HIGHLIGHTS

2021 Vishal Patel*, Sunjae Lee* et al., “Rifaximin reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS Randomised-Controlled Trial”, J Hepatology 

2017                  Sunjae Lee*, Cheng Zhang*, Muhammad Arif*, Zhengtao Liu, Rui Benfeitas, Gholamreza Bidkhori, Sumit Deshmukh, Mohamed Al Shobky, Alen Lovric, Jan Boren, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu, “TCSBN: a database of tissue and cancer specific biological networks”, Nucleic Acids Research

2017                  Sunjae Lee*, Cheng Zhang*, Zhengtao Liu* Martina Klevstig, Bani Mukopadhyay, Matthias Bergentall, Resat Cinar, Marcus Ståhlman, Natasha Sikanic, Joshua K Park, Sumit Deshmukh, Azadeh M Harzandi, Tim Kuijpers, Morten Grøtli, Simon J Elsässer, Brain D Piening, Michael Snyder, Ulf Smith, Jens Nielsen, Fredrik Bäckhed, George Kunos, Mathias Uhlen, Jan Boren#, Adil Mardinoglu#, “Network analyses identify liver-specific targets for treating liver diseases”, Molecular Systems Biology

2016                 Sunjae Lee*, Cheng Zhang*, Murat Kilicarslan*, Brian D. Piening, Elias Bjornson, Björn M. Hallström, Albert K. Groen, Ele Ferrannini, Markku Laakso, Michael Snyder, Matthias Blüher, Mathias Uhlen, Jens Nielsen, Ulf Smith, Mireille J. Serlie, Jan Boren, Adil Mardinoglu, “Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance”, Cell Metabolism – Highlighted at Nature Reviews Endocrinology

2016                 Sunjae Lee, Adil Mardinoglu, Cheng Zhang, Doheon Lee, and Jens Nielsen, “Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis”, Nucleic Acids Research

PUBLICATIONS

* first authors # corresponding authors

2024 Vikas Singh et al., "Normalization of RNA-Seq Data using Adaptive Trimmed Mean with Multi-reference", Briefings in Bioinformatics (accepted)

2024 Choong-Jae Lee*, Tae-Young Jang*, Jee-Heun Kim*, Songwon Lim, Sunjae Lee, Jeong-Seok Nam, "The dysadherin/FAK axis promotes individual cell migration in colon cancer", International Journal of Biological Sciences

2023 Jiseung Kang et al., "Slow gut transit increases the risk of Alzheimer’s disease: an integrated study of the bi-national cohort in South Korea and Japan and Alzheimer’s disease model mice", Journal of Advanced Research

2023 Xinjie Song, Nikhil Kirtipal#, Sunjae Lee#, Petr Malý#, and Shiv Bharadwaj#, "Current therapeutic targets and multifaceted physiological impacts of caffeine", Phytotherapy Research

2023 Yeongmin Kim*, So-Yeon Shin*, Jihun Jeung*, Yumin Kim, Yun-Won Kang,  Sunjae Lee#, Chang-Myung Oh#, "Integrative analysis of mitochondrial metabolic reprogramming in early-stage colon and liver cancer", Frontiers in Oncology

2023 Jeong-Su Park et al., "Trogocytic molting of T cell microvilli upregulates T cell receptor surface expression and promotes clonal expansion", Nature Communications

2023 Jibeom Lee, Jiseung Kang, Yumin Kim, Sunjae Lee, Chang-Myung Oh, Tae Kim, "Integrated analysis of the microbiota-gut-brain axis in response to sleep deprivation and diet-induced obesity", Frontiers in Endocrinology

2023 Bouchra Ezzamouri, Dorines Rosario, Gholamreza Bidkhori, Sunjae Lee, Mathias Uhlen, Saeed Shoaie, "Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment", NPJ Systems Biology and Applications 

2022 Neelu Begum, Azadeh Harzandi, Sunjae Lee, Mathias Uhlen, David L Moyes, Saeed Shoaie, "Host-mycobiome metabolic interactions in health and disease",  Gut Microbes

2022 Yu Sim Lee, Seunghee Kang, Nayeon Kang, Jaehong Yu, Taesung Park, Sunjae Lee, Oran Kwon, "Effect of Ecklonia cava polyphenol on adiposity reduction is associated with gut microbiota composition in subjects with abdominal obesity: A secondary analysis", Journal of Functional Foods

2022 Abeer Shaalan*, Sunjae Lee*, Catherine Feart, Esther Garcia-Esquinas, David Gomez-Cabrero, Esther Lopez-Garcia, Martine Morzel, Eric Neyraud, Fernando Rodriguez-Artalejo, Ricarda Streich, Gordon Proctor, "Alterations in the Oral Microbiome Associated With Diabetes, Overweight, and Dietary Components", Frontiers in Nutrition

2022 Ceri Proffitt, Gholamreza Bidkhori, Sunjae Lee  et al., "Genome-scale metabolic modelling of the human gut microbiome reveals changes of the glyoxylate and dicarboxylate metabolism in metabolic disorders", iScience

2022 Namjeong Choi, Ha Na Jang, Jagyeong Oh, Jiyeon Ha, Hyungbin Park, Xuexiu Zheng, Sunjae Lee#, Haihong Shen#, "SRSF6 regulates alternative splicing of apoptotic Fas gene by targeting a novel RNA sequence", Cancers

2022 Byong-Sop Song*, Ji Sun Moon*, Jingwen Tian, Ho Yeop Lee, Seok-Hwan Kim, Seul Gi Kang, Jung Tae Kim, Ha Thi Nga, Rui Benfeitas, Yeongmin Kim, Sanghee Park, Robert R. Wolfe, Minho Shong, Sunjae Lee#, Il-Young Kim#, Hyon-Seung Yi#, "Mitoribosomal defects aggravate liver cancer via aberrant glycolytic flux and T cell exhaustion", Journal of ImmunoTherapy of Cancer (JITC)

2022 So-Young Yoon, Eunhong Jang, Naho Ko, Minseok Kim, Su Yoon Kim, Yeojin Moon, Jeong-Seok Nam, Sunjae Lee, Youngsoo Jun, "A Genome-Wide Screen Reveals That Endocytic Genes Are Important for Pma1p Asymmetry during Cell Division in Saccharomyces cerevisiae",   International Journal of Molecular Sciences (IJMS)

2021 Jinmyung Jung, Yongdeuk Hwang, Hongryul Ahn, Sunjae Lee# and Sunyong Yoo#, "Precise Characterization of Genetic Interactions in Cancer via Molecular Network Refining Processes", International Journal of Molecular Sciences (IJMS)

2021 Vishal Patel*, Sunjae Lee* et al., “Rifaximin reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS Randomised-Controlled Trial”, J Hepatology 

2021 Chang-Hyun Kim*, Sang-Moo Park*, Sun-jae Lee*, Young-Dae Kim, Se-Hwan Jang, Seon-Min Woo, Taeg-Kyu Kwon, Zee-Yong Park, Ik-Joo Chung, Hye-Ran Kim#, Chang-Duk Jun#, "NSrp70 is a lymphocyte-essential splicing factor that controls thymocyte development", Nucleic Acids Research 

2021 So-Yeon Park, Ji-Young Kim, Gyu-Beom Jang, Jang-Hyun Choi, Jee-Heun Kim, Choong-Jae Lee, Sunjae Lee, Jeong-Heum Baek, Kwan-Kyu Park, Jin-Man Kim, Hee Jin Chang, Nam-Chul Cho, Jeong-Seok Nam, “Aberrant activation of the CD45-Wnt signaling axis promotes stemness and therapy resistance in colorectal cancer cells”, Theranostics

2021 Suhyeon Park, Yumin Kim, Jibeom Lee, Jeong Yun Lee, Hail Kim, Sunjae Lee# and Chang-Myung Oh#, “A Systems Biology Approach to Investigating the Interaction Between Serotonin Synthesis by Tryptophan Hydroxylase and the Metabolic Homeostasis”, International Journal of Molecular Sciences (IJMS)

2021 Azadeh Harzandi, Sunjae Lee, Gholamreza Bidkhori et al., “Acute kidney injury leading to CKD is associated with a persistence of metabolic dysfunction and hypertriglyceridemia”, iScience

2021                  Dorines Rosario, Gholamreza Bidkhori, Sunjae Lee at al., “Systematic Analysis of Host-Microbiome Interactions Revealed the Key Role of Bacterial Folate and Homocysteine Metabolism in Parkinson’s Disease”, Cell Reports

2020                  Stefania Vaga*, Sunjae Lee* et al., “Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals”, Scientific Reports (Top 100 in Microbiology Collection, 2020)

2020                 Abdellah Tebani, Anders Gummesson, Wen Zhong, Ina Schuppe Koistinen, Tadepally Lakshmikanth, Lisa M Olsson, Fredrik Boulund, Maja Neiman, Hans Stenlund, Cecilia Hellström, Max J Karlsson, Muhammad Arif, Tea Dodig-Crnković, Adil Mardinoglu, Sunjae Lee, Cheng Zhang, Yang Chen, Axel Olin, Jaromir Mikes, Hanna Danielsson, Kalle von Feilitzen, Per-Anders Jansson, Oskar Angerås, Mikael Huss, Sanela Kjellqvist, Jacob Odeberg, Fredrik Edfors, Valentina Tremaroli, Björn Forsström, Jochen M Schwenk, Peter Nilsson, Thomas Moritz, Fredrik Bäckhed, Lars Engstrand, Petter Brodin, Göran Bergström, Mathias Uhlen and Linn Fagerberg, “Integration of molecular profiles in a longitudinal wellness profiling cohort”, Nature Communications

2020                  Jang Won Son, Saeed Shoaie, and Sunjae Lee#, “Systems Biology: A Multi-Omics Integration Approach to Metabolism and Microbiome”, Endocrinology and Metabolism

2020                  Christian Lieven et al., “Memote for standardized genome-scale metabolic model testing”, Nature Biotechnology Correspondence

2020                  Victoria R Carr#, Elizabeth A. Witherden, Sunjae Lee, Saeed Shoaie, Peter Mullany, Gordon B. Proctor, David Gomez-Cabrero, and David L. Moyes#, “Abundance and diversity of resistomes differ between healthy oral cavities and gut”, Nature Communications

2019                  Sara Omenetti, Claudio Bussi, Amina Metidji, Adrea Iseppon, Sunjae Lee, Mauro Tolaini, Ying Li, Gavin Kelly, Probir Chakravarty, Saeed Shoaie, Maxmiliano G. Gutierrez, Brigitta Stockinger, “The intestine harbours functionally distinct homeostatic tissue-resident and inflammatory Th17 cells”, Immunity

2019                  Petia Kovatcheva-Datchary*, Saeed Shoaie*, Sunjae Lee, Annika Wahlstrom, Intawat Nookaew, Anna Hallen, Rosie Perkins, Jens Nielsen, Fredrik Backhed, “Simplified intestinal microbiota to study microbe-diet-host interactions in a mouse model”, Cell Reports – Highlighted in Nature Methods

2019                  Matthew J. Harms, Qian Li, Sunjae Lee, Cheng Zhang, Bengt Kull, Stefan Hallen, Anders Thorell, Ida Alexandersson, Carolina Hagberg, Xiao-Rong Peng, Adil Mardinoglu, Kirsty Spalding, Jeremie Boucher, “Mature human white adipocytes cultured under permeable membranes maintain identity, function, and can transdifferentiate into brown-like adipocytes”, Cell Reports

2019                  Zhengtao Liu*, Cheng Zhang*, Sunjae Lee, Woonghee Kim, Martina Klevstig, Azadeh M. Harzandi, Natasa Sikanic, Muhammad Arif, Marcus Ståhlman, Jens Nielsen, Mathias Uhlen, Jan Boren, and Adil Mardinoglu, “Pyruvate kinase L/R is regulator of lipid metabolism and mitochondrial function”, Metabolic Engineering

2019                  Rui Benfeitas*, Gholamreza Bidkhori*, Bani Mukhopadhyay*, Martina Klevstig, Muhammad Arif, Cheng Zhang, Sunjae Lee, Resat Cinar, Jens Nielsen, Mathias Uhlen, Jan Boren, George Kunos, and Adil Mardinoglu, “Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis”, EBioMedicine

2018                  Cheng Zhang, Gholamreza Bidkhori, Rui Benfeitas, Sunjae Lee, Muhammad Arif, Adil Mardinoglu, “ESS: a tool for genome-scale quantification of essentiality score for reaction/genes in constraint-based modeling”, Frontiers in Physiology

2018                  Brian Piening*, Wenyu Zhou*, Kevin Contrepois*, Hannes Rost*, Gucci Gu, Tejaswini Mishra, Blake Hansen, Eddy Bautista, Shana Leopold, Christine Yeh, Daniel Spakowicz, Kimberly Kukurba, Dalia Perelman, Colleen Craig, Elizabeth Colbert, Denis Salins, Shannon Rego, Sunjae Lee, Cheng Zhang, Jessica Wheeler, M. Reza Sailani, Liang Liang, Charles Abbott, Mark Gerstein, Adil Mardinoglu, Sharon Pitteri, Erica Sodergren, Tracey McLaughlin#, George M. Weinstock# and Michael Snyder#, “Integrative Personal Omics Profiles During Periods of Weight Gain and Loss”, Cell Systems

2018                  Adil Mardinoglu*#, Hao Wu*, Elias Bjornson, Cheng Zhang, Antti Hakkarainen, Sari M. Räsänen, Sunjae Lee, Rosellina M. Mancina, Mattias Bergentall, Leonie Bogl, Kirsi H. Pietiläinen, Sanni Söderlund, Niina Matikainen, Marcus Ståhlman, Per-Olof Bergh, Martin Adiels, Brian D. Piening, Marit Granér, Nina Lundbom, Kevin J Williams, Stefano Romeo, Jens Nielsen, Michael Snyder, Mathias Uhlén, Göran Bergström, Rosie Perkins, Hanns-Ulrich Marschall, Fredrik Bäckhed#, Marja-Riitta Taskinen and Jan Borén#, “An integrated understanding of the rapid metabolic benefits of a carbohydrate-restricted diet on hepatic steatosis in humans”, Cell Metabolism – Highlighted at Science Translational Medicine, 2018

2017                  Sunjae Lee*, Cheng Zhang*, Muhammad Arif*, Zhengtao Liu, Rui Benfeitas, Gholamreza Bidkhori, Sumit Deshmukh, Mohamed Al Shobky, Alen Lovric, Jan Boren, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu, “TCSBN: a database of tissue and cancer specific biological networks”, Nucleic Acids Research

2017                  Sunjae Lee*, Cheng Zhang*, Zhengtao Liu* Martina Klevstig, Bani Mukopadhyay, Matthias Bergentall, Resat Cinar, Marcus Ståhlman, Natasha Sikanic, Joshua K Park, Sumit Deshmukh, Azadeh M Harzandi, Tim Kuijpers, Morten Grøtli, Simon J Elsässer, Brain D Piening, Michael Snyder, Ulf Smith, Jens Nielsen, Fredrik Bäckhed, George Kunos, Mathias Uhlen, Jan Boren#, Adil Mardinoglu#, “Network analyses identify liver-specific targets for treating liver diseases”, Molecular Systems Biology

2017                 Mathias Uhlen, Cheng Zhang, Sunjae Lee, Evelina Sjöstedt, Linn Fagerberg, Gholamreza Bidkhori, Rui Benfeitas, Muhammad Arif, Zhengtao Liu, Fredrik Edfors, Kemal Sanli, Kalle von Feilitzen, Per Oksvold, Emma Lundberg, Sophia Hober, Peter Nilsson, Johanna Mattson,  Jochen M. Schwenk, Hans Brunnström, Bengt Glimelius, Tobias Sjöblom, Per-Henrik Edqvist, Dijana Djureinovic, Patrick Micke, Cecilia Lindskog, Adil Mardinoglu, Fredrik Ponten, “A pathology atlas of the human cancer transcriptome”, Science – Highlighted at Nature, 2017 

2017                 Jim Bosley*, Christofer Boren*, Sunjae Lee, Morten Grøtli, Jens Nielsen, Mathias Uhlen, Jan Boren, Adil Mardinoglue, “Improving the economics of NASH/NAFLD treatment through the use of systems biology”, Drug Discovery Today

2017                 Peter J. Thul*, Lovisa Åkesson*, Mikaela Wiking, Diana Mahdessian, Aikaterini Geladaki, Hammou Ait Blal, Tove Alm, Anna Asplund, Lars Björk, Lisa M. Breckels, Anna Bäckström, Frida Danielsson, Linn Fagerberg, Jenny Fall, Laurent Gatto, Christian Gnann, Sophia Hober, Martin Hjelmare, Fredric Johansson, Sunjae Lee, Cecilia Lindskog, Jan Mulder, Claire M. Mulvey, Peter Nilsson, Per Oksvold, Johan Rockberg, Rutger Schutten, Jochen M. Schwenk, Åsa Sivertsson, Evelina Sjöstedt, Marie Skogs, Charlotte Stadler, Devin P. Sullivan, Hanna Tegel, Casper Winsnes, Cheng Zhang, Martin Zwahlen, Adil Mardinoglu, Fredrik Pontén, Kalle von Feilitzen, Kathryn S. Lilley, Mathias Uhlén#, Emma Lundberg#, “A subcellular map of the human proteome”, Science – Highlighted at perspective in Science

2016                 Sunjae Lee*, Cheng Zhang*, Murat Kilicarslan*, Brian D. Piening, Elias Bjornson, Björn M. Hallström, Albert K. Groen, Ele Ferrannini, Markku Laakso, Michael Snyder, Matthias Blüher, Mathias Uhlen, Jens Nielsen, Ulf Smith, Mireille J. Serlie, Jan Boren, Adil Mardinoglu, “Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance”, Cell Metabolism – Highlighted at Nature Reviews Endocrinology 

2016                 Sunjae Lee, Adil Mardinoglu, Cheng Zhang, Doheon Lee, and Jens Nielsen, “Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis”, Nucleic Acids Research

2016                 Cheng Zhang, Sunjae Lee, Adil Mardinoglu#, and Qiang Hua#, “Investigating the Combinatory effects of biological networks on Gene Co-expression”, Frontiers in physiology

2015                 Docyong Kim, Jaeheyun Lee, Sunjae Lee, Junseok Park, and Doheon Lee, “Predicting Unintended Effects of Drugs based on Off-target Tissue Effects”, Biochem Biophys Res Commun

2014                 Sunjae Lee*, KiYoung Lee*, Seyeol Yoon, Jae W. Lee#, and Doheon Lee#, “Anomalies in network bridges involved in bile acid metabolism predict outcomes of colorectal cancer patients”, PLOS ONE

2013                 Woochang Hwang, Yongdeuk Hwang, Sunjae Lee, and Doheon Lee, “Rule-based multi-scale simulation for drug effect pathway analysis”, BMC Med Inform Decis Mak

2013                 Jaesub Park, Sunjae Lee, Kiseong Kim, and Doheon Lee, “Systematic Approach for Analyzing Drug Combination by Using Target-Enzyme Distance”, Interdisciplinary Bio Central

2012                 Hyojung Paik, Junho Kim, Sunjae Lee, Hyoung-Sam Heo, Cheol-Goo Hur#, and Doheon Lee#, “Prioritization of SNPs for genome-wide association studies using an interaction model of genetic variation, gene expression, and trait variation”, Mol Cells

2011                 Dokyun Na, Sunjae Lee, Gwan-Su Yi#, and Doheon Lee#, “Synthetic inter-species cooperation of host and virus for targeted genetic evolution”, J Biotechnol

2010                 Dokyun Na, Sunjae Lee, and Doheon Lee, “Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes.” BMC Syst Biol

2007                 Taewoo Ryu, Juhyun Jung, Sunjae Lee, Ho Jung Nam, Sun Woo Hong, Jae Wook Yoo, Dong-ki Lee, and Doheon Lee, “bZIPDB: a database of regulatory information for human bZIP transcription factors”, BMC Genomics