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Mark Ziemann 🇺🇦🌻🦩

@mdziemann@genomic.social
mastodon 4.7.3
  • Open on genomic.social

Bioinformatics researcher.
Supports Ukraine.
Hates fascism.

266 Followers
629 Following
29 Posts
Joined July 10, 2023
Blog:
https://genomespot.blogspot.com/
Gravatar:
https://gravatar.com/markziemann
Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

I think it is a bunch of separate issues. Firstly, how AI companies have used all material from the internet without permission and without any compensation to the authors of the original works. Next, the excess consumption of water and energy for a loss-making enterprise that is straining the local communities. Next is the surveillance aspect and the storage of sensitive data on each user. These all need very strong regulation. cont.

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

Funding for science in Australia is running out, and will have a terrible impact on our economic situation. The so called progressive labour government has let this get worse and worse. Liam Mannix reports on what this means for CSIRO

https://moe_6a5h.api-02.moengage.com/v1/emailview?q=CNz4uh8jqq2uEhkLFlo7IUkhMSU5F8Tg9z4IacY.EifL2EcQTPeFdGg3jqc9-QdJMVv9TS3iWECzOR9xKY1shZ6rGOBBykMpcg6ngGE6LowYSz.wJVTV5WIC8AcCOagWm0vER2U2jB.qYkL2D8vvlr6S0VsAIGMci.kaemEV.Cp8Z.acKGbm6Lj1GEV2nB.QLVwf1T.ocSoI-JeFRTNL.fV9Mq.NQCdiJASFjKTwf2k1qYLp65y2iHF6dWH72u.Q1vqWkw64VcpJX8uyf63_lnA&event_date=2026-07-28&event_time=1785265344

moe_6a5h.api-02.moengage.com

Examine

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 4mo ago
Replying to
For example, a note for each citation that justifies why it should be included. For example "Smith 2022 data in Fig 3A shows XX trend" because some of the texts we cite are complex and huge. Page and line numbers or quotes would be useful. I think this could make it easier for peer reviewers to flag problematic citations and provide the interested reader a bit more detail.
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago

Pleased to share with you our latest article "Ten common mistakes that could ruin your enrichment analysis", featuring Anusuiya Bora, Matthew McKenzie.

This article condenses what we've learned about best practices in pathway enrichment analysis over the past 15 years. We hope you find it useful.

https://doi.org/10.1371/journal.pcbi.1014122

#bioinformatics #genomics

doi.org
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

Shared and niche-specific transcriptional signatures of macrophage aging revealed by a cross-tissue meta-analysis
https://link.springer.com/article/10.1186/s12915-026-02672-x
#genomics #Bioinformatics

link.springer.com
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

RE: @EuromaidanPress@mastodon.social

It is crazy how one of russia's strategic goals was to expand access to warm deepwater ports, and now as a consequence of their war, they are losing control of Crimean ports, Azov Sea and therefore river access to the Black Sea.

mastodon.social

Euromaidan Press: "14 more Russian vessels hit overnight — July's ta…" - Mastodon

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 4mo ago
Replying to
This would also put more emphasis on academics to actually read the full source and not just cite articles based on the abstract or title alone.
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 6mo ago

73% of research papers in social and behavioural sciences are reproducible when data is provided. The problem is that out of 600 studies sampled, only 144 made data publicly available or shared data upon request.
https://www.nature.com/articles/s41586-026-10203-5
#academicchatter #reproducibility

nature.com
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago

I hate this so much.
Noone wants AI slop in scholarship.
If you need a nice looking graphic, please engage a graphic designer!
https://arxiv.org/abs/2603.16159
#AI #slop

arxiv.org
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 4mo ago
Replying to
@satrevik@fediscience.org @lakens@mastodon.social Perfect. Thank you!
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 4mo ago

RE: @hn50@social.lansky.name

The amount of cash getting burned for #AI capex is astonishing. So big and unprofitable that it will likely never pay back. Well worth a read from Ed Zitron

social.lansky.name

Hacker News 50: "AI is too expensive Link: https://www.wheresyour…" - Mastodon

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago

Consumer-grade PCs are better suited to R-based data analysis tasks compared to servers or workstations
https://genomespot.blogspot.com/2026/05/benchmarking-r-based-bioinformatics.html
#Bioinformatics
#dataAnalytics

genomespot.blogspot.com

Benchmarking R based bioinformatics speed across different computer types

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago
Replying to
Also what's the point of doing all this work unless you're going to name the worst offending journals and publishers??
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago
Replying to
When registering, please use your institutional email address. Registration is free, but registrants will need to fill out a 10 minute survey. If you are in the commercial sector, please use your employer's email address. This is to avoid spam registrations. Thanks!
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 6mo ago
Replying to
@petergleick full desperation mode. Pathetic.
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 4mo ago

Interesting story about Russia trying to send North Korea a nuclear sub reactor.
https://edition.cnn.com/2026/05/12/world/a-russian-ship-sank-in-mysterious-circumstances-it-may-have-been-carrying-nuclear-reactors-to-north-korea

edition.cnn.com
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago

RE: @noelreports@mstdn.social

Well this is something new

mstdn.social

NOELREPORTS 🇪🇺 🇺🇦: "A Ukrainian drone armed with a recoilless shotgun…" - Mastodon 🐘

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago

Seems that Retraction Watch doesn't have an account on fedi. Let's fix that. Anyone know how to make a bot repost their blog articles?

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago

RE: @mdziemann@genomic.social

Last chance to register for our workshop on reproducible pathway enrichment analysis. There are 2 sessions, 1st one is focused on GUI-web tools and 2nd will be based on R Markdown. We'll also be discussing best practices from our related article in PLOS Comp Biol
Register here: https://tinyurl.com/ye262hzx
#Bioinformatics #genomics

genomic.social
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 5mo ago

RE: @mdziemann@genomic.social

🚨 Reminder about the upcoming workshop - you will learn best practices in pathway enrichment analysis!

🔗 Registration: https://tinyurl.com/ye262hzx

genomic.social
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 4mo ago

You folks noticed an uptick of YT ads for chatGPT in the past few weeks? Seems kinda desperate.

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

Suspect patterns of citations indicate paper mills are responsible for 5-10% of articles in some top ranked cancer journals.
https://www.biorxiv.org/content/10.64898/2026.05.25.727627v1

biorxiv.org
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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

Just went for a jog here in Melbourne as I normally do after putting the kids to bed. It felt unseasonably warm. Just checked the temperature now is 13C at 11pm. Normally it's around 5-10C at this time of year. I guess this is climate change in real-time

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

Probably the most insane thing I've heard about North Korea 💩
https://youtu.be/bEKzFiWDGJc

The politics of poo in North Korea

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

If you want a laugh, check out what kitboga is doing to scam caller AI bots. Absolute gold.
https://youtu.be/lk3jCuITwcE

Don't Hang Up On AI Scammers. Do THIS Instead.

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Open post
Mark Ziemann 🇺🇦🌻🦩 @mdziemann@genomic.social
· 2mo ago

Really liking this new #postrock album from If These Trees Could Talk we waited 10 years for a new one and it doesn't disappoint.
https://ifthesetreescouldtalk.bandcamp.com/album/the-hidden-hand

The Hidden Hand, by If These Trees Could Talk
If These Trees Could Talk

The Hidden Hand, by If These Trees Could Talk

9 track album

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