Haris Zafeiropoulos
LightNews LightNews
banner
hariszaf.bsky.social
Haris Zafeiropoulos
@hariszaf.bsky.social
72 followers 70 following 12 posts
microbial systems biologist, bioinformatician
hariszaf.github.io/
Posts Replies Media Videos
hariszaf.bsky.social
🧪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
asm.org
#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
Model for the interaction between P. aeruginosa and K. pneumoniae. These bacteria can co-exist in nutrient-replete conditions. Under iron-limiting conditions, siderophore synthesis is induced in both bacteria. Iron limitation can also turn on the synthesis of biosurfactants, rhamnolipids, in P. aeruginosa, allowing it to push away K. pneumoniae.
June 16, 2025 at 5:57 PM
hariszaf.bsky.social
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
hariszaf.bsky.social
annas-archive.li/blog/an-upda...
An update from the team
About recent events.
annas-archive.li
August 27, 2025 at 9:08 AM
Reposted by Haris Zafeiropoulos
economic-cell.bsky.social
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
hariszaf.bsky.social
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
hariszaf.bsky.social
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
hariszaf.bsky.social
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
hariszaf.bsky.social
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
cpavloud.bsky.social
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...

🧬🖥️🧪🦠🌊
Graphical abstract of a publication. The original abstract is "Major oil spills can impose a significant environmental hazard on the marine ecosystem, and a promising mitigation measure is in-situ oil burning (ISB). However, our knowledge of the impact of the burned residues and soot deposition on the marine ecosystem is still limited. We investigated the effects of burned oil residue and soot deposition on the marine plankton communities of the oligotrophic Eastern Mediterranean Sea with a mesocosm experiment. Three triplicated treatments were tested: (1) Iranian crude oil was added and burned (Burned treatment); (2) soot was collected and deposited with artificial rain (Soot); and (3) a non-contaminated Control. Results revealed that Low Nucleic Acid heterotrophic bacteria, Synechococcus spp., and pigmented pico-nano Eukaryotes (pnEuk) were negatively affected in the Burned and Soot treatments. Viruses, heterotrophic pnEuk and ciliates (in Soot) were crucial for controlling the High Nucleic Acid bacteria. Ciliates and most dinoflagellates showed a negative response to the burned residues but were less affected or were even favored when exposed to soot. Our results show that ISB affected the structure and dynamics of the plankton food web through burned residues and soot depositions. However, since the effects appeared at least three days after the ignition, ISB could be combined with subsequent burned residue collection to minimize its impact on the pelagic ecosystem."
December 4, 2024 at 9:57 AM
Reposted by Haris Zafeiropoulos
mdboer.bsky.social
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
stevenjrobbins.bsky.social
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
wcratcliff.bsky.social
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