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Mark Ziemann 🇺🇦🌻🦩

@mdziemann.genomic.social.ap.brid.gy

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

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Mark Ziemann 🇺🇦🌻🦩@mdziemann.genomic.social.ap.brid.gy · 2w ago

Yesterday marked 10 years since the publication of our article on how Excel spreadsheets cause autocorrect errors to genomics data. https://link.springer.com/article/10.1186/s13059-016-1044-7 #bioinformatics #genomics

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.

link.springer.com

Mark Ziemann 🇺🇦🌻🦩@mdziemann.genomic.social.ap.brid.gy · 2w ago

A straightforward and up-to-date guide to functional enrichment analysis https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1895224/full #genomics #bioinformatics #pathwayEnrichment

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...

frontiersin.org

Mark Ziemann 🇺🇦🌻🦩@mdziemann.genomic.social.ap.brid.gy · 2w ago

How is using Docker containers any better than strict descriptiuons of all packages with requirements.txt (Python) or Renv (R)? Let's discuss. https://genomespot.blogspot.com/2026/08/on-computational-reproducibility-surely.html #Bioinformatics #Reproducibility

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 ...

genomespot.blogspot.com

Mark Ziemann 🇺🇦🌻🦩@mdziemann.genomic.social.ap.brid.gy · last mo.

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

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

biorxiv.org