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Since there is a discussion regarding the proteasome system, I am posting the relevant section from the document I circulated in 2018. Of interest could be the part where it is described how viral infections can negatively affect UPS and ERAD functioning :

@Hutan Yes, this is straight from o3 reasoning engine. Very impressive indeed.

I have increased confidence when different methods converge on the same results. I would like to point the convergences here. 1) The paper mentions PTPN11 and GRB2. They both appear on figure 2B. These have been found since 2018 (note in one tweet, Michael Snyder - one of the authors is tagged)...

@jnmaciuch Thank you so much for your work. One of the problematic areas in metabolomics and its results is to try to understand why certain metabolites are different from healthy controls. I would like to provide an example of how different types of analysis can be used to -hopefully- help in...

Good question. Let's assume that 4 LLMs named A,B,C,D are given the same prompt. It basically has to do with the rate of agreement. B,C,D will evaluate facts given by A (=metabolite 1 and metabolite 2 are all 5 alpha reductase metabolites). If all 3 LLMs agree that this is indeed true then we...

This is an important moment I believe. This is something I have been working on and it involves the use of Ensemble Learning for Large Language Models (LLMs) which we can call "EnsembleLLMs". What does this mean? Essentially, a single prompt is passed to many LLMs -for example, to find causal...

@Jonathan Edwards I dream of a day where unbiased AI algorithms will be making the right decisions for us. Probably the biggest hurdle to move ME/CFS research has been -and still is- the "Selfish gene"

From my understanding, Unutmaz has primarily used a paper he very recently published and he also directed AI to collect other papers using metabolomics. You can see the prompt he used here : https://manus.im/share/RiwQh3pvyc1xXSxAgq9yZP?replay=1 The data I used cannot have significant...

Here is a relevant thread based on the findings of Derya Unutmaz and the work that I have been doing. Peroxisome proliferators, PGC1a, MERTK, Bile acid metabolism have been previously identified. It is usually a good sign when research targets converge. CC @Simon M @wigglethemouse

Of note, 4-BPA is an ER Stress inhibitor. Also , peroxisomes have been identified as early as 2017 through Network Analysis https://www.s4me.info/threads/machine-learning-assisted-research-on-me-cfs.5015/page-9#post-456267 and regarding ER Stress https://pmc.ncbi.nlm.nih.gov/articles/PMC8194262/

With the help of Grok 3, I realized that the study found several metabolites below that are related to dehydrotestosterone and more specifically 5 alpha reductase - related metabolites. Given my story ( I got ME/ CFS from Finasteride which is a 5 alpha reductase inhibitor) these results may...

@To anyone interested, I could send some relevant information, perhaps @DMissa ? The Ubiquitin Proteasome system has been one research target appearing for quite some time using machine learning and information retrieval methods. See attached from an email (september 2021) I sent to an...

I would like for a research group to test for glycosylation disruption. So Transferrin Isoform Analysis, N-Glycan profiling, Dolichol Phosphate and Lipid-linked Oligosaccharides

Absolutely right , I only wanted to mention that the family of sulfotransferases have been previously identified as a potential research "hotspot"

Regarding the SULT1A1 that @Hutan mentioned. Machine Learning has identified several Sulfotransferases genes as important. Post in 2017 Also regarding viral persistence and the association of LXR and SULT2B1 : (2023) During a presentation I made to the team of Wenzhong Xiao,the medical...

I spoke with Professor Osborne in 2021 and presented my work to him. I also introduced him to some researchers I happened to know. Unfortunately there was no further collaboration. He is a really nice person and wants to help us. I could speak to him again if there is a certain need.

My favorite topic (=liver) comes up again. cc @Chris Ponting and from another study. Note that ACLF = Acute Liver failure. References https://www.sciencedirect.com/science/article/abs/pii/S1079979609000138 https://www.spandidos-publications.com/10.3892/ijmm.2018.3946 EDIT : Going...

Or it may be that the decisions we have been taking regarding which research will be funded or which collaborations will take place have been largely ineffective. An example here (note, I am the author) : Having used machine learning and network analysis methods to research ME/CFS since 2015...

As this being the last day of the year, I wanted to share the yearly update for 2024 regarding a software framework I have been using to identify biological targets of high predictive value . The framework uses machine learning, natural language processing and network analysis algorithms to...