Coupling flux balance analysis with reactive transport modeling through machine learning for rapid and stable simulation of microbial metabolic switching

Authors: Hyun-Seob Song, Firnaaz Ahamed, Joon-Yong Lee, Christopher S. Henry, Janaka N. Edirisinghe, William C. Nelson, Xingyuan Chen, J. David Moulton, Timothy D. Scheibe

Source: Scientific Reports, Vol 15, Iss 1, Pp 1-10 (2025)

Subject Terms: Artificial neural networks, Surrogate model, Flux balance analysis, Reactive transport modeling, Metabolic switching, Medicine, Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/b77c0880a62c4f35b899a7832394a28b

LipidOz enables automated elucidation of lipid carbon–carbon double bond positions from ozone-induced dissociation mass spectrometry data

Authors: Dylan H. Ross, Joon-Yong Lee, Aivett Bilbao, Daniel J. Orton, Josie G. Eder, Meagan C. Burnet, Brooke L. Deatherage Kaiser, Jennifer E. Kyle, Xueyun Zheng

Source: Communications Chemistry, Vol 6, Iss 1, Pp 1-11 (2023)

Subject Terms: Chemistry, QD1-999

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3669

Access URL: https://doaj.org/article/da325e63f1314553a0a38f572cd4ecf3

Metabolomic, photoprotective, and photosynthetic acclimatory responses to post‐flowering drought in sorghum

Authors: Christopher R. Baker, Dhruv Patel‐Tupper, Benjamin J. Cole, Lindsey G. Ching, Oliver Dautermann, Armen C. Kelikian, Cayci Allison, Julie Pedraza, Julie Sievert, Aivett Bilbao, Joon‐Yong Lee, Young‐Mo Kim, Jennifer E. Kyle, Kent J. Bloodsworth, Vanessa Paurus, Kim K. Hixson, Robert Hutmacher, Jeffery Dahlberg, Peggy G. Lemaux, Krishna K. Niyogi

Source: Plant Direct, Vol 7, Iss 11, Pp n/a-n/a (2023)

Subject Terms: antioxidants, drought tolerance, galactinol, metabolomics, photoprotection, photosynthesis, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/2475-4455

Access URL: https://doaj.org/article/d9564b6e95344982a7f8a2f72d85b144

A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants

Authors: Scotland E. Farley, Jennifer E. Kyle, Hans C. Leier, Lisa M. Bramer, Jules B. Weinstein, Timothy A. Bates, Joon-Yong Lee, Thomas O. Metz, Carsten Schultz, Fikadu G. Tafesse

Source: Nature Communications, Vol 13, Iss 1, Pp 1-14 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/8045e4b0f34b44b689fa4b922259ce55

Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes

Authors: Ryan McClure, Yuliya Farris, Robert Danczak, William Nelson, Hyun-Seob Song, Aimee Kessell, Joon-Yong Lee, Sneha Couvillion, Christopher Henry, Janet K. Jansson, Kirsten S. Hofmockel

Source: mSystems, Vol 7, Iss 5 (2022)

Subject Terms: soil microbiome, consortia, model microbiome, chitin decomposition, metabolic interactions, chitin, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/d0fb3cb1aea643bd847c8447a403177f

A global lipid map defines a network essential for Zika virus replication

Authors: Hans C. Leier, Jules B. Weinstein, Jennifer E. Kyle, Joon-Yong Lee, Lisa M. Bramer, Kelly G. Stratton, Douglas Kempthorne, Aaron R. Navratil, Endale G. Tafesse, Thorsten Hornemann, William B. Messer, Edward A. Dennis, Thomas O. Metz, Eric Barklis, Fikadu G. Tafesse

Source: Nature Communications, Vol 11, Iss 1, Pp 1-15 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/e3700eeb09074ab692ee327211963128

Deep learning predicts microbial interactions from self-organized spatiotemporal patterns

Authors: Joon-Yong Lee, Natalie C. Sadler, Robert G. Egbert, Christopher R. Anderton, Kirsten S. Hofmockel, Janet K. Jansson, Hyun-Seob Song

Source: Computational and Structural Biotechnology Journal, Vol 18, Iss , Pp 1259-1269 (2020)

Subject Terms: Machine learning, Agent-based modeling, Soil microbiomes, Microscopy imaging technology, Network inference, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037020302865; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/eb89b03151474034ac3a7ad15c35281f

Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling

Authors: Hyun-Seob Song, James C. Stegen, Emily B. Graham, Joon-Yong Lee, Vanessa A. Garayburu-Caruso, William C. Nelson, Xingyuan Chen, J. David Moulton, Timothy D. Scheibe

Source: Frontiers in Microbiology, Vol 11 (2020)

Subject Terms: substrate-explicit modeling, microbial-explicit modeling, enzyme-explicit modeling, integrative biogeochemical modeling, high-resolution metabolomics, FTICR-MS, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2020.531756/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/9c5047d0c79a47e49319fdd8abbc009e

Blazing Signature Filter: a library for fast pairwise similarity comparisons

Authors: Joon-Yong Lee, Grant M. Fujimoto, Ryan Wilson, H. Steven Wiley, Samuel H. Payne

Source: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-12 (2018)

Subject Terms: Pairwise similarity comparison, Filtering, Large-scale data mining, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-018-2210-6; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/dc6ed44605af44c883360d5a458797b6

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

Access URL: https://doaj.org/article/c60a0facea3342e3a5ea835dc0c84575

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations

Authors: Taniya Roy Chowdhury, Joon-Yong Lee, Eric M. Bottos, Colin J. Brislawn, Richard Allen White, Lisa M. Bramer, Joseph Brown, Jeremy D. Zucker, Young-Mo Kim, Ari Jumpponen, Charles W. Rice, Sarah J. Fansler, Thomas O. Metz, Lee Ann McCue, Stephen J. Callister, Hyun-Seob Song, Janet K. Jansson

Source: mSystems, Vol 4, Iss 4 (2019)

Subject Terms: metaphenome, metatranscriptome, multi-omics, soil microbiome, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/47047ddab7ff4fd997a736f630733e1b

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

Statistical Modeling of Indirect Paths for UWB Sensors in an Indoor Environment

Authors: Moona Lee, Joon-Yong Lee

Source: Sensors, Vol 17, Iss 1, p 43 (2016)

Subject Terms: ultra-wideband, indirect path, human tracking, Chemical technology, TP1-1185

File Description: electronic resource

Relation: http://www.mdpi.com/1424-8220/17/1/43; https://doaj.org/toc/1424-8220

Access URL: https://doaj.org/article/d7d23d39cc00412f9bbbbaa217545252

Multi-objective evolutionary design of fuzzy logic controllers for car parking problem

Authors: Joon-Yong Lee, Min-Soeng Kim, Ju-Jang Lee

Source: 9th IEEE International Workshop on Advanced Motion Control, 2006. Advanced Motion Control, 2006. 9th IEEE International Workshop on. :607-612 2006

Relation: 2006 9th IEEE International Workshop on Advanced Motion Control

Accuracy Enhancement for UWB Indoor Positioning Using Ray Tracing

Authors: Yung-Hoon Jo, Joon-Yong Lee, Dong-Heon Ha, Shin-Hoo Kang

Source: 2006 IEEE/ION Position, Location, And Navigation Symposium Position, Location, And Navigation Symposium, 2006 IEEE/ION. :565-568 2006

Relation: 2006 IEEE/ION Position, Location, And Navigation Symposium

Ranging Performance of UWB radio in Multipath and Multiuser environments

Authors: Joon-Yong Lee, Sungyul Yoo

Source: 2005 IEEE 16th International Symposium on Personal, Indoor and Mobile Radio Communications Personal, Indoor and Mobile Radio Communications Personal, Indoor and Mobile Radio Communications, 2005. PIMRC 2005. IEEE 16th International Symposium on. 1:496-500 2005

Relation: 2005 IEEE 16th International Symposium on Personal, Indoor and Mobile Radio Communications

Large error performance of UWB ranging

Authors: Joon-Yong Lee, Sungyul Yoo

Source: 2005 IEEE International Conference on Ultra-Wideband Ultra-wideband Ultra-Wideband, 2005. ICU 2005. 2005 IEEE International Conference on. :308-313 2005

Relation: 2005 IEEE International Conference on Ultra-Wideband

Modeling of the emotional model with friendship for familiarity of robot

Authors: Tae-Yong Choi, Joon-Yong Lee, Jun-ho Shin, Ju-Jang Lee

Source: 2005 IEEE/RSJ International Conference on Intelligent Robots and Systems Intelligent robots and systems Intelligent Robots and Systems, 2005. (IROS 2005). 2005 IEEE/RSJ International Conference on. :1235-1240 2005

Relation: 2005 IEEE/RSJ International Conference on Intelligent Robots and Systems

Multi-objective walking trajectories generation for a biped robot

Authors: Joon-Yong Lee, Min-Soeng Kim, Ju-Jang Lee

Source: 2004 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (IEEE Cat. No.04CH37566) Intelligent robots and systems Intelligent Robots and Systems, 2004. (IROS 2004). Proceedings. 2004 IEEE/RSJ International Conference on. 4:3853-3858 vol.4 2004

Relation: 2004 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)

Optimal walking trajectory generation for a biped robot using multi-objective evolutionary algorithm

Authors: Joon-Yong Lee, Ju-Jang Lee

Source: 2004 5th Asian Control Conference (IEEE Cat. No.04EX904) Asian control conference Control Conference, 2004. 5th Asian. 1:357-364 Vol.1 2004

Relation: 2004 5th Asian Control Conference