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Haris Zafeiropoulos

@hariszaf.bsky.social

microbial systems biologist, bioinformatician hariszaf.github.io/

19 Posts89 Follower89 Folgt
Haris Zafeiropoulos@hariszaf.bsky.social · 12mo ago

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

Haris Zafeiropoulos@hariszaf.bsky.social · last yr.

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

Christina Pavloudi@cpavloud.bsky.social · 2y ago

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."
@mdboer.bsky.social · 2y ago

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

Steven Robbins@stevenjrobbins.bsky.social · 2y ago

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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Will Ratcliff@wcratcliff.bsky.social · 2y ago

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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