Publications

2024

• Wootaek Lim, Jitae Kim, Songhyeon Kim, Hyunsu Bong, Kwang-su Park*, Minji Jeon* "DR.DEGMON: Self-explainable deep neural network for drug-induced cell viability prediction incorporating differentially expressed genes and Gene Ontology" The 18th International Conference on Data and Text Mining in Biomedical Informatics (2024)

• Songhyeon Kim, Hyunsu Bong, Minji Jeon* "Dr.Emb Appyter: A web platform for drug discovery using embedding vectors." Journal of Computational Chemistry (2024) 

2023

• Junhyun Lee†, Bumsoo Kim†, Minji Jeon*, Jaewoo Kang* "Co-attention Graph Pooling for Efficient Pairwise Graph Interaction Learning." IEEE Access (2023).

• Letizia Amadori, Claudia Calcagno, Dawn M Fernandez, Simon Koplev, Nicolas Fernandez, Ravneet Kaur, Pauline Mury, Nayaab S Khan, Swathy Sajja, Roza Shamailova, Yannick Cyr, Minji Jeon, Christopher A Hill, Peik Sean Chong, Sonum Naidu, Ken Sakurai, Adam Ali Ghotbi, Raphael Soler, Natalia Eberhardt, Adeeb Rahman, Peter Faries, Kathryn J Moore, Zahi A Fayad, Avi Ma’ayan, Chiara Giannarelli "Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis." Nature Cardiovascular Research (2023): 1-22.

• Giacomo B Marino, Megan L Wojciechowicz, Daniel JB Clarke, Maxim V Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma’ayan "lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs." Database 2023 (2023): baad009.

• Alexander Lachmann, Kaeli A Rizzo, Alon Bartal, Minji Jeon, Daniel JB Clarke, Avi Ma’ayan "PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices." PeerJ 11 (2023): e14927.

2022

• Amanda L Charbonneau, Arthur Brady, Karl Czajkowski, Jain Aluvathingal, Saranya Canchi, Robert Carter, Kyle Chard, Daniel JB Clarke, Jonathan Crabtree, Heather H Creasy, Mike D'Arcy, Victor Felix, Michelle Giglio, Alicia Gingrich, Rayna M Harris, Theresa K Hodges, Olukemi Ifeonu, Minji Jeon, Eryk Kropiwnicki, Marisa CW Lim, R Lee Liming, Jessica Lumian, Anup A Mahurkar, Meisha Mandal, James B Munro, Suvarna Nadendla, Rudyard Richter, Cia Romano, Philippe Rocca-Serra, Michael Schor, Robert E Schuler, Hongsuda Tangmunarunkit, Alex Waldrop, Cris Williams, Karen Word, Susanna-Assunta Sansone, Avi Ma'ayan, Rick Wagner, Ian Foster, Carl Kesselman, C Titus Brown, Owen White "Making Common Fund data more findable: catalyzing a data ecosystem." GigaScience 11 (2022). 

• Yerin Kim, Chaeeun Kim, Hojin Lee, Minseok Kim, Haiyan Zheng, Ji Yeon Lim, Hye-In Yun, Minji Jeon, Jungmin Choi, Sun Wook Hwang "Gpr83 Tunes Nociceptor Function, Controlling Pain." Neurotherapeutics (2022): 1-13. 

• Minji Jeon, Zhuorui Xie, John E. Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke & Avi Ma’ayan* "Transforming L1000 profiles to RNA-seq-like profiles with deep learning." BMC Bioinformatics 23, 374 (2022). https://doi.org/10.1186/s12859-022-04895-5

• Zhuorui Xie, Eryk Kropiwnicki, Megan L Wojciechowicz, Kathleen M Jagodnik, Ingrid Shu, Allison Bailey, Daniel JB Clarke, Minji Jeon, John Erol Evangelista, Maxim V. Kuleshov, Alexander Lachmann, Abhijna A Parigi, Jose M Sanchez, Sherry L Jenkins, Avi Ma'ayan*  "Getting Started with LINCS Datasets and Tools." Current Protocols 2.7 (2022): e487. 

• John Erol Evangelista†, Daniel JB Clarke†, Zhuorui Xie†, Alexander Lachmann†, Minji Jeon, Kerwin Chen, Kathleen M Jagodnik, Sherry L Jenkins, Maxim V Kuleshov, Megan L Wojciechowicz, Stephan C Schürer, Mario Medvedovic, Avi Ma’ayan* "SigCom LINCS: data and metadata search engine for a million gene expression signatures." Nucleic Acids Research (2022). 

2021

• Zhaoping Xiong†, Minji Jeon†, Robert J Allaway†, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Minyue Zheng, Aik Choon Tan, Xindi Guo, The Multi-Targeting Drug DREAM Challenge Community, Kristen K Dang, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger*, Ross Cagan* "Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: the Multi-Targeting Drug DREAM Challenge" PLoS computational biology 17.9 (2021): e1009302.

• Mujeen Sung, Jinhyuk Lee, Sean Yi, Minji Jeon, Sungdong Kim, Jaewoo Kang* "Can Language Models be Biomedical Knowledge Bases?" EMNLP 2021

• Anna Cichońska, Balaguru Ravikumar, Robert J. Allaway, Fangping Wan, Sungjoon Park, Olexandr Isayev, Shuya Li, Michael Mason, Andrew Lamb, Ziaurrehman Tanoli, Minji Jeon, Sunkyu Kim, Mariya Popova, Stephen Capuzzi, Jianyang Zeng, Kristen Dang, Gregory Koytiger, Jaewoo Kang, Carrow I. Wells, Timothy M. Willson, The IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Tudor I. Oprea, Avner Schlessinger, David H. Drewry, Gustavo Stolovitzky, Krister Wennerberg, Justin Guinney*, Tero Aittokallio* "Crowdsourced mapping of unexplored target space of kinase inhibitors." Nature communications 12.1 (2021): 1-18.

• Daniel J. B. Clarke, Minji Jeon, Sherry Xie, Daniel J. Stein, Nicole Moiseyev, Charles Dai, Megan L. Wojciechowicz, Skylar Litz, Jason Hom, John Erol Evangelista, Lucas Goldman, Serena Zhang, Christine Yoon, Sherry L. Jenkins, Avi Ma’ayan* "Appyters: Turning Jupyter Notebooks into Data Driven Web Apps", Patterns (In press)

• Allison Bailey, Zhuorui Xie, Maxim Kuleshov, Daniel Clarke, John Evangelista, Sherry Jenkins, Alexander Lachmann, Megan Wjciechowicz, Eryk Kropiwnicki, Kathleen Jagodnik, Minji Jeon, Avi Ma'ayan* "Gene Set Knowledge Discovery with Enrichr" Current protocols 1.3 (2021): e90.

• Minji Jeon†, Kathleen M. Jagodnik†, Eryk Kropiwnicki, Daniel J. Stein, Avi Ma'ayan* "Prioritizing Pain-Associated Targets with Machine Learning" Biochemistry 60.18 (2021): 1430-1446.

• Eryk Kropiwnicki, John E Evangelista, Daniel J Stein, Daniel J B Clarke, Alexander Lachmann, Maxim V Kuleshov, Minji Jeon, Kathleen M Jagodnik, Avi Ma’ayan* "Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning." Database 2021 (2021).

• Amanda L Charbonneau*, Arthur Brady, Saranya Canchi, Robert Carter, Kyle Chard, Daniel J.B. Clarke, Heather H Creasy, Mike D’Arcy, Michelle Giglio, Alicia Gingrich, Rayna M Harris, Theresa K Hodges, Minji Jeon, Eryk Kropiwnicki, Marisa C.W. Lim, R. Lee Liming, Meisha Mandal, James B Munro, Suvarna Nadendla, Cia Romano, Philippe Rocca-Serra, Robert E. Schuler, Alex Waldrop, Cris Williams, Karen Word, Susanna-Assunta Sansone, Avi Ma’ayan, Rick Wagner, Ian Foster, Carl Kesselman, C. Titus Brown, Owen White "Making Common Fund data more findable: Catalyzing a Data Ecosystem." bioRxiv (2021).

• Alexander Lachmann, Kaeli Rizzo, Alon Bartal, Minji Jeon, Daniel JB Clarke, Avi Ma'ayan* "PrismExp: Predicting Human Gene Function by Partitioning Massive RNA-seq Co-expression Data." bioRxiv (2021).

2020

• Mi Yang, Francesca Petralia, Zhi Li, Hongyang Li, Weiping Ma, Xiaoyu Song, Sunkyu Kim, Heewon Lee, Han Yu, Bora Lee, Seohui Bae, Eunji Heo, Jan Kaczmarczyk, Piotr Stępniak, Michał Warchoł, Thomas Yu, Anna P Calinawan, Paul C Boutros, Samuel H Payne, Boris Reva, Tunde Aderinwale, Ebrahim Afyounian, Piyush Agrawal, Mehreen Ali, Alicia Amadoz, Francisco Azuaje, John Bachman, Sherry Bhalla, José Carbonell-Caballero, Priyanka Chakraborty, Kumardeep Chaudhary, Yonghwa Choi, Yoonjung Choi, Cankut Çubuk, Sandeep Kumar Dhanda, Joaquín Dopazo, Laura L Elo, Ábel Fóthi, Olivier Gevaert, Kirsi Granberg, Russell Greiner, Marta R Hidalgo, Vivek Jayaswal, Hwisang Jeon, Minji Jeon, Sunil V Kalmady, Yasuhiro Kambara, Jaewoo Kang, Keunsoo Kang, Tony Kaoma, Harpreet Kaur, Hilal Kazan, Devishi Kesar, Juha Kesseli, Daehan Kim, Keonwoo Kim, Sang-Yoon Kim, Sajal Kumar, Yunpeng Liu, Roland Luethy, Swapnil Mahajan, Mehrad Mahmoudian, Arnaud Muller, Petr V Nazarov, Hien Nguyen, Matti Nykter, Shujiro Okuda, Sungsoo Park, Gajendra Pal Singh Raghava, Jagath C Rajapakse, Tommi Rantapero, Hobin Ryu, Francisco Salavert, Sohrab Saraei, Ruby Sharma, Ari Siitonen, Artem Sokolov, Kartik Subramanian, Veronika Suni, Tomi Suomi, Léon-Charles Tranchevent, Salman Sadullah Usmani, Tommi Välikangas, Roberto Vega, Hua Zhong, Emily Boja, Henry Rodriguez, Gustavo Stolovitzky, Yuanfang Guan, Pei Wang, David Fenyö, Julio Saez-Rodriguez "Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics." Cell Systems 11.2 (2020): 186-195.

• Doyeong Hwang†, Minji Jeon†, Jaewoo Kang* “A Drug-Induced Liver Injury Prediction Model using Transcriptional Response Data with Graph Neural Network” 2020 IEEE International Conference on Big Data and Smart Computing

• Anna Cichonska, Balaguru Ravikumar, Robert J Allaway, Sungjoon Park, Fangping Wan, Olexandr Isayev, Shuya Li, Michael J Mason, Andrew Lamb, Minji Jeon, Sunkyu Kim, Mariya Popova, Jianyang Zeng, Kristen Dang, Gregory Koytiger, Jaewoo Kang, Carrow I Wells, Timothy M Willson, Tudor I Oprea, Avner Schlessinger, David H Drewry, Gustavo A Stolovitzky, Krister Wennerberg, Justin Guinney, Tero Aittokallio "Crowdsourced mapping of unexplored target space of kinase inhibitors" BioRxiv (2020): 2019-12.

2019

• Minji Jeon, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Sunkyu Kim, Yonghwa Choi, Aik-Choon Tan, Jaewoo Kang* "ReSimNet: Drug Response Similarity Prediction using Siamewe Neural Networks" Bioinformatics 35.24 (2019): 5249-5256.

• Buru Chang†, Yonghwa Choi†, Minji Jeon, Junhyun Lee, Kyu-Man Han, Aram Kim, Byung-Joo Ham, Jaewoo Kang* “ARPNet: Antidepressant Response Prediction Network for Major Depressive Disorder” Genes 10.11 (2019): 907. 

• Michael Patrick Menden, Dennis Wang, Yuanfang Guan, Michael Mason, Bence Szalai, Krishna C Bulusu, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, Tin Nguyen, Mikhail Zaslavskiy, AstraZeneca-Sanger Drug Combination DREAM Consortium, In Sock Jang, Zara Ghazoui, Mehmet Eren Ahsen, Robert Vogel, Elias Chaibub Neto, Thea Norman, Eric KY Tang, Mathew J Garnett, Giovanni Di Veroli, Stephen Fawell, Gustavo Stolovitzky, Justin Guinney, Jonathan R Dry, Julio Saez-Rodriguez*, "Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen"  Nature Communications, 10.1 (2019): 2674. 

2018

• Minji Jeon, Sunkyu Kim, Sungjoon Park, Heewon Lee, Jaewoo Kang* "In silico drug combination discovery for personalized cancer therapy" BMC systems biology, 2018, 12.2: 16. 

• Sungjoon Park, Jung Min Kim, Wonho Shin, Sung Won Han, Minji Jeon, Hyun Jin Jang, Ik-Soon Jang, Jaewoo Kang* "BTNET: boosted tree based gene regulatory network inference algorithm using time-course measurement data" BMC systems biology, 2018, 12.2: 16. 

• Seongsoon Kim, Donghyeon Park, Yonghwa Choi, Kyubum Lee, Byounggun Kim, Minji Jeon, Jihye Kim, Aik Choon Tan, Jaewoo Kang* "A Pilot Study of Biomedical Text Comprehension using an Attention-Based Deep Neural Reader: Design and Experimental Analysis" JMIR medical informatics, 2018, 6.1. 

• Yonghwa Choi, Minji Jeon , Sunkyu Kim, Kyu-Man Han, Eunsoo Won, Aram Kim, Byung-Joo Ham, and Jaewoo Kang* "Diagnostic Model for Korean Major Depressive Disorder using Multi-Modal Data" Korean Institute of Information Scientists and Engineers (KIISE), 2018

2016

• Sunwon Lee, Donghyeon Kim, Kyubum Lee, Jaehoon Choi, Seongsoon Kim, Minji Jeon, Sangrak Lim, Donghee Choi, Sunkyu Kim, Aik-Choon Tan, Jaewoo Kang*  "BEST: next-generation biomedical entity search tool for knowledge discovery from biomedical literature" PloS one, 2016, 11.10: e0164680. 

• Kyubum Lee, Wonho Shin, Byounggun Kim, Sunwon Lee, Yonghwa Choi, Sunkyu Kim, Minji Jeon, Aik Choon Tan, Jaewoo Kang* "HiPub: translating PubMed and PMC texts to networks for knowledge discovery" Bioinformatics, 2016, 32.18: 2886-2888.  

2015

• Minjae Yoo, Jimin Shin, Jihye Kim, Karen A Ryall, Kyubum Lee, Sunwon Lee, Minji Jeon, Jaewoo Kang, Aik Choon Tan*, "DSigDB: drug signatures database for gene set analysis" Bioinformatics, 2015, 31.18: 3069-3071. 

• Ashis Saha† , Minji Jeon† , Aik Choon Tan, Jaewoo Kang* "iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data" PloS one, 2015, 10.7: e0131656. 

• Woo-Keun Seo, Jaewoo Kang, Minji Jeon, Kyubum Lee, Sunwon Lee, Ji Hyun Kim, Kyungmi Oh, Seong-Beom Koh, "Feasibility of Using a Mobile Application for the Monitoring and Management of Stroke-Associated Risk Factors" Journal of Clinical Neurology, 2015, 11.2: 142-148. 

• Sunkyu Kim, Sunwon Lee, Kyubum Lee, Minji Jeon, Kwanghun Choi, Sungjoon Park, and Jawoo Kang* "Development and utilization of BEST(Biomedical Entity Search Tool) API" Korean Institute of Information Scientists and Engineers (KIISE), 2015

2012-2014

• Minji Jeon, Jaewoo Kang* "Research trends on drug response prediction for personalized cancer therapeutics" Korean Institute of Information Scientists and Engineers (KIISE), 2014

• Minji Jeon, Sunwon Lee, Kyubum Lee, Aik-Choon Tan, Jaewoo Kang*  "BEReX: biomedical entity-relationship eXplorer", Bioinformatics, 2013, 30.1: 135-136. 

• Kyubum Lee, Sunwon Lee, Minji Jeon, Jaehoon Choi, Jaewoo Kang* "Drug-drug interaction analysis using heterogeneous biological information network" Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on. IEEE, 2012. p. 1-5.