Muzaffer Arikan

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

I woke up to some very sad news...

Peer was a giant of bioinformatics and computational biology and an inspiring mentor to everyone who had been in his group. I find myself repeating things he said all the time and will probably keep doing so for the rest of my life

www.embl.org/news/embl-an...

gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti

GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...

MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes https://www.biorxiv.org/content/10.1101/2025.10.28.685052v1

Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs Nature Communications - Here, the authors systematically map metaproteomic responses of ex vivo human gut microbiota to common therapeutics, identifying several drug classes inducing strong...

Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs.
@quadraminstitute.bsky.social

rdcu.be/eMmcT

Practical Guidance for Training Machine Learning Models in Metabolomics and Mass Spectrometry Research This tutorial offers a step-by-step guide for analytical chemists to train machine learning models for MS-based metabolomics. It covers data preparation, feature engineering, model selection, evaluati...

Practical Guidance for Training Machine Learning Models in Metabolomics and Mass Spectrometry Research | Analytical Chemistry pubs.acs.org/doi/full/10....

Seen this in grant applications too... One even claimed the “undoubted” existence of placental microbiome while citing studies that actually refuted it.

Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson’s disease and cognitive decline pathophysiology The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the con...

Our recent publication has appeared in Gut Microbes. Access it through the link below:
www.tandfonline.com/doi/full/10....

Dominant taxa in microbiomes are obviously important but here's a discussion on low abundance taxa that are highly persisting/prevalent. We can see a lot of these in metagenomics, often obscured by a high false negative rate.
🔗 www.sciencedirect.com/science/arti...

Mass-spectrometry-based proteomics: from single cells to clinical applications - Nature This Review summarizes advances in mass-spectrometry-based proteomics and explores the potential applications of these technologies in the clinic.

Mass-spectrometry-based proteomics: from single cells to clinical applications www.nature.com/articles/s41...

‘Dark proteins’ hiding in our cells could hold clues to cancer and other diseases The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do.

"Dark proteins." Also known as microproteins. There are thousands of them in our cells and we're still struggling to define their function. Succinctly reviewed @nature.com www.nature.com/articles/d41...

Propagation of pathologic α-synuclein from kidney to brain may contribute to Parkinson’s disease - Nature Neuroscience Yuan et al. find that the kidney can serve as a site of initiation for the spread of pathological α-synuclein to the brain, contributing to the development of Parkinson’s disease (PD) and providing a ...

We knew about the potential origin of Parkinson's disease from the gut (known as Braak’s hypothesis). But the kidney?!
www.nature.com/articles/s41...

5,562 proteins were found to have tissue-specific enrichment across 32 human tissues.

The majority of them (3,088) are enriched at the protein but not RNA level.

The brain hosts the largest number of proteins that are only enriched at the protein level but not RNA level.

How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding Abstract. The intestinal epithelium is protected from direct contact with gut microbes by a mucus layer. This mucus layer consists of secreted mucin glycop

Some gut microbes can degrade mucus. 🍬🦠🍭

✂️ What enzymes do they use to degrade mucin glycans and how does that lead to cross-feeding?

#glycotime
#microbiology

academic.oup.com/glycob/artic...

AI in microbiome‐related healthcare Artificial intelligence (AI) has the potential to transform clinical practice and healthcare. Following impressive advancements in fields such as computer vision and medical imaging, AI is poised to ...

AI in microbiome-related healthcare

A framework for understanding collective microbiome metabolism - Nature Microbiology This Perspective explores why microbiome members perform partial metabolism of substrates and suggests that proteome efficiency is a driver of collective microbiome metabolism.

worth a read: A framework for understanding collective microbiome metabolism

Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla.
doi.org/10.1101/2024...
@wwood @rhysnewell @CMR_QUT
🧵1/6

Can you please add me? Thanks!

Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases In metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large is critical for the peptide identification step. Therefore, the availabili...

Here is our recent review on constructing protein sequence databases for metaptoteomics
#microbiome #metaproteomics
pubs.acs.org/doi/10.1021/...