Jonathan Jacobs
@bioinformer.bsky.social
UofArizona #Aggie > UofMaryland PhD > NIH/NCI PostDoc > Biodefense, Pathogen #Genomics, #Bioinformatics, Data Authenticity, #BioSecurity. ++PC gaming, DnD, EDM, punk, goth, backcountry backpacking, porsche
🎲♟️👾🎮 🎸 🧪 🧬 🖥 🦠🚀🏎️
he/him. On Steam: @bioinformer
🎲♟️👾🎮 🎸 🧪 🧬 🖥 🦠🚀🏎️
he/him. On Steam: @bioinformer
Museum island and the Cathedral
December 3, 2025 at 5:43 AM
Museum island and the Cathedral
Guo, Yufeng, Liqiu Su, Qi Liu, Yan Zhu, Zongjie Dai, and Qinhong Wang. 2022. “Dissecting Carbon Metabolism of Yarrowia Lipolytica Type Strain W29 Using Genome-Scale Metabolic Modelling.” Computational and Structural Biotechnology Journal 20: 2503–11. www.sciencedirect.com/science/arti...
Engineering Yarrowia lipolytica for enhanced lipid productivity in nutrient-rich conditions: A scalable approach to microbial lipid production
Climate change is reducing crop yields and increasing price volatility for commodities like cocoa and palm oil, thereby driving the need for sustainab…
www.sciencedirect.com
November 7, 2025 at 5:59 PM
Guo, Yufeng, Liqiu Su, Qi Liu, Yan Zhu, Zongjie Dai, and Qinhong Wang. 2022. “Dissecting Carbon Metabolism of Yarrowia Lipolytica Type Strain W29 Using Genome-Scale Metabolic Modelling.” Computational and Structural Biotechnology Journal 20: 2503–11. www.sciencedirect.com/science/arti...
Guo, Yufeng, Liqiu Su, Qi Liu, Yan Zhu, Zongjie Dai, and Qinhong Wang. 2022. “Dissecting Carbon Metabolism of Yarrowia Lipolytica Type Strain W29 Using Genome-Scale Metabolic Modelling.” Computational and Structural Biotechnology Journal 20: 2503–11.
www.csbj.org/article/S200...
www.csbj.org/article/S200...
Dissecting carbon metabolism of Yarrowia lipolytica type strain W29 using genome-scale metabolic modelling
The growing environmental concerns of fossil-based chemical production urge the development
of alternative microbial bioproduction [1,2]. As a non-conventional model oleaginous
yeast [3], Yarrowia lip...
www.csbj.org
November 7, 2025 at 5:59 PM
Guo, Yufeng, Liqiu Su, Qi Liu, Yan Zhu, Zongjie Dai, and Qinhong Wang. 2022. “Dissecting Carbon Metabolism of Yarrowia Lipolytica Type Strain W29 Using Genome-Scale Metabolic Modelling.” Computational and Structural Biotechnology Journal 20: 2503–11.
www.csbj.org/article/S200...
www.csbj.org/article/S200...
Liu, Qianxi, Haoran Bi, Kai Wang, et al. 2023. “Revealing the Mechanisms of Enhanced β-Farnesene Production in Yarrowia Lipolytica through Metabolomics Analysis.” International Journal of Molecular Sciences 24 (24): 17366. doi.org/10.3390/ijms...
doi.org
November 7, 2025 at 5:59 PM
Liu, Qianxi, Haoran Bi, Kai Wang, et al. 2023. “Revealing the Mechanisms of Enhanced β-Farnesene Production in Yarrowia Lipolytica through Metabolomics Analysis.” International Journal of Molecular Sciences 24 (24): 17366. doi.org/10.3390/ijms...
Qiao, He, Zaihang Dong, Bofan Yu, Xiao Hong, and Xuye Lang. 2025. “Transcriptomics-Driven Engineering of Yarrowia Lipolytica for Enhanced Fatty Acid Biosynthesis.” ACS Synthetic Biology 14 (9): 3520–29. doi.org/10.1021/acss....
Transcriptomics-Driven Engineering of Yarrowia lipolytica for Enhanced Fatty Acid Biosynthesis
While Yarrowia lipolytica has gained prominence as a microbial chassis for biomanufacturing, its broader application faces two critical limitations: incomplete genetic annotation and insufficient char...
doi.org
November 7, 2025 at 5:59 PM
Qiao, He, Zaihang Dong, Bofan Yu, Xiao Hong, and Xuye Lang. 2025. “Transcriptomics-Driven Engineering of Yarrowia Lipolytica for Enhanced Fatty Acid Biosynthesis.” ACS Synthetic Biology 14 (9): 3520–29. doi.org/10.1021/acss....
Patterson, Kurt, James Yu, Jenny Landberg, et al. 2018. “Functional Genomics for the Oleaginous Yeast Yarrowia Lipolytica.” Metabolic Engineering 48 (July): 184–96. www.sciencedirect.com/science/arti...
Functional genomics for the oleaginous yeast Yarrowia lipolytica
Oleaginous yeasts are valuable systems for biosustainable production of hydrocarbon-based chemicals. Yarrowia lipolytica is one of the best characteri…
www.sciencedirect.com
November 7, 2025 at 5:59 PM
Patterson, Kurt, James Yu, Jenny Landberg, et al. 2018. “Functional Genomics for the Oleaginous Yeast Yarrowia Lipolytica.” Metabolic Engineering 48 (July): 184–96. www.sciencedirect.com/science/arti...
Xie, Dongming, Ethel N. Jackson, and Quinn Zhu. 2015. “Sustainable Source of Omega-3 Eicosapentaenoic Acid from Metabolically Engineered Yarrowia Lipolytica: From Fundamental Research to Commercial Production.” Applied Microbiology and Biotechnology 99 (4): 1599–610. doi.org/10.1007/s002....
Sustainable source of omega-3 eicosapentaenoic acid from metabolically engineered Yarrowia lipolytica: from fundamental research to commercial production - Applied Microbiology and Biotechnology
The omega-3 fatty acids, cis-5, 8, 11, 14, and 17-eicosapentaenoic acid (C20:5; EPA) and cis-4, 7, 10, 13, 16, and 19-docosahexaenoic acid (C22:6; DHA), have wide-ranging benefits in improving heart h...
doi.org
November 7, 2025 at 5:59 PM
Xie, Dongming, Ethel N. Jackson, and Quinn Zhu. 2015. “Sustainable Source of Omega-3 Eicosapentaenoic Acid from Metabolically Engineered Yarrowia Lipolytica: From Fundamental Research to Commercial Production.” Applied Microbiology and Biotechnology 99 (4): 1599–610. doi.org/10.1007/s002....
Metz, James G., Paul Roessler, Daniel Facciotti, et al. 2001. “Production of Polyunsaturated Fatty Acids by Polyketide Synthases in Both Prokaryotes and Eukaryotes.” Science 293 (5528): 290–93. doi.org/10.1126/scie...
Production of Polyunsaturated Fatty Acids by Polyketide Synthases in Both Prokaryotes and Eukaryotes
Polyunsaturated fatty acids (PUFAs) are essential membrane components in higher eukaryotes and are the precursors of many lipid-derived signaling molecules. Here, pathways for PUFA synthesis are descr...
doi.org
November 7, 2025 at 5:59 PM
Metz, James G., Paul Roessler, Daniel Facciotti, et al. 2001. “Production of Polyunsaturated Fatty Acids by Polyketide Synthases in Both Prokaryotes and Eukaryotes.” Science 293 (5528): 290–93. doi.org/10.1126/scie...
Xue, Zhixiong, Pamela L Sharpe, Seung-Pyo Hong, et al. 2013. “Production of Omega-3 Eicosapentaenoic Acid by Metabolic Engineering of Yarrowia Lipolytica.” Nature Biotechnology 31 (8): 734–40. doi.org/10.1038/nbt....
Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica - Nature Biotechnology
Metabolic engineering of the oleaginous yeast Yarrowia lipolytica greatly enhances yields of omega-3 eicosapentaenoic acid.
doi.org
November 7, 2025 at 5:59 PM
Xue, Zhixiong, Pamela L Sharpe, Seung-Pyo Hong, et al. 2013. “Production of Omega-3 Eicosapentaenoic Acid by Metabolic Engineering of Yarrowia Lipolytica.” Nature Biotechnology 31 (8): 734–40. doi.org/10.1038/nbt....
Bigey, Frédéric, Emilie Pasteur, Xymena Połomska, et al. 2023. “Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia Lipolytica.” Journal of Fungi 9 (1): 76. www.mdpi.com/2309-608X/9/...
www.mdpi.com
November 7, 2025 at 5:59 PM
Bigey, Frédéric, Emilie Pasteur, Xymena Połomska, et al. 2023. “Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia Lipolytica.” Journal of Fungi 9 (1): 76. www.mdpi.com/2309-608X/9/...
And for those who are interest - here's a list of recent papers we've included in the JC 👇
November 7, 2025 at 5:59 PM
And for those who are interest - here's a list of recent papers we've included in the JC 👇
So far - this journal club has been one of the best and most fun scientific discussion groups I've had in years.
Highly recommend doing something like this for your own team if you don't already do so. It's been just excellent.
Highly recommend doing something like this for your own team if you don't already do so. It's been just excellent.
November 7, 2025 at 5:59 PM
So far - this journal club has been one of the best and most fun scientific discussion groups I've had in years.
Highly recommend doing something like this for your own team if you don't already do so. It's been just excellent.
Highly recommend doing something like this for your own team if you don't already do so. It's been just excellent.
Everyone's busy too - so we didn't want people saying they would show up, but then cancelling last minute or not showing. So... i scheduled it for 4pm on Fridays on purpose. This time slot has worked really well to make sure everyone who shows up actually wants to be there and is engaged.
November 7, 2025 at 5:59 PM
Everyone's busy too - so we didn't want people saying they would show up, but then cancelling last minute or not showing. So... i scheduled it for 4pm on Fridays on purpose. This time slot has worked really well to make sure everyone who shows up actually wants to be there and is engaged.
We (try) to not talk about project topics and keep things on the science, on the papers we're reviewing.
We also have some basic rules around presenting vs. being a "lurker" (attending but not presenting), and expectations on at least reading the abstract and some of the figures.
We also have some basic rules around presenting vs. being a "lurker" (attending but not presenting), and expectations on at least reading the abstract and some of the figures.
November 7, 2025 at 5:59 PM
We (try) to not talk about project topics and keep things on the science, on the papers we're reviewing.
We also have some basic rules around presenting vs. being a "lurker" (attending but not presenting), and expectations on at least reading the abstract and some of the figures.
We also have some basic rules around presenting vs. being a "lurker" (attending but not presenting), and expectations on at least reading the abstract and some of the figures.
While it was originally intended to be only for co-workers and collaborators working on a shared (DARPA funded) research program focused on Y. lipolytica engineering - it has grown to include over 30 scientists, postdocs and students from industry and academia.
November 7, 2025 at 5:59 PM
While it was originally intended to be only for co-workers and collaborators working on a shared (DARPA funded) research program focused on Y. lipolytica engineering - it has grown to include over 30 scientists, postdocs and students from industry and academia.