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Jeongbin Park
Charité
25Publications
11H-index
1,298Citations
Publications 24
Newest
#1Stephan M. Tirier (DKFZ: German Cancer Research Center)
#2Jeongbin Park (Charité)H-Index: 11
Last.Christian ConradH-Index: 18
view all 20 authors...
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....
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#1Jeongbin Park (Charité)H-Index: 11
#2Wonyl Choi (BU: Boston University)
Last.Naveed Ishaque (Charité)H-Index: 9
view all 12 authors...
Multiplexed fluorescence in situ hybridization techniques have enabled cell class or type identification by mRNA quantification in situ. However, inaccurate cell segmentation can result in incomplete cell-type and tissue characterization. Here, we present a robust segmentation-free computational framework, applicable to a variety of in situ transcriptomics platforms, called Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation (SSAM). SSAM assumes that spatial distrib...
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#1Teresa G Krieger (Charité)
#2Stephan M. Tirier (DKFZ: German Cancer Research Center)
Last.Christian Conrad (Charité)H-Index: 1
view all 8 authors...
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...
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#1Manuel Rodríguez-Paredes (DKFZ: German Cancer Research Center)H-Index: 11
#2Felix Bormann (DKFZ: German Cancer Research Center)H-Index: 4
Last.Frank LykoH-Index: 53
view all 20 authors...
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...
11 CitationsSource
#1Gue-Ho Hwang (Hanyang University)H-Index: 3
#2Jeongbin Park (Charité)H-Index: 11
Last.Sangsu Bae (Hanyang University)H-Index: 15
view all 10 authors...
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...
6 CitationsSource
#1Rabea Wagener (CAU: University of Kiel)H-Index: 8
#2Cristina López (CAU: University of Kiel)H-Index: 17
Last.Reiner Siebert (CAU: University of Kiel)H-Index: 86
view all 34 authors...
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...
3 CitationsSource
#1Jeongbin Park (Charité)H-Index: 11
#2Liam Childs (DKFZ: German Cancer Research Center)H-Index: 1
Last.Roland Eils (Charité)H-Index: 5
view all 4 authors...
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...
Source
#1Gue-Ho Hwang (Hanyang University)H-Index: 3
#2Jeongbin Park (DKFZ: German Cancer Research Center)H-Index: 11
Last.Sangsu Bae (Hanyang University)H-Index: 15
view all 9 authors...
Background: 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 facilitat...
3 CitationsSource
#1Stephan M. Tirier (DKFZ: German Cancer Research Center)
#2Jeongbin Park (DKFZ: German Cancer Research Center)H-Index: 11
Last.Christian Conrad (DKFZ: German Cancer Research Center)H-Index: 7
view all 19 authors...
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...
Source
#1Daniel B. Lipka (DKFZ: German Cancer Research Center)H-Index: 17
#2Tania Witte (DKFZ: German Cancer Research Center)H-Index: 7
Last.Christoph Plass (DKFZ: German Cancer Research Center)H-Index: 77
view all 40 authors...
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 ...
12 CitationsSource
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