Ashish Malik
@ashish-malik.bsky.social
Microbial Ecology | Soil Carbon | Land Use & Climate Change | Chancellor's Fellow at University of Edinburgh 🏴 | Global Citizen 🌏 | Green Politics | 🏳️🌈 he/him
Pinned
Ashish Malik
@ashish-malik.bsky.social
· Sep 16
📢 Funded PhD opportunities for UK candidates in beautiful Edinburgh. Get in touch if you're interested in a PhD on understanding the mechanisms of soil carbon cycling and the role of microbes. We work in different ecosystems: peatlands, forests and agricultural soils. Please repost/spread the word.
Reposted by Ashish Malik
Genomic GC bias correction improves species abundance estimation from metagenomic data | Nature Communications https://www.nature.com/articles/s41467-025-65530-4
Genomic GC bias correction improves species abundance estimation from metagenomic data - Nature Communications
Differences in genomic GC content skew species abundances in microbial communities. Here, the authors develop GuaCAMOLE, a computational method that quantifies this GC bias from metagenomic sequencing data and corrects abundances accordingly, showing its application increases abundances of some pathogenic bacteria up to twofold in human gut microbiomes.
www.nature.com
November 26, 2025 at 10:42 PM
Genomic GC bias correction improves species abundance estimation from metagenomic data | Nature Communications https://www.nature.com/articles/s41467-025-65530-4
Reposted by Ashish Malik
🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.”
Explore the full study: https://doi.org/10.1093/bioadv/vbaf280
Explore the full study: https://doi.org/10.1093/bioadv/vbaf280
November 26, 2025 at 10:01 AM
🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.”
Explore the full study: https://doi.org/10.1093/bioadv/vbaf280
Explore the full study: https://doi.org/10.1093/bioadv/vbaf280
Reposted by Ashish Malik
We're at 735 registrants and counting! 🎉🦠
If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.
Please share with your networks. 🔗👇
isbscience.org/events/2025-...
If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.
Please share with your networks. 🔗👇
isbscience.org/events/2025-...
November 26, 2025 at 5:19 PM
We're at 735 registrants and counting! 🎉🦠
If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.
Please share with your networks. 🔗👇
isbscience.org/events/2025-...
If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.
Please share with your networks. 🔗👇
isbscience.org/events/2025-...
Reposted by Ashish Malik
You know those labs that keep harming students, again and again? Some reflections on why it's so hard to stop this from happening and where our responsibilities lie.
scienceforeveryone.science/bad-mentors-... 🧪
scienceforeveryone.science/bad-mentors-... 🧪
Bad mentors hurt people
What to do about bad mentors?
scienceforeveryone.science
November 25, 2025 at 6:38 PM
You know those labs that keep harming students, again and again? Some reflections on why it's so hard to stop this from happening and where our responsibilities lie.
scienceforeveryone.science/bad-mentors-... 🧪
scienceforeveryone.science/bad-mentors-... 🧪
Reposted by Ashish Malik
Aren't foreign student fees pretty much the only thing keeping universities solvent?
i: Reeves to unveil £600m raid on foreign student
university fees #TomorrowsPapersToday
university fees #TomorrowsPapersToday
November 23, 2025 at 9:59 PM
Aren't foreign student fees pretty much the only thing keeping universities solvent?
Reposted by Ashish Malik
" A small number of rogue nations can not be allowed to block progress for the rest of the world..."
November 23, 2025 at 7:04 AM
" A small number of rogue nations can not be allowed to block progress for the rest of the world..."
Reposted by Ashish Malik
Reposted by Ashish Malik
COP30 TEXT ANALYSIS: One way to read dense COP text is to focus on the verbs. These are helpfully italicised – and for good reason.
MOSTLY INACTIVE: Carbon Brief analysis of the “global mutirão” text finds 69 inactive verbs, requiring no action, against 32 active verbs.
1/4
MOSTLY INACTIVE: Carbon Brief analysis of the “global mutirão” text finds 69 inactive verbs, requiring no action, against 32 active verbs.
1/4
November 22, 2025 at 8:21 PM
COP30 TEXT ANALYSIS: One way to read dense COP text is to focus on the verbs. These are helpfully italicised – and for good reason.
MOSTLY INACTIVE: Carbon Brief analysis of the “global mutirão” text finds 69 inactive verbs, requiring no action, against 32 active verbs.
1/4
MOSTLY INACTIVE: Carbon Brief analysis of the “global mutirão” text finds 69 inactive verbs, requiring no action, against 32 active verbs.
1/4
Reposted by Ashish Malik
Things move quickly in politics. The idea of a Sunday broadsheet dedicating it's entire front page to @greenparty.org.uk is huge, and let's be honest, a sign of changing times.
People are sitting up and noticing @zackpolanski.bsky.social
join.greenparty.org.uk
People are sitting up and noticing @zackpolanski.bsky.social
join.greenparty.org.uk
November 23, 2025 at 12:27 PM
Things move quickly in politics. The idea of a Sunday broadsheet dedicating it's entire front page to @greenparty.org.uk is huge, and let's be honest, a sign of changing times.
People are sitting up and noticing @zackpolanski.bsky.social
join.greenparty.org.uk
People are sitting up and noticing @zackpolanski.bsky.social
join.greenparty.org.uk
Reposted by Ashish Malik
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Ashish Malik
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
Reposted by Ashish Malik
Lecturer/Senior Lecturer in Plant Ecology at Flinders Uni just advertised. Such a great place + city to live in. So nice to see an Adelaide wide cluster of grassy ecology expertise developing that would be v exciting to be part of! Apply!
Lecturer/Senior Lecturer in Plant Ecology
Position Details Full Time | Continuing Academic Level B I AU$113,211 - $133,974 p.a.I View Position Description Academic Level C |AU $138,124 - $158,885 pa I View Position Description Location: Bedfo...
flinders.wd3.myworkdayjobs.com
November 21, 2025 at 11:31 AM
Lecturer/Senior Lecturer in Plant Ecology at Flinders Uni just advertised. Such a great place + city to live in. So nice to see an Adelaide wide cluster of grassy ecology expertise developing that would be v exciting to be part of! Apply!
Reposted by Ashish Malik
If you use GMail, AI (Gemini) was turned on yesterday by default and now scans all of your content for machine learning. To turn off, go to Settings>General and scroll down. Uncheck the box for "Smart features."
There's other "Smart" add-ons as well, but that's the one that reads your content.
There's other "Smart" add-ons as well, but that's the one that reads your content.
November 20, 2025 at 5:32 PM
If you use GMail, AI (Gemini) was turned on yesterday by default and now scans all of your content for machine learning. To turn off, go to Settings>General and scroll down. Uncheck the box for "Smart features."
There's other "Smart" add-ons as well, but that's the one that reads your content.
There's other "Smart" add-ons as well, but that's the one that reads your content.
Reposted by Ashish Malik
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
November 20, 2025 at 6:42 PM
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Reposted by Ashish Malik
Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.
Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...
pubs.acs.org
November 20, 2025 at 9:24 PM
Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.
Reposted by Ashish Malik
I really hate it when scientists keep saying that “we need to rebuild trust in science,” because it implies that scientists are to blame for the mistrust rather than the millions of dollars of dark money that have funded political attacks on science in order to advance a far right agenda.
November 19, 2025 at 9:48 PM
I really hate it when scientists keep saying that “we need to rebuild trust in science,” because it implies that scientists are to blame for the mistrust rather than the millions of dollars of dark money that have funded political attacks on science in order to advance a far right agenda.
Reposted by Ashish Malik
🧵 1/ New preprint alert! From the FUTURE OAK project, led by the super talented @alejandra1909.bsky.social
Large-scale culturing of the tree microbiome enables targeted disease suppression
Here's what we found... 👇
www.biorxiv.org/content/10.1...
Large-scale culturing of the tree microbiome enables targeted disease suppression
Here's what we found... 👇
www.biorxiv.org/content/10.1...
Large-scale culturing of the tree microbiome enables targeted disease suppression
The tree microbiome is essential for host health and pathogen suppression. Synthetic microbial communities (SynComs) are emerging as important tools to understand microbiome dynamics and engineer micr...
www.biorxiv.org
November 19, 2025 at 3:05 PM
🧵 1/ New preprint alert! From the FUTURE OAK project, led by the super talented @alejandra1909.bsky.social
Large-scale culturing of the tree microbiome enables targeted disease suppression
Here's what we found... 👇
www.biorxiv.org/content/10.1...
Large-scale culturing of the tree microbiome enables targeted disease suppression
Here's what we found... 👇
www.biorxiv.org/content/10.1...
Reposted by Ashish Malik
I had a great conversation with the wonderful @zackpolanski.bsky.social on his podcast. Do please listen in. I don't think you'll have heard anything quite like it. And there's a LOT more here than the title suggests. podcasts.apple.com/gb/podcast/h...
How Labour Negate Progressive Ideas Through ‘Divide and Rule’ | George Monbiot | Zack Polanski
Podcast Episode · Bold Politics with Zack Polanski · 19/11/2025 · 40m
podcasts.apple.com
November 19, 2025 at 10:14 AM
I had a great conversation with the wonderful @zackpolanski.bsky.social on his podcast. Do please listen in. I don't think you'll have heard anything quite like it. And there's a LOT more here than the title suggests. podcasts.apple.com/gb/podcast/h...
Reposted by Ashish Malik
📢 Extra, extra: our collaborative study on trace gas oxidizers in a warmer soil is out as a preprint
www.biorxiv.org/content/10.1...
Big thanks to @thanh0109.bsky.social @bobpmleung.bsky.social @wutkowska.bsky.social @andreasrichter.bsky.social @mathildebio.bsky.social @greening.bsky.social
...
www.biorxiv.org/content/10.1...
Big thanks to @thanh0109.bsky.social @bobpmleung.bsky.social @wutkowska.bsky.social @andreasrichter.bsky.social @mathildebio.bsky.social @greening.bsky.social
...
Soil trace gas oxidizers divergently respond to short- and long-term warming
The upland soil microbiome is dominated by aerobic bacteria that oxidize atmospheric trace gases, including CO, H2, and CH4. As a result, soils are the largest biological sink for these climate-active...
www.biorxiv.org
November 19, 2025 at 9:02 AM
📢 Extra, extra: our collaborative study on trace gas oxidizers in a warmer soil is out as a preprint
www.biorxiv.org/content/10.1...
Big thanks to @thanh0109.bsky.social @bobpmleung.bsky.social @wutkowska.bsky.social @andreasrichter.bsky.social @mathildebio.bsky.social @greening.bsky.social
...
www.biorxiv.org/content/10.1...
Big thanks to @thanh0109.bsky.social @bobpmleung.bsky.social @wutkowska.bsky.social @andreasrichter.bsky.social @mathildebio.bsky.social @greening.bsky.social
...
Reposted by Ashish Malik
Soils contain an amazing diversity of functions encoded in plasmids.
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
November 18, 2025 at 7:18 PM
Soils contain an amazing diversity of functions encoded in plasmids.
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
Reposted by Ashish Malik
#Review
Bacteria can “remember” past environments through genetic & biochemical imprints helping them adapt and thrive! 🦠🧠
#MicroSky
www.nature.com/articles/s41...
Bacteria can “remember” past environments through genetic & biochemical imprints helping them adapt and thrive! 🦠🧠
#MicroSky
www.nature.com/articles/s41...
Exploring the concept of bacterial memory - Nature Microbiology
This Perspective discusses the concept, mechanisms and evidence for memory in bacteria at individual and community levels.
www.nature.com
November 18, 2025 at 8:51 AM
#Review
Bacteria can “remember” past environments through genetic & biochemical imprints helping them adapt and thrive! 🦠🧠
#MicroSky
www.nature.com/articles/s41...
Bacteria can “remember” past environments through genetic & biochemical imprints helping them adapt and thrive! 🦠🧠
#MicroSky
www.nature.com/articles/s41...
Reposted by Ashish Malik
My colleague @avnimalh0tra.bsky.social is hiring a Postdoctoral Research Associate to investigate rhizosphere processes influencing methane (CH₄) dynamics in northern peatlands! Super cool opening -- please circulate careers.pnnl.gov/jobs/11061?l...
Post Doctorate Research Associate - Peatland Rhizosphere and Trace Gas Processes in Richland, Washington | Pacific Northwest National Laboratory
PNNL is hiring a Post Doctorate Research Associate - Peatland Rhizosphere and Trace Gas Processes in Richland, Washington. Review all of the job details and apply today!
careers.pnnl.gov
November 17, 2025 at 6:58 PM
My colleague @avnimalh0tra.bsky.social is hiring a Postdoctoral Research Associate to investigate rhizosphere processes influencing methane (CH₄) dynamics in northern peatlands! Super cool opening -- please circulate careers.pnnl.gov/jobs/11061?l...
Reposted by Ashish Malik
Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
ECR connection: Meet Meren when you need to
A means for ECRs to get advice from a senior scientist outside of their support network
merenlab.org
November 16, 2025 at 4:56 PM
Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Reposted by Ashish Malik
Join us at #EGU26 in Vienna for our session SSS4.2 on microbial physiology, co-organized with @jpausch.bsky.social and @aguilart.bsky.social, featuring @edithhammer.bsky.social as Invited Speaker - meetingorganizer.copernicus.org/EGU26/sessio...
Deadline for abstract submissions is 15th of January.
Deadline for abstract submissions is 15th of January.
November 16, 2025 at 12:26 PM
Join us at #EGU26 in Vienna for our session SSS4.2 on microbial physiology, co-organized with @jpausch.bsky.social and @aguilart.bsky.social, featuring @edithhammer.bsky.social as Invited Speaker - meetingorganizer.copernicus.org/EGU26/sessio...
Deadline for abstract submissions is 15th of January.
Deadline for abstract submissions is 15th of January.
Reposted by Ashish Malik
