Jeongbin Park
Publications 20
Published on Dec 1, 2019in Scientific Reports4.01
Stephan M. Tirier (DKFZ: German Cancer Research Center), Jeongbin Park8
Estimated H-index: 8
+ 17 AuthorsBjörn Eismann (DKFZ: German Cancer Research Center)
Patient-derived 3D cell culture systems are currently advancing cancer research since they potentiate the molecular analysis of tissue-like properties and drug response under well-defined conditions. However, our understanding of the relationship between the heterogeneity of morphological phenotypes and the underlying transcriptome is still limited. To address this issue, we here introduce “pheno-seq” to directly link visual features of 3D cell culture systems with profiling their transcriptome....
Published on May 7, 2019in bioRxiv
Teresa G Krieger (Charité), Stephan Marius Tirier (DKFZ: German Cancer Research Center)+ 5 AuthorsChristian Conrad (Charité)
Glioblastoma multiforme (GBM) are devastating neoplasms with high invasive capacity. GBM has been difficult to study in vitro. Therapeutic progress is also limited by cellular heterogeneity within and between tumors. To address these challenges, we present an experimental model using human cerebral organoids as a scaffold for patient-derived glioblastoma cell invasion. By tissue clearing and confocal microscopy, we show that tumor cells within organoids extend a network of long microtubes, recap...
Published on Dec 1, 2018in Nature Communications11.88
Manuel Rodríguez-Paredes9
Estimated H-index: 9
(DKFZ: German Cancer Research Center),
Felix Bormann3
Estimated H-index: 3
(DKFZ: German Cancer Research Center)
+ 17 AuthorsHorst Wenck28
Estimated H-index: 28
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer and usually progresses from a UV-induced precancerous lesion termed actinic keratosis (AK). Despite various efforts to characterize these lesions molecularly, the etiology of AK and its progression to cSCC remain partially understood. Here, we use Infinium MethylationEPIC BeadChips to interrogate the DNA methylation status in healthy, AK and cSCC epidermis samples. Importantly, we show that AK methylation patterns alr...
Published on Dec 1, 2018in BMC Bioinformatics2.51
Gue-Ho Hwang2
Estimated H-index: 2
(Hanyang University),
Jeongbin Park8
Estimated H-index: 8
+ 7 AuthorsSangsu Bae13
Estimated H-index: 13
(Hanyang University)
As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of...
Published on Nov 22, 2018in Blood16.56
Rabea Wagener7
Estimated H-index: 7
(University of Ulm),
Cristina López16
Estimated H-index: 16
(CAU: University of Kiel)
+ 31 AuthorsHolger Thiele71
Estimated H-index: 71
(University of Cologne)
The "WHO Classification of Tumours of Haematopoietic and Lymphoid Tissue" notes instances of Burkitt lymphoma/leukemia (BL) with IG- MYC -rearrangement displaying a B-cell precursor immunophenotype (termed herein "preBLL"). To characterize the molecular pathogenesis of preBLL we investigated 13 preBLL cases (including one cell line) of which 12 were analyzable using genome, exome, and targeted sequencing, imbalance mapping, and DNA-methylation profiling. In five patients with reads across the IG...
Published on Aug 27, 2018in bioRxiv
Jeongbin Park (Charité), Liam H Childs (DKFZ: German Cancer Research Center)+ 1 AuthorsRoland Eils3
Estimated H-index: 3
Background: An increasing number of bioinformatics tools are developed in JavaScript to provide an interactive visual interface to users. However, there are no tools yet that enable fast client-side analysis of large, high-throughput sequencing file formats, such as BAM and VCF files. Results: We present HTSlib-js, an asm.js-based JavaScript wrapper for HTSlib, the de facto standard for processing BAM and VCF files. HTSlib-js exploits recent technological advances in web browser engines that dra...
Published on May 1, 2018in bioRxiv
Stephan Marius Tirier (DKFZ: German Cancer Research Center), Jeongbin Park8
Estimated H-index: 8
(DKFZ: German Cancer Research Center)
+ 16 AuthorsMarta Gut36
Estimated H-index: 36
3D-culture systems have advanced cancer modeling by reflecting physiological characteristics of in-vivo tissues, but our understanding of functional intratumor heterogeneity including visual phenotypes and underlying gene expression is still limited. Transcriptional heterogeneity can be dissected by single-cell RNA-sequencing, but these technologies suffer from low RNA-input and fail to directly correlate gene expression with contextual cellular phenotypes. Here we present "pheno-seq" for integr...
Published on Dec 1, 2017in Nature Communications11.88
Daniel B. Lipka15
Estimated H-index: 15
(DKFZ: German Cancer Research Center),
Tania Witte7
Estimated H-index: 7
(DKFZ: German Cancer Research Center)
+ 37 AuthorsJeongbin Park8
Estimated H-index: 8
(DKFZ: German Cancer Research Center)
Juvenile myelomonocytic leukemia (JMML) is an aggressive myeloproliferative disorder of early childhood characterized by mutations activating RAS signaling. Established clinical and genetic markers fail to fully recapitulate the clinical and biological heterogeneity of this disease. Here we report DNA methylome analysis and mutation profiling of 167 JMML samples. We identify three JMML subgroups with unique molecular and clinical characteristics. The high methylation group (HM) is characterized ...