Sign in

iiinova is part of the Atmosphere — an open, public network where you own your identity.

Mark Ziemann 🇺🇦🌻🦩

@mdziemann.genomic.social.ap.brid.gy
54 followers 18 following 205 posts

Bioinformatics researcher. Supports Ukraine. Hates fascism. 🌉 bridged from ⁂ genomic.social/@mdziemann, follow @ap.brid.gy to interact

PostsRepliesMedia
Reposted by Mark Ziemann 🇺🇦🌻🦩
Dmitry Grozoubinski @explaintrade.com · 10/10/2026
For those playing along at home: To give the appearance of action on the impacts of his humiliating blunder on the world stage, the President of the United States is making a humiliating blunder on the world stage by bailing the Russian president out of a humiliating blunder on the world stage.
12635175 635
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 10/10/2026
More quality content from the chaser chaser.com.au
Trump meme says:
Aussies miss when morning routine didn't involve finding out whatever the fuck this cunt did today.
100 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 08/10/2026
Exciting news -- The 1st RN4CB Seminar is locked in for the 29th Oct! Dr Daniel Mietchen (FIZ Karlsruhe — Leibniz Institute for Information, Germany) will present his work on "Observing computational reproducibility in the wild". Register here […] [Original post on genomic.social]
Reproducibility Network for Computational Biology Webinar
Dr Daniel Mietchen from FIZ Karlsruhe — Leibniz Institute for Information will present a seminar titled "Observing computational reproducibility in the wild"
Seminar hosts: Drs Sheeba Samuel and Mark Ziemann
Register here to receive the Zoom meeting invitation: https://forms.gle/FeUwFX9KzX1UjCfHA

Thursday October 29, 2026
11pm - 12am CET - Berlin
6pm EDT - New York
3pm PDT - San Fran
9am AEDT 30th Oct - Syd/Melb
7am JST 30th Oct - Tokyo

More info: RN4CB.org
002 2
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 07/10/2026
How to generate QRcodes in R for FREE! genomespot.blogspot.com/2026/10/cre… #Rstats
genomespot.blogspot.com
Create a QR code for FREE using R
R is a very versatile programming language and can do many graphical tasks with ease. Here, I demonstrate how to use R to generate QRcodes. ...
002 2
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 01/10/2026
Currently reading this review. The writing seems a bit... off. www.nature.com/articles/s41591-026-…
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 26/09/2026
Me walking up to the cave entrance in Hastings through temperature rainforest which is typical in southern Tasmania
010 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 26/09/2026
Caves in Hastings, south of Hobart in Tasmania.
Inside a cave there are many stalagtites illuminated for the tour group.
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 15/09/2026
My FediFriends, you're invited to join us for special guest seminar from one of the world leaders in research integrity, Professor Jennifer Byrne, which will be held on the 21st September 10:30am AEST and you are welcome to join us in person at the Burnet Institute (Commercial Rd, Melbourne).
Scholarly seminar flyer featuring a photo portrait, seminar synopsis and biosketch of the speaker, Professor Jennifer Byrne.

Join us for a timely discussion on research paper mills and the challenges they pose to biomedical publication integrity. Drawing on her internationally recognised work, Professor Byrne will explore how fabricated publications can be identified and how emerging risks, including generative AI, are reshaping scientific publishing.

About the Speaker
Professor Jennifer Byrne is a recognised leader in research integrity and biomedical publication quality. She is Director of Biobanking-NSW Health and Professor of Molecular Oncology at the University of Sydney, where she leads the PRIMeR group — Publication and Research Integrity in Medical Research.

Her work has brought international attention to the risks posed by paper mills and flawed research outputs, including her identification of repetitive human gene research papers containing critical reagent errors.

Professor Byrne was named one of Nature’s 10 people in 2017 and was one of three experts invited to testify before the US Congress at its 2022 hearing into paper mills and research misconduct. She is also the recipient of the Australian Academy of Science’s Professor David Vaux Research Integrity Fellowship for 2025–2026.
022 2
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 14/09/2026
Australian Epigenetics conference is about to kick-off! Looking forward to some amazing science! #AEpiA #Epigenetics
Officials standing on a podium opening a scientific conference
030 3
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 11/09/2026
So, Houthi forces have expanded control of the red sea coast including the port of Mokha. Yemeni forces surrendered en masse and Houthis seized a large amount of US-made millitary hardware sent by Saudi Arabia. Houthis look to continue south and take full […] [Original post on genomic.social]
Millitary map of the Yemen's Red Sea Coast showing advances of Houthi forces capturing Mokha from the north. Original Source: ISW https://understandingwar.org/research/middle-east/iran-update-september-10-2026/
001 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 08/09/2026
RE: c.im/@cdarwin/117233488078293128 LLMs are MaaS, misconduct as a service #AI
001 1
Reposted by Mark Ziemann 🇺🇦🌻🦩
Karandeep(Singh) @kdpsingh.bsky.social · 01/09/2026
!!! www.bbc.com/news/article...
bbc.com
Duane "Keffe D" Davis found guilty in 1996 murder of rapper Tupac Shakur
The verdict ends decades of mystery as to who was behind the rapper's death.
111 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 31/08/2026
The idea that thousands of corps are going to be using fleets of AI agents to make money at all costs is just... scary shit. cdn.openai.com/pdf/67869394-cb91-4c…
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 28/08/2026
Sydney, Canberra and Melbourne record warmest ever Winter, 2C higher than the long term average www.abc.net.au/news/2026-08-29/spri… #Climate
011 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 27/08/2026
More from Reese Richardson: "It cannot be overstated how much biomedical research rides on antibodies (ABs) performing as intended and how much time researchers lose to working with ABs that do not perform. Increased recognition of the importance of AB validation has led to vendors […]
genomic.social
Original post on genomic.social
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 27/08/2026
RE: flipboard.com/@naturenewsteam/lates… Life scientists rely on validated reagents - one bad antibody could undermine years of work #biology #molbio
flipboard.com
121 2
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 26/08/2026
Was anything useful achieved? Fuck knows. But I wonder about the carbon footprint of this type of "research" www.biorxiv.org/content/10.64898/20… #bioinformatics #AI
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 24/08/2026
RE: genomic.social/@tangming2005/117145… I think this meme is really accurate. The biologist with AI is using a rocket launcher in a crowded room. The user - a pop star - probably doesn't know how to use the tool, but if they did manage to get it working, everyone in that […]
genomic.social
Original post on genomic.social
001 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 24/08/2026
Happy 🇺🇦 Ukrainian Independence Day! Celebrating 35 years of independence from the USSR kyivindependent.com/ukraines-35-yea…
001 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 24/08/2026
I still monitor these spreadsheet errors and publish monthly reports on my group's webpage. You can see that rates of affected articles are still 15-25%. ziemann-lab.net/public/gene_name_er…
ziemann-lab.net
Gene Name Error Monthly Dashboard
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 24/08/2026
Yesterday marked 10 years since the publication of our article on how Excel spreadsheets cause autocorrect errors to genomics data. link.springer.com/article/10.1186/s… #bioinformatics #genomics
link.springer.com
Gene name errors are widespread in the scientific literature - Genome Biology
The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.
1212 12
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 21/08/2026
Today we just added 4195 human gene expression studies to the dee2.io data resource -- that is ~200k samples. We're still running way behind what is released by NCBI, but with the current prices of computer parts we're doing the best we can with the limited funding we got. #rnaseq […]
genomic.social
Original post on genomic.social
020 2
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 21/08/2026
Do I have any followers in cancer research who could review an article on the use of NanoString gene expression data? #genomics #cancer
001 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 20/08/2026
A straightforward and up-to-date guide to functional enrichment analysis www.frontiersin.org/journals/bioinf… #genomics #bioinformatics #pathwayEnrichment
frontiersin.org
Frontiers | A practical guide to functional enrichment analysis
Functional Enrichment Analysis (FEA) has become a critical step in the analysis of omics data in recent years. As a result, numerous approaches have been rap...
010 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 20/08/2026
It is great to see that the background genelist problem in pathway enrichment is getting picked up in different domain areas. Like here in GWAS/exome analysis. #genomics #bioinformatics #pathwayEnrichment www.biorxiv.org/content/10.64898/20…
010 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 18/08/2026
How is using Docker containers any better than strict descriptiuons of all packages with requirements.txt (Python) or Renv (R)? Let's discuss. genomespot.blogspot.com/2026/08/on-… #Bioinformatics #Reproducibility
genomespot.blogspot.com
On computational reproducibility -- surely requirements.txt​ is enough? Right?
Image credit: Paul .T (@hooverpaul55) I got an interesting question by email today. How is using Docker containers any better than strict ...
011 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 12/08/2026
Have you noticed how biorxiv has been intermittently down lately? Some sites/features not working? Or is it just me? For example, the link for the article shown below is dead. Strange. www.biorxiv.org/content/10.64898/20… #academicchatter
bioRxiv preprint toot: "Most published human disease RNA-seq cannot be uniformly reanalyzed: a population-scale audit of reprocessability in the Gene Expression Omnibus"
The bioRxiv link appears to be dead.
011 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 07/08/2026
We started a Reproducibility Network for Computational Biology! 🎉 🥳 🍾 Improving research quality is the main aim. There will be opportunities to get involved later in the year as a general member or position on the committee. More details here […] [Original post on genomic.social]
Screenshot showing the members of the steering committee of the Reproducibility Network for Computational Biology. There are 12 prominent researchers across 7 countries.
0114 11
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 30/07/2026
Suspect patterns of citations indicate paper mills are responsible for 5-10% of articles in some top ranked cancer journals. www.biorxiv.org/content/10.64898/20…
biorxiv.org
Suspected distortion of citations in high-impact cancer journals
Research and scholarship are shaped by article citations, which underpin the communication of ideas, assignment of credit, journal impact factors, and author career progression. Given their key influence on author and journal metrics, citations can be intentionally manipulated to inflate the reputation of journals and researchers. Paper mills, unethical organisations that produce and sell manuscripts and publishing services, may also be manipulating citations, but the extent of this manipulation is unknown. Here, we show that molecular cancer articles sharing features with retracted papers from paper mills display citation patterns that suggest systematic inflation. These articles were published in journals in the top decile of journal rankings. Suspected paper mill articles received 50 to 100% more citations than other papers 1 to 3 years after publication, while paradoxically attracting fewer readers and online accesses. Suspected paper mill articles also cited – and were cited by – other suspected paper mill articles and appeared in journals previously reported as paper mill targets. The resulting citations from suspected paper mill articles measurably inflated journal citation metrics. These findings suggest that paper mills inflate the citation metrics of supported publications and affected journals. The manipulation of citation metrics at scale may amplify unreliable findings, slowing scientific progress, and providing unreasonable citation benchmarks for research articles, journals and authors. Our findings highlight new risks in relying on citation metrics for research and journal evaluation and support the use of more robust metrics to describe article and journal quality. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council, 2029249
010 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 29/07/2026
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 moe_6a5h.api-02.moengage […]
genomic.social
Original post on genomic.social
010 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 26/07/2026
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
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 24/07/2026
Probably the most insane thing I've heard about North Korea 💩 youtu.be/bEKzFiWDGJc
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 22/07/2026
If you want a laugh, check out what kitboga is doing to scam caller AI bots. Absolute gold. youtu.be/lk3jCuITwcE
000 0
Reposted by Mark Ziemann 🇺🇦🌻🦩
David Roberts @volts.wtf · 14/07/2026
An amazing quote from Lindsey Graham in this Atlantic story. It really captures an essential truth about politics that too few people ever really come to terms with. www.theatlantic.com/ideas/2026/0...
14353951168 5.4K
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 15/07/2026
Shared and niche-specific transcriptional signatures of macrophage aging revealed by a cross-tissue meta-analysis link.springer.com/article/10.1186/s… #genomics #Bioinformatics
A scientific chart shows certain gene ontology and reactome pathways are consistently upregulated in aging across dozens of public mouse datasets
032 3
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 13/07/2026
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 […]
genomic.social
Original post on genomic.social
100 1
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 12/07/2026
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. ifthesetreescouldtalk.bandcamp.com/…
ifthesetreescouldtalk.bandcamp.com
The Hidden Hand, by If These Trees Could Talk
9 track album
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 12/07/2026
RE: mastodon.social/@EuromaidanPress/11… 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
000 0
Reposted by Mark Ziemann 🇺🇦🌻🦩
Defending Ukraine @ukrdef.mstdn.social.ap.brid.gy · 06/07/2026
KYIV INDEPENDENT: Russia’s largest oil refinery in flames as Ukraine strikes Omsk, 2,500 km away from border kyivindependent.com/russias-largest… The Omsk refinery was the last of Russia's 11 largest gasoline […]
mstdn.social
Original post on mstdn.social
021 2
Reposted by Mark Ziemann 🇺🇦🌻🦩
Ada Palmer @adapalmer.wandering.shop.ap.brid.gy · 28/03/2026
‘Truly spectacular’ drug for sleeping sickness simplifies treatment, raising hopes for eradication. European regulators have approved acoziborole, a new treatment for sleeping sickness that cures the disease with a single oral dose. The drug replaces complex regimens requiring hospitalisation […]
wandering.shop
Original post on wandering.shop
0021 21
Reposted by Mark Ziemann 🇺🇦🌻🦩
tante @tante.tldr.nettime.org.ap.brid.gy · 25/06/2026
RE: discuss.systems/@dev/11680746072586… It's kinda fun how this is basically Marx' theory in goose form. "Eggs do not lay eggs" is code for "all value is produced by the worker".
discuss.systems
2226 26
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 25/06/2026
One of my favourite small youtube creators Fredo Rockwell discusses the situation in Crimea. #Ukraine www.youtube.com/watch?v=_20F1tSdz9g
000 0
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 24/06/2026
The Australasian Epigenetics Alliance conference is quickly approaching in September. In fact the early bird registration and abstract submission deadline is 20th June Details: 2026aepia.com.au #Epigenetics #Genomics
The Australasian Epigenetics 2026 conference flyer. Details about the event can be found on the website https://2026aepia.com.au/
011 1
Reposted by Mark Ziemann 🇺🇦🌻🦩
Judith Beyer @judithbeyer.bsky.social · 23/06/2026
I am a member of an international editorial board of a regionally oriented journal, the flagship journal for the region. We had a board meeting and the journal editor shared the latest numbers: 70% desk rejects due to #AI at a submission rate of over 1000 articles p.a. Countless hours of extra work.
274 7
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 23/06/2026
I am having the life drained out of me by this "compliance training" slop BS #CorporateLife
A mindnumbing "compliance traning" quiz question that asks "True or false: Security awareness traning can play a valuable part in compliance" duuuh
000 0
Reposted by Mark Ziemann 🇺🇦🌻🦩
Operator Starsky🇺🇦 @starskyua.bsky.social · 10/06/2026
Fresh daily brief is here, my friends and family - WHAT A NIGHT! It was insane! Ukrainian "Flamingo" filmed for the first time by grateful russian witnesses, russian colonel becomes a best russian on Earth, a bunch of russian facilities partying really hard and many more news! youtu.be/hzFD13SXY1s
youtu.be
Ukraine Daily Brief: "Flamingo" comes to RUSSIA | Sochi vacation spoiled | Breaking News & Updates
YouTube video by Operator Starsky 🇺🇦
59023 90
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 10/06/2026
If you're in Melbourne and interested in genomics and epigenetics, come along to the #Melbourne #Epigenetics club 4pm today. Visit the website to get club email updates: www.eckmaslab.com/melbourne-epigene…
Seminar poster featuring Nir Eynon, Natasha Jansz and William Hamilton. Hosted at Melbourne Uni 10th June
023 3
Reposted by Mark Ziemann 🇺🇦🌻🦩
Chris Alemany🇺🇦🇨🇦🇪🇸 @chris.mstdn.chrisalemany.ca.ap.brid.gy · 10/06/2026
OK folks, I need some #docker advice for those gurus out there. A boost would be appreciated to get it in front of knowledgeable eyes. I have a container running postgresql for mastodon. I would like to tweak the conf file for postgresql now that I […] [Original post on mstdn.chrisalemany.ca]
111 1
Reposted by Mark Ziemann 🇺🇦🌻🦩
PKs Powerfromspace1 @powerfromspace1.mstdn.social.ap.brid.gy · 06/06/2026
@MilitaryNewsUA ❗️From tomorrow in Crimea, the sale of gasoline to civilians is completely stopped, — Occupying authorities. Previously there was a limit of 20 liters per person. They say they will try to resume sales in the coming days 🤷‍♂️​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​​ […]
mstdn.social
Original post on mstdn.social
012 2
Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 02/06/2026
This is a result of a real Google search my son did...
000 0