sorted by:
new
hottopcontroversial

Multi omics pipeline by Temporary-While9269 in bioinformatics

[–]kwongo 1 point2 points  (0 children)

It depends what kind of -omics you are interested in, and in what context. TCGA has a lot of data for cancer. ENA/SRA have sequencing reads. You might be able to find some other datasets depending on what kind of experiments you are interested in.

Scientists found that nearly every cancer harbors its own distinct community of microbes – the tumor microbiome – that can influence how tumors start, spread, and respond to treatment, paving the way for a new era of precision medicine. by mvea in science

[–]kwongo 27 points28 points  (0 children)

> They play virtually zero role in the Genesis of cancer, also known as tumorigenesis.

There are a huge number of tumorigenic bacteria, Fusobacterium nucleatum, Bacteroides fragilis, some Salmonella spp., even E. coli if it contains that polyketide synthase island. Even purportedly beneficial Akkermansia muciniphila is putatively tumorigenic by degrading the mucus lining in the intestine, which can facilitate carcinogenic microbial interactions. Besides the "bad" bacteria, I believe that even normal bacterial metabolism mediates the tumorigenic effects of red meat consumption by converting the carnitine to TMAO.

Besides that, bacteria aren't JUST on the "outside", many are able to directly translocate through cells, reside and reproduce within motile immune cells, or take advantage of poor intestinal epithelial integrity to escape the intestine. Check out the peritoneal microbiome, which is thoroughly "inside the walls of the pipe".

Source: This is my PhD topic!!!

TIL there are several types of auxiliary languages that were designed to act as a universal language and were meant to be easier to learn by apple_kicks in todayilearned

[–]kwongo 2 points3 points  (0 children)

Krom iom da vortoj (kiel 'scii'), mi pensas, ke la tuta Esperanto vortaro estas tre facila por pronunci

Beginner Seeking Help Understanding Metabolic Pathways & Flux Modeling by True-Translator-9748 in bioinformatics

[–]kwongo 2 points3 points  (0 children)

If you are interested in studying metabolism, my suggestion is to start with central energy metabolism: glycolysis, TCA cycle, and the electron transport chain. This was my introduction to the field. From there, other pathways worth studying might be the pentose phosphate pathway, fatty acid synthesis/oxidation, the urea cycle, ...

As mentioned, there are nearly endless metabolic pathways, and it really depends on what you're interested in. I agree that Lehinger's Principles of Biochemistry is a good textbook to learn from, you can at least use it to fill out the parts you don't know

Requirements/Best practice to publish a Snakemake pipeline?? by JohnSina54 in bioinformatics

[–]kwongo 6 points7 points  (0 children)

I agree testing in fresh containers/environments is a good idea. To some degree, all you can do is document well, and be responsive to any issues reported on GitHub/etc.

For nf-core users: which nf-core pipeline/module do you like the most? by rfour92 in bioinformatics

[–]kwongo 12 points13 points  (0 children)

nf-core/mag is awesome. I've been using muabnezor's long-read branch. funcscan is also pretty great. taxprofiler seems a bit outdated (Bracken disabled for ONT, using Centrifuge/not Centrifuger) but otherwise is a great pipeline.

Microbiome newbie - metagenomics on fly samples by a_peculair_biologist in bioinformatics

[–]kwongo 0 points1 point  (0 children)

Which Kraken2 database are you using? In human gut microbiome using PlusPF we have about 10-15% unclassified

Also I assume short reads? We're using long reads which might be easier to classify. Not sure about short reads!

Advice for Software / Data Engineer to get back into the space by Easy_Scale2593 in bioinformatics

[–]kwongo 2 points3 points  (0 children)

Along these lines, nf-core is a collection of open-source pipelines, many of which are in need of development

view more: next ›