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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

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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

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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.

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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

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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/

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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

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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.

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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.

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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

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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/

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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

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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

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 02/06/2026

This is a result of a real Google search my son did...

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 20/04/2026

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊 Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices. 📅 When: 12 and 13 May 2026 🕑 Time: 2:00 PM – 4:00 PM (AEST) 📍 Where: Online 💰 Cost: FREE […] [Original post on genomic.social]

Image is a flyer describing the "Mastering Reproducible Enrichment Analysis" workshop. It states "A workshop where you can learn to (1) perform pathway enrichment analysis using web-tools and programming tools (2) Reproducible methods and documentation. 12th and 13th May 2PM to 4PM Melbourne time (AEST). Free registration! (Limited placed available). Presented by Dr Mark Ziemann and Ms Anusuiya Bora from Deakin University and Burnet Institute." There is a QR code to the registration form: https://forms.cloud.microsoft/pages/responsepage.aspx?id=7Hgj0IgW1UaFQBwotfRw9jybGyPjBPZFraF6WJ9taAxUNEs4MjZWWTlLTDhUR1NLR1NKUUVLNVJYVS4u&route=shorturl

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 23/02/2026

It has been four years since russia invaded Ukraine. Four years of resistance, innovation and sheer determination. Sanctions are working, our support is making a difference to help the heroes defend their country. We need to keep up the pressure at all levels. In the end #Ukraine will be VICTORIOUS!

Ukranian flag flies proudly in front of a clear blue sky.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 19/02/2026

Jeffrey Epstein was a CIA asset, involved in global armaments trade and corruption. Excellent reporting from Ex-infantryman turned youtuber Chris Cappy #Epstein youtu.be/cvy1DQt_ZRQ

A post fom @Cappyarmy on X formerly Twitter:
"The extent of Jeffery Epstein's involvement in black market weapons smuggling is becoming more clear with the file dump. Arms deals that the CIA, Mossad and MI6 were heavily involved in. He was a new species of "global fixer" that emerged in the post ww2 cold war era to fill a novel demand. Countries needed plausible deniability for the first time.

So, Epstein / Adnan Kashoggi (saudi arms dealer he managed money for) those types filled that emerging demand. Shadow black market arms deals exploded and billions in commissions needed to be hidden in the financial system. But what happens in the dark is more horrifying than we could have imagined."

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 05/02/2026

Just upgraded my work keyboard. Makes typing a bit more enjoyable. Would recommend.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 03/01/2026

Yes, you can use a single stick of DDR5 for bioinformatics and data analysis, incurring only a small drop in performance. genomespot.blogspot.com/2026/01/yes… #bioinformatics #RAM #DDR5 #ddr5memory

A line diagram showing benchmarking of a bioinformatics data processing workflow involving four different memory configurations 2 modules with stock settings, 2 modules with memory overclocking, 1 module with stock settings and 1 module with overclocking. It shows a 15% boost when using the tweaked settings, and 3% slowdown when using only 1 module.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 20/12/2025

Family enjoyed a visit to Point Cook and had the beach all to ourselves

Point Cook beach deserted despite perfect weather.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 08/12/2025

Holy shit RAM prices have gone nuts. In August I built a workstation with 192GB DDR5 costing $758 AUD for the memory. Same memory now would cost $2498 #RAM

92GB Crucial DDR5 kit for the extortionate price of AUD$1249

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 02/12/2025

Looks like biorxiv.org is down - can we blame this on AI scrapers?

A cloudflare timeout page suggests biorxiv.org is down.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 02/11/2025

My tip to academics - never publish in Elsevier journals. They are charging exorbident APCs like a mafia. If you get a lot of review invitations, always reply with a demand for 10% of the APC for the peer review. I'm not doing free work for those parasites.

My reply to an invitation to d oa voluntary peer review for an Elsevier Journal. The journal charges authors $4400 USD publication fee.

My reviews for for-profit publishers are charged at $100 USD/hr. A typical manuscript takes 3 hrs to review. I can return the review to you in 3 days after payment. Let me know how you would like to proceed.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 16/10/2025

There's an early + mid-career #Epigenetics symposium taking place across Australia and online, supported by AEpiA. This will be a great opportunity to present your work, learn about other research happening in the region and network with other epigenetics peeps!

The symposium takes place on the 4th December at 12:30
Registration is required, but it free --> https://www.aepia.org.au/emcr-symposium
Abstract deadline 31st October

In addition to scientific talks, there will be a career development panel discussion featuring Drs Luke Isbel, Dhanya Sooraj and Phillipa Taberlay

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 28/08/2025

New merch from Wild Hornets. Proceeds go to produce FPV drones to defend #Ukraine The range includes T-shirts, hoodies and long sleeve shirts (my fav) in male and female variants www.bonfire.com/wild-hornets-offici…

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 22/08/2025

Put together this workstation PC for CPU and I/O intensive work to support the dee2.io project. This is only my 2nd computer build but it's performance is just astonishing and with undervolting it is also super efficient for 24/7 use. 1/2

Ryzen PC for scientific computing with wood trim. Front view.

Ryzen PC for scientific computing. Side view shows oversize air cooler.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 14/08/2025

Today I gave a talk entitled "Computational reproducibility and the struggle for reliable science" I've uploaded the slides here: ziemann-lab.net/2025/08/14/plenery-… 1/2 #Bioinformatics #Genomics #reproducibility #academicchatter

Title slide for Mark Ziemann's plenery presentition entitled "Computational reproducibility and the struggle for reliable science"
Other details include the event: LES Graduate Researcher Conference
Date: 2025-08-14
Licence: CC-BY-4.0

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 31/07/2025

A few weeks ago, Sydney #PostRock legends We Lost The Sea released an new album "A Single Flower" welostthesea.bandcamp.com/album/a-s… This is a captivating journey full of emotions high and low in the band's iconic and epic style.

Cover art for We Lost The Sea's new album "A Single Flower". It features a sillhouette of a black crow on a white background. The bird isn't in a flying possition but seemingly on its back, possibley falling. There is a red poppy flower in the middle of the picture. There is a thick black border around the picture.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 17/06/2025

If you ever need to sign PDFs on #linux <a href="https://xournalpp.github.io/"> Xournal++</a> has got you covered. While LibreOffice can in theory edit the PDF, it ruins text alignment. Xournal++ keeps original PDF content and is designed for annotating. #FOSS

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 03/06/2025

Australia's Monash University to build a AUD$60M AI computing facility, to be operational in 2026 www.monash.edu/news/articles/monash… #AI

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 22/05/2025

The Australasian Epigenetics Alliance continues tomorrow with a talk from A/Prof Siddharth Dey (University of California, USA) Title: ‘Developing integrated single-cell epigenome and transcriptome sequencing technologies to study early mammalian embryogenesis’ […] [Original post on genomic.social]

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 15/05/2025

From the Zachgo lab, an authoratative review of the evolutionary biology of sex in plants. 🌱 🌲 🌻 And the figures are just gorgeous! doi.org/10.1007/s00497-025-00522-4 #evolution #biology #plants

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 14/04/2025

🔬 𝗛𝗲𝗹𝗽 𝗜𝗺𝗽𝗿𝗼𝘃𝗲 𝘁𝗵𝗲 𝗥𝗲𝗽𝗿𝗼𝗱𝘂𝗰𝗶𝗯𝗶𝗹𝗶𝘁𝘆 𝗼𝗳 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 𝗧𝗼𝗼𝗹𝘀 𝗶𝗻 𝗕𝗶𝗼𝗺𝗲𝗱𝗶𝗰𝗮𝗹 𝗦𝗰𝗶𝗲𝗻𝗰𝗲𝘀 + 𝗪𝗶𝗻 𝗮 𝗩𝗼𝘂𝗰𝗵𝗲𝗿! 🎟️ My wonderful PhD student (not on fedi) is runnning a survey about researcher views about pathway enrichment analysis. If you are a life scientist who has […] [Original post on genomic.social]

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 02/04/2025

The mitch R/Bioconductor package for enrichment analysis gets new network visualisation function in the devel branch. See these examples for how lung cells respond to C19 infection. Here red=up regulated, blue=down. Details and quickstart guide […] [Original post on genomic.social]

Pathway network chart focusing on those upregulated by SARS-COV-2 infection. It includes Reactome pathways like EGRF, FLT3 and interleukin signaling.

Pathway network chart focusing on those down-regulated by SARS-COV-2 infection. It includes DNA replication and DNA repair pathways.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 19/02/2025

Now isn’t the time to back down. 🇺🇦 needs our help now more than ever. I supported Liberty Ukraine with a donation www.libertyukraine.org #Ukraine

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 06/02/2025

Just tried DeepSeek-R1-Distill-Qwen-32B model on my PC and noticed that it swapped into Chinese in one of my questions 😂 (1st screenshot) Q) If I knew a nuclear explosion was imminent in my city in 5 minutes and I was at home, what would be the best way to […] [Original post on genomic.social]

In response to my question, DeepSeek started the answer in English then swapped to Chinese.

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 05/02/2025

Today thinking of Dr Nick Wong who passed away on the 3rd of February 2023 and who was a friend to many in the bioinformatics and life sciences community in Australia and NZ 🕯️

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 05/12/2024

I'm not an expert on the Syrian conflict but holy shit the situation is getting crazy. Last week the largest city Alleppo (AL) was seized by the Turkish backed rebels (green) without severe battles and just yesterday the city of Hama (HA) also fell. If the […] [Original post on genomic.social]

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Mark Ziemann 🇺🇦🌻🦩 @mdziemann.genomic.social.ap.brid.gy · 26/11/2024

That feeling when... a 2.5 hr compulsory workshop is cancelled just before it was meant to start #worklife

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