iiinova — where your digital self keeps evolving

Reposted by Paul Gardner

Ellen Leffler @ellenleffler.bsky.social · 5h

My department at University of Utah is recruiting new faculty, with "Human" and "Genetics" broadly defined. It is a fantastic place to start a lab, with collaboration, creativity and conviviality encouraged. Applications due Oct 16. Please share and apply! utah.peopleadmin.com/postings/208...

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Michael Hiller @hillermich.bsky.social · 23/09/2026

Happy to share results of the @bat1kgenomes.bsky.social phase 1, providing reference genomes covering 21 bat families. New insights into bat phylogeny, ancestral genome reconstruction, European origin & ancestral echolocation. Great work by a team of 100+ colleagues www.nature.com/articles/s41...

nature.com

Reference genomes and fossils revise bat family phylogeny and biogeography - Nature

An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.

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Paul Gardner @ppgardne.bsky.social · 24/09/2026

This is well worth a read by anyone thinking about the impacts of AI on education IMHO: aiandeducation.mit.edu/report/

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Arc Institute @arcinstitute.org · 23/09/2026

Many important bacterial non-coding RNAs and structural elements remain undiscovered. To help, David Li, Garyk Brixi, Michael Fischbach, @brianhie.bsky.social & team introduce Minerva, which uses a genome language model to predict RNA base pairing, repeats, & other interactions from sequence alone.

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Zamin Iqbal @zaminiqbal.bsky.social · 21/09/2026

Careful implementation of Bayesian phylogenetics in Delphy allows huge speed gains and identical results to BEAST, but runs on your laptop browser www.nature.com/articles/s41... Amazing work from @pardissabeti.bsky.social , Patrick Varilly, @benfry.com and co.

Two plots showing tMRCA and support are incredibly tightly correlated between Delphy and BEAST

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Igor Ulitsky @igorulitsky.bsky.social · 24/08/2026

One of the (well, >1) problems in the lncRNA field is that some of the lncRNAs are not real genes, i.e., do not represent a standalone locus that produces independent transcripts. Some cases are more 🤔 than others, e.g. lncDACH that Matt Bennet from Andy Baker's lab took a deep dive into. 🧵

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Paul Gardner @ppgardne.bsky.social · 18/09/2026

How not to build a lncRNA annotation tool: 1. assume the genome & transcriptome consists of only lncRNAs and mRNAs:

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Reposted by Paul Gardner

George Slim @bureauchem.bsky.social · 11/09/2026

Juliet Gerrard's book on her time as Prime Minister's Chief Science Advisor is out. Practical and approachable with a nice frame of how and where science advice works. (I get mentioned! - only time I've asked my boss if I can have a shower). aucklanduniversitypress.co.nz/front-row-se...

aucklanduniversitypress.co.nz

Front Row Seat: How Science Can (and Can’t) Shape Public Decision-Making

A scientist and three prime ministers – the inside story.

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Paul Gardner @ppgardne.bsky.social · 10/09/2026

Four of twelve faked systematic reviews received identical replies overnight from TB Emran. MS Mubarak wrote much the same response a month ago - with no update or retraction yet. At this stage I have put more effort in than this papermill crowd.

We have rechecked Figure 1 and accept your findings, including that the included count equals the number of references and that the arithmetic does not follow PRISMA 2020. Figure 1 does not document an executed search. This review was a narrative synthesis presented as a systematic review, which is a methodological misreporting. This review was conducted as a topic-focused narrative synthesis rather than a systematic review. Sources were selected by the authors on relevance to each section; screening was not duplicated, and no protocol was registered. The article does not describe itself that way: it cites Page et al. and presents Figure 1 in PRISMA form with specific counts. That is a misreporting of the methodology, and it is a matter for the published record rather than for this thread. We will write to the publisher requesting a corrigendum for this article that withdraws Figure 1 and its caption, removes the citation to Page et al., and the claim of PRISMA-conformant selection and replaces the search paragraph with an accurate description of the narrative methodology, stating that the selection is not reproducible from a documented search. We will post the outcome here.

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Paul Gardner @ppgardne.bsky.social · 08/09/2026

I'm happy to say I have managed to report all 12 faked systematic reviews that we discovered on PubPeer. The corresponding URLs are in the ALT text. I'm awaiting responses from most of the publishers/authors -- other than one author admission:

1. https://pubpeer.com/publications/E858A6B3492DB679121B1358E1CDEA#null
2. https://pubpeer.com/publications/E223A9D5CF9F48D2BA6E31A5B7B163
3. https://pubpeer.com/publications/5EA00303B5EDCCDAF82304D93F0A1C
4. https://pubpeer.com/publications/339F22D24DEBFB96025FC31675A9F4
5. https://pubpeer.com/publications/650876481D7FC858E2F95148AB264C#null
6. https://pubpeer.com/publications/BE8365B6373075786A0DE05323125A#null
7. https://pubpeer.com/publications/ABE3AB3258181CD400EDFC900E3851
8. https://pubpeer.com/publications/A87CFEBAA1950F2D96195B8B8088B8
9. https://pubpeer.com/publications/233E9B0E67EAB1C92CD3904F5587C2#null
10. https://pubpeer.com/publications/365A43971AC6C7292696BA05F2300D
11. https://pubpeer.com/publications/A8F0DC88104363F2E9334CE67A03EA
12. https://pubpeer.com/publications/FFC531637B4932529E46082BC0004E

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Paul Gardner @ppgardne.bsky.social · 07/09/2026

I'm experimenting with a co-author basic network analysis to explore dubious quality publication. Last year we reported a (now retracted) review by Abdur Rauf, then we found faked systematic reviews by Talha Bin Emran. Now checking the other high degree authors in the network...

A co-authorship network of authors linked to low-quality & faked reviews. Author name is followed by the degree of the network node.

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Paul Gardner @ppgardne.bsky.social · 01/09/2026

This looks like an important read. The image captures what many educators have suspected for the last few years -- & is the reason we are moving away from written internal assessments. papers.ssrn.com/sol3/papers....

The figures to the left plot the distribution of our outcomes, split by student-month observations for students who eventually adopt
generative AI before adoption (Pre AI), after adoption (Post AI) and for student-month observations associated with students who have no
adopted generative AI by June 2025 (Never AI). The figures to the right plot the mean outcomes by event time for students who
eventually adopt generative AI before adoption (Ever-AI Students). For the Never-AI Students, we construct a reweighted mean
comparison series so that, at each event time, the control observations have the same distribution over month, grade, and school as the
corresponding Ever-AI observations. The data is at the student-month level and the samples are shown in Table 1. In panel A, the outcome
is the average score (percent relative to baseline average) on the homework assignments. In panel B, the outcome is the average homework
completion time in minutes. In Panel C, the outcome is the average score (percent relative to baseline average) on the closed-book exams
in class.

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Paul Gardner @ppgardne.bsky.social · 31/08/2026

Major spliceosomal RNA secondary structures, interactions (PDB), evolutionary conservation (PhyloP & Rfam SEEDs), and disease associations (D’Souza et al 2026). All in one monstrously busy plot. 😁

The major spliceosomal RNAs layed around a circle: U1, U2, U4, U5 and U6. Blue arcs indicate secondary structures, orange and green arcs indicate RNA:RNA interactions between snRNA & mRNA respectively. RNA:protein interaction regions are indicated with arcs & purple labels. Variable sites associated with recessive or dominant disease are indicated with red or black triangles respectively (D'Douza et al 2026). The outer rings are heatmaps indicating evolutionary conservation from Rfam seed alignments (%identity) & maximum phyloP scores (phyloP447way).

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Paul Gardner @ppgardne.bsky.social · 28/08/2026

Well I like it! For the human spliceosomal RNA fans -- secondary structures & interactions mined from PDB & indicated by arcs between snRNA nucleotides which are plotted around the circle. Evolutionary conservation is from Rfam seed alignments and phyloP scores.

Circular plot showing human spliceosomal RNAs U1, U2, U4, U5 & U6, inner arcs indicate basepairs, outer rings are heatmaps indicating evolutionary conservation.

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Paul Gardner @ppgardne.bsky.social · 23/08/2026

New paper day! What started as an overly ambitious summer student project is now published. We asked which genomic signals best distinguish protein-coding, short ncRNA and long ncRNA genes from the genomic background. doi.org/10.1093/g3jo...

doi.org

Genomic indicators of gene function: a systematic assessment of the human genome

Abstract. Proteins and non-coding RNAs are functional products of the genome that are central for crucial cellular processes. With recent technological adv

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Reposted by Paul Gardner

Neil Hall @neilhall.bsky.social · 20/08/2026

Biological Databases are critical infrastructure - not projects. As so much effort is put into harnessing AI to solve all our problems, we are allowing the foundational data resources crumble. Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...

nature.com

Treat biological databases as infrastructure, not projects

Letter to the Editor

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David Hood @thoughtfulnz.bsky.social · 20/08/2026

With this weeks release of provisional deaths as part of the quarterly population/births/deaths data for NZ, I can remake my expected vs. actual weekly mortality graph. I've. said before that in 2029 we should all look at the peak covid period from both time directions to look at inflection points.

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Reposted by Paul Gardner

Shaun Hendy @hendysh.bsky.social · 16/08/2026

None of this is about whether reallocating science funding is a bad idea. Maybe there is a case to be made? But it illustrates the perils of centrally prioritising funding without using the right data to make meaningful comparisons with other countries. 8/n

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Reposted by Paul Gardner

Adam Phillippy @aphillippy.bsky.social · 06/08/2026

🎯 Goodhart’s law: if you make a list of variants the target, people will get really good at calling those variants. But those variants are not a genome! As a result, we’ve been stuck trying to read genomes under the lamppost of short reads [4/15]

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Reposted by Paul Gardner

PaulEKruger @paulekruger.bsky.social · 06/08/2026

Excellent speech from Reuben Davidson here. @nicgaston.bsky.social and I had the pleasure of hosting Reuben last Friday at UC as he toured MacDiarmid Inst labs, he gets it, he appreciates the dire straits the science sector is in! #nzpol

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Reposted by Paul Gardner

Noah Whiteman @nkwhiteman.bsky.social · 06/08/2026

I’m thrilled to share that our search for a tenure-track colleague in my *truly wonderful and collegial* Genetics, Genomics, Evolution and Development Division in the MCB Department at Berkeley @berkeleymcb.bsky.social is live! Please share this broad search widely: aprecruit.berkeley.edu/JPF05481

aprecruit.berkeley.edu

Assistant Professor -Genetics, Genomics, Evolution, and Development - Molecular and Cell Biology

University of California, Berkeley is hiring. Apply now!

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Liz Miller @lizmillercu.bsky.social · 31/07/2026

Job alert! I'm recruiting a new post-doc to work on mechanisms of co-translational quality control in the ER. Looking for expertise in ribosome biology and yeast genetics/cell biology. Please reach out to me with any questions. www.dundee.ac.uk/work-for-us/...

dundee.ac.uk

Postdoctoral Research Assistant - UOD2336

Closing date: Thursday 27 August 2026, 23:59

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Brent Toderian @brenttoderian.bsky.social · 30/07/2026

“According to the finance ministry’s calculations, the cost to society of trips by car is close to one euro/km. On the other hand, every km travelled by bike yields societal gains of 60 euro cents thanks to the health benefits of cycling, transport efficiency gains, & lower infrastructure spending.”

theprogressplaybook.com

Copenhagen Cycling Revolution: Lessons for Cities

Close to two-thirds of the city’s residents commute by bike to school or work every day.

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Bart Janssen @bjjanssen.bsky.social · 30/07/2026

Brutally improve Parliament by imposing a 50% wealth tax on all MPs

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Phil Garnock-Jones @theobrominated.eurosky.social · 30/07/2026

Let's brutally transform Parliament by giving these numpties the bum's rush in November.

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Paul Gardner @ppgardne.bsky.social · 29/07/2026

What other sectors could the NZ Prime Minister brutally transform? --Brutally increase tomato production by halving water use? --Brutally improve literacy by closing libraries? --Brutally strengthen bridges by removing beams? --Brutally improve health by closing clinics?

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Reposted by Paul Gardner

Meg Mindlin @invertebabe.bsky.social · 29/07/2026

New research just dropped today that makes octopuses even weirder than they already are… let me explain🧵🧪🐙🐡🦑

OCTOPUSES JUST GOT WEIRDER
Featuring an illustration of a two spot octopus with a blue and purple ribosome behind it

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Paul Gardner @ppgardne.bsky.social · 28/07/2026

I walked the GENE 4th years through this story yesterday. They were suitably horrified. On a related note, how many retractions, links to papermills, research misconduct etc. should be allowed before the entirety of a group's work can be delisted from the academic record?

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Reposted by Paul Gardner

Ronald Breaker @ronbreaker.bsky.social · 24/07/2026

My lab at #Yale has two #riboswitch research openings: 1. Postdoc with mammalian gene manipulation experience (tinyurl.com/zzb269em); 2. Postdoc (or BS, MS) with bioinformatics skills (tinyurl.com/3j73jfcn). Send your cv to me or to Kavita at kumari.thakur@yale.edu.

tinyurl.com

Postdoctoral Associate in Eukaryotic Cellular Molecular Genetics and RNA Biology — Department of Molecular, Cellular and Developmental Biology (MCDB)

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Sally Greaves @cardiokiwi.bsky.social · 23/07/2026

Following initial vaccination of a limited number of key native species, a further 23 have been deemed priority for vaccination, including the Rowi and Haast kiwi, the Southern Brown kiwi, black robin, hoiho/yellow-eyed penguin and pāteke/brown teal. www.stuff.co.nz/nz-news/3610...

stuff.co.nz

Some of New Zealand’s rarest kiwi to be vaccinated as bird flu threat grows

Kiwi will now be vaccinated against bird flu after the Ministry for Primary Industries approved the second stage of the Department of Conservation’s vaccine plan.

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Emily Troyer @fishfetisher.bsky.social · 23/07/2026

Beetles beetles beetles beetles !

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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026

Today I am so incredibly excited to share with you a new tool from the lab, #RFviewJS (and its stand-alone version #RFview). Two tools I built to fill a gap that has frustrated me for years. #RNA secondary structure visualization (1/n)

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Paul Gardner @ppgardne.bsky.social · 15/07/2026

1/8 Systematic reviews and meta-analyses are at the top of the evidence hierarchy. They influence clinical practice, policy and future research. So I was surprised to find a series of 12 reviews with remarkably similar PRISMA literature-search figures.

Evidence pyramid from: https://commons.wikimedia.org/wiki/File:Research_design_and_evidence_-_Capho.svg

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Paul Gardner @ppgardne.bsky.social · 15/07/2026

I spent months hunting for missing essential & highly conserved ncRNAs in avian genomes -- eventually we realized they were all on microchromosomes.

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Rod Emmerson @rodemmerson.bsky.social · 14/07/2026

In today’s NZ Herald

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Margot Finn @eicathomefinn.bsky.social · 13/07/2026

In an outspoken attack on the “incredibly profitable” but “completely unregulated” scientific publishing industry, Thomas Südhof...said he wanted to see US or European Union agencies establish minimum standards for journals that wish to describe themselves as “peer reviewed”. 1/3

timeshighereducation.com

‘Broken journal system’ needs government oversight, says Nobelist

Federal authorities should enforce minimum standards for peer review in ‘unregulated’ journal sector, argues Thomas Südhof

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Torsten Schwede @torstenschwede.bsky.social · 11/07/2026

CASP17, the 17th Critical Assessment of Structure Prediction conference, will take place in person in Rome, Italy, December 1–5, 2026. Registration is open now. What is the state-of-the-art in predicting protein and RNA structures, immune complexes, and ligands? events.humanitix.com/casp17 🧪 #AI

events.humanitix.com

CASP17

CASP17 - Critical Assessment of Structure Prediction 3D Structure of Proteins, RNA, and Complexes, Immune Complexes, Ligand Binding, Conformational Ensembles

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Elena Rivas @rivaselenarivas.bsky.social · 05/07/2026

New! R-scape version v2.6.11 github.com/EddyRivasLab... with drawings of R-scape annotated RNA consensus structures with many fewer overlaps!! Using RFview github.com/dincarnato/R... Shout out to @incarnatolab.bsky.social for displaying R-scape's covariation outputs + CaCoFold-R3D structures.

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