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List of works by Jan Korbel

A cell-based model system links chromothripsis with hyperploidy

scientific article published on 28 September 2015

A comprehensive map of mobile element insertion polymorphisms in humans

scientific article

A draft human pangenome reference

scientific article published on 10 May 2023

A scalable CRISPR/Cas9-based fluorescent reporter assay to study DNA double-strand break repair choice

scientific article published on 14 August 2020

A structured open dataset of government interventions in response to COVID-19

scientific preprint published on 09 May 2020

A structured open dataset of government interventions in response to COVID-19

scientific article published on 27 August 2020

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge

scientific article

Acquisition of chromosome instability is a mechanism to evade oncogene addiction

scientific article published on 06 February 2020

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

scientific article published on 27 January 2016

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis

scientific article

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

scientific article published on 08 October 2008

Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies

article

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms ⬇️

scientific article published on June 2015

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

scientific article (publication date: July 2004)

Assembly and diploid architecture of an individual human genome via single-molecule technologies

scientific article published on 29 June 2015

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

BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence

scientific article

Butler enables rapid cloud-based analysis of thousands of human genomes

scientific article published on 05 February 2020

Challenges in studying genomic structural variant formation mechanisms: the short-read dilemma and beyond

scientific article published on 30 September 2011

Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors

scientific article published on 05 August 2020

Clinical significance of different types of p53 gene alteration in surgically treated prostate cancer

scientific article published on 26 April 2014

Combining frequency and positional information to predict transcription factor binding sites

scientific article published in November 2001

Comment on "Rényi entropy yields artificial biases not in the data and incorrect updating due to the finite-size data"

scientific article published on 01 August 2019

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

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads

scientific article

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

scientific article published in Nature

Criteria for Inference of Chromothripsis in Cancer Genomes ⬇️

scientific article published on March 14, 2013

DELLY: structural variant discovery by integrated paired-end and split-read analysis

scientific article

Deletion lengthening at chromosomes 6q and 16q targets multiple tumor suppressor genes and is associated with an increasingly poor prognosis in prostate cancer

scientific article published on 11 November 2017

Dense and accurate whole-chromosome haplotyping of individual genomes.

scientific article published on 3 November 2017

Dissecting the genomic complexity underlying medulloblastoma

scientific article

Distinct genomic aberrations associated with ERG rearranged prostate cancer

scientific article published on April 2009

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

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

scientific article published on 30 May 2016

Empirical social triad statistics can be explained with dyadic homophylic interactions

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

scientific article

Extracting information from cDNA arrays

scientific article

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

scientific article published on 07 December 2020

GE-23ENHANCER HIJACKING ACTIVATES GFI1 FAMILY ONCOGENES IN MEDULLOBLASTOMA.

scientific article published in November 2014

Genetic code expansion for multiprotein complex engineering.

scientific article

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

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

scientific article published on 29 March 2019

Genomic data sharing in Europe is stumbling-Could a code of conduct prevent its fall?

scientific article published on 18 February 2020

Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy.

scientific article

Germline Elongator mutations in Sonic Hedgehog medulloblastoma

scientific article published on 01 April 2020

Germline GPR161 Mutations Predispose to Pediatric Medulloblastoma

scientific article published on 14 October 2019

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

article

Global identification and characterization of transcriptionally active regions in the rice genome

scientific article

Heterogeneity of ERG expression in prostate cancer: a large section mapping study of entire prostatectomy specimens from 125 patients.

scientific article

High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution

scientific article

High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations

High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays

scientific article

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

scientific article published on 15 July 2019

ICGC PedBrain - dissecting the genomic complexity underlying medulloblastoma using whole-genome sequencing.

scientific article

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

scientific article published in June 2007

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

scientific article published on 6 December 2012

Information Geometric Duality of <i>ϕ</i>-Deformed Exponential Families

scientific article published on 24 January 2019

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

scientific article

International network of cancer genome projects

scientific article

MB-25REGULATION OF MEDULLOBLASTOMA FORMATION BY Gfi1 AND Gfi1b.

scientific article published on 21 April 2015

MBCL-44. THE MOLECULAR AND CLINICAL LANDSCAPE OF INFANT MEDULLOBLASTOMA (iMB): RESULTS AND MOLECULAR ANALYSIS FROM A PROSPECTIVE, MULTICENTER PHASE II TRIAL (SJYC07)

MSB: a mean-shift-based approach for the analysis of structural variation in the genome

scientific article published on 26 November 2008

Mapping copy number variation by population-scale genome sequencing

scientific article

Maximum Entropy Principle in Statistical Inference: Case for Non-Shannonian Entropies

scientific article published on 01 March 2019

Missense variants in NOX1 and p22phox in a case of very-early-onset inflammatory bowel disease are functionally linked to NOD2

scientific article published on 01 February 2019

Mitochondrial mutations drive prostate cancer aggression

scientific article published on 22 September 2017

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories

scientific article published on 01 December 2018

Multi-platform discovery of haplotype-resolved structural variation in human genomes

scientific article published on 16 April 2019

No correlation between NF1 mutation position and risk of optic pathway glioma in 77 unrelated NF1 patients

scientific article published on 11 March 2016

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

scientific article

PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia

scientific article published on 01 December 2018

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

scientific article (publication date: 23 February 2009)

PM-09REGULATION OF MEDULLOBLASTOMA FORMATION BY Gfi1 AND Gfi1B

scientific article published in November 2014

Paired-end mapping reveals extensive structural variation in the human genome

scientific article

Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation

scientific article

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking.

scientific article

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

scientific article published on 05 February 2020

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

scientific article published on 11 April 2022

Phenotypic impact of genomic structural variation: insights from and for human disease ⬇️

scientific article published on February 1, 2013

Point Divergence Gain and Multidimensional Data Sequences Analysis

scientific article published on 03 February 2018

Predicting collapse of adaptive networked systems without knowing the network

scientific article published on 27 January 2020

Prediction of effective genome size in metagenomic samples

scientific article published on January 2007

Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes

scientific article published on 12 February 2020

Quantifying environmental adaptation of metabolic pathways in metagenomics

scientific article

Recurrent inversion toggling and great ape genome evolution

scientific article published on 15 June 2020

Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing

scientific article

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

scientific article

Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions

scientific article

Risk-adapted therapy for young children with medulloblastoma (SJYC07): therapeutic and molecular outcomes from a multicentre, phase 2 trial

scientific article published on 16 May 2018

SHOT: a web server for the construction of genome phylogenies

scientific article published on 01 March 2002

STRUCTURAL VARIANTS SHUFFLE CHROMATIN TO ACTIVATE GFI1 FAMILY ONCOGENES IN MEDULLOBLASTOMA.

scientific article published in July 2014

Similar gene expression profiles do not imply similar tissue functions

scientific article

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing

scientific article published on 23 December 2019

Somatic structural variant formation is guided by and influences genome architecture

scientific article published on 17 February 2022

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

scientific article

Structured RNAs in the ENCODE selected regions of the human genome

scientific article

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

scientific article

Systematic Identification of Determinants for Single Strand Annealing Mediated Deletion Formation in Saccharomyces cerevisiae

scientific article

Systematic association of genes to phenotypes by genome and literature mining

scientific article

Systematic discovery of analogous enzymes in thiamin biosynthesis

scientific article

Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity

scientific article

Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome

scholarly article

Systems approaches identify the consequences of monosomy in somatic human cells

scientific article published on 22 September 2021

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

scientific article published on 30 May 2016

TMPRSS2-ERG fusions are strongly linked to young patient age in low-grade prostate cancer

scientific article published on 9 July 2014

Targeted Perturb-seq enables genome-scale genetic screens in single cells

scientific article published on 01 June 2020

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

scientific article

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.

scientific article published in January 2004

The NSL complex maintains nuclear architecture stability via lamin A/C acetylation

scientific article published on 01 October 2019

The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis

scientific article

The current excitement about copy-number variation: how it relates to gene duplications and protein families

scientific article

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies

scholarly article

The landscape of genomic alterations across childhood cancers

scientific article published on 28 February 2018

The molecular landscape of ETMR at diagnosis and relapse

scientific article published on 04 December 2019

The whole-genome landscape of medulloblastoma subtypes

scientific article published in July 2017

Transgene methylation in mice reflects copy number but not expression level.

scientific article published in March 2004

Tsallis thermostatics as a statistical physics of random chains. ⬇️

scientific article published on 3 February 2017

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism

article

Variation in transcription factor binding among humans

scientific article

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