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  1. Article: PyOncoPrint: a python package for plotting OncoPrints.

    Park, Jeongbin / Paramasivam, Nagarajan

    Genomics & informatics

    2023  Volume 21, Issue 1, Page(s) e14

    Abstract: OncoPrint, the plot to visualize an overview of genetic variants in sequencing data, has been widely used in the field of cancer genomics. However, still, there have been no Python libraries capable to generate OncoPrint yet, a big hassle to plot ... ...

    Abstract OncoPrint, the plot to visualize an overview of genetic variants in sequencing data, has been widely used in the field of cancer genomics. However, still, there have been no Python libraries capable to generate OncoPrint yet, a big hassle to plot OncoPrints within Python-based genetic variants analysis pipelines. This paper introduces a new Python package PyOncoPrint, which can be easily used to plot OncoPrints in Python. The package is based on the existing widely used scientific plotting library Matplotlib, the resulting plots are easy to be adjusted for various needs.
    Language English
    Publishing date 2023-03-31
    Publishing country Korea (South)
    Document type Journal Article
    ZDB-ID 2802682-2
    ISSN 2234-0742 ; 1598-866X
    ISSN (online) 2234-0742
    ISSN 1598-866X
    DOI 10.5808/gi.22079
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: SpatialSPM: statistical parametric mapping for the comparison of gene expression pattern images in multiple spatial transcriptomic datasets.

    Ohn, Jungyoon / Seo, Mi-Kyoung / Park, Jeongbin / Lee, Daeseung / Choi, Hongyoon

    Nucleic acids research

    2024  

    Abstract: Spatial transcriptomic (ST) techniques help us understand the gene expression levels in specific parts of tissues and organs, providing insights into their biological functions. Even though ST dataset provides information on the gene expression and its ... ...

    Abstract Spatial transcriptomic (ST) techniques help us understand the gene expression levels in specific parts of tissues and organs, providing insights into their biological functions. Even though ST dataset provides information on the gene expression and its location for each sample, it is challenging to compare spatial gene expression patterns across tissue samples with different shapes and coordinates. Here, we propose a method, SpatialSPM, that reconstructs ST data into multi-dimensional image matrices to ensure comparability across different samples through spatial registration process. We demonstrated the applicability of this method by kidney and mouse olfactory bulb datasets as well as mouse brain ST datasets to investigate and directly compare gene expression in a specific anatomical region of interest, pixel by pixel, across various biological statuses. Beyond traditional analyses, SpatialSPM is capable of generating statistical parametric maps, including T-scores and Pearson correlation coefficients. This feature enables the identification of specific regions exhibiting differentially expressed genes across tissue samples, enhancing the depth and specificity of ST studies. Our approach provides an efficient way to analyze ST datasets and may offer detailed insights into various biological conditions.
    Language English
    Publishing date 2024-04-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkae293
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Low-Molecular Collagen Peptide Supplementation and Body Fat Mass in Adults Aged ≥ 50 Years: A Randomized, Double-Blind, Placebo-Controlled Trial.

    Park, Jeongbin / Kim, Minji / Shin, Hyeri / Ahn, Hyejin / Park, Yoo Kyoung

    Clinical nutrition research

    2023  Volume 12, Issue 4, Page(s) 245–256

    Abstract: A randomized, double-blind, placebo-controlled trial was conducted to confirm whether collagen peptide supplementation for 12 week has a beneficial effect on body fat control in older adults at a daily physical activity level. Participants were assigned ... ...

    Abstract A randomized, double-blind, placebo-controlled trial was conducted to confirm whether collagen peptide supplementation for 12 week has a beneficial effect on body fat control in older adults at a daily physical activity level. Participants were assigned to either the collagen group (15 g/day of collagen peptide) or the placebo group (placebo drink). Body composition was measured by bioelectrical impedance analysis (BIA) and dual-energy X-ray absorptiometry (DEXA). In total, 74 participants (collagen group, n = 37; placebo group, n = 37) were included in the final analysis. The collagen group showed a significant reduction in total body fat mass compared with the placebo group, as evidenced by both BIA (p = 0.021) and DEXA (p = 0.041) measurements. Body fat mass and percent body fat of the whole body and trunk reduced at 12 weeks compared with baseline only in the collagen group (whole body: body fat mass, p = 0.002; percent body fat, p = 0.002; trunk: body fat mass, p = 0.001; percent body fat, p = 0.000). Total fat mass change (%) (collagen group, -0.49 ± 3.39; placebo group, 2.23 ± 4.20) showed a significant difference between the two groups (p = 0.041). Physical activity, dietary intake, and biochemical parameters showed no significant difference between the groups. The results confirmed that collagen peptide supplementation had a beneficial effect on body fat reduction in older adults aged ≥ 50 years with daily physical activity level. Thus, collagen peptide supplementation has a positive effect on age-related changes.
    Language English
    Publishing date 2023-10-31
    Publishing country Korea (South)
    Document type Journal Article
    ZDB-ID 2684656-1
    ISSN 2287-3740 ; 2287-3732
    ISSN (online) 2287-3740
    ISSN 2287-3732
    DOI 10.7762/cnr.2023.12.4.245
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online ; Thesis: Segmentation-free inference of cell types from in situ transcriptomics data

    Park, Jeongbin [Verfasser] / Eils, Roland [Akademischer Betreuer]

    2020  

    Author's details Jeongbin Park ; Betreuer: Roland Eils
    Keywords Naturwissenschaften ; Science
    Subject code sg500
    Language English
    Publisher Universitätsbibliothek Heidelberg
    Publishing place Heidelberg
    Document type Book ; Online ; Thesis
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  5. Article ; Online: Development of finely tuned liposome nanoplatform for macrophage depletion.

    Choi, Tae Hyeon / Yoo, Ran Ji / Park, Ji Yong / Kim, Ji Yoon / Ann, Young Chan / Park, Jeongbin / Kim, Jin Sil / Kim, Kyuwan / Shin, Yu Jin / Lee, Yong Jin / Lee, Kyo Chul / Park, Jisu / Chung, Hyewon / Seok, Seung Hyeok / Im, Hyung-Jun / Lee, Yun-Sang

    Journal of nanobiotechnology

    2024  Volume 22, Issue 1, Page(s) 83

    Abstract: Background: Immunotherapy with clodronate-encapsulated liposomes, which induce macrophage depletion, has been studied extensively. However, previously reported liposomal formulation-based drugs (Clodrosome: Results: We developed four types of click ... ...

    Abstract Background: Immunotherapy with clodronate-encapsulated liposomes, which induce macrophage depletion, has been studied extensively. However, previously reported liposomal formulation-based drugs (Clodrosome
    Results: We developed four types of click chemistry-based liposome nanoplatforms that were uniformly sized and encapsulated with clodronate, for effective macrophage depletion, followed by conjugation with Man-N
    Conclusion: The newly-developed liposome nanoplatform, with finely tuned size control, high in vivo stability, and excellent ex vivo M2 macrophage targeting and depletion effects, is a promising macrophage-depleting agent.
    MeSH term(s) Male ; Humans ; Liposomes/pharmacology ; Clodronic Acid/pharmacology ; Tissue Distribution ; Macrophages
    Chemical Substances Liposomes ; Clodronic Acid (0813BZ6866)
    Language English
    Publishing date 2024-02-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2100022-0
    ISSN 1477-3155 ; 1477-3155
    ISSN (online) 1477-3155
    ISSN 1477-3155
    DOI 10.1186/s12951-024-02325-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Spatial Transcriptomics-Based Identification of Molecular Markers for Nanomedicine Distribution in Tumor Tissue.

    Park, Jeongbin / Choi, Jinyeong / Lee, Jae Eun / Choi, Hongyoon / Im, Hyung-Jun

    Small methods

    2022  Volume 6, Issue 11, Page(s) e2201091

    Abstract: The intratumoral accumulation of nanomedicine has been considered a passive process, referred to as the enhanced permeability and retention effect. Recent studies have suggested that the tumor uptake of nanomedicines follows an energy-dependent pathway ... ...

    Abstract The intratumoral accumulation of nanomedicine has been considered a passive process, referred to as the enhanced permeability and retention effect. Recent studies have suggested that the tumor uptake of nanomedicines follows an energy-dependent pathway rather than being a passive process. Herein, to explore the factor candidates that are associated with nanomedicine tumor uptake, a molecular marker identification platform is developed by integrating microscopic fluorescence images of a nanomedicine distribution with spatial transcriptomics information. When this approach is applied to PEGylated liposomes, molecular markers related to hypoxia, glycolysis, and apoptosis can be identified as being related to the intratumoral distribution of the nanomedicine. It is expected that the method can be applied to explain the distribution of a wide range of nanomedicines and that the data obtained from this analysis can enhance the precise utilization of nanomedicines.
    MeSH term(s) Humans ; Nanomedicine/methods ; Transcriptome/genetics ; Liposomes ; Neoplasms/diagnosis ; Permeability
    Chemical Substances Liposomes
    Language English
    Publishing date 2022-09-30
    Publishing country Germany
    Document type Journal Article
    ISSN 2366-9608
    ISSN (online) 2366-9608
    DOI 10.1002/smtd.202201091
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  7. Article ; Online: Development of Spleen Targeting H

    Oh, Chiwoo / Lee, Wooseung / Park, Jeongbin / Choi, Jinyeong / Lee, Somin / Li, Shengjun / Jung, Han Na / Lee, Jeong-Seob / Hwang, Jee-Eun / Park, Jiwoo / Kim, MinKyu / Baek, Seungki / Im, Hyung-Jun

    ACS nano

    2023  Volume 17, Issue 5, Page(s) 4327–4345

    Abstract: Nanoparticles are primarily taken up by immune cells after systemic administration. Thus, they are considered an ideal drug delivery vehicle for immunomodulation. Because the spleen is the largest lymphatic organ and regulates the systemic immune system, ...

    Abstract Nanoparticles are primarily taken up by immune cells after systemic administration. Thus, they are considered an ideal drug delivery vehicle for immunomodulation. Because the spleen is the largest lymphatic organ and regulates the systemic immune system, there have been studies to develop spleen targeting nanoparticles for immunomodulation of cancer and immunological disorders. Inflammatory bowel disease (IBD) includes disorders involving chronic inflammation in the gastrointestinal tract and is considered incurable despite a variety of treatment options. Hydrogen sulfide (H
    MeSH term(s) Humans ; Liposomes/adverse effects ; Spleen ; Inflammatory Bowel Diseases/drug therapy ; Colitis/drug therapy ; Immunomodulation
    Chemical Substances Liposomes
    Language English
    Publishing date 2023-02-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.2c08898
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: CFD-based design optimization of ducted hydrokinetic turbines.

    Park, Jeongbin / Knight, Bradford G / Liao, Yingqian / Mangano, Marco / Pacini, Bernardo / Maki, Kevin J / Martins, Joaquim R R A / Sun, Jing / Pan, Yulin

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 17968

    Abstract: Hydrokinetic turbines extract kinetic energy from moving water to generate renewable electricity, thus contributing to sustainable energy production and reducing reliance on fossil fuels. It has been hypothesized that a duct can accelerate and condition ... ...

    Abstract Hydrokinetic turbines extract kinetic energy from moving water to generate renewable electricity, thus contributing to sustainable energy production and reducing reliance on fossil fuels. It has been hypothesized that a duct can accelerate and condition the fluid flow passing the turbine blades, improving the overall energy extraction efficiency. However, no substantial evidence has been provided so far for hydrokinetic turbines. To investigate this problem, we perform a CFD-based optimization study with a blade-resolved Reynolds-averaged Navier-Stokes (RANS) solver to explore the design of a ducted hydrokinetic turbine that maximizes the efficiency of energy extraction. A gradient-based optimization approach is utilized to effectively deal with the high-dimensional design space of the blade and duct geometry, with gradients being calculated through the adjoint method. The final design is re-evaluated through higher-fidelity unsteady RANS (URANS) simulations. Our optimized ducted turbine achieves an efficiency of about 54% over a range of operating conditions, higher than the typical 46% efficiency of unducted turbines.
    Language English
    Publishing date 2023-10-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-43724-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1.

    Park, Jeongbin / Bae, Sangsu

    Bioinformatics (Oxford, England)

    2017  Volume 34, Issue 6, Page(s) 1077–1079

    Abstract: Summary: Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs ( ...

    Abstract Summary: Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5'-TTTN-3' at the 5' ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time.
    Availability and implementation: Free access at http://www.rgenome.net/cpf1-database/.
    Contact: sangsubae@hanyang.ac.kr.
    MeSH term(s) CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Endonucleases/metabolism ; Gene Editing ; Gene Knockout Techniques ; Genome ; Genomic Library ; Internet ; RNA, Guide, CRISPR-Cas Systems/genetics
    Chemical Substances RNA, Guide, CRISPR-Cas Systems ; Endonucleases (EC 3.1.-)
    Language English
    Publishing date 2017-11-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btx695
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    In stock of ZB MED Cologne/Königswinter

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  10. Article ; Online: Discovery of potential imaging and therapeutic targets for severe inflammation in COVID-19 patients

    Hyunjong Lee / Jeongbin Park / Hyung-Jun Im / Kwon Joong Na / Hongyoon Choi

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 9

    Abstract: Abstract The Coronavirus disease 2019 (COVID-19) has been spreading worldwide with rapidly increased number of deaths. Hyperinflammation mediated by dysregulated monocyte/macrophage function is considered to be the key factor that triggers severe illness ...

    Abstract Abstract The Coronavirus disease 2019 (COVID-19) has been spreading worldwide with rapidly increased number of deaths. Hyperinflammation mediated by dysregulated monocyte/macrophage function is considered to be the key factor that triggers severe illness in COVID-19. However, no specific targeting molecule has been identified for detecting or treating hyperinflammation related to dysregulated macrophages in severe COVID-19. In this study, previously published single-cell RNA-sequencing data of bronchoalveolar lavage fluid cells from thirteen COVID-19 patients were analyzed with publicly available databases for surface and imageable targets. Immune cell composition according to the severity was estimated with the clustering of gene expression data. Expression levels of imaging target molecules for inflammation were evaluated in macrophage clusters from single-cell RNA-sequencing data. In addition, candidate targetable molecules enriched in severe COVID-19 associated with hyperinflammation were filtered. We found that expression of SLC2A3, which can be imaged by [18F]fluorodeoxyglucose, was higher in macrophages from severe COVID-19 patients. Furthermore, by integrating the surface target and drug-target binding databases with RNA-sequencing data of severe COVID-19, we identified candidate surface and druggable targets including CCR1 and FPR1 for drug delivery as well as molecular imaging. Our results provide a resource in the development of specific imaging and therapy for COVID-19-related hyperinflammation.
    Keywords Medicine ; R ; Science ; Q
    Subject code 616 ; 610
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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