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List of works by Lukas Chavez

17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells

scientific article

A biobank of patient-derived pediatric brain tumor models

scientific article published on 22 October 2018

A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells

scientific article published on 21 May 2010

A mouse model for embryonal tumors with multilayered rosettes uncovers the therapeutic potential of Sonic-hedgehog inhibitors

scientific article published on 11 September 2017

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways

scientific article published on 14 March 2016

ATRT-09. CHROMATIN SEGMENTATION ANALYSES IN ATYPICAL TERATOID/RHABDOID TUMORS REVEAL H3K27ME3-MEDIATED EPIGENETIC SILENCING OF TUMOR SUPPRESSOR GENES AND IDENTIFY A NOVEL ROLE OF EZH2, ASSOCIATED WITH ACTIVE CHROMATIN.

scientific article

Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling

scientific article published on 01 September 2018

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

scientific article published on 27 January 2016

Acute loss of TET function results in aggressive myeloid cancer in mice

scientific article

An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays

scientific article published on 05 December 2018

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

Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma

scientific article published on 04 April 2019

Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development

scientific article

Comparative Analysis of Human Embryonic Stem Cell and Induced Pluripotent Stem Cell-Derived Hepatocyte-Like Cells Reveals Current Drawbacks and Possible Strategies for Improved Differentiation ⬇️

scientific article published on January 24, 2011

Comparative molecular portraits of human unfertilized oocytes and primordial germ cells at 10 weeks of gestation ⬇️

scientific article published on January 1, 2012

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

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

scientific article

DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis

scientific article published on 14 March 2017

DNA methylation-based classification of central nervous system tumours

scientific article published on 14 March 2018

DNA-methylation profiling discloses significant advantages over NanoString method for molecular classification of medulloblastoma

scientific article published on 13 October 2017

DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer

scientific article

Deep sequencing of WNT-activated medulloblastomas reveals secondary SHH pathway activation.

scientific article published on 12 February 2018

Desmoplastic Infantile Ganglioglioma/Astrocytoma (DIG/DIA) Are Distinct Entities with Frequent BRAFV600 Mutations

article

Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells

scientific article published on 13 January 2014

Dynamic Changes in Chromatin Accessibility Occur in CD8+ T Cells Responding to Viral Infection.

scientific article published on 5 December 2016

Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming.

scientific article published on 9 February 2018

EMBR-01. MOLECULAR AND CLINICAL HETEROGENEITY IN HISTOLOGICALLY-DIAGNOSED CNS-PNET PATIENTS PROSPECTIVELY TREATED AS A SINGLE ENTITY: A REPORT FROM THE CHILDREN’S ONCOLOGY GROUP ACNS0332 TRIAL.

scientific article

EMBR-02. RECURRENT HOMOZYGOUS DELETION OF DROSHA AND MICRODUPLICATION OF PDE4DIP CONTAINING THE ANCESTRAL DUF1220 DOMAIN IN PINEOBLASTOMA

EPEN-23. MOLECULAR HETEROGENEITY AMONG PEDIATRIC POSTERIOR FOSSA EPENDYMOMA

EPEN-24. YAP1 FUSION PROTEINS MEDIATE ONCOGENIC ACTIVITY IN EPENDYMOMA VIA INTERACTION WITH TEAD TRANSCRIPTION FACTORS.

scientific article published on 22 June 2018

EPIG-04THE CHROMATIN LANDSCAPE OF MEDULLOBLASTOMA.

scientific article

EPN-34EPIGENOMIC ANALYSIS OF EPENDYMAL TUMORS IDENTIFIES SUBGROUP SPECIFIC ENHANCERS CONTROLLING DISTINCT REGULATORY CIRCUITRIES.

scientific article published on 30 May 2016

EPND-01. THE ACTIVE REGULATORY LANDSCAPE OF EPENDYMAL TUMORS.

scientific article published on 31 May 2017

EPND-07. MOLECULAR HETEROGENEITY AMONG PEDIATRIC POSTERIOR FOSSA EPENDYMOMA.

scientific article published on 31 May 2017

Engineering Genetic Predisposition in Human Neuroepithelial Stem Cells Recapitulates Medulloblastoma Tumorigenesis

scientific article published on 13 June 2019

Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility

scientific article

Epithelioid glioblastomas stratify into established diagnostic subsets upon integrated molecular analysis.

scientific article

Evidence of H3 K27M mutations in posterior fossa ependymomas

scientific article

Extensive Molecular and Clinical Heterogeneity in Patients With Histologically Diagnosed CNS-PNET Treated as a Single Entity: A Report From the Children's Oncology Group Randomized ACNS0332 Trial

scientific article published on 17 October 2018

GENE-02. CHROMOSOME CONFORMATION ANALYSIS OF EPENDYMOMA IDENTIFIES PUTATIVE TUMOR DEPENDENCY GENES ACTIVATED BY DISTAL ONCOGENIC ENHANCERS

scientific article published on 23 April 2019

Genetic confirmation that ependymoma can arise as part of multiple endocrine neoplasia type 1 (MEN1) syndrome.

scientific article published on 25 February 2017

H3-/IDH-wild type pediatric glioblastoma is comprised of molecularly and prognostically distinct subtypes with associated oncogenic drivers

scientific article published on 11 April 2017

Immunohistochemical analysis of H3K27me3 demonstrates global reduction in group-A childhood posterior fossa ependymoma and is a powerful predictor of outcome

scientific article

In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach

scientific article published on 15 July 2009

InTAD: chromosome conformation guided analysis of enhancer target genes

article

Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression

scientific article published on 21 November 2019

Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

scientific article published on 18 April 2016

Integrated molecular characterization of IDH-mutant glioblastomas

scientific article published on 15 November 2018

Large conserved domains of low DNA methylation maintained by Dnmt3a

scientific article published on 24 November 2013

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

scientific article

MEDU-20. TARGETING OF MYC BY HDAC INHIBITION IN MYC AMPLIFIED GROUP 3 MEDULLOBLASTOMA.

scientific article

MRI Features of Histologically Diagnosed Supratentorial Primitive Neuroectodermal Tumors and Pineoblastomas in Correlation with Molecular Diagnoses and Outcomes: A Report from the Children's Oncology Group ACNS0332 Trial

scientific article published on 10 October 2019

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX.

scientific article published on 7 April 2013

Molecular characterization of cultured adult human liver progenitor cells

scientific article published on October 2010

Molecular heterogeneity and CXorf67 alterations in posterior fossa group A (PFA) ependymomas

scientific article published on 16 June 2018

Opposing Effects of CREBBP Mutations Govern the Phenotype of Rubinstein-Taybi Syndrome and Adult SHH Medulloblastoma

scientific article published on 9 March 2018

PATH-32. MOLECULAR HETEROGENEITY AMONG PEDIATRIC POSTERIOR FOSSA EPENDYMOMA

PDCT-05. MOLECULAR DIAGNOSTICS REVEAL 60% HIGHER SURVIVAL FOR MOLECULARLY-VERIFIED VERSUS HISTOPATHOLOGICALLY-DIAGNOSED PEDIATRIC SUPRATENTORIAL CENTRAL NERVOUS SYSTEM EMBRYONAL TUMORS AND PINEOBLASTOMAS; A REPORT FROM THE CHILDREN’S ONCOLOGY GROUP

PDTM-23. THE ACTIVE REGULATORY LANDSCAPE OF EPENDYMAL TUMORS

PDTM-49. GLOBAL REDUCTION IN H3K27me3, SIMILAR TO H3K27M MUTANT GLIOMAS, IS A MOLECULAR SURROGATE FOR PEDIATRIC POSTERIOR FOSSA- GROUP A EPENDYMOMAS

scientific article published on 6 November 2017

PNR-12GENOME-WIDE PROFILING OF EMBRYONAL TUMORS WITH MULTILAYERED ROSETTES (ETMR).

scientific article published on 30 May 2016

Polymorphous low-grade neuroepithelial tumor of the young (PLNTY): an epileptogenic neoplasm with oligodendroglioma-like components, aberrant CD34 expression, and genetic alterations involving the MAP kinase pathway.

scientific article

Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data

scientific article published in 2013

Publisher Correction: Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

scientific article published on 01 December 2019

QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments

scientific article

Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data.

scientific article

Recurrent homozygous deletion of DROSHA and microduplication of PDE4DIP in pineoblastoma

scientific article published in Nature Communications

Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma

scientific article published on 21 August 2020

Second-generation molecular subgrouping of medulloblastoma: an international meta-analysis of Group 3 and Group 4 subtypes

scientific article published on 10 May 2019

Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis

scientific article

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea

scientific article

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.

scientific article

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

scientific article published on 30 May 2016

TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells

scientific article published on 21 November 2016

TMOD-05. MOLECULAR CHARACTERIZATION OF ORTHOTOPIC PATIENT-DERIVED XENOGRAFT MODELS OF PEDIATRIC BRAIN TUMORS AND THEIR USE IN PRECLINICAL EXPERIMENTS.

scientific article

Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock

scientific article published on 27 August 2019

Telomerase activation in posterior fossa group A ependymomas is associated with dismal prognosis and chromosome 1q gain

scientific article

Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling

scientific article published on 05 December 2016

The Meningioma Enhancer Landscape Delineates Novel Subgroups and Drives Druggable Dependencies

scientific article published on 23 July 2020

The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine.

scientific article published on 27 April 2015

The landscape of genomic alterations across childhood cancers

scientific article published on 28 February 2018

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

Transcription Elongation Machinery Is a Druggable Dependency and Potentiates Immunotherapy in Glioblastoma Stem Cells

scientific article published in 2022

YAP1 subgroup supratentorial ependymoma requires TEAD and nuclear factor I-mediated transcriptional programmes for tumorigenesis

scientific article published on 02 September 2019

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