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Article ; Online: A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response.

Park, Sung-Joon / Nakai, Kenta

NAR genomics and bioinformatics

2024 Volume 6, Issue 2, Page(s) lqae050

Abstract: Delineating the intricate interplay between promoter-proximal and -distal regulators is crucial for understanding the function of transcriptional mediator complexes implicated in the regulation of gene expression. The present study aimed to develop a ... ...

Abstract	Delineating the intricate interplay between promoter-proximal and -distal regulators is crucial for understanding the function of transcriptional mediator complexes implicated in the regulation of gene expression. The present study aimed to develop a computational method for accurately modeling the spatial proximal and distal regulatory interactions. Our method combined regression-based models to identify key regulators through gene expression prediction and a graph-embedding approach to detect coregulated genes. This approach enabled a detailed investigation of the gene regulatory mechanisms for germinal center B cells, accompanied by dramatic rearrangements of the genome structure. We found that while the promoter-proximal regulatory elements were the principal regulators of gene expression, the distal regulators fine-tuned transcription. Moreover, our approach unveiled the presence of modular regulators, such as cofactors and proximal/distal transcription factors, which were co-expressed with their target genes. Some of these modules exhibited abnormal expression patterns in lymphoma. These findings suggest that the dysregulation of interactions between transcriptional and architectural factors is associated with chromatin reorganization failure, which may increase the risk of malignancy. Therefore, our computational approach helps decipher the transcriptional
Language	English
Publishing date	2024-05-06
Publishing country	England
Document type	Journal Article
ISSN	2631-9268
ISSN (online)	2631-9268
DOI	10.1093/nargab/lqae050
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Article ; Online: Dual Representation Learning for Predicting Drug-side Effect Frequency using Protein Target Information.

Park, Sungjoon / Lee, Sangseon / Pak, Minwoo / Kim, Sun

IEEE journal of biomedical and health informatics

2024 Volume PP

Abstract: Knowledge of unintended effects of drugs is critical in assessing the risk of treatment and in drug repurposing. Although numerous existing studies predict drug-side effect presence, only four of them predict the frequency of the side effects. ... ...

Abstract	Knowledge of unintended effects of drugs is critical in assessing the risk of treatment and in drug repurposing. Although numerous existing studies predict drug-side effect presence, only four of them predict the frequency of the side effects. Unfortunately, current prediction methods (1) do not utilize drug targets, (2) do not predict well for unseen drugs, and (3) do not use multiple heterogeneous drug features. We propose a novel deep learning-based drug-side effect frequency prediction model. Our model utilized heterogeneous features such as target protein information as well as molecular graph, fingerprints, and chemical similarity to create drug embeddings simultaneously. Furthermore, the model represents drugs and side effects into a common vector space, learning the dual representation vectors of drugs and side effects, respectively. We also extended the predictive power of our model to compensate for the drugs without clear target proteins using the Adaboost method. We achieved state-of-the-art performance over the existing methods in predicting side effect frequencies, especially for unseen drugs. Ablation studies show that our model effectively combines and utilizes heterogeneous features of drugs. Moreover, we observed that, when the target information given, drugs with explicit targets resulted in better prediction than the drugs without explicit targets. The implementation is available at https://github.com/eskendrian/sider.
Language	English
Publishing date	2024-01-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2695320-1
ISSN	2168-2208 ; 2168-2194
ISSN (online)	2168-2208
ISSN	2168-2194
DOI	10.1109/JBHI.2024.3350083
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Zs.A 5483: Show issues

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Article ; Online: Reply: Ischemia With Nonobstructive Coronary Artery Disease.

Hwang, Doyeon / Park, Sungjoon / Koo, Bon-Kwon

JACC. Asia

2023 Volume 3, Issue 4, Page(s) 687

Language	English
Publishing date	2023-07-25
Publishing country	United States
Document type	Journal Article
ISSN	2772-3747
ISSN (online)	2772-3747
DOI	10.1016/j.jacasi.2023.06.003
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Article ; Online: Transverse Magnetization in Spin-Orbit Coupled Antiferromagnets.

Oh, Taekoo / Park, Sungjoon / Yang, Bohm-Jung

Physical review letters

2023 Volume 130, Issue 26, Page(s) 266703

Abstract: Some antiferromagnets under a magnetic field develop magnetization perpendicular to the field as well as more conventional ones parallel to the field. So far, the transverse magnetization (TM) has been attributed to either the spin canting effect or the ... ...

Abstract	Some antiferromagnets under a magnetic field develop magnetization perpendicular to the field as well as more conventional ones parallel to the field. So far, the transverse magnetization (TM) has been attributed to either the spin canting effect or the presence of cluster magnetic multipolar ordering. However, a general theory of TM based on microscopic understanding is still missing. Here, we construct a general microscopic theory of TM in antiferromagnets with cluster magnetic multipolar ordering by considering classical spin Hamiltonians with spin anisotropy that arises from the spin-orbit coupling. First, from general symmetry analysis, we show that TM can appear only when all crystalline symmetries are broken other than the antiunitary mirror, antiunitary twofold rotation, and inversion symmetries. Moreover, by analyzing spin Hamiltonians, we show that TM always appears when the degenerate ground state manifold of the spin Hamiltonian is discrete, as long as it is not prohibited by symmetry. On the other hand, when the degenerate ground state manifold is continuous, TM generally does not appear except when the magnetic field direction and the spin configuration satisfy specific geometric conditions under single-ion anisotropy. Finally, we show that TM can induce the anomalous planar Hall effect, a unique transport phenomenon that can be used to probe multipolar antiferromagnetic structures. We believe that our theory provides a useful guideline for understanding the anomalous magnetic responses of the antiferromagnets with complex magnetic structures.
MeSH term(s)	Anisotropy ; Magnetic Fields
Language	English
Publishing date	2023-01-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.130.266703
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Article ; Online: OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data.

Park, Sung-Joon / Nakai, Kenta

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 18, Page(s) 3021–3022

Abstract: Summary: Microorganisms infect and contaminate eukaryotic cells during the course of biological experiments. Because microbes influence host cell biology and may therefore lead to erroneous conclusions, a computational platform that facilitates ... ...

Abstract	Summary: Microorganisms infect and contaminate eukaryotic cells during the course of biological experiments. Because microbes influence host cell biology and may therefore lead to erroneous conclusions, a computational platform that facilitates decontamination is indispensable. Recent studies show that next-generation sequencing (NGS) data can be used to identify the presence of exogenous microbial species. Previously, we proposed an algorithm to improve detection of microbes in NGS data. Here, we developed an online application, OpenContami, which allows researchers easy access to the algorithm via interactive web-based interfaces. We have designed the application by incorporating a database comprising analytical results from a large-scale public dataset and data uploaded by users. The database serves as a reference for assessing user data and provides a list of genera detected from negative blank controls as a 'blacklist', which is useful for studying human infectious diseases. OpenContami offers a comprehensive overview of exogenous species in NGS datasets; as such, it will increase our understanding of the impact of microbial contamination on biological and pathological traits. Availability and implementation: OpenContami is freely available at: https://openlooper.hgc.jp/opencontami/. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Humans ; Software ; Algorithms ; Databases, Factual ; High-Throughput Nucleotide Sequencing ; Internet ; Computational Biology
Language	English
Publishing date	2021-02-08
Publishing country	England
Document type	Review ; 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/btab101
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Zs.A 2374: Show issues

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Article ; Online: Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress.

Zhao, Xiaoyu / Singhal, Akshat / Park, Sungjoon / Kong, JungHo / Bachelder, Robin / Ideker, Trey

Cancer discovery

2024 Volume 14, Issue 3, Page(s) 508–523

Abstract: Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways that are incompletely understood. Here, we develop an ... ...

Abstract	Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways that are incompletely understood. Here, we develop an ensemble of predictive models that elucidate how cancer mutations impact the response to common RS-inducing (RSi) agents. The models implement recent advances in deep learning to facilitate multidrug prediction and mechanistic interpretation. Initial studies in tumor cells identify 41 molecular assemblies that integrate alterations in hundreds of genes for accurate drug response prediction. These cover roles in transcription, repair, cell-cycle checkpoints, and growth signaling, of which 30 are shown by loss-of-function genetic screens to regulate drug sensitivity or replication restart. The model translates to cisplatin-treated cervical cancer patients, highlighting an RTK-JAK-STAT assembly governing resistance. This study defines a compendium of mechanisms by which mutations affect therapeutic responses, with implications for precision medicine. Significance: Zhao and colleagues use recent advances in machine learning to study the effects of tumor mutations on the response to common therapeutics that cause RS. The resulting predictive models integrate numerous genetic alterations distributed across a constellation of molecular assemblies, facilitating a quantitative and interpretable assessment of drug response. This article is featured in Selected Articles from This Issue, p. 384.
MeSH term(s)	Humans ; Female ; Mutation ; Uterine Cervical Neoplasms ; Signal Transduction ; Cisplatin/pharmacology ; Cisplatin/therapeutic use ; Machine Learning
Chemical Substances	Cisplatin (Q20Q21Q62J)
Language	English
Publishing date	2024-01-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2625242-9
ISSN	2159-8290 ; 2159-8274
ISSN (online)	2159-8290
ISSN	2159-8274
DOI	10.1158/2159-8290.CD-23-0641
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Zs.A 6916: Show issues

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Article ; Online: HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.

Zhang, Weihang / Cui, Yang / Liu, Bowen / Loza, Martin / Park, Sung-Joon / Nakai, Kenta

Briefings in bioinformatics

2024 Volume 25, Issue 3

Abstract: Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality cell labels ... ...

Abstract	Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality cell labels are still lacking in single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) data, because of extreme sparsity and inconsistent chromatin accessibility between datasets. Here, we present a novel automated cell annotation method that transfers cell type information from a well-labeled scRNA-seq reference to an unlabeled scATAC-seq target, via a parallel graph neural network, in a semi-supervised manner. Unlike existing methods that utilize only gene expression or gene activity features, HyGAnno leverages genome-wide accessibility peak features to facilitate the training process. In addition, HyGAnno reconstructs a reference-target cell graph to detect cells with low prediction reliability, according to their specific graph connectivity patterns. HyGAnno was assessed across various datasets, showcasing its strengths in precise cell annotation, generating interpretable cell embeddings, robustness to noisy reference data and adaptability to tumor tissues.
MeSH term(s)	Reproducibility of Results ; Chromatin ; Neural Networks, Computer
Chemical Substances	Chromatin
Language	English
Publishing date	2024-04-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbae152
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Zs.A 6262: Show issues

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Article ; Online: SUPERA stent placement for salvaging early recurrent arteriovenous graft thrombosis after percutaneous transluminal angioplasty: A single-center study.

Lee, Hyoung Nam / Park, Sung-Joon / Cho, Youngjong / Lee, Sangjoon

The journal of vascular access

2023 , Page(s) 11297298231160196

Abstract: Background: The aim of this study was to evaluate the patency of the helical interwoven SUPERA stent for salvaging prosthetic arteriovenous (AV) grafts with rapidly recurrent thrombotic occlusion developed within a short time period after successful ... ...

Abstract	Background: The aim of this study was to evaluate the patency of the helical interwoven SUPERA stent for salvaging prosthetic arteriovenous (AV) grafts with rapidly recurrent thrombotic occlusion developed within a short time period after successful percutaneous transluminal angioplasty. Methods: From December 2019 to September 2021, the data of 20 patients with AV graft who had the SUPERA stent inserted satisfying the following conditions were consecutively collected. (1) More than 1 year has passed since the AV access operation; (2) Thrombotic re-occlusion of AV graft occurred within 3 months after previous successful endovascular treatment; (3) Residual stenosis is greater than 30% after full effacement of balloon angioplasty in the primary lesion. Post-interventional target lesion primary patency (TLPP), access circuit primary patency (ACPP), and secondary patency (SP) were calculated. Results: Primary lesions of early recurrent arteriovenous graft thrombosis were found in 13 patients with graft-vein anastomosis, six patients with intra-graft stenosis, and one patient with outflow vein complications. The lesions showed residual stenosis in 47.4% (interquartile range: 44.1%-55.3%) of patients despite full-effacement balloon angioplasty. Clinical success was achieved in all patients with full-expansion of the stents at the 1-month follow-up. The TLPP was 70.7% and 32% at 6 and 12 months, respectively, and ACPP was 47.5% and 6.8% at 6 and 12 months, respectively. The SP was 76.1% and 57.1% at 6 and 12 months, respectively. No cannulation complications occurred in the six patients with installation inside the graft. No hemodialysis or stent fracture occurred in any patient during the follow-up period. Conclusions: The SUPERA stent may have a role in salvaging AV grafts with early recurrent thrombosis due to its greater radial force and its conformability and can be useful in treating stenosis involving the elbow or axilla, with fair patency and low complication rates.
Language	English
Publishing date	2023-03-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2252820-9
ISSN	1724-6032 ; 1129-7298
ISSN (online)	1724-6032
ISSN	1129-7298
DOI	10.1177/11297298231160196
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Article: Thinking-with favorite reads in the anthropology of global health and environmental health

Park, Sung-Joon

Curare

2019 Volume 42, Issue 1/2, Page(s) 96

Language	German ; English
Document type	Article
ZDB-ID	303901-8
ISSN	0344-8622
Database	Current Contents Medicine

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Article ; Online: Phonon Angular Momentum Hall Effect.

Park, Sungjoon / Yang, Bohm-Jung

Nano letters

2020 Volume 20, Issue 10, Page(s) 7694–7699

Abstract: The spin Hall effect is the transverse flow of the electron spin in response to an external electric field. Similarly, the temperature gradient in magnets can drive a transverse flow of the magnon spin, which provides a thermal alternative for spin ... ...

Abstract	The spin Hall effect is the transverse flow of the electron spin in response to an external electric field. Similarly, the temperature gradient in magnets can drive a transverse flow of the magnon spin, which provides a thermal alternative for spin manipulation. Recently, phonon angular momentum (PAM), the angular momentum of atoms resulting from their orbital motion around their equilibrium positions, has garnered attention as a quantity analogous to the magnon spin. Here, we report that the temperature gradient generally induces a transverse flow of PAM, which we term the phonon angular momentum Hall effect (PAMHE). The PAMHE arises whenever there are transverse and longitudinal acoustic phonons, and it is therefore ubiquitous in condensed matter systems. As a consequence of the PAMHE, PAM accumulates at the crystal edges. When the atoms in the crystal carry a non-zero Born effective charge, the edge PAM induces edge magnetization, which can be observed through optical measurement.
Language	English
Publishing date	2020-09-28
Publishing country	United States
Document type	Journal Article
ISSN	1530-6992
ISSN (online)	1530-6992
DOI	10.1021/acs.nanolett.0c03220
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