iiinova — where your digital self keeps evolving

Haris Zafeiropoulos @hariszaf.bsky.social · 03/04/2026

Great phd opportunity ! www.jsmc-phd.de/admission/va...

Haris Zafeiropoulos @hariszaf.bsky.social · 25/03/2026

Hi ! I am Haris, a bioinformatician keen on microbial ecology and interactions. Here is my scholar scholar.google.com/citations?us... and here is my webpage hariszaf.github.io.

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Reposted by Haris Zafeiropoulos

Microbiome Virtual International Forum @microbiomevif.bsky.social · 09/03/2026

Happy Monday! We can't wait to welcome #MVIF 47 speakers and YOU 🤩 Highlights 🇧🇪 Andrey Radev 🇮🇷 Zahra Nezamivand Chegini Keynote 🇬🇧 Lindsay Hall (@halllab.bsky.social) Talks 🇺🇸 Chris Robinson 🇨🇭 @lukasmalf.bsky.social 🇮🇷 Mohammad Salimi Free registration: cassyni.com/s/mvif-47

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Haris Zafeiropoulos @hariszaf.bsky.social · 08/12/2025

If you are interested in contributing a video article on your methods, either message me or submit an abstract here: app.jove.com/methods-coll...

app.jove.com

JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Jove

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Haris Zafeiropoulos @hariszaf.bsky.social · 08/12/2025

JoVE articles are indexed in PubMed, Web of Science, SciFinder, EMBASE, and Scopus. Authors submit a traditional text manuscript, after which JoVE handles all the video production.

app.jove.com

JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Jove

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Haris Zafeiropoulos @hariszaf.bsky.social · 08/12/2025

New indices or predictive approaches, as well as research investigating the role or evolution of metabolic interactions in microbial communities, are also welcome.

app.jove.com

JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Jove

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Haris Zafeiropoulos @hariszaf.bsky.social · 08/12/2025

The purpose of this collection is to bring together methodological innovation, benchmarking strategies, and real-world applications that illuminate how complementary metabolic capabilities shape microbial interactions and ecosystem processes.

app.jove.com

JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Jove

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Haris Zafeiropoulos @hariszaf.bsky.social · 08/12/2025

To anyone keen on hashtag #microbial metabolic interactions, I have opened a Topical Collection with JoVE on “Methods and Applications for the Prediction and Verification of Metabolic Complementarity in Microbial Communities”: tiny.cc/ui5w001

app.jove.com

JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Jove

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Haris Zafeiropoulos @hariszaf.bsky.social · 14/10/2025

If you worry about your data getting scooped, μGrowthDB provides embargo dates, so your data would only be publicly available after the expiration of that date.Meanwhile, your entry will already appear in the db, acknowledging your contribution & showing that you’ve done your part for the community.

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Haris Zafeiropoulos @hariszaf.bsky.social · 14/10/2025

Transforming μGrowthDB into a truly representative resource of microbial culturing efforts would require a collective community effort. Therefore, give it a shot and share your #FAIR data!

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Haris Zafeiropoulos @hariszaf.bsky.social · 14/10/2025

🧪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

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Reposted by Haris Zafeiropoulos

ASM @asm.org · 16/06/2025

#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.

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Haris Zafeiropoulos @hariszaf.bsky.social · 23/09/2025

microbetag comes as a Python package you can use on your own genomes or as an on-the-fly service mapping your taxa to their closest GTDB genomes

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Reposted by Haris Zafeiropoulos

Economic Principles in Cell Biology @economic-cell.bsky.social · 01/07/2025

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...

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Haris Zafeiropoulos @hariszaf.bsky.social · 08/04/2025

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

msysbiology.com

Summer School on Data integration with Microbial Networks and Community Models

Bootstrap 5 Tech Conference Template

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Haris Zafeiropoulos @hariszaf.bsky.social · 19/03/2025

DNNGIOR gapfiller: doi.org/10.1016/j.is... dingo Python library for flux sampling: doi.org/10.1093/bioa...

doi.org

Redirecting

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Haris Zafeiropoulos @hariszaf.bsky.social · 19/03/2025

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

hariszaf.github.io

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...

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Haris Zafeiropoulos @hariszaf.bsky.social · 05/01/2025

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.com

Cassyni | Science starts with a seminar

Seamlessly organise, run and publish academic research seminars. Get started in minutes.

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Haris Zafeiropoulos @hariszaf.bsky.social · 10/12/2024

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

apps.cytoscape.org

Cytoscape App Store - MGG

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Reposted by Haris Zafeiropoulos

Christina Pavloudi @cpavloud.bsky.social · 04/12/2024

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."

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Reposted by Haris Zafeiropoulos

mdboer.bsky.social @mdboer.bsky.social · 26/11/2024

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

shorturl.at

Improving genome-scale metabolic models of incomplete genomes with deep learning

Microbial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.

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Reposted by Haris Zafeiropoulos

Steven Robbins @stevenjrobbins.bsky.social · 10/11/2024

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

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Reposted by Haris Zafeiropoulos

Will Ratcliff @wcratcliff.bsky.social · 04/11/2024

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

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