PNU students' names are underlined and Prof. Giltae Song bolded (* corresponding author)
Bo Zhou*, Joseph G. Arthur, Hanmin Guo, Taeyoung Kim, Yiling Huang, Reenal Pattni, Tao Wang, Soumya Kundu, Jay X.J. Luo, HoJoon Lee, Daniel C. Nachun, Carolin Purmann, Emma M. Monte, Annika K. Weimer, Ping-Ping Qu, Minyi Shi, Lixia Jiang, Xinqiong Yang, John F. Fullard, Jaroslav Bendl, Kiran Girdhar, Minsu Kim, Xi Chen, PsychENCODE Consortium, William J. Greenleaf, Laramie Duncan, Hanlee P. Ji, Xiang Zhu, Giltae Song, Stephen B. Montgomery, Dean Palejev, Heinrich zu Dohna, Panos Roussos, Anshul Kundaje, Joachim F. Hallmayer, Michael P. Snyder, Wing H. Wong*, Alexander E. Urban*. Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. Cell, DOI: 10.1016/j.cell.2024.09.014. 2024.
Hwayeong Kim, Sangwoo Moon, Joohwang Lee, EunAh Kim, Sang Wook Jin, Jung Lim Kim, Seung Uk Lee, Jinmi Kim, Seungtae Yoo, Jiwon Lee, Giltae Song*, Jiwoong Lee*. Fuzzy clustering of 24–2 visual field patterns can detect glaucoma progression. PLoS ONE, 19(9): e0309011. 2024.
Minwook Kim, Donggil Kang, Min Sun Kim, Jeong Cheon Choe, Sun-Hack Lee, Jin Hee Ahn, Jun-Hyok Oh, Jung Hyun Choi, Han Cheol Lee, Kwang Soo Cha, Kyungtae Jang, WooRI Bong, Giltae Song*, Hyewon Lee*. Acute myocardial infarction prognosis prediction with reliable and interpretable artificial intelligence system. Journal of the American Medical Informatics Association, ocae114. 2024.
Incheol Shin, Keumseok Kang, Juseong Kim, Sanghun Sel, Jeonghoon Choi, Jae-Wook Lee, Ho Young Kang, Giltae Song*. AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders. BMC Bioinformatics, 24:447. 2023.
Jae-Won Lee, Jong-Hyun Won, Seonggwang Jeon, Yujin Choo, Yubin Yeon, Jin-Seon Oh, Minsoo Kimm, SeonHwa Kim, InSuk Joung, Cheongjae Jang, Sung Jong Lee, Tae Hyun Kim, Kyong Hwan Jin, Giltae Song, Eun-Sol Kim, Jejoong Yoo, Eunok Paek, Yung-Kyun Noh, Keehyoung Joo. DeepFold: Enhancing Protein Structure Prediction through Optimized Loss Functions, Improved Template Features, and Re-optimized Energy Function. Bioinformatics, btad712. 2023.
Jongseong Lim, Sunghun Jung, Chan JeGal, Gwanghoon Jung, Jung Ho Yoo, Jin Kyu Gahm, Giltae Song*. LEQNet: Light Earthquake Deep Neural Network for Earthquake Detection and Phase Picking. Frontiers in Earth Science, 10:848237. 2022.
Dohyeon Lee, Giltae Song*. FastqCLS: a FASTQ Compressor for Long-read Sequencing via read reordering using a novel scoring model. Bioinformatics, btab696. 2021.
Gwangho Lee, Gun Hyuk Jang, Ho Young Kang, Giltae Song*. Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach. PLoS ONE, 16(6):e0253760. 2021.
Firda Aminy Maruf, Rian Pratama Giltae Song*. DNN-Boost: Somatic mutation identification of tumor-only whole-exom sequencing data using deep neural network and XGBoost. Journal of Bioinformatics and Computational Biology, 2140017. 2021.
Rian Pratama, Jae Joon Hwang, Ji Hye Lee, Giltae Song*, Hae Ryoun Park*. Authentication of differential gene expression in oral squamous cell carcinoma using machine learning applications. BMC Oral Health, 21:281. 2021.
Dongpin Oh, J. Seth Strattan, Junho Hur, Jose Bento, Alexander Eckehart Urban, Giltae Song*, J. Michael Cherry. CNN-Peaks: ChIP-Seq peak detection pipeline using convolution neural networks that imitate human visual inspection. Scientific Reports, 10, 7933. 2020.
Morteza Roodgar, Afshin Babveyh, Lan H Nguyen, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B Hanks, Mohan Avula, Lihua Jiang, Ruiqi Jian, Hoyong Lee, Giltae Song, Hassan Chaib, Irv L Weissman, Serafim Batzoglou, Susan Holmes, David G Smith, Joseph L Mankowski, Stefan Prost, Michael P Snyder. Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. Giga Science, Vol 9(7):giaa069. 2020.
Seonghyeon Kim, Seokwoo Kang, Kwang Ryel Ryu, Giltae Song*. Real-time occupancy prediction in a large exhibition hall using deep learning approach. Energy and Buildings, Vol 199:216-222. 2019.
Giltae Song, Jongin Lee, Juyeon Kim, Seokwoo Kang, Hoyong Lee, Daehong Kwon, Daehwan Lee, Gregory I. Lang, J. Michael Cherry, Jaebum Kim. Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies. PLoS ONE, 14(8): e0221858. 2019.
Taegeun Bae, Woo Chang Hwang, Dohyeon Lee, Giltae Song, Junseok W Hur, Junho K Hur. Characterization of distinct mutation patterns by CRISPR-Cas9 and CRISPRCpf1 genome editing systems. Molecular & Cellular Toxicology, 15:383–389. 2019.
Bo Zhou, Steve S Ho, Stephanie U Greer, Noah Spies, John M Bell, Xianglong Zhang, Xiaowei Zhu, Joseph G Arthur, Seunggyu Byeon, Reenal Pattni, Ishan Saha, Giltae Song, Hanlee P Ji, Dimitri Perrin, Wing H Wong, Alexej Abyzov, Alexander E Urban. Haplotype-resolved and integrated genome analysis of ENCODE cell line HepG2. Nucleic Acids Research, Vol 47(8):3846-3861. 2019.
Bo Zhou, Steve S Ho, Xiaowei Zhu, Xianglong Zhang, Noah Spies, Seunggyu Byeon, Joseph G Arthur, Reenal Pattni, Noa Ben-Efraim, Michael S Haney, Rajini R Haraksingh, Giltae Song, Dimitri Perrin, Wing H Wong, Alexej Abyzov, Alexander E Urban. Comprehensive, Integrated, and Phased Whole-Genome Analysis of the Primary ENCODE Cell Line K562. Genome Research, Vol 29: 472-484. 2019
Doo-Hee Hwang, Seok-Hwan Choi, Jin-Myeong Shin, Giltae Song, Yoon-Ho Choi. Privacy-Preserving Compressed Reference-Oriented Alignment Map Using Decentralized Storage. IEEE Access, Vol 6: 45990-46001. 2018.
Fadhilah Kurnia Putri, Giltae Song, Joonho Kwon, Praveen Rao. DISPAQ: Distributed Profitable-Area Query from Big Taxi Trip Data. Sensors, Vol 17(10):2201. 2017.
Giltae Song, Rama Balakrishnan, Gail Binkley, Maria Costanzo, Kyla Dalusag, Stacia Engel, Sage Hellerstedt, Benjamin Hitz, Kalpana Karra, Rob Nash, Kelley Paskov, Travis Sheppard, Marek Skrzypek, Shuai Weng, Edith Wong, and J. Michael Cherry. Integration of new alternative reference strain genome sequences into the Saccharomyces Genome Database. Database (Oxford), Vol. 2016: article ID baw074. 2016.
Stacia Engel, Shuai Weng, Gail Binkley, Kelley Paskov, Giltae Song, and J. Michael Cherry. From one to many: Expanding the Saccharomyces cerevisiae reference genome panel. Database (Oxford), Vol. 2016: article ID baw020. 2016.
Travis Sheppard, Benjamin Hitz, Stacia Engel, Giltae Song, Rama Balakrishnan, Gail Binkley, Maria Costanzo, Kyla Dalusag, Sage Hellerstedt, Kalpana Karra, Rob Nash, Kelley Paskov, Marek Skrzypek, Shuai Weng, Edith Wong, and J. Michael Cherry. The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Research, 44 (D1): D698-D702. 2015.
Giltae Song*, Benjamin Dickins, Janos Demeter, Stacia Engel, Jennifer Gallagher, Kisurb Choe, Barbara Dunn, Michael Snyder, J. Michael Cherry. AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae. PLoS ONE, 10(3):e0120671. 2015.
Giltae Song*, Cathy Riemer, Benjamin Dickins, Hie Lim Kim, Louxin Zhang, Yu Zhang, Chih-Hao Hsu, Ross Hardison, NISC Comparative Sequencing Program, Eric Green, Webb Miller. Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. Genome Biology and Evolution, 4(4):586-601. 2012.
Giltae Song*, Chih-Hao Hsu, Cathy Riemer, Yu Zhang, Hie Lim Kim, Federico Hoffmann, Louxin Zhang, Ross Hardison, NISC Comparative Sequencing program, Eric Green, Webb Miller. Conversion events in gene clusters. BMC Evolutionary Biology, 11:226. 2011.
The ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biology, 9(4):e1001046. 2011.
Giltae Song*, Chih-Hao Hsu, Cathy Riemer, Webb Miller. Evaluation of methods for detecting conversion events in gene clusters. BMC Bioinformatics, 12(Suppl 1):S45. 2011. (Presented in the 9th Asia Pacific Bioinformatics Conference [APBC2011].)
Giltae Song*, Louxin Zhang, Tomas Vinar, Webb Miller. CAGE: Combinatorial Analysis of Gene-cluster Evolution. Journal of Computational Biology, 17(9):1227-1242. 2010.
Tomas Vinar, Brona Brejova, Giltae Song, Adam C. Siepel. Reconstructing histories of complex gene clusters on a phylogeny. Journal of Computational Biology, 17(9):1267-1279. 2010.
Giltae Song*, Louxin Zhang, Tomas Vinar, Webb Miller. Inferring the recent duplication history of a gene cluster. In F. D. Ciccarelli, I. Miklos, ed., Comparative Genomics, International Workshop (RECOMB-CG), 5817 volume of Lecture Notes in Bioinformatics, pp. 111-125, Budapest, September 2009. Springer. (Invited to Journal of Computational Biology.)
Tomas Vinar, Brona Brejova, Giltae Song, Adam Siepel. Reconstructing histories of complex gene clusters on a phylogeny. In F. D. Ciccarelli, I. Miklos, ed., Comparative Genomics, International Workshop (RECOMB-CG), 5817 volume of Lecture Notes in Bioinformatics, pp. 150-163, Budapest, September 2009. Springer. (Invited to Journal of Computational Biology.)
Yu Zhang, Giltae Song, Tomas Vinar, Eric D. Green, Adam Siepel, Webb Miller. Evolutionary history reconstruction for mammalian complex gene clusters. Journal of Computational Biology, 16(8):1051-1070. 2009.
Yu Zhang, Giltae Song, Chih-Hao Hsu, and Webb Miller. Simultaneous history reconstruction for complex gene clusters in multiple species. Pacific Symposium on Biocomputing, 14:162-173(2009).
Yu Zhang, Giltae Song, Tomas Vinar, Eric D. Green, Adam Siepel, Webb Miller. Reconstructing the evolutionary history of complex human gene clusters. RECOMB, 4955 volume of Lecture Notes in Computer Science, pp. 29-49, Singapore, January 2008. Springer. (Invited to Journal of Computational Biology.)