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Tae-Soo Kim

Ewha Womans University · Biochemistry, Genetics and Molecular Biology

About the Lab

Professor Tae-Soo Kim's research lab specializes in computational and systems biology, with a focus on understanding the molecular mechanisms underlying gene regulation, epigenetic modifications, and transcriptional dynamics. The lab investigates how epigenetic enzymes such as histone demethylases and deacetylases regulate transcriptional memory and stress responses in model organisms like budding yeast. Additionally, the lab explores the application of machine learning and deep learning techniques—particularly Temporal Convolutional Networks (TCNs)—to decode complex biological signals, including 3D human action recognition and gene expression patterns. The integration of computational modeling with experimental validation defines the lab’s interdisciplinary approach to systems biology and biomedical applications.

transcriptional regulationepigeneticscomputational biologydeep learninggene expression

Research Overview

Papers
401
Total Citations
12,506
Papers (5y)
109
Primary Field
Biochemistry, Genetics and Molecular Biology

Research Output Trend

Figures are computed from collected data and may differ slightly.

Publications per year (5y)
109total
2021
2022
2023
2024
2025
Citations per year (5y)
1,037total
20212022202320242025

Selected Papers

15
1
Article|721 citations·2017
Interpretable 3D Human Action Analysis with Temporal Convolutional Networks
Tae Soo Kim, Austin Reiter

The discriminative power of modern deep learning models for 3D human action recognition is growing ever so potent. In conjunction with the recent resurgence of 3D human action representation with 3D skeletons, the quality and the pace of recent progress have been significant. However, the inner workings of state-of-the-art learning based methods in 3D human action recognition still remain mostly black-box. In this work, we propose to use a new class of models known as Temporal Convolutional Neur

Computer Vision and Pattern RecognitionComputer Science
2
Article|318 citations·2009
Dimethylation of H3K4 by Set1 Recruits the Set3 Histone Deacetylase Complex to 5′ Transcribed Regions
Tae Soo Kim, Stephen Buratowski
SJR Q1CellOA
Molecular BiologyBiochemistry, Genetics and Molecular Biology
3
Article|203 citations·2012
Set3 HDAC Mediates Effects of Overlapping Noncoding Transcription on Gene Induction Kinetics
Tae Soo Kim, Zhenyu Xu, Sandra Clauder‐Münster, Lars M. Steinmetz, Stephen Buratowski
SJR Q1CellOA
Molecular BiologyBiochemistry, Genetics and Molecular Biology
4
Article|180 citations·2000
Mac-based mode-tracking in structural topology optimization
Tae Soo Kim, Yoon Young Kim
SJR Q1Computers & Structures
Civil and Structural EngineeringEngineering
5
Article|105 citations·2003
Induction of the mitochondrial permeability transition by selenium compounds mediated by oxidation of the protein thiol groups and generation of the superoxide
Tae Soo Kim, Byung Yup Yun, Ick Young Kim
SJR Q1Biochemical Pharmacology
Nutrition and DieteticsNursing
6
Article|69 citations·2007
Two Saccharomyces cerevisiae JmjC Domain Proteins Demethylate Histone H3 Lys36 in Transcribed Regions to Promote Elongation
Tae Soo Kim, Stephen Buratowski
SJR Q1Journal of Biological ChemistryOA

Histone methylation is a reversible modification regulated by the antagonistic functions of residue-specific histone methyltransferases and demethylases. Although methylation of histone H3 at lysines 4 and 36 is linked to transcription, the roles of histone demethylases in transcription regulation are not understood. Here we show that overexpression of either Jhd1 or Rph1, two JmjC-domain proteins, bypasses the requirement for the positive elongation factor gene BUR1. Biochemical analysis and ch

Molecular BiologyBiochemistry, Genetics and Molecular Biology
7
Article|65 citations·2019
Objective assessment of intraoperative technical skill in capsulorhexis using videos of cataract surgery
Tae Soo Kim, Molly O’Brien, Sidra Zafar, Gregory D. Hager, Shameema Sikder, S. Swaroop Vedula
SJR Q2International Journal of Computer Assisted Radiology and Surgery
OphthalmologyMedicine
8
Article|64 citations·2012
Antioxidant capacities of α-tocopherol, trolox, ascorbic acid, and ascorbyl palmitate in riboflavin photosensitized oil-in-water emulsions
Tae Soo Kim, Eric A. Decker, JaeHwan Lee
SJR Q1Food Chemistry
BiochemistryMedicine
9
Article|60 citations·2010
RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast
Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J. Rando
SJR Q1Genome biologyOA

BACKGROUND: The use of genome-wide RNA abundance profiling by microarrays and deep sequencing has spurred a revolution in our understanding of transcriptional control. However, changes in mRNA abundance reflect the combined effect of changes in RNA production, processing, and degradation, and thus, mRNA levels provide an occluded view of transcriptional regulation. RESULTS: To partially disentangle these issues, we carry out genome-wide RNA polymerase II (PolII) localization profiling in budding

Molecular BiologyBiochemistry, Genetics and Molecular Biology
10
Article|57 citations·2010
Formation of NOx from Air and N2/O2 Mixtures Using a Nonthermal Microwave Plasma System
Tae Soo Kim, Soonho Song, Joongsoo Kim, Ryuichi Iwasaki
SJR Q3Japanese Journal of Applied Physics

We present an experimental study of NO x (NO and NO 2 ) formation from air and N 2 /O 2 /NO x mixtures using a nonthermal microwave plasma device. The tests were performed considering the energy consumed to generate plasma gas and the flow rate of air. The results demonstrated that NO x production was proportional to input power and the inverse of air flow rate. In the experiments that used N 2 and O 2 mixtures instead of air, the maximum NO x concentration produced at equilibrium was 16.02 ×10

Radiology, Nuclear Medicine and ImagingMedicine
11
Article|52 citations·2002
Dysfunction of rat liver mitochondria by selenite: induction of mitochondrial permeability transition through thiol-oxidation
Tae Soo Kim, Daewon Jeong, Byung Yup Yun, Ick Young Kim
SJR Q2Biochemical and Biophysical Research Communications
Nutrition and DieteticsNursing
12
Article|52 citations·2018
Rpd3L HDAC links H3K4me3 to transcriptional repression memory
Bo Bae Lee, Ahyoung Choi, Ji Hyun Kim, Yukyung Jun, Hyeonju Woo, So Dam Ha, Chae Young Yoon, Jin-Taek Hwang, Lars M. Steinmetz, Stephen Buratowski, Sanghyuk Lee, Hye Young Kim
SJR Q1Nucleic Acids ResearchOA

Transcriptional memory is critical for the faster reactivation of necessary genes upon environmental changes and requires that the genes were previously in an active state. However, whether transcriptional repression also displays 'memory' of the prior transcriptionally inactive state remains unknown. In this study, we show that transcriptional repression of ∼540 genes in yeast occurs much more rapidly if the genes have been previously repressed during carbon source shifts. This novel transcript

Molecular BiologyBiochemistry, Genetics and Molecular Biology
13
Article|50 citations·2012
Determination of the degree of oxidation in highly-oxidised lipids using profile changes of fatty acids
Tae Soo Kim, JuDong Yeo, Ji Young Kim, Mi‐Ja Kim, JaeHwan Lee
SJR Q1Food Chemistry
Organic ChemistryChemistry
14
Article|49 citations·2022
Terminalia chebula Retz. extract ameliorates the symptoms of atopic dermatitis by regulating anti-inflammatory factors in vivo and suppressing STAT1/3 and NF-ĸB signaling in vitro
Hye Jin Kim, Hyun‐Kyung Song, Sun Haeng Park, Seol Jang, Ki-Sun Park, Kwang Hoon Song, Sang Kook Lee, Tae Soo Kim
SJR Q1PhytomedicineOA

Overall, TC extract alleviated AD-like symptoms by regulating anti-inflammatory factors in vivo and suppressing STAT1/3 and NF-κB signaling in vitro. In addition, our results show the in vivo effect of partial improvements in AD, as well as the in vitro effect on inflammatory factors by the constituents of TC. This finding provides that TC extract and its components could be potential therapeutic drugs for AD.

DermatologyMedicine
15
Article|47 citations·2004
Recruitment of the Swi/Snf Complex by Ste12-Tec1 Promotes Flo8-Mss11-Mediated Activation of STA1 Expression
Tae Soo Kim, Hye Young Kim, Jin Ho Yoon, Hyen Sam Kang
SJR Q2Molecular and Cellular BiologyOA

In the yeast Saccharomyces diastaticus, expression of the STA1 gene, which encodes an extracellular glucoamylase, is activated by the specific DNA-binding activators Flo8, Mss11, Ste12, and Tec1 and the Swi/Snf chromatin-remodeling complex. Here we show that Flo8 interacts physically and functionally with Mss11. Flo8 and Mss11 bind cooperatively to the inverted repeat sequence TTTGC-n-GCAAA (n = 97) in UAS1-2 of the STA1 promoter. In addition, Flo8 and Mss11 bind indirectly to UAS2-1 of the STA1

Molecular BiologyBiochemistry, Genetics and Molecular Biology

Research Areas

Molecular BiologySensory SystemsOncologyNuclear and High Energy PhysicsPhysiologyImmunology

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