Seoul National University Biological Sciences Website

Publications

Laboratory of Computational Biology

BMB reports

Doyeon Kim, Hee Ryung Chang, and Daehyun Baek (2017). Rules for functional microRNA targeting. BMB reports

Cell Host & Microbe

Sungchul Kim, Daekwan Seo, Dongwoo Kim, Yujin Hong, Hyeshik Chang, Daehyun Baek, V. Narry Kim, Sungwook Lee, and Kwangseog Ahn (2015). Temporal Landscape of MicroRNA-Mediated Host-Virus Crosstalk during Productive Human Cytomegalovirus Infection. Cell Host & Microbe

Sanghyun Lee, Jaewon Song, Sungchul Kim, Jongkyu Kim, Yujin Hong, Youngkyun Kim, Donghyun Kim, Daehyun Baek, and Kwangseog Ahn (2013). Selective degradation of host microRNAs by an intergenic HCMV noncoding RNA accelerates virus production. Cell Host & Microbe

Clinical Cancer Research

Seongmin Choi*, Hyeong Ryul Kim*, Chang Ohk Sung*, Jongkyu Kim, Sukjun Kim, ..., Gu Kong^#, Daehyun Baek^#, and Se Jin Jang^# (2015). Genomic alterations in the RB pathway indicate prognostic outcomes of early-stage lung adenocarcinoma. Clinical Cancer Research

eLife

Yoo Kyusang*, Jo Young-Woo, Yoo Takwon, Hann Sang-Hyeon, Park Inkuk, Kim Yea-Eun, Kim Ye Lynne, Rhee Joonwoo, Song In-Wook, Kim Ji-Hoon, Baek Daehyun, Kong Young-Yun^# (2024). Muscle-resident mesenchymal progenitors sense and repair peripheral nerve injury via the GDNF-BDNF axis. eLife

Experimental & Molecular Medicine

Hyeonseo Hwang, Hyeonseong Jeon, Nagyeong Yeo and Daehyun Baek (2024). Big data and deep learning for RNA biology. Experimental & Molecular Medicine

Hyeonseong Jeon*, Junhak Ahn*, Byunggook Na, Soona Hong, Lee Sael, Sun Kim, Sungroh Yoon^#, and Daehyun Baek^# (2023). AIVariant: a deep learning-based somatic variant detector for highly contaminated tumor samples. Experimental & Molecular Medicine

Jeongeun Lee*, Jean Lee*, Sungwon Jeon, Jeongha Lee, Insu Jang, Jin Ok Yang, Soojin Park, Byungwook Lee, Jinwook Choi, Byung-Ok Choi, Heon Yung Gee, Jaeseong Oh, In-Jin Jang, Sanghyuk Lee, Daehyun Baek, Youngil Koh, Sung-Soo Yoon, Young-Joon Kim, Jong-Hee Chae, Woong-Yang Park, Jong Hwa Bhak^# & Murim Choi^# (2022). A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population. Experimental & Molecular Medicine

Genes & Development

H. Rosaria Chiang, Lori W. Schoenfeld, J. Graham Ruby, Vincent C. Auyeung, Noah Spies, Daehyun Baek, ... and David P. Bartel (2010). Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes & Development

Genome Research

Daehyun Baek^#, Colleen Davis, Brent Ewing, David Gordon and Phil Green^# (2007). Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Research

Hepatology

Sung-Min Ahn, Se Jin Jang, Ju Hyun Shim, Deokhoon Kim, ... Daehyun Baek, Farhan Haq, Adnan Ahmed Ansari, Sun Young Lee, Sung-Min Chun, Seongmin Choi, Hyun-Jeung Choi, Jongkyu Kim, Sukjun Kim, ... and Gu Kong (2014). Genomic portrait of resectable hepatocellular carcinomas: Implications of RB1 and FGF19 aberrations for patient stratification. Hepatology

IEEE/ACM transactions on computational biology and bioinformatics

Donghe Li, Wonji Kim, Longfei Wang, Kyong-Ah Yoon, Boyoung Park, Charny Park, Sun-Young Kong, Yongdeuk Hwang, Daehyun Baek, Eun Sook Lee, and Sungho Won (2019). Comparison of INDEL calling tools with simulation data and real short-read data. IEEE/ACM transactions on computational biology and bioinformatics

Journal of Neuroscience

Su-Eon Sim, Chae-Seok Lim, Jae-Ick Kim, Daekwan Seo, Heejung Chun, Nam-Kyung Yu, ..., Daehyun Baek, Yong-Seok Lee, and Bong-kiun Kaang (2016). The brain-enriched microRNA miR-9-3p regulates synaptic plasticity and memory. Journal of Neuroscience

Molecular Cell

Stephen W. Eichhorn, Huili Guo, Sean E. McGeary, Ricard A. Rodriguez-Mias, Chanseok Shin, Daehyun Baek, Shu-hao Hsu, Kalpana Ghoshal, Judit Villén, and David P. Bartel (2014). mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Molecular Cell

Molecular Oncology

Namhee Yu, Seunghui Yong, Hong Kwan Kim, Yoon‐La Choi, Yeonjoo Jung, Doyeon Kim, Jihae Seo, Ye Eun Lee, Daehyun Baek, Jinseon Lee, Seungjae Lee, Jong Eun Lee, Jaesang Kim, Jhingook Kim^#, and Sanghyuk Lee^# (2019). Identification of tumor suppressor microRNAs by integrative microRNA and mRNA sequencing of matched tumor-normal pairs in lung adenocarcinoma. Molecular Oncology

Molecules and Cells

Hyeonseo Hwang, Hee Ryung Chang, and Daehyun Baek (2023). Determinants of Functional MicroRNA Targeting. Molecules and Cells

Doyeon Kim, Jongkyu Kim, and Daehyun Baek (2014). Global and local competition between exogenously introduced microRNAs and endogenously expressed microRNAs. Molecules and Cells

Nature Biomedical Engineering

Jang-il Sohn*, Min-Hak Choi*, Dohun Yi*, Vipin A. Menon, Yeon Jeong Kim, Junehawk Lee, Jung Woo Park, Sungkyu Kyung, Seung-Ho Shin, Byunggook Na, Je-Gun Joung, Young Seok Ju, Min Sun Yeom, Youngil Koh, Sung-Soo Yoon, Daehyun Baek, Tae-Min Kim & Jin-Wu Nam^# (2022). Ultrafast prediction of somatic structural variations by filtering out reads matched to pan-genome k-mer sets. Nature Biomedical Engineering

Nature communications

Doyeon Kim*, Sukjun Kim*, Joori Park*, Hee Ryung Chang*, Jeeyoon Chang*, Junhak Ahn*, Heedo Park*, Junehee Park, Narae Son, Gihyeon Kang, Jeonghun Kim, Kisoon Kim, Man-Seong Park^#, Yoon Ki Kim^#, and Daehyun Baek^# (2021). A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome. Nature communications

Sukjun Kim*, Soyoung Kim*, Hee Ryung Chang*, Doyeon Kim*, Junehee Park, Narae Son, Joori Park, Minhyuk Yoon, Gwangung Chae, Young-Kook Kim, V. Narry Kim, Yoon Ki Kim, Jin-Wu Nam, Chanseok Shin^#, and Daehyun Baek^# (2021). The regulatory impact of RNA-binding proteins on microRNA targeting. Nature communications

Nature genetics

Doyeon Kim*, You Me Sung*, Jinman Park*, Sukjun Kim, Jongkyu Kim, Junhee Park, Haeok Ha, Jung Yoon Bae, SoHui Kim and Daehyun Baek (2016). General rules for functional microRNA targeting. Nature genetics

Commentary:
Principles of Systems Biology. Cell Systems (2016) [Link]
Deciphering rules of microRNA targeting. Nature Reviews Genetics (2016) [Link]
기능적 microRNA Targeting 규칙의 포괄적 발굴. 생화학분자생물학회 우수논문소개 (2017) [Link]

Nature Medicine

Jeongmin Ryoo, Jongsu Choi, Changhoon Oh, Sungchul Kim, Minji Seo, Seok-Young Kim, Daekwan Seo, Jongkyu Kim, Tommy E White, ... Daehyun Baek, and Kwangseog Ahn (2014). The ribonuclease activity of SAMHD1 is required for HIV-1 restriction. Nature Medicine

Nature Structural & Molecular Biology

Young-Kook Kim, Gabbine Wee, Joha Park, Jongkyu Kim, Daehyun Baek, Jin-Soo Kim, and V. Narry Kim (2013). TALEN-based knockout library for human microRNAs. Nature Structural & Molecular Biology

David M Garcia*, Daehyun Baek*^#, Chanseok Shin, George W Bell, Andrew Grimson, and David P. Bartel^# (2011). Weak seed-pairing stability and high target-Site abundance decrease the proficiency of lsy-6 and other miRNAs. Nature Structural & Molecular Biology

Nature

Daehyun Baek*, Judit Villén*, Chanseok Shin*, Fernando D. Camargo, Steven P. Gygi and David P. Bartel (2008). The impact of microRNAs on protein output. Nature

Nucleic Acids Research

Jeeyoon Chang*, Min-Kyung Shin*, Joori Park*, Hyun Jung Hwang, Nicolas Locker, Junhak Ahn, Doyeon Kim, Daehyun Baek, Yeonkyoung Park, Yujin Lee, Sung Ho Boo, Hyeong-In Kim, Yoon Ki Kim^# (2023). An interaction between eIF4A3 and eIF3g drives the internal initiation of translation. Nucleic Acids Research

PLoS Genetics

Kiwon Park*, Jeongmin Ryoo*, Heena Jeong, Minsu Kim, Sungwon Lee, Sung-Yeon Hwang, Jiyoung Ahn, Doyeon Kim, Hyungseok C Moon, Daehyun Baek, Kwangsoo Kim, Hye Yoon Park, Kwangseog Ahn^# (2021). Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription-replication conflict regions. PLoS Genetics

Proceedings of the National Academy of Sciences U.S.A.

Daehyun Baek^# and Phil Green^# (2005). Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proceedings of the National Academy of Sciences U.S.A.

Scientific Reports

Hyojin Song, Yoojoo Lim, Hogune Im, Jeong Mo Bae, Gyeong Hoon Kang, Junhak Ahn, Daehyun Baek, Tae-You Kim, Sung-Soo Yoon^#, and Youngil Koh^# (2019). Interpretation of EBV infection in pan-cancer genome considering viral life cycle: LiEB (Life cycle of Epstein-Barr virus). Scientific Reports

Scientific Reports

Sangmoon Lee*, Jihae Seo*, Jinman Park*, ... Jong-Hee Chae, In-Jin Jang, Sanghyuk Lee, Woong-Yang Park, Daehyun Baek^#, and Murim Choi^# (2017). Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population. Scientific Reports