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Johnbosco

@biocodebreaker.bsky.social
154 followers 1.1K following 27 posts

Bioinformatician | Cancer Omics | Health informatics | FAIR Principles | Reproducible Research orcid.org/0000-0002-2355-8475

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Reposted by Johnbosco
Oxford Nanopore @nanoporetech.com · 29/06/2026
Many RNAs originally annotated as non-coding may encode proteins, with signals found across UTRs and overlapping known ORFs. Mike Clark shares how Oxford Nanopore enables this kind of transcript-level insight. Learn more: bit.ly/3SgUa19
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Laura Helmuth @laurahelmuth.bsky.social · 29/06/2026
Springer Nature retracted two studies by Max Planck. In response to a question from @samkean.bsky.social, they issued this statement: "Detailed information about specific retractions is usually confidential and can only be shared with the relevant authors.”
science.org
Why have papers by one of history’s most famous physicists been retracted?
Springer Nature has removed two studies by Max Planck. A bot may be to blame
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GenomeWeb @genomeweb.bsky.social · 29/06/2026
Researchers have identified over 460 "problematic" Western blot images in Thermo Fisher's online antibody catalog, while the company denies any wrongdoing.
ebx.sh
Thermo Fisher's Response to Antibody Image Controversy Sparks Outcry From Researchers
Thermo Fisher's Response to Antibody Image Controversy Sparks Outcry From Researchers
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Open Research Knowledge Graph @orkg.bsky.social · 15/05/2026
📣 Celebrating 7 years since the alpha release of the ORKG🎉, the Living Journal of Reviews in Science and Technology lets the research community rethink literature reviews as living, #FAIR, semantically structured machine-actionable knowledge resources supporting sustainable scholarly communication.
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Open Research Knowledge Graph @orkg.bsky.social · 23/06/2026
“Scientific publishing should not be seen as the final product of research. Rather, it is the beginning of a new cycle.” That's the motto of TIB Knowledge Loom, co-founded by @laurendsnyder.bsky.social. Follow her to learn about reproducible and reusable research! #INWED26 #EngineeringIntelligence
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Symbiosky @symbiosky.bsky.social · 06/05/2026
The “publish or perish” incentive system has collapsed — and AI just exposed it. #AcademicSky
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Nature @nature.com · 08/05/2026
An audit of 2.5 million academic papers has identified nearly 3,000 biomedical-science papers that contain fake references. go.nature.com/42iMcX4
go.nature.com
Surge in fake citations uncovered by audit of 2.5 million biomedical science papers
An analysis of 97 million citations has found that rates of fabricated citations have climbed steeply since 2023.
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Magdalena Skipper @magdalenaskipper.bsky.social · 08/05/2026
Happy 100th birthday to Sir David Attenborough! 🎉 An inspiration to me & millions of others around the globe & across the generations! We share more than our passion for the natural world but also a deep appreciation for ceramics! His collection is magnificent! 🧪 www.nature.com/immersive/d4...
nature.com
A life in pictures: Celebrating Attenborough at 100
As the British naturalist celebrates a milestone birthday, we take a look at how his work has shaped science.
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The Jackson Laboratory @jax.org · 07/05/2026
67 years. One enduring vision for genetics in medicine. 🧪 🧬 The JAX Short Course—founded by Victor McKusick—continues to shape the field and the people driving it forward. Be part of what’s next - go.jax.org/mckusick26
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Lauren Snyder, PhD @laurendsnyder.bsky.social · 16/02/2026
The TIB Knowledge Loom is live! If you believe scientific knowledge should be reusable, reproducible & open, then this digital library is for you. We are an Open Science initiative promoting a cultural shift in how scientific knowledge is organized & published. Check it out: knowledgeloom.tib.eu
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Johnbosco @biocodebreaker.bsky.social · 24/10/2025
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Open Research Knowledge Graph @orkg.bsky.social · 23/10/2025
Meet Johnbosco (@biocodebreaker.bsky.social), our new #ORKGreborn curation grantee! As a bioinformatics researcher, he is helping us expand our open-source digital library into medical research. He shares his motivation for contributing to this initiative. Visit the library here: reborn.orkg.org
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Open Research Knowledge Graph @orkg.bsky.social · 01/10/2025
Meet the 2025 #ORKGreborn curation grantees who are helping us grow our #openscience digital library! Over the next few weeks, they’ll share why they’re invested in a future where all scientific knowledge is represented in open digital libraries like ORKG reborn: reborn.orkg.org/pages/submit
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Ian Hussey @ianhussey.mmmdata.io · 23/08/2025
I often find my students' code is littered with dependencies that are loaded and then not used. This is a bad coding practice, but it's also very boring to check. I updated {psychdsish} to include a function that does this for you.
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Claus Wilke @clauswilke.com · 15/08/2025
A simple design framework that will massively improve your slides and your public speaking clauswilke.substack.com/p/slides-tha...
clauswilke.substack.com
Slide designs that present themselves: The assertion–evidence template
Your slides are not your talk.
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Johnbosco @biocodebreaker.bsky.social · 13/08/2025
Anyone have difficulty accessing the Cold Spring Harbor Laboratory site? I haven't been able to access it in a long time! Perhaps I should try using a VPN? genome.cshlp.org/cgi/doi/10.1... @cshlnews.bsky.social
genome.cshlp.org
Highly accurate assembly polishing with DeepPolisher
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Jonathan Jacobs @bioinformer.bsky.social · 04/08/2025
New #bioinformatics Scientist opening at @officialatcc.bsky.social ! Love #genomics? Want to help build a digital biology future? We're sequencing our entire collection 😱 Our focus? Authenticated Reference Data. Digital Standards. Reproducibility. Join us! careers-atcc.icims.com/jobs/4000/sc...
careers-atcc.icims.com
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Johnbosco @biocodebreaker.bsky.social · 20/07/2025
www.nature.com/articles/s44...
nature.com
Writing is thinking - Nature Reviews Bioengineering
On the value of human-generated scientific writing in the age of large-language models.
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Johnbosco @biocodebreaker.bsky.social · 20/07/2025
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Ming Tommy Tang @tommytang.bsky.social · 12/07/2025
2. Ten Simple Rules for Reproducible Computational Research journals.plos.org/ploscompbio...
journals.plos.org
Ten Simple Rules for Reproducible Computational Research
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Oded Rechavi @odedrechavi.bsky.social · 14/07/2025
I love the idea of "micropublications" www.micropublication.org (preparing one now)
micropublication.org
microPublication - Get Your Data Out, Be Cited
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Gudrun Lotze @gudrunlotze.bsky.social · 11/07/2025
What can scientists or the public do when a publication says "data or code available upon reasonable request" - but the author doesn’t respond or refuses to share? #reproducibility #openscience #opensource #dataaccess #researchintegrity #AcademicSky #EduSky
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Johnbosco @biocodebreaker.bsky.social · 12/07/2025
Moreover, despite contacting the authors of the original papers, we were unable to obtain these data for 68% of the experiments. elifesciences.org/articles/67995
elifesciences.org
Reproducibility in Cancer Biology: Challenges for assessing replicability in preclinical cancer biology
A project to repeat experiments from high-impact papers in cancer biology encountered a series of challenges, many of which were caused by a lack of detail in the original papers.
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Johnbosco @biocodebreaker.bsky.social · 12/07/2025
Reproducibility Project: Cancer Biology to investigate the replicability of preclinical research in cancer biology. Conclusion: it is hard to assess whether reported findings are credible. elifesciences.org/articles/67995
elifesciences.org
Reproducibility in Cancer Biology: Challenges for assessing replicability in preclinical cancer biology
A project to repeat experiments from high-impact papers in cancer biology encountered a series of challenges, many of which were caused by a lack of detail in the original papers.
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4TU.ResearchData @4turesearchdata.bsky.social · 09/07/2025
❓How can we make reproducibility a routine part of the publishing process❓ CODECHECK is a community-led initiative that helps verify the computational reproducibility of #scientific research. Read more on its application on our website: community.data.4tu.nl/2025/07/09/c...
community.data.4tu.nl
CODECHECK in Practice: How TU Delft and 4TU.ResearchData Are Making Reproducibility Happen
How can we make reproducibility a routine part of the publishing process? That question is at the heart of a new pilot bringing together the TU Delft Digital Competence Centre (DCC) and the 4TU.Res…
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4TU.ResearchData @4turesearchdata.bsky.social · 11/06/2025
Are #engineering and #design research processes reproducible? Join the lunch session "Why does reproducibility matter and how to achieve it?" at @tue.nl on 17 June! See how 4TU.ResearchData piloted the facilitation of reproducibility checks within the #CODECHECK initiative ⬇️ shorturl.at/qyXkc
shorturl.at
Why does reproducibility matter and how to achieve it?
This session explores the importance of reproducibility in research and how 4TU.ResearchData supports researchers in making their work more transparent and trustworthy. We’ll reflect on how 4TU.Res…
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Johnbosco @biocodebreaker.bsky.social · 10/07/2025
x.com/kyleichan/st...
x.com
Kyle Chan on X: "Chinese universities ranked above MIT, Oxford, Stanford in the new 2025 Nature Index: Zhejiang, USTC, Peking, Tsinghua, Nanjing, Shanghai Jiaotong, Sun Yat-sen, Fudan, Sichuan China’s heavy investment in scientific research underpins all of its tech & industrial advances. https://t.co/EMT3yHMXJj" / X
Chinese universities ranked above MIT, Oxford, Stanford in the new 2025 Nature Index: Zhejiang, USTC, Peking, Tsinghua, Nanjing, Shanghai Jiaotong, Sun Yat-sen, Fudan, Sichuan China’s heavy investment in scientific research underpins all of its tech & industrial advances. https://t.co/EMT3yHMXJj
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Johnbosco @biocodebreaker.bsky.social · 10/07/2025
x.com/kyleichan/st...
x.com
Kyle Chan on X: "China’s scientific progress is real. Citation counts can be gamed. There is some fraud. And Chinese researchers have been incentivized with cash to target top journals. But the Nature Index, which looks at contributors to 145 top international journals, is solid. 1/ 🧵 https://t.co/8jZed6dpQU" / X
China’s scientific progress is real. Citation counts can be gamed. There is some fraud. And Chinese researchers have been incentivized with cash to target top journals. But the Nature Index, which looks at contributors to 145 top international journals, is solid. 1/ 🧵 https://t.co/8jZed6dpQU
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Prof Peter Hotez MD PhD DSc(hon) @peterhotezmdphd.bsky.social · 30/05/2025
No words
America’s brain drain
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Terry Christiani 👋 @terrychristiani.bsky.social · 29/05/2025
The Round 1 grants from the R Consortium Infrastructure Steering Committee have been announced. This is one of my favorite things about this working for this org. #rstats r-consortium.org/posts/r-cons...
r-consortium.org
R Consortium Awards First Round of 2025 ISC Grants – R Consortium
The R Consortium’s Infrastructure Steering Committee (ISC) is proud to announce the first round of 2025 grant recipients. These seven projects are receiving support to enhance and expand the capabilit...
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EMBL-EBI @ebi.embl.org · 29/05/2025
Long-read sequencing can reveal hidden cancer mutations, but existing tools often produce false positives. SAVANA is a machine learning algorithm trained on cancer genomes, built to make analysis faster and clinically reliable. @isidrolauscher.bsky.social www.ebi.ac.uk/about/news/r... #oncosky
ebi.ac.uk
Machine learning algorithm brings long-read sequencing to the clinic
SAVANA is a new tool designed for accurate detection of structural variations in clinical samples.
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Michael Love @mikelove.bsky.social · 20/05/2025
I'll be leading a workshop with Justin Landis at useR! in Durham on August 8. It will be a gentle introduction to how we model biological data using tidy data principles user2025.r-project.org
user2025.r-project.org
useR! 2025
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Andrea Love, PhD | Biomedical Scientist @drandrealove.bsky.social · 20/05/2025
A grade 9 prostate tumor IS NOT stage 9 cancer Cancer stages range from I to IV & are used for all cancers. Gleason grades: specific to prostate cancer, range from 6 to 10. They tell us different things. IF anyone confuses them, they have NO business talking about cancer in ANY capacity.
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Andrea Love, PhD | Biomedical Scientist @drandrealove.bsky.social · 20/05/2025
If you want to learn some basics on cancer biology, read this article: news.immunologic.org/p/cancer-hun...
news.immunologic.org
Cancer: hundreds of complex diseases that are plagued with misinformation
Lack of understanding of cancer underlies harmful pseudoscience that circulates rampantly
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Alex Rubinsteyn @alexr.bsky.social · 17/05/2025
It’s time: @benjamingvincent.bsky.social and I are going to do a cancer immunotherapy / cool research / accelerating future medicine podcast. Any tips for getting started?
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European Commission @ec.europa.eu · 08/05/2025
Choose Science. Choose Europe. A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open. With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond. Apply by 10 September → europa.eu/!fBTMgF
A graphic for the Marie Skłodowska-Curie Actions (MSCA), showing a historical portrait of Marie Skłodowska-Curie overlaid with an image of four young researchers walking down a hallway. The European Commission logo is in the top left. Text reads: "Marie Skłodowska-Curie Actions – €404.3 million to support postdoctoral researchers”
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Ming Tommy Tang @tommytang.bsky.social · 15/05/2025
I had a 26GB TSV file. R choked. So I turned to UNIX. And it worked. 1/ You only need 500 columns. But the file is 26GB. R freezes. Memory bleeds. You need the data—but you don’t need the pain. Here’s what I did.
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Open Research Knowledge Graph @orkg.bsky.social · 01/05/2025
📢New article alert. Open-source approach transforms the production of scientific results by making them machine-readable. Published in Scientific Data from @natureportfolio.nature.com Open access article: doi.org/10.1038/s415... Press release: bit.ly/4iKb6Vj #FAIRScience #pressrelease
doi.org
Rethinking the production and publication of machine-readable expressions of research findings - Scientific Data
Scientific Data - Rethinking the production and publication of machine-readable expressions of research findings
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Ming Tommy Tang @tommytang.bsky.social · 05/05/2025
A unified analysis of atlas single-cell data genome.cshlp.org/content/35/...
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