proteomics technology

CCM2 mediates death signaling by the TrkA receptor tyrosine kinase

Chromosome 17/17q gain and unaltered profiles in high resolution array-CGH are prognostically informative in neuroblastoma.

Chromothripsis in human breast cancer

Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states

Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation

Corrigendum: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies

DNA methylation-based classification of central nervous system tumours.

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

Differential clinical significance of individual NKG2D ligands in melanoma: soluble ULBP2 as an indicator of poor prognosis superior to S100B.

Differential proteome analysis of conditioned media to detect Smad4 regulated secreted biomarkers in colon cancer

Dissecting the genomic complexity underlying medulloblastoma

Divergent mechanisms underlie Smad4-mediated positive regulation of the three genes encoding the basement membrane component laminin-332 (laminin-5).

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

EPIG-04THE CHROMATIN LANDSCAPE OF MEDULLOBLASTOMA.

ERCC5 p.Asp1104His and ERCC2 p.Lys751Gln Polymorphisms Are Independent Prognostic Factors for the Clinical Course of Melanoma

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

GENE-06. DISTINCT MOLECULAR SUBGROUPS OF TUMORS OF THE PINEAL REGION CORRELATE WITH CLINICAL PARAMETERS AND GENETIC ALTERATIONS

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

Genome-wide identification of translationally inhibited and degraded miR-155 targets using RNA-interacting protein-IP.

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma

Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis

High-level inducible Smad4-reexpression in the cervical cancer cell line C4-II is associated with a gene expression profile that predicts a preferential role of Smad4 in extracellular matrix composition

Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma

Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration

Impact of the CCR5 gene polymorphism on the survival of metastatic melanoma patients receiving immunotherapy

Integrative genomic and transcriptomic analysis of leiomyosarcoma.

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks

Loss of Smad4 correlates with loss of the invasion suppressor E-cadherin in advanced colorectal carcinomas

Low p14ARF expression in neuroblastoma cells is associated with repressed histone mark status, and enforced expression induces growth arrest and apoptosis.

Lsd1 as a therapeutic target in Gfi1-activated medulloblastoma

MED12 mutations and NOTCH signalling in chronic lymphocytic leukaemia.

Merkel cell polyomavirus status is not associated with clinical course of Merkel cell carcinoma.

MicroRNA miR-885-5p targets CDK2 and MCM5, activates p53 and inhibits proliferation and survival

Microphthalmia-associated transcription factor gene amplification in metastatic melanoma is a prognostic marker for patient survival, but not a predictive marker for chemosensitivity and chemotherapy response

Molecular subgrouping of primary pineal parenchymal tumors reveals distinct subtypes correlated with clinical parameters and genetic alterations

Monitoring CSF proteome alterations in amyotrophic lateral sclerosis: obstacles and perspectives in translating a novel marker panel to the clinic

Oligonucleotide array-based comparative genomic hybridization (aCGH) of 90 neuroblastomas reveals aberration patterns closely associated with relapse pattern and outcome

Ontological Analysis and Pathway Modelling in Drug Discovery

PCM-15SOMATIC CRISPR/Cas9-MEDIATED TUMOR SUPPRESSOR DISRUPTION ENABLES VERSATILE BRAIN TUMOR MODELING.

Pilocytic Astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response

Postoperative serum proteomic profiles may predict recurrence-free survival in high-risk primary breast cancer

Proteomic analysis of field cancerization in pharynx and oesophagus: a prospective pilot study.

Proteomic bronchiolitis obliterans syndrome risk monitoring in lung transplant recipients

RNAi screening in glioma stem-like cells identifies PFKFB4 as a key molecule important for cancer cell survival.

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M mutant pediatric high-grade gliomas

Relevance of PTEN loss in brain metastasis formation in breast cancer patients

Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays

Serum amyloid A as a prognostic marker in melanoma identified by proteomic profiling

Serum proteomics and disease-specific biomarkers of patients with advanced gastric cancer

Smad4 deficiency in cervical carcinoma cells.

Survivin-specific T-cell reactivity correlates with tumor response and patient survival: a phase-II peptide vaccination trial in metastatic melanoma

TB-17A COMPREHENSIVE PAN-CANCER ANALYSIS OF CHILDHOOD MALIGNANCIES.

Telomere dysfunction and chromothripsis

The FRA2C common fragile site maps to the borders of MYCN amplicons in neuroblastoma and is associated with gross chromosomal rearrangements in different cancers.

The branched-chain amino acid transaminase 1 sustains growth of antiestrogen-resistant and ERα-negative breast cancer

The landscape of chromothripsis across adult cancer types

The landscape of genomic alterations across childhood cancers

The landscape of viral associations in human cancers

The whole-genome landscape of medulloblastoma subtypes

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

Tumor suppressor Smad4 mediates downregulation of the anti-adhesive invasion-promoting matricellular protein SPARC: Landscaping activity of Smad4 as revealed by a "secretome" analysis.

Tumor-derived exosomes modulate PD-L1 expression in monocytes.

Tumor-microenvironment interactions studied by zonal transcriptional profiling of squamous cell lung carcinoma

Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli

confFuse: High-Confidence Fusion Gene Detection across Tumor Entities.

qPCR in gastrointestinal stromal tumors: Evaluation of reference genes and expression analysis of KIT and the alternative receptor tyrosine kinases FLT3, CSF1-R, PDGFRB, MET and AXL.