Chrats Melkonian
@cmelkonian.bsky.social
Inspired by Microbial Ecology and Evolution - Microbial Bioinformatics. Postdoc at Theoretical Biology and Bioinformatics (UU) & Bioinformatics (WUR)
Reposted by Chrats Melkonian
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.
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.
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...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 9:28 PM
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.
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.
Reposted by Chrats Melkonian
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)
August 21, 2025 at 10:52 AM
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)
Reposted by Chrats Melkonian
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...
#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
July 28, 2025 at 2:13 PM
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...
#ISMEComms by Xiaoyu Zai et al
with @cmelkonian.bsky.social @vivianecordovez.bsky.social @marnixmedema.bsky.social
academic.oup.com/ismecommun/a...
Reposted by Chrats Melkonian
🚨 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
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
May 22, 2025 at 5:57 AM
🚨 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
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
Reposted by Chrats Melkonian
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
May 21, 2025 at 6:55 AM
Exciting PhD opportunity with @vivianecordovez.bsky.social : www.linkedin.com/jobs/view/ph...
Reposted by Chrats Melkonian
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! 😃
March 24, 2025 at 10:56 AM
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! 😃
Reposted by Chrats Melkonian
📣 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
@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
March 14, 2025 at 2:15 PM
📣 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
@ismepublications.bsky.social @isme-microbes.bsky.social
doi.org/10.1093/isme...
#microsky #mevosky
Reposted by Chrats Melkonian
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!
Thank the organizers @cmelkonian.bsky.social and @marnixmedema.bsky.social for this amazing event!
February 26, 2025 at 3:28 PM
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!
Thank the organizers @cmelkonian.bsky.social and @marnixmedema.bsky.social for this amazing event!
Reposted by Chrats Melkonian
Reposted by Chrats Melkonian
Reposted by Chrats Melkonian
February 24, 2025 at 3:14 PM
🚨 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
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
February 18, 2025 at 10:51 AM
🚨 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
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
📢 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!
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
January 6, 2025 at 12:34 PM
📢 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!
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!
Reposted by Chrats Melkonian
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/...
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
December 16, 2024 at 11:38 AM
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/...
www.science.org/doi/10.1126/...
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!
Please comment if you would like to be added: go.bsky.app/5h7VaGm
Looking forward to the discussions!
December 15, 2024 at 9:22 AM
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!
Please comment if you would like to be added: go.bsky.app/5h7VaGm
Looking forward to the discussions!
Reposted by Chrats Melkonian
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
December 10, 2024 at 8:05 AM
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-...
Reposted by Chrats Melkonian
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/...
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
December 2, 2024 at 5:51 PM
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/...
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/...
📢 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
📅 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
November 28, 2024 at 11:37 AM
📢 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
📅 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
Reposted by Chrats Melkonian
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
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
Reposted by Chrats Melkonian
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
May 13, 2024 at 10:12 AM
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)
Reposted by Chrats Melkonian
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...
#ISMEComms by Katarina Hrovat, Bas Dutilh, @marnixmedema.bsky.social and @cmelkonian.bsky.social
academic.oup.com/ismecommun/a...
March 9, 2024 at 1:05 PM
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...
#ISMEComms by Katarina Hrovat, Bas Dutilh, @marnixmedema.bsky.social and @cmelkonian.bsky.social
academic.oup.com/ismecommun/a...
Reposted by Chrats Melkonian
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
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
January 16, 2024 at 2:30 PM
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
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
My first post is a Christmas present to all the cheese lovers and microbiome enthusiast! The key message is that the cheese flavour is not the result of individual microbes alone but of the community. Fantastic teamwork and collaboration between industry and academia. 🎄🎁🧀 rdcu.be/ducw0
December 21, 2023 at 6:32 PM
My first post is a Christmas present to all the cheese lovers and microbiome enthusiast! The key message is that the cheese flavour is not the result of individual microbes alone but of the community. Fantastic teamwork and collaboration between industry and academia. 🎄🎁🧀 rdcu.be/ducw0