Evaluating oleaginous yeasts for enhanced microbial lipid production using sweetwater as a sustainable feedstock

Authors: Valériane Malika Keita, Yi Qing Lee, Meiyappan Lakshmanan, Dave Siak-Wei Ow, Paul Staniland, Jessica Staniland, Ian Savill, Kang Lan Tee, Tuck Seng Wong, Dong-Yup Lee

Source: Microbial Cell Factories, Vol 23, Iss 1, Pp 1-17 (2024)

Subject Terms: Oleaginous yeasts, Microbial oil, Microbial cell factories, Sweetwater, Comparative omics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/1475-2859

Access URL: https://doaj.org/article/405144ec2f70414e94c01bea0a8ed6d3

Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations

Authors: Yoon-Mi Choi, Dong-Hyuk Choi, Yi Qing Lee, Lokanand Koduru, Nathan E. Lewis, Meiyappan Lakshmanan, Dong-Yup Lee

Source: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 3736-3745 (2023)

Subject Terms: Flux balance analysis (FBA), Parsimonious flux balance analysis (pFBA), Biomass equation, Ensemble modeling, Macromolecular composition, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037023002532; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/0a884a6507744c7babcf42477f68670a

Genome-scale metabolic modeling and in silico analysis of opportunistic skin pathogen Cutibacterium acnes

Authors: Su-Kyung Kim, Minouk Lee, Yi Qing Lee, Hyun Jun Lee, Mina Rho, Yunkwan Kim, Jung Yeon Seo, Sung Hun Youn, Seung Jin Hwang, Nae Gyu Kang, Choong-Hwan Lee, Seo-Young Park, Dong-Yup Lee

Source: Frontiers in Cellular and Infection Microbiology, Vol 13 (2023)

Subject Terms: skin microbiome, skin pathogen, Cutibacterium acnes, acne vulgaris, genome-scale metabolic model, Wood-Werkman cycle, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcimb.2023.1099314/full; https://doaj.org/toc/2235-2988

Access URL: https://doaj.org/article/fb5a3fc5aef7466a9bcb573719d232c5

Liver’s influence on the brain through the action of bile acids

Authors: Xin Yi Yeo, Li Yang Tan, Woo Ri Chae, Dong-Yup Lee, Yong-An Lee, Torsten Wuestefeld, Sangyong Jung

Source: Frontiers in Neuroscience, Vol 17 (2023)

Subject Terms: liver, brain, bile acid, neurodegeneration, gut microbiome, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnins.2023.1123967/full; https://doaj.org/toc/1662-453X

Access URL: https://doaj.org/article/51a3148005c24580b290d41f0f4f9e6f

Editorial: Heterologous Protein Expression and Production Platforms: The How, Now and Wow of It, Volume II

Authors: Jacinta S. D’Souza, Siddhesh B. Ghag, Dong-Yup Lee

Source: Frontiers in Bioengineering and Biotechnology, Vol 10 (2022)

Subject Terms: recombinant proteins, genetic engineering, overexpression platform, expression tags, microbial factories, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fbioe.2022.946381/full; https://doaj.org/toc/2296-4185

Access URL: https://doaj.org/article/5bb8f6692aa146ecbb42de5d0804b84c

Metabolomic Elucidation of the Effect of Sucrose on the Secondary Metabolite Profiles in Melissa officinalis by Ultraperformance Liquid Chromatography–Mass Spectrometry

Authors: Sooah Kim, Jungyeon Kim, Nahyun Kim, Dongho Lee, Hojoung Lee, Dong-Yup Lee, Kyoung Heon Kim

Source: ACS Omega, Vol 5, Iss 51, Pp 33186-33195 (2020)

Subject Terms: Chemistry, QD1-999

File Description: electronic resource

Relation: https://doaj.org/toc/2470-1343

Access URL: https://doaj.org/article/8aaef5fdcbca4e5fb61644e54960b809

Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics

Authors: Lokanand Koduru, Meiyappan Lakshmanan, Shawn Hoon, Dong-Yup Lee, Yuan Kun Lee, Dave Siak-Wei Ow

Source: Frontiers in Microbiology, Vol 13 (2022)

Subject Terms: systems biology, gut microbiota, inflammatory disorders, probiotics, postbiotics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2022.846555/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/b8c41423612f4c6c9344cde186afbac3

Editorial: Predictive Modeling of Human Microbiota and Their Role in Health and Disease

Authors: Hyun-Seob Song, Stephen R. Lindemann, Dong-Yup Lee

Source: Frontiers in Microbiology, Vol 12 (2021)

Subject Terms: microbial biomarkers, machine learning, microbial association networks, species and gene profiling, precision nutrition, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2021.782871/full; https://doaj.org/toc/1664-302X

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In silico model-guided identification of transcriptional regulator targets for efficient strain design

Authors: Lokanand Koduru, Meiyappan Lakshmanan, Dong-Yup Lee

Source: Microbial Cell Factories, Vol 17, Iss 1, Pp 1-12 (2018)

Subject Terms: Model-guided strain design, Genome-scale metabolic model, Constraint-based flux analysis, Transcriptional regulator, Systems biology, Microbiology, QR1-502

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12934-018-1015-7; https://doaj.org/toc/1475-2859

Access URL: https://doaj.org/article/238318946ea24da7bd64cb630c054822

Improving catalytic activity of the Baeyer–Villiger monooxygenase-based Escherichia coli biocatalysts for the overproduction of (Z)-11-(heptanoyloxy)undec-9-enoic acid from ricinoleic acid

Authors: Ji-Min Woo, Eun-Yeong Jeon, Eun-Ji Seo, Joo-Hyun Seo, Dong-Yup Lee, Young Joo Yeon, Jin-Byung Park

Source: Scientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/798a8107b85d4efabf5957a7c2422088

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng

Authors: Murukarthick Jayakodi, Beom-Soon Choi, Sang-Choon Lee, Nam-Hoon Kim, Jee Young Park, Woojong Jang, Meiyappan Lakshmanan, Shobhana V. G. Mohan, Dong-Yup Lee, Tae-Jin Yang

Source: BMC Plant Biology, Vol 18, Iss 1, Pp 1-7 (2018)

Subject Terms: Panax ginseng, Genome database, Ginseng annotation, Ginseng genome browser, Botany, QK1-989

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12870-018-1282-9; https://doaj.org/toc/1471-2229

Access URL: https://doaj.org/article/b38e4088d25145da8fd2f7b606d947ec

Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data

Authors: Joon-Yong Lee, Shin Haruta, Souichiro Kato, Hans C. Bernstein, Stephen R. Lindemann, Dong-Yup Lee, Jim K. Fredrickson, Hyun-Seob Song

Source: Frontiers in Microbiology, Vol 10 (2020)

Subject Terms: microbial communities, microbial ecology, context dependence, network inference, interspecies interactions, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2019.03049/full; https://doaj.org/toc/1664-302X

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Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

Authors: Hyun-Seob Song, Joon-Yong Lee, Shin Haruta, William C. Nelson, Dong-Yup Lee, Stephen R. Lindemann, Jim K. Fredrickson, Hans C. Bernstein

Source: Frontiers in Microbiology, Vol 10 (2019)

Subject Terms: context dependence, network inference, rule-based approach, microbiome modeling, microbial ecology, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2019.01264/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/8fd17fce878643669876b87b6a956ee3

Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars

Authors: Yun Sun Lee, Hyun-Seung Park, Dong-Kyu Lee, Murukarthick Jayakodi, Nam-Hoon Kim, Sang-Choon Lee, Atreyee Kundu, Dong-Yup Lee, Young Chang Kim, Jun Gyo In, Sung Won Kwon, Tae-Jin Yang

Source: Journal of Ginseng Research, Vol 41, Iss 1, Pp 60-68 (2017)

Subject Terms: adventitious root, metabolome, Panax ginseng, primary metabolic pathways, transcriptome, Botany, QK1-989

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S1226845316000026; https://doaj.org/toc/1226-8453

Access URL: https://doaj.org/article/209e6b2f2bd740aa959e9127d427d184

Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii

Authors: Na-Rae Lee, Choong Hwan Lee, Dong-Yup Lee, Jin-Byung Park

Source: Microorganisms, Vol 8, Iss 4, p 539 (2020)

Subject Terms: Megasphaera elsdenii, hexanoic acid, bifurcated pathway, genome-scale metabolic model, constraint-based modeling, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/8/4/539; https://doaj.org/toc/2076-2607

Access URL: https://doaj.org/article/0503c8df86924c7d947aa78e03f41d7a

Comprehensive Secondary Metabolite Profiling Toward Delineating the Solid and Submerged-State Fermentation of Aspergillus oryzae KCCM 12698

Authors: Su Y. Son, Sunmin Lee, Digar Singh, Na-Rae Lee, Dong-Yup Lee, Choong H. Lee

Source: Frontiers in Microbiology, Vol 9 (2018)

Subject Terms: Aspergillus oryzae, solid state fermentation, submerged fermentation, metabolomics/metabolite profiling, antimicrobial activity, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2018.01076/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/8f4b0b2305284d7287af4e6ab037144c

Modeling rice metabolism: from elucidating environmental effects on cellular phenotype to guiding crop improvement

Authors: Meiyappan Lakshmanan, Maurice C. Y. Cheung, Bijayalaxmi Mohanty, Dong-Yup Lee

Source: Frontiers in Plant Science, Vol 7 (2016)

Subject Terms: Metabolism, Systems Biology, rice, Flux-balance analysis, -omics data, genome-scale metabolic networks and models, Plant culture, SB1-1110

File Description: electronic resource

Relation: http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01795/full; https://doaj.org/toc/1664-462X

Access URL: https://doaj.org/article/3e437bed02614c22bc95e7e2570840bf

Coopetitive Supply Chain Relationship Model: Application to the Smartphone Manufacturing Network.

Authors: Jeremy Jie Ming Kwok, Dong-Yup Lee

Source: PLoS ONE, Vol 10, Iss 7, p e0132844 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4506052?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/52884377f8db4f3b98aa02d3b7acb2a1

Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells.

Authors: Vanessa M Y Ding, Paul J Boersema, Leong Yan Foong, Christian Preisinger, Geoffrey Koh, Subaashini Natarajan, Dong-Yup Lee, Jos Boekhorst, Berend Snel, Simone Lemeer, Albert J R Heck, Andre Choo

Source: PLoS ONE, Vol 6, Iss 3, p e17538 (2011)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21437283/pdf/?tool=EBI; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/adbbe8a9de054032b918e4b6a0ff1945

Integrated transcriptome and binding sites analysis implicates E2F in the regulation of self-renewal in human pluripotent stem cells.

Authors: Hock Chuan Yeo, Thian Thian Beh, Jovina Jia Ling Quek, Geoffrey Koh, Ken Kwok Keung Chan, Dong-Yup Lee

Source: PLoS ONE, Vol 6, Iss 11, p e27231 (2011)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3208628?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/80176bfd331747cdbe27f6e8c02fd493