Jonathan Jacobs

This week be like…

That’s awesome! I’d love to see the results! Can you send a link? My group at ATCC has sequenced, assembled, annotated over 6500 microbial genomes including about 560 fungi as well as part of our authenticated reference genome initiative. You may be interested! Take a look over here genomes.atcc.org

Complete Diploid Genome of the Type Strain Yarrowia lipolytica YB-423 (ATCC 18942™) Abstract. Here, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a co

First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics

Complete Diploid Genome of the Type Strain Yarrowia lipolytica YB-423 (ATCC 18942™) Abstract. Here, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a co

First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics

“I just checked—it turns out that Art. II, Sec. 1 of the Constitution of the United States does *not* say ‘The executive Power shall be vested in a bunch of sociopaths who think they can do whatever the f*ck they want and make sh*t up as they go along.’” — George Conway

LIke... people just throw data format standards out the window in bioinformatics space to suit their needs? Who knew? 😭

the XKCD comic seems appropriate here...

Wondering how this count of retrotransposons in Yarrowia lipolytica compare to other yeasts... bc it seems really high and may explain why this species has such incredible genomic plasticity at the structural level.

(for context - this is from our recent publication on type-strain in JIMB)

It's a beautiful thing when this happens...

Also realizing that biologists, engineers, data scientists often use the same words differently.

Standards fail when semantic alignment fails.

Also see my post on providence vs provenance — this actually happened today. 🤦🏻‍♂️

Thing heard at lunch:

“AI magnifies data quality—for better or worse.” 🎯

“Biology needs to treated like a programming language…” 🤔

Audience question: “how is your work applicable to real world challenges, needs, or opportunities?”

Speaker: SynBio always has this tension btwn application of a new tech vs. can we do something in the first place. Personally, I like to try new things first and then find an application later.

🧐

Some takeaways from today’s meeting: 1/n

Engineers: “Why do we need so many replicates?”

Biologists: “Why are you iterating without statistical confidence?”

Looking forward to participating in today’s session at the MidAtlantic Synthetic Biology Symposium on digital biology & data standards in synthetic biology.

Lots of work to do in this space - and very happy NIST is organized a session on this topic.

#synbio

Attending MidAtlantic Synthetic Biology Symposium - happy to see @genegirl007.bsky.social presenting on her work at GATech! “Harnessing synthetic biology for next-generation therapeutics” #synbio #stemcells

But they post the salary ranges and I just can’t wrap my head around it.

Nope.

a man with curly hair and glasses is making a funny face and saying `` wait ... what ? '' ALT: a man with curly hair and glasses is making a funny face and saying `` wait ... what ? ''

Ok so the salary ranges for bioinformaticians at AI/ML companies (Anthropocene, OpenAI etc) - is ABSOLUTELY INSANE.

$250k - $450k+ salary plus equity… no PhD and only a few years experience required . Whut???

🧪🖥️ This was funny AF so I feel compelled to share it. 🧵

So … if you ever are confused or read / hear / think someone else is confused about

Providence vs. Provenance

Please share this thread. 👇

#AIxBio #Bioinformatics

🧪🖥️ This was funny AF so I feel compelled to share it. 🧵

So … if you ever are confused or read / hear / think someone else is confused about

Providence vs. Provenance

Please share this thread. 👇

#AIxBio #Bioinformatics

Just a reminder that Large Language Models is just one type of AI. It is not synonymous with AI and indeed the key aspects which make LLMs work - big attention networks, very large embedding spaces - have many applications.

Museum island and the Cathedral

Oh hey… what’s all this now?

THATS RIGHT!

The ATCC Genome Portal now has whole exome and RNAseq data for 900+ cell lines and organoids models, with more data coming. Currently >4k datasets : all produced in house by my team under ISO using benchmarked and standardized methods.

genomes.ATCC.org

Something wicked this way comes... 🧬🧬🧬

(to the ATCC Genome Portal on Monday, Dec 1st...)

(wicked in a good, different, leap forward way... 😄)

In 2003, Dr. Nathan Myhrvold pointed out that GenBank was doubling in size every 18 months - much like Moore's Law.

22 years later - that trend is continuing. (www.ncbi.nlm.nih.gov/genbank/stat...)

How much longer is that going to be sustainable?

#bioinformatics #genomics

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…

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...

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...

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...

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...

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...

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....

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…

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...

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...

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....