Julien Roux (@julienroux.bsky.social on 🦋)

Bioinformatician in @DepBiomedicine at @UniBasel_en. @isbsib member. Interested in omics data analysis, exp design, data viz

@julienroux.bsky.social on 🦋

[Vince Buffalo @vsbuffalo]

Utterly depressing this kinda study is drawing attention. Dilutes scientific validity for paper creation.
Massively underpowered (n=18, n=16, n=14 for 85% & 75% dark chocolate, and control), they see no effect of 75% and then do a bunch of gut microbiome 16s analyses. QRP galore.

[Sergio Marco @sergiomarco96]

1/🧬 Excited our latest preprint titled:
"Exploration of RNA outside segmented cells in spatial transcriptomics reveals extrasomatic RNA organization"

🔖 Read it here: https://t.co/0CKJulYDKH

Details on motivation and findings 👇

[Elisabeth Bik @MicrobiomDigest]

@DefenderOfBasic Let me introduce you to PubPeer and its plugin. Over 200,000 papers commented on (9,500 by me!) and counting.
https://t.co/TpTQHdPOsj

[gen0m1cs @gen0m1cs]

This looks great.

SCT (i.e., XXY, XYY, XXX chromosome individuals) PheWAS analysis was conducted for disease diagnosis associations.

[Julien Roux (@julienroux.bsky.social on 🦋) @_julien_roux]

I'm not posting here anymore, but this is worth an exception! See the thread on 🦋:
https://t.co/JcPUUo9paT

[medRxiv @medrxivpreprint]

Rapid and long-lasting remodelling of the blood transcriptome following bariatric surgery https://t.co/155Tl465Bb #medRxiv

[Misha Khodak @khodakmoments]

🧵 on surprising revelations from our study of specialized foundation models (FMs beyond vision/text): after evaluating dozens of scientific & time series FMs we found that most weren’t even competitive with simple supervised models, some with as little as 513 parameters.
1/n

[Christophe Dessimoz @cdessimoz]

Find me and other @ISBSIB colleagues on bluesky: https://t.co/CKa3ZF9wF0
(If you are a SIB member and are missing from the list, please let me know and I will add you).

[Charlie Hebdo @Charlie_Hebdo_]

🔴 COMPETITION | Charlie Hebdo is launching a cartoon competition on the following theme: mocking God ! Draw your anger at the stranglehold all religions are having on your freedoms. More info 👉 https://t.co/10wCWxlstx

[Publishing with Integrity @fake_journals]

eLife won’t get an impact factor, says @Clarivate | @RetractionWatch | https://t.co/fBtxU2Vw3E

[AukeHoekstra @AukeHoekstra]

BlueSky is still small and a bit of a bubble. But there are many good reasons for being on BlueSky too.

It feels almost exactly like twitter but under the hood it has some substantial improvements.

[SIB @ISBSIB]

🚀Big News! 🚀SIB will host the 25th European Conference on Computational Biology (eccb) in Geneva, Switzerland, from 31 Aug-4 Sept 26!🇨🇭
Save the date and stay tuned for more updates as we get ready for #eccb2026 @ECCBinfo @ISBSIB https://t.co/zbVGozvwrs

[Current Biology @CurrentBiology]

😶

[Mark R@markrobinsonca@{genomic.social,bsky.social} @markrobinsonca]

This is getting exciting. Over 20 abstracts submitted. The committee will be looking at them next week. Looking forward to these discussions.

There is still time to submit (due Monday 18th).

Google form link:
https://t.co/zGGZ9Xd60E

[Anshul Kundaje @anshulkundaje]

This is not at all why we're leaving X. It's become a misinformation cesspool and it's impossible to have thoughtful arguments here any more. Have you tried engaging with any "vaccine skeptics" here? Evidence and facts have no meaning here. It's a pure propaganda engine. 1/

[Publishing with Integrity @fake_journals]

Who reviewed this paper?

A few days ago @gcabanac tweeted about a paper that had published a remark that it had been forced to cite irrelevant papers. You can see the tweet here: https://t.co/FpSr5QLPfW. We remarked that if it was not so serious, it would be funny.

Since reading that tweet, we have not been able to get it out of our head, so we thught that we would document it in a little more detail. We are doing this for three reasons.

1️⃣ In our view, it descerves more detail to be made available.

2️⃣ We'd like these details to be be kept as a matter of public record, so we are posting similar posts on our X account and our LinkedIn account.

3️⃣ It should be of interest to this community, so we hope that this raises even further the ethical issues around this topic.

The first image shows the paper that we are looking at. What is interesting is the text that appears on at the end of the introduction (highlighted in red). This appears to show that the reviewer insisted that a set of 13 papers be cited, else they would not accept the paper. It would be interesting to see the review repport, so that we could be certain what had been said. If you want to see the paper, it is available here: https://t.co/mlv5UDdp5T

In the rest of this 🧵, we show the papers that have been asked to be cited (i.e. [35]-[47]). These have been taken from the paper mentioned above. You'll notice (as we have highlighted it) that every paper is "et al." meaning, of course, that there are quite a few authors on each paper.

Gicven that we cannot see all the authors, the other images on this 🧵 shows the full set of authors on each of these 13 papers.

We leave it an an exercise for the reader to hazard a guess as to the reviewr is?

[Simon Cox is on BlueSky @SimonFRCox]

Hey followers - if you haven’t moved to Bluesky yet, I really encourage you to try it. It’s MUCH better than Twitter and so many of the people you follow are already there.

I’m on https://t.co/3ajOXHwWBx

Here’s some tips if you make the move.

Hope to see you there.

[Mike Morrison @mikemorrison]

🚨Announcing new #OpenHardware project to measure traffic patterns in scientific poster sessions (w/anonymous & IRB-safe data).

The single most powerful thing we can do to improve poster sessions is create better measures.

Details & how you can test/contribute:
https://t.co/ucpv3AfEiw

[Dr. Jean Fan @JEFworks]

I didn't noticed all these co-first authors because such status is not available/visible on PubMed. It is also not displayed on most journal websites unless you click for more details.

I've discussed this issue before on my blog with recommendations: https://t.co/m5j0psPEcN 2/3

[Richard Sever @cshperspectives]

@srikosuri @mbeisen bioRxiv/arXiv have shown people find ways to pick what to read before such proxies are assigned. Meanwhile, HHMI have shown you can assess people without resorting to those proxies. 2/2

[MA Oviedo-Garcia @maoviedogarcia]

#ReviewLikeATweet #StrangerThings @MDPIOpenAccess @Diagnostics_mdpi

1 art-Round 1
🥇0 words (Lucian Puscasiu)
🥈13 words (Mihai Cristian Dumitrascu)
🥉 26 words (Anonymous)
🗞️ 34 words (Ana Valea)

Thorough review of the original manuscript❓

@PubPeer

https://t.co/clNADTTaOA