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Matthew McCullen

@nkcell.bsky.social
218 followers 491 following 3 posts
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Reposted by Matthew McCullen
Stephan P. Rosshart @srosshart.bsky.social · 05/10/2026
Reposts appreciated! Natural microbiota-based mouse models - particularly Wildlings - improve reproducibility & translation across a remarkable range of biomedical fields. Our new @jem.org Found in Translation! Thanks Isabel, Mario & @jonatcoquet.bsky.social! doi.org/10.1084/jem....
doi.org
Natural microbiota–based mouse models: A platform to fast-track translation of fundamental discoveries into the clinic
Conventional laboratory mice are invaluable tools in biomedical research, but their restricted microbial complexity limits their translational relevance. H
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Reposted by Matthew McCullen
John Stott @jpsastro.bsky.social · 24/09/2026
Had a UKRI funded grant proposal rejected at the "AI triage stage". "This AI-based triage was used only to identify approximately 50% of the strongest proposals to take forward to full human review." 🧪 #academicsky
I am writing to let you know that, unfortunately, your application was not successful.

Review process

As part of the initial triage of the 179 proposals submitted to this call, each was assessed using an AI-based review. Every proposal was read independently by several different AI models against the same seven criteria used to shape this call (including cyber security relevance, research quality and novelty, importance of the problem addressed, feasibility of the project plan, likely outputs and impact, value for money, and responsible research practice), with each model asked to give a score and a written justification with supporting quotations from the text. To guard against any one model's idiosyncrasies, we also ran a second, independent process in which different AI models debated the merits and weaknesses of each proposal before reaching a judgement, again against the same criteria. Scores from both processes were combined to produce an overall ranking. 

This AI-based triage was used only to identify approximately 50% of the strongest proposals to take forward to full human review.  Projects selected for funding were drawn from those that progressed to the full human review stage. We recognise that AI-assisted assessment is a new and evolving part of the review process, and we are continuing to evaluate how well it aligns with the judgements of human reviewers on this call. We will soon produce a document detailing our method, so that others can build upon it and improve it.

Feedback on your application

Your application was not selected to progress beyond the AI triage stage.  To provide transparency on the outcome of this assessment, we are sharing below the scores (out of 5) from each of the two AI review processes described above, together with the mean score across the two processes.
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Reposted by Matthew McCullen
Pam Rosato @pcrosato1.bsky.social · 24/09/2026
inpreparation.substack.com/p/opinion-re...
inpreparation.substack.com
Opinion: I Miss When The NIH Payline Was 40% And We All Mouth-Pipetted Phenol
By Dr. Douglas R. Waverly, Professor Emeritus of Biochemistry, Yale University
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Reposted by Matthew McCullen
Open Box Science @openboxscience.bsky.social · 23/09/2026
Hao Hu's talk is now on YouTube! Priming of CD8+ T cells by peripheral dendritic cells exacerbates tau-mediated neurodegeneration youtu.be/4up0OQQA-wA
youtu.be
[Hao Hu] Priming of CD8+ T cells by peripheral DCs exacerbates tau-mediated neurodegeneration
Priming of CD8+ T cells by peripheral dendritic cells exacerbates tau-mediated neurodegeneration *Speaker: Hao Hu (Washington University in St. Louis) *Moderator: Jerry Lin (Massachusetts General…
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Reposted by Matthew McCullen
Anita Devineni @anitadevineni.bsky.social · 13/09/2026
My department (Biology at Emory) is hiring for a teaching track position! These are stable, well-respected, long-term positions with a path to promotion and ppl often staying for decades. The dept is wonderfully supportive and filled with amazing humans (faculty + staff) apply.interfolio.com/191814
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Reposted by Matthew McCullen
Grace Lindsay @neurograce.bsky.social · 27/08/2026
MIT has put out an "AI and Education" report summarizing what they've found at their own institution. Seems thoughtful. aiandeducation.mit.edu/report/
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Reposted by Matthew McCullen
Nonia Pariente @npariente.bsky.social · 12/09/2026
Experimenting with new models of peer review is essential to move to a future of #publishing that better serves science and researchers ⬇️ DiscoveryStack is an interesting attempt, aiming to separate the assessment of quality & impact @maxkrummel.bsky.social @richardsever.bsky.social 🧪
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Reposted by Matthew McCullen
Jeffrey Perkel (he/him) @jperkel.bsky.social · 09/09/2026
The policy change was “necessitated because of financial realities”, says @briannosek.bsky.social: it costs US$4-5 million annually to manage the OSF. New @nature.com, @cos.io to stop hosting data & code, plus private data, from 16 Nov. By @dalmeet.bsky.social 🧪 www.nature.com/articles/d41...
nature.com
Popular open-science platform to stop hosting data and code amid funding concerns
Changes to the Open Science Framework’s policies will come into effect in November, forcing researchers to reconsider their workflows.
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Reposted by Matthew McCullen
Open Box Science @openboxscience.bsky.social · 08/09/2026
OBS Neuroimmunology Webinar — Monthly on the 3rd Thu at 12 PM ET Priming of CD8+ T cells by peripheral dendritic cells exacerbates tau-mediated neurodegeneration *Speaker: Hao Hu (WashU) *Moderator: Jerry Lin (MGH/Harvard) *Zoom link: us02web.zoom.us/meeting/regi...
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Reposted by Matthew McCullen
Stephen Turner @stephenturner.us · 03/05/2026
Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪
doi.org
Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
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Reposted by Matthew McCullen
Adrian Liston @labliston.bsky.social · 27/08/2026
Two post-doc positions available in our lab! It is a supportive environment and on which boosts careers! Historically, of our ~30 post-docs 27% have gone on to tenure-track positions, 27% did another post-doc, and 42% have gone on to positions in biotech or pharma.
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Reposted by Matthew McCullen
Johan Duchêne @johanduchene.bsky.social · 26/08/2026
Wow! Only Good Antibodies has developed a new tool that lets you see, directly in a paper, which antibodies were tested and validated. A tool that comes at the right time, given all the issues surrounding antibody validation. Definitively a tool to get onlygoodantibodies.co.uk/extension/
onlygoodantibodies.co.uk
Browser Extension — Only Good Antibodies
A free browser extension that marks antibodies cited in a paper with their knockout-controlled validation status, for the application they were used in.
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Reposted by Matthew McCullen
keven-pittsinger.bsky.social @keven-pittsinger.bsky.social · 26/08/2026
Linux turns 35 today. Here's your cake. Enjoy.
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Reposted by Matthew McCullen
Reese Richardson @reeserichardson.bsky.social · 25/08/2026
A massive update: At least ~15 companies~ are selling scientists antibodies using faked validation data. We've documented 18,000+ manipulated images on 17,000+ products sold by leading laboratory suppliers including Thermo Fisher, Abcam, Santa Cruz Biotechnology, Millipore Sigma and Bio-Techne. 1/🧵
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Reposted by Matthew McCullen
Richard Van Noorden @richvn.bsky.social · 25/08/2026
More than 18,000 questionable images found in antibody catalogues of 15 companies. This "...raises questions about the practices of commercial antibody suppliers" by @dangaristo.bsky.social in @nature.com. Sleuthing led by @reeserichardson.bsky.social. www.nature.com/articles/d41...
nature.com
More than 18,000 questionable images found in antibody catalogues of 15 companies
Science sleuth’s findings raise questions for researchers working to improve the reliability of commercial antibodies.
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Reposted by Matthew McCullen
Richard Sever @richardsever.bsky.social · 25/08/2026
"Jupyter notebooks associated with papers are using software versions beyond their support window[s]...This contributes to reproducibility issues...Similar issues arise with datasets" A paper's a permanent scientific record. If dependencies aren't, it isn't. 1/2 academic.oup.com/gigascience/...
academic.oup.com
Validate User
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Reposted by Matthew McCullen
Sholto David @sholtodavid.bsky.social · 25/08/2026
Today I'm posting a new blog! Nearly two hundred papers have muddled the names for different proteins and recorded using the wrong antibody for a range of experiments. This time it's PERK vs. p-ERK. Including researchers from Harvard, the Mayo Clinic, and more. sholto.substack.com/p/perk-vs-p-...
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Reposted by Matthew McCullen
Sholto David @sholtodavid.bsky.social · 21/08/2026
www.nature.com/articles/d41...
nature.com
Sleuth identifies dozens of studies that used the wrong antibody
The case is the latest example of a scientific workhorse being misused in experiments.
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Reposted by Matthew McCullen
Richard Sever @richardsever.bsky.social · 18/08/2026
In the past I [could] detect fraudulent stuff...formulaic, tortured phrases, too good to be true...This [was] different... I wonder if I'd have identified [it] if it hadn't concerned my own datasets. I have strong doubts academic publishing is ready for this" deevybee.blogspot.com/2026/08/acce...
deevybee.blogspot.com
Acceleration of the arms race between fraudsters and honest researchers
I was recently asked to review a paper that piqued my curiosity. From the abstract it sounded as if it was a secondary analysis of a datas...
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Reposted by Matthew McCullen
elizabethginexi.bsky.social @elizabethginexi.bsky.social · 14/08/2026
‼️NIH is proposing to change NIH Peer Review outcomes. Instead of impact scores they propose 3 categories: "Most competitive" "Competitive", or "Not discussed" This RFI link will accept your comments/feedback on this proposal until 10/13/26. grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-26-088: Request for Information (RFI) on Proposed Changes to Reporting Outcomes from NIH Peer Review
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Request for Information (RFI) on Proposed Changes to Reporting Outcomes from NIH Peer Review NOT-OD-26-088. NIH
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Reposted by Matthew McCullen
vincentholst.bsky.social @vincentholst.bsky.social · 13/08/2026
In 2023, @nature.com published 'Papers and patents are becoming less disruptive over time', receiving world-wide media attention. Our Matters Arising, published after a 32 month delay (more on that soon), shows that the reported decline can largely be attributed to dataset artefacts. 🧵
The average CD_5 index per year for Web of Science. The original Park et al. decline (top curve) becomes essentially flat (bottom curve) when removing papers with CD_5=1. Those papers largely correspond to dataset artefacts.
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Reposted by Matthew McCullen
Robert Aboukhalil @robert.bio · 13/08/2026
I made a Nextflow tutorial you can run from your browser!! Nothing to install, and cloud costs are sponsored by @carolinacloud.io You build a pipeline to find how much sequencing you need to detect Listeria in ice cream, with interactive challenges along the way. sandbox.bio/tutorials/ne...
sandbox.bio
Introduction to Nextflow
Interactive Nextflow tutorial: write your first pipeline and run it on real cloud infrastructure, for free and with no installation. Also learn to use existing nf-core pipelines.
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Reposted by Matthew McCullen
Richard Sever @richardsever.bsky.social · 13/08/2026
bioRxiv/medRxiv have been dealing with endless bot attacks recently (plus usual DDOS stuff, etc). Tricky to address without impacting genuine users - many of you affected. Apologies. We're working with our hosting service on solutions & think we're getting there [he shouts in his Red Queen costume].
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Reposted by Matthew McCullen
Carl T. Bergstrom @carlbergstrom.com · 21/07/2026
1. We—@eduede.bsky.social, @mjcrockett.bsky.social, Kevin Gross, and I—have a new preprint on the arXiv today, based on ideas that emerged during an @sfiscience.bsky.social workshop in November 2024: The unintended consequences of large language models as a labor-augmenting technology in science.
arxiv.org
The unintended consequences of large language models as a labor-augmenting technology in science
As a labor-augmenting technology, large language models (LLMs) have the potential to accelerate scientific activity across the research pipeline. But even if LLMs perform on par with human experts at ...
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Reposted by Matthew McCullen
Adrian Liston @labliston.bsky.social · 18/07/2026
We want to make sure that anyone who needs to read this book can, so if you can't buy the book you can now read for free online. Essential reading for scientists suffering a bout of self-doubt or imposter's syndrome heyzine.com/flip-book/a5...
heyzine.com
Online Flipbook
Created with the Heyzine flipbook maker
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Reposted by Matthew McCullen
Valérie Masson-Delmotte @valmasdel.bsky.social · 16/07/2026
AI in scientific publishing: Slower, worse, and more expensive | Science www.science.org/doi/10.1126/...
science.org
AI in scientific publishing: Slower, worse, and more expensive
There’s a saying in the management world, popularized by NASA administrator Daniel Goldin in the 1990s, that the goal of technological improvements is to make products faster, better, and cheaper. Alt...
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bioRxiv Immunology @biorxiv-immuno.bsky.social · 09/07/2026
Bcl11b dose-dependently regulates positive selection of CD8 T cells to the virtual memory fate www.biorxiv.org/content/10.64898/20…
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Reposted by Matthew McCullen
Julia Métraux @juliametraux.bsky.social · 07/07/2026
Scoop: NIH is on a mission to enlist one million Americans to share their genetic data to help with health research through a precision medicine program called “All of Us.” What participants don’t know is that at one research site, Palantir stores the data. www.motherjones.com/politics/202...
motherjones.com
Palantir has a hand in NIH's most ambitious health initiative
The defense tech firm's work with public health data has largely flown under the radar.
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Paul Jenkins @pjenkinslab.bsky.social · 30/06/2026
Nice article from The Scientist about the antibody "problem". www.the-scientist.com/altered-anti... @reeserichardson.bsky.social @sholtodavid.bsky.social @jwoodgett.bsky.social @mbonini.bsky.social @bwjones.bsky.social
the-scientist.com
Altered Antibody Validation Data on Vendor Sites Alarms Researchers | The Scientist
After several examples of undisclosed alterations in reagent suppliers’ antibody catalogues surfaced, researchers call for transparency to rebuild trust.
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Reposted by Matthew McCullen
MwahahahahahadScientist @mads100tist.bsky.social · 26/06/2026
Don't use slop. Someone's trying to make money out of you and your colleagues and your friends. Do yourself a favor and read 100% human-crated content in @prelights.bsky.social Upload preprints. Read preprints. Cite preprints. Fuck AI 🧪
prelights.biologists.com
Homepage - preLights
Welcome to preLights, the preprint highlights service run by the biological community and supported by The Company of Biologists. Here, a team of scientists regularly review, highlight and comment on ...
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Aydan Bulut-Karslioglu @bulutkarslioglu.bsky.social · 26/06/2026
I have been thinking since yesterday about why I find the 1% thing so, so disturbing. It's a visceral reaction of 'just no', which goes beyond the general yuck towards the enshittification of/via AI. I have finally put my finger on it: it is the feeling you get when
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Reposted by Matthew McCullen
Richard Sever @richardsever.bsky.social · 26/06/2026
“the academic community is enormously heterogeneous and it’s almost impossible to keep everyone happy” Never a truer word said in this analysis of downstream consequences of openness by @jacoates.bsky.social ripplingideas.org/2026/06/26/t...
ripplingideas.org
The 1% club and the rocky road ahead for bioRxiv
The recent launch of qed’s “top 1%” preprint ranking has sparked controversy, with concerns about its arbitrary nature, potential harm to authors, and low-quality inclusions. Whil…
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Reposted by Matthew McCullen
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 24/06/2026
Beyond statistical significance: ranking transcription factor binding motifs by effect size www.biorxiv.org/content/10.64898/20…
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Retraction Watch @retractionwatch.com · 24/06/2026
Nature Medicine has retracted a paper on whether time of day makes a difference in chemotherapy efficacy.
nature.com
Retraction Note: Time-of-day immunochemotherapy in non-small cell lung cancer: a randomized phase 3 trial - Nature Medicine
Nature Medicine - Retraction Note: Time-of-day immunochemotherapy in non-small cell lung cancer: a randomized phase 3 trial
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Ram Savan @ramlabuw.bsky.social · 10/06/2026
Our new manuscript, by lead author Gargi Mishra, shows that the IFN-I locus in pDCs is poised for rapid interferon production, as PU.1 and IRF8 establish an open chromatin architecture. #Immunology #Interferons #InnateImmunity #Epigenetics
urldefense.com
Lineage-specific chromatin poising enforced by ETS-IRF composite elements determines the divergent interferon responses of plasmacytoid dendritic cells and epithelial cells
Plasmacytoid dendritic cells (pDCs) produce robust type I interferons (IFN-I) within hours of viral sensing, while epithelial cells at mucosal surfaces mount a delayed response dominated by type III i...
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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 23/06/2026
Our Dept of Microbiology & Immunology @Geisel School of Medicine @Dartmouth has an opening for an Assistant Professor. Looking for programs bridging multiple areas in Micro & Immuno. A great place to be! Programs: www.M2P2.org www.dartmouthbiofilm.org Job ad: apply.interfolio.com/187637
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Adrian Liston @labliston.bsky.social · 24/06/2026
Ever wonder how your career (and life!) could have turned out differently if you had picked that PhD project in London instead, or gone into #patientadvocacy rather than a #postdoc? What different lives could you have lived? Now you can find out! www.amazon.co.uk/Professor-Pi...
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Nikolai Slavov @slavov-n.bsky.social · 23/06/2026
A decade ago, the money wasted on poor antibodies was estimated to be US $800 million / year. Global research antibody spending is ~$4-6B/year now vs $1.6B in 2015. What is your estimate for money wasted on poor antibodies in 2026 ?
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Miguel Branco @brancolab.bsky.social · 23/06/2026
open.substack.com
Opinion: I Was Not Allowed To Type Prompts Into ChatGPT During My Chalk Talk And This Is Discrimination
By Dr. Rachel Simmons, Postdoctoral Fellow, Stanford University
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Reese Richardson @reeserichardson.bsky.social · 05/06/2026
The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
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Sholto David @sholtodavid.bsky.social · 02/06/2026
Today I'm posting a new blog about an astonishing scientific own goal. Hundreds of papers have reported using a totally wrong antibody to investigate the tumor suppressor p16. This mistake has happened because scientists have muddled the names of two proteins. forbetterscience.com/2026/06/02/m...
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Matthew McCullen @nkcell.bsky.social · 02/06/2026
In @eLife.bsky.social: TGF-β drives the conversion of conventional NK cells into uterine tissue-resident NK cells to support murine pregnancy doi.org/10.7554/eLif...
doi.org
TGF-β drives the conversion of conventional NK cells into uterine tissue-resident NK cells to support murine pregnancy
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Reposted by Matthew McCullen
Reese Richardson @reeserichardson.bsky.social · 29/05/2026
@dangaristo.bsky.social reports on the brouhaha for @nature.com : www.nature.com/articles/d41...
nature.com
Science sleuths uncover more than 100 suspicious images in Thermo Fisher antibody catalogue
Scientists have long worried about the reliability of commercial antibodies, and the latest findings have sparked fresh concerns.
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Reposted by Matthew McCullen
Reese Richardson @reeserichardson.bsky.social · 28/05/2026
Thermo Fisher has now made public the company line, which is ?!??!?!??!?!?! you really gotta read it. cen.acs.org/research-int...
In a statement emailed to C&EN, Thermo Fisher Scientific chief communications offer Sandy Pound says, “We take antibody validation, specificity and accurate product documentation seriously, and we are committed to the transparent and ethical generation, analysis and presentation of scientific data. In the process of preparing antibody images for publication on our website, some images may have been adjusted to clarify for presentation purposes.”...In the company statement, Pound says that the company plans on “providing the original and adjusted versions of the relevant images, as well as ensuring that users are informed that antibody images may have been optimized for presentation on the website.” https://cen.acs.org/research-integrity/Sleuths-say-Thermo-Fisher-doctored/104/web/2026/05https://cen.acs.org/research-integrity/Sleuths-say-Thermo-Fisher-doctored/104/web/2026/05
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Marieke Oudelaar @mariekeoudelaar.bsky.social · 26/05/2026
📣 Preprint alert! We developed a method to analyze concurrent interactions between multiple chromatin regions at single alleles at sub-nucleosome resolution (multi-way Micro-Capture-C, mwMCC) & used this to study structural synergy within super-enhancers. 1/14 www.biorxiv.org/content/10.6...
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Sholto David @sholtodavid.bsky.social · 22/05/2026
Earlier this week I posted an example of a fake western blot provided by ThermoFisher to demonstrate the validity of a p53 antibody. I considered it an amusing curiosity. In fact Thermo Fisher Scientific has systematically manipulated antibody validation data!
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The American Association of Immunologists @aai.org · 22/05/2026
📢 Calling all AAI Members! The RESTORE Grants Program is accepting applications on a rolling basis. If your research has been impacted by federal funding disruptions unrelated to scientific merit, we want to hear from you. Apply now: ow.ly/ABtJ50YZxGC.
Three scientists in lab coats discussing research data inside a circular graphic with AAI Restore Grants Program details.
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Matthew J Kuiper @matthewjkuiper.bsky.social · 20/05/2026
No matter how innocently it's seemingly done, this act of inputting others' (published or unpublished, copyrighted or not) creative work into a chatbot makes one an accomplice to intellectual property theft.
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Waggoner Lab @labwaggoner.bsky.social · 20/05/2026
@biorxivpreprint.bsky.social A scRNA-seq atlas of chronic inflammatory skin diseases www.biorxiv.org/content/10.6... isd-atlas.derma.meduniwien.ac.at
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