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Colin Davenport

@colindaven.bsky.social
343 followers 1.9K following 15 posts

Bioinformatics, genomics, metagenomics, nextflow and sequencing.

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Reposted by Colin Davenport
Angelo Iulianella @aineurolab.bsky.social · 25/09/2026
Folks, it’s been a loooong week. We’re all a bit exhausted, and need some cheering up. How about a couple of jokes? Which biochemicals wash up on beaches? …..nucleotides! 🧪
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Dave Baltrus 🦦 @surtlab.bsky.social · 25/09/2026
“We thank the reviewer for their comments! We have rewritten this section to provide concrete evidence * of biological function” *evidence is that Claude says so
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The Tennessee Holler @thetnholler.bsky.social · 23/09/2026
TALARICO: “The richest 1% now owns more wealth than the entire middle class. 3 dudes (Musk, Zuckerberg, Bezos) now own more wealth than 165 million Americans combined… they aren’t just buying yachts and jets anymore. They’re now buying power.” 🇺🇸 (From @teamtalaricohq.bsky.social )
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Willem van Schaik @wvschaik.bsky.social · 20/09/2026
I guess this is how AI will kill us all, because US military intelligence (lol) mistakes it for reality.
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Nature Portfolio @natureportfolio.nature.com · 19/09/2026
A paper in Nature Aging presents a new atlas that identifies 1,067 unannotated microproteins in the human frontal cortex. A subset is differentially expressed in Alzheimer’s disease independently of their canonical genes. go.nature.com/4rkDEKP 🧪
This is figure 1, which shows MS evidence of MPs in the aged human frontal cortex.
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Carl T. Bergstrom @carlbergstrom.com · 19/09/2026
We’re Google. Don’t crawl us, we’ll crawl you.
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David Hoey @davidjhoey.bsky.social · 16/09/2026
Introducing PhyloDig: a small command-line tool I am developing to make comparative phylogenetic analyses easier. github.com/davidjhoey/P...
github.com
GitHub - davidjhoey/PhyloDig: PhyloDig is a command line pipeline for automated homology mining across collections of protein and coding sequence databases. It combines HMMER searches, optional Pfam d...
PhyloDig is a command line pipeline for automated homology mining across collections of protein and coding sequence databases. It combines HMMER searches, optional Pfam domain filtering, and sequen...
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Dr. K. Lotterhos @drk-lo.bsky.social · 15/09/2026
I'm hiring a bioinformatician! Review of applications starts October 1 with a start date as soon as possible. 🧪 #Genomics #popGen #CompBio northeastern.wd1.myworkdayjobs.com/careers/job/...
northeastern.wd1.myworkdayjobs.com
Bioinformatician - Lotterhos Lab
About the Opportunity About the Center for Marine Ecological Genomics The successful candidate will be based at the Lotterhos Lab and the Center for Marine Ecological Genomics at Northeastern Marine S...
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Beyond Fossil Fuels @beyondfossilfuels.bsky.social · 16/09/2026
🚨BREAKING: New report by @ketanjoshi.co finds NVIDIA’s indirect emissions have risen 725% since 2020. Reminder, there is no evidence to say AI is a net benefit for climate, and Europe can't lock itself into more fossil gas to power data centres for Big Tech profits. ketanjoshi.co/2026/09/16/n...
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James Murray @james-bg.bsky.social · 13/09/2026
This is a critical point that’s repeatedly ignored. If you’re under 45 there’s a good chance you’re still working in 2050 when we should be at net zero. If you’re under 25 there’s a good chance you’re alive in 2100 when current trends suggest we’ll be at 3C of warming and all that comes with it.
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Ketan Joshi @ketanjoshi.co · 13/09/2026
This post from SemiAnalysis is well worth reading, to get a direct insight into how the AI industry is completely disconnected from the climate consequences of what they're doing.
Stacked bars showing cumulative onsite generation by quarter from Q1 2024 to Q3 2026 rising to ~75 GW, with a line indicating named suppliers reaching 22; colored segments represent gas turbines, recip engines, steam turbines, fuel cells and other.
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David Ho @davidho.bsky.social · 12/09/2026
I resigned from ExxonMobil today. I spent the last three years doing fossil fuel extraction research at both BP and ExxonMobil. Neither company is acting responsibly. They are racing to maximize extraction while the window to act closes, and gambling with our lives. More below.
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David Sünderhauf @davvi36.bsky.social · 10/09/2026
Please share! We are looking for a PhD student excited about gene transfer, and tackling Antimicrobial Resistance in Klebsiella pneumoniae. 🧬 More details & applications on funder website by 21st Oct 👇🏻 gw4biomed.ac.uk/developing-c...
gw4biomed.ac.uk
Developing CRISPR-Cas antimicrobials to tackle antibiotic resistance spread in Klebsiella pneumoniae - GW4 BioMed MRC DTP
Project Code IIAR27Ex van Houte Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Antimicrobial resistance (AMR) poses a major thre...
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Jason Moore @moorejh.bsky.social · 09/09/2026
Ironic given US companies used copyrighted materials to train their models www.engadget.com/2253604/us-a... #openai #anthropic #china
engadget.com
US authorities accuse Chinese AI companies of industrial-scale campaigns to copy American models - Engadget
The NSA, CISA and the FBI have accused DeepSeek, Moonshot and other Chinese AI companies of “distilling” American frontier AI models.
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Jeffrey Keese @jeffreykeese.bsky.social · 09/09/2026
Statistical confirmation that a majority of small children are agents of chaos.
Chart confirming that a majority of children want to let the pigeon drive the bus (9-7 in favor).
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Aarne Granlund @aarnegranlund.eurosky.social · 06/09/2026
”Europe hosted more than half of the world's 1.5 billion international arrivals. With global travel projected to hit 1.8 billion arrivals by 2030, governments are scrambling to manage the pressure.” More extreme weather, more flying? Or perhaps #Sufficiency instead www.bbc.com/travel/artic...
bbc.com
Extreme ways countries are combatting overtourism
As global travel surges toward 1.8 billion arrivals, destinations are testing controversial new measures to control the crowds.
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Alejandra Caraballo @esqueer.net · 09/09/2026
The alarms are all flashing red.
Screenshot of a thread on X by user Jacob Coxon (@hilbertspaess) detailing his resignation from Anthropic.
​The first post reads: "I resigned from Anthropic today. I spent the last three years doing pretraining research at both OpenAI and Anthropic. Neither company is acting responsibly. They are racing straight to self-improving superintelligence and gambling with our lives. More thoughts below."
​The second post reads: "Do not underestimate the power of this technology. These will soon be superhuman systems that can hack anything, revolutionize any field overnight, and acquire real power and resources. We have all witnessed the progress in each of these domains, and progress is not slowing."
​The third post reads: "The people building AI earnestly believe that it could kill us all by the end of the decade. This is not a marketing stunt. If anything, many executives and senior researchers will couch their phrasing in the press to sound sensible - but I hear the same people express fear privately. No other human activity poses this level of danger."Screenshot continuing the thread on X by Jacob Coxon (@hilbertspaess).
​The first post reads: "A common response is 'if they truly believe this, why are they still building it?' At OpenAI, many have not deeply internalized the civilizational stakes. At Anthropic, the stakes are well-understood, but they are locked in a race to get there first - they believe no one else will act responsibly, so they must do it themselves, despite the risk."
​The second post reads: "Accepting this race and entering the 'endgame' is a hubristic gamble that should not be launched from a private company's Slack. Attempting to speedrun alignment should require extraordinary confidence that there are no better trajectories available."
​The third post reads: "I am optimistic about the potential for coordination. Warning shots like the Hugging Face attack have made pacing agreements between U.S. labs more viable. I don’t feel like we’re on track to prevent a global race, which may require costly actions such as a temporary ban on improving model capabilities."
​The fourth post reads: "If you are a lab researcher, I urge you to consider what the next few years will actually feel like. Do you want to kick off a superintelligent RL run without a rigorous understanding of its mind? Should you put your head down because 'it’s happening anyway' - or take this moment to call for different conditions?"
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Prof Ian Hall @ianhall.bsky.social · 05/09/2026
If you privatise the profits from fossil fuels, you can’t keep socialising the costs of the damage. Those who’ve profited should pay their fair share of the impacts. That’s why Spain’s push for an EU oil and gas tax to help fund climate adaptation is worth supporting. www.ft.com/content/86da...
ft.com
Spain pushes for EU oil and gas tax to pay for climate change response
Rising extreme weather costs fuel campaign ahead of new resilience strategy
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Tim Stephens @proftimstephens.bsky.social · 05/09/2026
“The International Energy Agency estimates that data-center emissions could more than double by 2030—becoming one of the fastest-growing sources of greenhouse gases in the world.” www.theatlantic.com/magazine/202...
theatlantic.com
Inside the Dirty, Dystopian World of AI Data Centers
The race to power AI is already remaking the physical world.
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David Roberts @volts.wtf · 03/09/2026
This is demonstrably, measurably improving the health of the people who live there. Most notably, it increases the respiratory *& cognitive* health of children. They literally do better in school. If this country really gave a shit about children, this would be at the top of the public-policy list.
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Stephen Turner @stephenturner.us · 01/09/2026
I use AI frequently but my god I'd do anything to read English instead of Claudish for a single day across my emails, assignments, socials, Substackistan, academic literature, product announcements, etc. www.nature.com/articles/d41...
nature.com
Bland new world: is AI making us all think the same?
Researchers worry that generative AI is homogenizing culture and cognition.
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Albert Vilella, PhD. @albertvilella.bsky.social · 02/09/2026
Commoditizing the $ per million tokens at a fast pace
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Pablo González-Suárez @pablidopsis.bsky.social · 02/09/2026
One of my recent In Brief articles for @theplantcell.bsky.social below 👇 I highlight findings from Li and colleagues, who comprehensively characterized the seasonal chromatin landscape of hybrid aspen during dormancy and bud release 🌡️🧬
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Thiago Carvalho @cyrilpedia.bsky.social · 31/08/2026
The study "GPT detectors are biased against non-native English writers" www.cell.com/patterns/ful...
cell.com
GPT detectors are biased against non-native English writers
GPT detectors frequently misclassify non-native English writing as AI generated, raising concerns about fairness and robustness. Addressing the biases in these detectors is crucial to prevent the marginalization of non-native English speakers in evaluative and educational settings and to create a more equitable digital landscape.
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Q-Lab @leandroquadrana.bsky.social · 28/08/2026
What if transposases are already transcription factors in disguise? Our new preprint shows that transcriptional regulatory activity is an intrinsic property of transposases, revealing a direct route for their domestication into transcription factors. www.biorxiv.org/content/10.6...
doi.org
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Dare Obasanjo @carnage4life.bsky.social · 30/08/2026
An AI-native startup just restricted most new hires from using AI until they actually learn their jobs. Employees were using expensive frontier models for simple work while senior people cleaned up the AI slop. They now expect token spend to fall from $15–20M to $4–5M. I feel similar pain daily.
businessinsider.com
One CEO's fix for AI-generated slop: Make new hires learn their jobs without AI
Valon's CEO said he imposed the mandate after AI overuse drove up costs and left tenured employees with AI slop to fix.
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Michael Hobbes @michaelhobbes.bsky.social · 30/08/2026
Why were there only 3 measles deaths in the last 10 years Robert
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David Ho @davidho.bsky.social · 26/08/2026
The news and videos out of Nepal are horrific. Climate change makes the world a more chaotic and dangerous place. Even if your home isn’t affected, you might go on holidays or to a meeting and get caught up in it. I’m particularly thinking about this as our next IPCC lead author meeting is in Nepal.
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Mark Chadbourn @chadbourn.bsky.social · 27/08/2026
Germany’s Far Right AfD plans to expand Russian language teaching and reinstate school exchanges with Russia if it wins the Saxony-Anhalt regional election on September 6. It also says it would remove refugee and disabled children from mainstream schools and educate them separately.
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Justin Mikulka @justinmikulka.bsky.social · 27/08/2026
"The debate over data centers’ water use tends to focus on how much is needed to cool servers on-site. But that fails to capture the largest and least visible part of their overall use: the water used at the power plants fueling data centers’ rising energy needs." Solar and wind use very little H20
latitudemedia.com
Data centers’ hidden water footprint is linked to the grid
A Ceres analysis shows that data centers’ indirect water footprint from power plants dwarfs direct cooling.
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KWS Group @kwsgroup.bsky.social · 19/08/2026
📣 We are hiring a Computational Biologist – Genome Editing Trait Discovery in Einbeck, Germany. This is an interesting role for someone with strong analytical skills and a collaborative mindset. #PlantSciJobs #AgSciJobs jobs.kws.com/job/Einbeck-...
jobs.kws.com
Computational Biologist (m/f/d) - Genome Editing Trait Discovery
Computational Biologist (m/f/d) - Genome Editing Trait Discovery
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Nils Homer @nilshomer.com · 25/08/2026
fgumi v0.7.0 is released: github.com/fulcrumgenom... 1. sort is 28% faster; 2-3x faster than samtools 2. improved CODEC consensus calling 3. dedup now outputs metrics closer to picard MarkDuplicates and dupblaster 4. retag is a new tool that can copy/move/delete SAM tags
github.com
Release v0.7.0 · fulcrumgenomics/fgumi
For those running the fgumi command line tools v0.7.0 makes sort faster, hardens CODEC consensus, and brings dedup metrics to Picard/dupblaster parity. Sort is up to 28% faster — and 2–3× faster th...
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MadScientist @mads100tist.bsky.social · 25/08/2026
For the academics in the crowd 🧪
The post below, but all 'book' are crossed out in red, and replaced by 'paper'
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Adolfo Neto @adolfoneto.elixiremfoco.com · 23/08/2026
Is "AI" the least efficient thing that has ever happened in software engineering history?
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The Tennessee Holler @thetnholler.bsky.social · 22/08/2026
Couldn’t make it up if we tried
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George Monbiot @georgemonbiot.bsky.social · 19/08/2026
This is what the billionaire press and many politicians were campaigning so hard to destroy. Their freedom to drive took precedence over our children's freedom to thrive. www.theguardian.com/environment/...
theguardian.com
Ulez led to better lung size and function among London children, study finds
Researchers find capacity stunted by pollution restored after introduction of ultra-low emission zone
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Marc Somssich @somssich.bsky.social · 18/08/2026
I have said it before: Trait Discovery is one of the most difficult steps in our research here @kwsgroup.bsky.social. We need more help for this! We are looking for a Computational Biologist to help with trait discovery in our #GenomeEditing Team. #PlantScience #PlantScienceJobs #PlantSciJobs
jobs.kws.com
Computational Biologist (m/f/d) - Genome Editing Trait Discovery
Computational Biologist (m/f/d) - Genome Editing Trait Discovery
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Marc Somssich @somssich.bsky.social · 18/08/2026
We are looking for a Group Leader in #Wheat research for pre-breeding here @kwsgroup.bsky.social. This is a full-time, permanent position at KWS France. You would be working on a research station near Lille or Paris. jobs.kws.com/job/Mons-en-... #PlantScience #PlantSciJobs #PlantScienceJobs
jobs.kws.com
Group Lead Wheat Research & Pre-Breeding (m/f/d)
Group Lead Wheat Research & Pre-Breeding (m/f/d)
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Urbmonger @crowshair.bsky.social · 12/08/2026
Hell of a graphic
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cira-csu.bsky.social @cira-csu.bsky.social · 12/08/2026
Totality observed in Spain as the moon's shadow arrived at the Iberian Peninsula moments ago.
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John Trant @trantteam.bsky.social · 12/08/2026
We cant fold proteins computationally generally. A bunch of reasons, but a major one is that proteins dont fold alone. They fold with all sorts of help. And we dont normally know what that is. Many proteins do not adopt a global minimum fold. Its all complicated.
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Dr Paul Dorfman @drpauldorfman.bsky.social · 06/08/2026
Broxted Estate solar farm in Suffolk has had a 41% increase in its biodiversity since 2011 - a future where nature and renewables co-exsist. www.energylivenews.com/2026/08/05/s...
energylivenews.com
Solar panel farm has 41% increase in biodiversity - Energy Live News
The Broxted solar farm in Suffolk has generated more than 350GWh of electricity since 2013
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Climate Centre @climatecentreuk.bsky.social · 06/08/2026
Changing paved gardens back to grass and trees could reduce night-time temperatures by as much as 1C. Over 55% of the UK's front gardens have been paved over. Researchers at Nature Scientific Report found that those hard surfaces are absorbing the day's heat. www.theguardian.com/news/2026/au...
theguardian.com
Weatherwatch: Paving over front gardens is leading to hotter nights
Changing paved areas to grass and planting trees can reduce urban heat island effect by as much as 1C, study shows
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Prem Sikka @premnsikka.bsky.social · 05/08/2026
Major oil firms make $93bn profits in just 3 months amid war and climate crisis. They shift profits, dodge taxes, fuel poverty and inflation. They don't bear the social cost of their business. Forever holding people/govts to ransom. Polluters must pay. Need windfall tax now.
theguardian.com
Revealed: major oil firms make $93bn profits amid war and climate crisis
Iran conflict windfall over three months reignites calls for companies ‘cashing in on human misery’ to pay for environmental damage
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bioRxivpreprint @biorxivpreprint.bsky.social · 05/08/2026
An industry perspective on whole genome-informed hybrid maize disease resistance characterization to improve breeding decisions www.biorxiv.org/content/10.64898/20…
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Dr Paul Dorfman @drpauldorfman.bsky.social · 03/08/2026
Today, 34.1% of the European nuclear capacity is shuttered due to climate impact.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026
Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
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James Ball @jamesrball.com · 03/08/2026
"Kew Gardens has had a weather station since 1871. This July was, based on third party analysis of Met Office data collected at the site, the first calendar month on record where no rainfall was measured at Kew."
londoncentric.media
London's first month without rain
Plus: There's nowhere to bury the dead • London wants to keep its money • When will it stop being so damn hot • Who is to blame for turning off the air conditioning in the tower block?
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Cold War Steve @coldwarsteve.bsky.social · 06/07/2026
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