Haris Zafeiropoulos
banner
hariszaf.bsky.social
Haris Zafeiropoulos
@hariszaf.bsky.social
microbial systems biologist, bioinformatician
hariszaf.github.io/
🧪If you are interested in #microbial growth data, you may have have a look at μGrowthDB; an open repository designed to store, visualize, analyze & share quantitative measurements of species abundances and metabolite profiles from monocultures & communities of known composition.
#microsky #mevosky
October 14, 2025 at 8:59 AM
Reposted by Haris Zafeiropoulos
#MicrobiologyMonday: Pseudomonas aeruginosa releases a surfactant that displaces Klebsiella pneumoniae from solid surfaces. By pushing K. pneumoniae away, the detergent allows P. aeruginosa to better compete for limited iron. Learn more in #mBio: asm.social/2sH
June 16, 2025 at 5:57 PM
our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just published

A Cytoscape app is also available to make your life easier (and prettier)

#microbiome #metabolic-modeling #networks
microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis - Genome Biology
Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. No...
doi.org
September 23, 2025 at 9:42 AM
Reposted by Haris Zafeiropoulos
First day of July brings us the Summer 2025 edition of our open-access textbook! Join Piglette in stargazing and exploring newest additions to our book principlescellphysiology.org/book-economi...
July 1, 2025 at 9:43 AM
Hi #microbiome community.

If you are interested in microbial networks, feel free to have a look and register in our summer school!

Two days with talks and hands-on on how to annotate your networks and come up with testable hypotheses.
24 and 25 Sep 2025, Leuven , Belgium

@3domics.bsky.social
Summer School on Data integration with Microbial Networks and Community Models
Bootstrap 5 Tech Conference Template
msysbiology.com
April 8, 2025 at 1:41 AM
If you're new in #metabolic #modelling or just interested, we had a workshop last week and here is a set of notebooks we wrote.

Among other things, we discussed our recently published gapfiller, DNNGIOR and the dingo flux sampling Python library we built with the GeomScale group!

#microbiome #flux
Metabolic modeling for microbiomes
Daniel Garza, Meine Boer and I, we organized a 3-days workshop at INRAE/PROSE in Antony, on the basics of metabolic modelling, our new gap-filler, called DNNGIOR and applications of the methodology on...
hariszaf.github.io
March 19, 2025 at 10:04 PM
If you're interested in microbial co-occurrence networks and how to make sense out of them, feel free to join my seminar at @microbiomevif.bsky.social on microbetag; a recently developed software of ours!
#microbiome #networks
Cassyni | Science starts with a seminar
Seamlessly organise, run and publish academic research seminars. Get started in minutes.
cassyni.com
January 5, 2025 at 10:44 PM
Here's our new tool for annotating microbial co-occurrence networks with phenotypic traits & potential metabolic complementarities.

Cytoscape App
apps.cytoscape.org/apps/mgg

Documentation
hariszaf.github.io/microbetag/

bioRxiv
doi.org/10.1101/2024...

#microbiome #microbiology #metagenomics
Cytoscape App Store - MGG
apps.cytoscape.org
December 10, 2024 at 1:49 AM
Reposted by Haris Zafeiropoulos
Did we set fire to the rain? 🔥
Well, not exactly, but we did set it to the water. Or technically, to our artificial oil spill! 🛢️

Was there smoke on the water? 💨
Yes, there was!

Is this the first publication of, quite a few, more to come? Indeed!

Check it out here:
doi.org/10.1016/j.sc...

🧬🖥️🧪🦠🌊
December 4, 2024 at 9:57 AM
Reposted by Haris Zafeiropoulos
Exciting news! 🎉 My article is out in iScience presenting DNNGIOR, a deep learning tool advancing gap-filling in metabolic models. Huge thanks to co-authors @cmelkonian.bsky.social, @hariszaf.bsky.social, Daniel Garza, Andreas Haas and @bedutilh.bsky.social. Read at shorturl.at/REOm8
Improving genome-scale metabolic models of incomplete genomes with deep learning
Microbial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.
shorturl.at
November 26, 2024 at 12:25 PM
Reposted by Haris Zafeiropoulos
Love this idea for helping the community make the transition to Bluesky, so I’ve compiled a woefully incomplete list of microbial ecologists and -omics peeps I know are here.

Please make suggestions and share. Let me know if you’d like to be added.

go.bsky.app/TQpaTqF
November 10, 2024 at 11:21 AM
Reposted by Haris Zafeiropoulos
Excited to share: The inaugural Alma Dal Co School on Collective Behavior is coming to Venice (Sep 29-Oct 4, 2025). This unique school honors Alma (1989-2022), whose brilliant work bridging physics and microbiology revealed how metabolic interactions structure microbial communities. 1/12
November 4, 2024 at 3:26 PM