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Reposted by Chrats Melkonian

Ragnar {Groot Koerkamp} @curiouscoding.nl · 11d

Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.

Rick Beeloo @rickbitloo.bsky.social · 11d

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:

www.biorxiv.org/content/10.1...

Want to get started? github.com/rickbeeloo/b...

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Reposted by Chrats Melkonian

Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21

Into natural product biosynthesis & tailoring enzymes? Frustrated by the lack of a dedicated resource to explore their functions? Tired of endless literature searches for reaction info? Meet the MITE database, freely available at mite.bioinformatics.nl. Preprint: doi.org/10.26434/che... (1/8)

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Reposted by Chrats Melkonian

Ákos T Kovács @evolvedbiofilm.bsky.social · Jul 28

Harnessing the phyllosphere microbiota of wild foxtail millet for designing beneficial cross-kingdom synthetic communities

#ISMEComms by Xiaoyu Zai et al
with @cmelkonian.bsky.social @vivianecordovez.bsky.social @marnixmedema.bsky.social

academic.oup.com/ismecommun/a...

Harnessing the phyllosphere microbiota of wild foxtail millet for designing beneficial cross-kingdom synthetic communities

Abstract. Understanding the interplay between mechanisms in plant microbiome assembly and functioning of wild ancestors has led to the proposal of a novel

academic.oup.com

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Reposted by Chrats Melkonian

Viviane Cordovez @vivianecordovez.bsky.social · May 22

🚨 Open position
We are hiring a PhD student to investigate the ecology and genomics of phyllosphere yeasts combining lab experiments with computational approaches. Joins us at @niooknaw.bsky.social in collaboration with @micropresearch.bsky.social @cmelkonian.bsky.social @marnixmedema.bsky.social

PhD position: Ecology and Genomics of Phyllosphere Yeasts

The phyllosphere - the aerial parts of plants - harbors a rich and diverse microbial community, including bacteria, filamentous fungi, yeasts and viruses. This environment is both harsh and dynamic, e...

nioo.knaw.nl

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Reposted by Chrats Melkonian

Marnix Medema @marnixmedema.bsky.social · May 21

Exciting PhD opportunity with @vivianecordovez.bsky.social : www.linkedin.com/jobs/view/ph...

KNAW - Koninklijke Nederlandse Akademie van Wetenschappen hiring PhD position: Ecology and Genomics of Phyllosphere Yeasts - NIOO-KNAW - Wageningen in Wageningen, Gelderland, Netherlands | LinkedIn

Posted 3:49:05 PM. The phyllosphere - the aerial parts of plants - harbors a rich and diverse microbial community…See this and similar jobs on LinkedIn.

www.linkedin.com

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Reposted by Chrats Melkonian

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · Mar 24

Excited to be hosting the Paired Omics Mining #community in #Wageningen this week with @marnixmedema.bsky.social! 😎 I hope you are all having safe travels here, and we just brought in some extra good care to make your stay an enjoyable one! 😃

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Reposted by Chrats Melkonian

Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · Mar 14

📣 New, free webtool by the Snoek lab! Meet SpeSpeNet, an intuitive platform for automated network analysis of microbiomes to uncover complex interactions between microbes and their environments

@ismepublications.bsky.social @isme-microbes.bsky.social
doi.org/10.1093/isme...

#microsky #mevosky

SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks

Abstract. Correlation networks are commonly used to explore microbiome data. In these networks, nodes are taxa and edges represent correlations between the

doi.org

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Reposted by Chrats Melkonian

Yang Song @y-song.bsky.social · Feb 26

It was a pleasure to speak at the Bioinformatics for Food Science Symposium—such an inspiring event! Great discussions and insights on the future of food science.
Thank the organizers @cmelkonian.bsky.social and @marnixmedema.bsky.social for this amazing event!

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Reposted by Chrats Melkonian

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · Feb 24

www.linkedin.com/posts/jjjvan...

#Bioinformatics #metabolomics #CompMetabolomics

Justin J.J. van der Hooft on LinkedIn: #bioinformatics #food #sciences #mite #mibig #fermo

Looking forward to a great #Bioinformatics in #Food #Sciences symposium today! 😎 Our team will also present on #MITE, #MIBiG, and #FERMO today with Mitja…

www.linkedin.com

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Reposted by Chrats Melkonian

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · Feb 24

www.linkedin.com/posts/jjjvan...

Justin J.J. van der Hooft on LinkedIn: #bioinformatics #food #wageningen

Looks indeed quite straightforward to me! 😎 Aschwin Schilperoort from dsm-firmenich presenting today during the #Bioinformatics for #Food Science symposium…

www.linkedin.com

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Reposted by Chrats Melkonian

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · Feb 24

www.linkedin.com/posts/jjjvan...

With @mmzdouc.bsky.social

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Reposted by Chrats Melkonian

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · Feb 24

www.linkedin.com/posts/jjjvan...

Justin J.J. van der Hooft on LinkedIn: #bioinformatics #food

Jos Boekhorst making a (significant?!) point during the #Bioinformatics and #Food Sciences symposium at Wageningen University & Research Wageningen Campus

www.linkedin.com

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Chrats Melkonian @cmelkonian.bsky.social · Feb 18

🚨 Last Call for the Bioinformatics in Food Science Symposium – Feb 24th! 🚨

We are almost at full house, approaching 110 attendees. Fortunately online participation is unlimited!

Register here to receive the meeting link: lnkd.in/dfXTcrCa

#Bioinformatics #FoodScience #Networking #Science

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Chrats Melkonian @cmelkonian.bsky.social · Jan 6

📢 Abstract Submission Extended Until January 12th.

Don't miss your chance to present at the upcoming Symposium on Bioinformatics in Food Science!

☯️ We encourage abstracts from female speakers. Submit here: forms.gle/nA6b5zx9qv5K...

~80 in-person attendees registered, few spots still available!

Symposium: Bioinformatics in Food Science

Join us to explore how bioinformatics and data science, including AI technologies, are transforming the science behind our food, from microbes in food fermentation and sustainable agriculture to advan...

forms.gle

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Reposted by Chrats Melkonian

Alvaro Sanchez @asanchezlab.bsky.social · Dec 16

Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...

Diverse phage communities are maintained stably on a clonal bacterial host

Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

www.science.org

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Chrats Melkonian @cmelkonian.bsky.social · Dec 15

Some help fixing it would be most welcome.

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Chrats Melkonian @cmelkonian.bsky.social · Dec 15

A new #StarterPack with scientist specialized in microbial bioinformatics - #MicroBioInf.
Please comment if you would like to be added: go.bsky.app/5h7VaGm

Looking forward to the discussions!

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Chrats Melkonian @cmelkonian.bsky.social · Dec 15

Hello, could you please add me, thanks!

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Reposted by Chrats Melkonian

Mitja M. Zdouc @mmzdouc.bsky.social · Dec 10

Are you working on natural products? We’ve just released version 4.0 of the MIBiG data standard and repository! It now includes 3059 biosynthetic gene clusters, thanks to the combined efforts of 288 expert contributors. A thread: (1/8) academic.oup.com/nar/advance-...

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Abstract. Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in ag

academic.oup.com

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Reposted by Chrats Melkonian

Daniel Probst @skepteis.bsky.social · Dec 2

Here's a first:
I'm hiring a PhD student.
If you have (or know someone who has) a strong background and interest in computational (bio)chemistry or computer science (especially 3D computer vision), let's work together 😊

www.wur.nl/nl/vacature/...

PhD student - Machine learning in bio- and cheminformatics

www.wur.nl

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Chrats Melkonian @cmelkonian.bsky.social · Nov 28

📢 Symposium: Bioinformatics in Food Science. Registrations are now open! Please repost to spread the word.
📅 The symposium is free of charge and will take place at February 24, 2025, at Omnia Auditorium, Wageningen Campus.
💻 Exciting speakers lined up - visit the link for details! lnkd.in/dkzfurdY

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Reposted by Chrats Melkonian

mdboer.bsky.social @mdboer.bsky.social · Nov 26

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

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Reposted by Chrats Melkonian

Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · May 13

The RAT is out! 🐀 Our new Read Annotation Tool integrates taxonomic signals from MAGs, contigs, and reads from #metagenomics 🧬 into one microbial community profile with great sensitivity and precision. Read the article at www.nature.com/articles/s41.... 🧵 (1/5)

Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes - Nature Communications

Metagenomic taxonomic profiling usually relies either on reads or assembled contigs/MAGs. Here, authors present RAT, a tool that integrates taxonomic signals from reads, contigs, and MAGs into one pro...

www.nature.com

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Reposted by Chrats Melkonian

Ákos T Kovács @evolvedbiofilm.bsky.social · Mar 9

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria

#ISMEComms by Katarina Hrovat, Bas Dutilh, @marnixmedema.bsky.social and @cmelkonian.bsky.social

academic.oup.com/ismecommun/a...

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Reposted by Chrats Melkonian

Bas E. Dutilh @bedutilh.bsky.social · Jan 16

Standardization of metagenomics is (not) required!
Join the symposium on 2 February in Utrecht: www.knvm.org/activities/6... with @cmelkonian.bsky.social @annecmg.bsky.social @aldertzomer.bsky.social and many more

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