Matthias Flotho
@mflot.bsky.social
📤 90
📥 306
📝 36
PhD candidate at Helmholtz Institute for Pharmaceutical Research Saarland
pinned post!
ggdiceplot 1.0.1 is out now! From today, {diceplot} is deprecated and treated as the legacy implementation, all new development and features will go into {ggdiceplot}. Repo:
github.com/maflot/ggdic...
Docs:
dice-and-domino-plot.readthedocs.io/en/latest/
Paper:
tinyurl.com/ggdiceplot
#rstats
#ggplot2
about 2 months ago
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Jens Hör
5 days ago
Great opportunity to join the lab of
@patrick-pausch.bsky.social
!
www.linkedin.com/feed/update/...
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PhD advertisement - Pausch lab | Patrick Pausch | 15 comments
Please share! 📤 The Pausch lab at Vilniaus universitetas / Vilnius University is looking to recruit PhD students to work on: ⚔️ 🛡️: Bacterial Immune Systems (CRISPR, retrons, & beyond) 🧬 ✂️: De...
https://www.linkedin.com/feed/update/urn:li:activity:7419288162033836032/
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Sholto David
6 days ago
Figure 5. Sudden quarrelling of spouse due to misuse of wireless sensor technology:
doi.org/10.5539/jpl....
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scverse
9 days ago
We will have our first community meeting of 2026 on Tue, Jan 20, 2026, 11AM CST/ 9AM PST ! Ian Ferenc Diks (
@ianfd.bsky.social
) will be presenting on SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale.
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Onisillos
9 days ago
"The target was numbers, and quality was mentioned only in terms of a journal’s prestige, never the work itself."
www.nature.com/articles/d41...
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I’m going to halve my publication output. You should consider slow science, too
If we don’t slow down, the research enterprise is going to crash, argues Adrian Barnett.
https://www.nature.com/articles/d41586-025-04061-w
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Pretty cool visualization tool for inspecting read alignments!
#datavis
#bioinformatics
#openscience
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12 days ago
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Helmholtz Institute Würzburg
13 days ago
Check out the latest paper by
@carmen-aguilar.bsky.social
, which also involved our
#HIRI
group leader
@emmanuel-saliba.bsky.social
and his lab. It was recently published in
@natmicrobiol.nature.com
:
doi.org/10.1038/s415...
Congratulations to all authors! 👏🎉
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The Parkinson's Disease Drug Tolcapone and Analogues are Potent Glycomimetic Lectin Inhibitors of Pseudomonas aeruginosa LecA
doi.org/10.1002/anie...
20 days ago
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Matthias Flotho
Allen Institute
22 days ago
Every brain tells a story. What will we learn when we listen? Together with
@uwmedicine.bsky.social
, we're embarking on an ambitious mission - building a functional, cellular map of the human brain.
https://alleninstitute.org/news/mapping-the-brain-to-improve-lives/
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Mapping the brain to improve lives
A collaborative effort between UW and the Allen Institute is creating a first-of-its-kind brain atlas, paving the way for breakthroughs in brain health.
https://alleninstitute.org/news/mapping-the-brain-to-improve-lives/
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Aligning Science Across Parkinson's
23 days ago
🧠 CRN Team Kordower developed a co-pathology mouse model combining tau, amyloid-β, & α-synuclein. They show co-pathologies synergistically trigger an amplified neuroimmune response, with expanded CD4+/CD8+ T cells & increased CD68+ microglia. 🔗 Check out the full
#preprint
:
https://bit.ly/4jAHzzl
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Matthias Flotho
ggdiceplot 1.0.1 is out now! From today, {diceplot} is deprecated and treated as the legacy implementation, all new development and features will go into {ggdiceplot}. Repo:
github.com/maflot/ggdic...
Docs:
dice-and-domino-plot.readthedocs.io/en/latest/
Paper:
tinyurl.com/ggdiceplot
#rstats
#ggplot2
about 2 months ago
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For anybody working on thermal imaging of faces: The thermal-face-alignment TFAN package has just dropped on pip.
github.com/openscivisio...
#computer-vision
#thermal-imaging
#thermal-recognition
#thermal-landmarks
#face-alignment
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about 1 month ago
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bioRxiv Bioinfo
about 2 months ago
Copula modeling of gene coexpression in single-cell RNA sequencing data
https://www.biorxiv.org/content/10.64898/2025.12.04.692380v1
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Chuan Wang
about 2 months ago
How does a bacterial small RNA evolve new functions? Our new study reveals the stepwise evolutionary journey of UhpU, a 3′UTR-derived sRNA in E. coli and relatives. It evolved from a metabolically-focused regulator to one with expanded targets and biogenesis manner.
www.pnas.org/doi/10.1073/...
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ggdiceplot 1.0.1 is out now! From today, {diceplot} is deprecated and treated as the legacy implementation, all new development and features will go into {ggdiceplot}. Repo:
github.com/maflot/ggdic...
Docs:
dice-and-domino-plot.readthedocs.io/en/latest/
Paper:
tinyurl.com/ggdiceplot
#rstats
#ggplot2
about 2 months ago
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Matthias Flotho
Nature Portfolio
about 2 months ago
Approximately 96% of the images from some space observatories in low Earth orbit could be tainted over the next decade due to light contamination from satellites, according to an analysis in Nature.
go.nature.com/3Y7eTUA
🔭 🧪
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Altmetric
about 2 months ago
THREAD One Year of tracking research communication on
@bsky.app
This time last year we officially added the Bluesky social platform to the places where we track research communication and article sharing. Here are some of the most viral articles that gained traction in the last 12 months. 1/14
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Erik Angner
2 months ago
"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week:
www.nature.com/articles/s41...
h/t
@asa.tsbalans.se
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Jens Zentgraf
2 months ago
We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (
doi.org/10.1093/bioi...
). You can find it at gitlab (
gitlab.com/rahmannlab/c...
) or install it via PyPI or Bioconda.
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Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
AbstractMotivation. The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many co
https://doi.org/10.1093/bioinformatics/btaf632
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Just out: PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation
doi.org/10.1093/nar/...
#openscience
#scRNAseq
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PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation
Abstract. Single-cell transcriptomic studies of peripheral blood mononuclear cells (PBMCs) offer valuable insights into immune states across diverse biolog
https://doi.org/10.1093/nar/gkaf1245
2 months ago
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Matthias Flotho
Global Antibiotic R&D Partnership (GARDP)
2 months ago
💥 Fewer than 3,000 scientists worldwide are working on antibiotic discovery, and progress is slowing. We need bold action to develop new antibiotics that are both innovative and accessible to everyone, everywhere. That’s what drives GARDP’s DER programme. This is BIG.
#WAAW2025
#AMR
#ThisIsBig
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Helena Klara Jambor
2 months ago
⏰ tomorrow, Nov 18, 5pm Berlin/4pm London “Data Vis for Cancer Patient Education“ - a
#DataVis
#BioVis
talk Link & Abstract: alt-text and also:
biovis.net/2025/meetup/
(right under picture)
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Matthias Flotho
Nature Portfolio
3 months ago
The Hektoria Glacier on the Antarctic Peninsula retreated by at least 8 km in two months, a rate nearly 10 times faster than previously measured for a grounded glacier, according to a study in Nature Geoscience.
go.nature.com/4nETBYJ
⚒️ 🧪
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World Conferences on Research Integrity
3 months ago
Chaos is coming for scholarly publishing
#AcademicPublishing
#WCRI2026
#WCRI
www.researchprofessionalnews.com/rr-news-uk-v...
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Chaos is coming for scholarly publishing - Research Professional News
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards
https://www.researchprofessionalnews.com/rr-news-uk-views-of-the-uk-2025-november-chaos-is-coming-for-scholarly-publishing/
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The EMBO Journal
3 months ago
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
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Prof. Stefan Rahmstorf
3 months ago
Here is our Exxon study in Science, with
@naomioreskes.bsky.social
and
@geoffreysupran.bsky.social
!
www.science.org/doi/10.1126/...
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Assessing ExxonMobil’s global warming projections
ExxonMobil’s own climate models showed that fossil fuel use would cause climate warming.
https://www.science.org/doi/10.1126/science.abk0063
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Now also online ggdiceplot:
github.com/maflot/ggdic...
#datavis
#openscience
add a skeleton here at some point
3 months ago
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www.youtube.com/watch?v=e15B...
add a skeleton here at some point
3 months ago
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doi.org/10.1371/jour...
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Ending publication bias: A values-based approach to surface null and negative results
Sharing knowledge is a fundamental principle within the scientific community, yet null and negative results are still being underreported. This Consensus View discusses the problem of such publication...
https://doi.org/10.1371/journal.pbio.3003368
3 months ago
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Albert Vilella, PhD.
3 months ago
Sad but true.
#AI
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The New York Times
3 months ago
See how the U.S. got hooked on ultraprocessed foods, one of the greatest health threats of our time.
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How America Got Hooked on Ultraprocessed Foods
They promised convenience and cheap nutrition. But they became one of the greatest health threats of our time.
https://nyti.ms/4obTFk3
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doi.org/10.1093/nar/...
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Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards
Abstract. MicroRNAs are by far the most extensively studied and best-characterized class of small RNAs. This depth of knowledge may partly explain the pers
https://doi.org/10.1093/nar/gkaf1049
3 months ago
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STADTRADELN
3 months ago
Droht durch die Einigung im Zollstreit der EU mit den USA eine Schwächung von EU-Fahrzeugstandards? 😟🚗🌍 Das befürchten zahlreiche europäische Städte und zivile Organisationen in einem Brief an die EU!
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Accepting US car standards would risk European lives, warn cities and civil society
Opening the EU market to vehicles certified under US standards would weaken the protections that save lives in Europe, say more than 80 civil society organisations and the administrations of…
https://etsc.eu/accepting-us-car-standards-would-risk-european-lives-warn-cities-and-civil-society/
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Fucking awesome work! "Hand-curated by three months"(the author)
doi.org/10.1093/nar/...
#openscience
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SmallBARNA 2026: a kingdom-wide bacterial sRNA resource
Abstract. Bacterial small RNA are important context-sensitive regulators of gene expression, especially in highly pathogenic bacteria, often controlling vi
https://doi.org/10.1093/nar/gkaf999
3 months ago
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Matthias Flotho
MCPmed is live🎉 Make biomedical APIs, and databases LLM-ready via the Model Context Protocol (MCP)! - MCPmed Templates: wrap APIs fast - Breadcrumbs: drop LLM-readable tags in your web service More projects online now. Star & follow:
github.com/MCPmed
#LLM
#Bioinformatics
#OpenScience
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MCPmed
MCPmed has 6 repositories available. Follow their code on GitHub.
https://github.com/MCPmed
7 months ago
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Albert Vilella, PhD.
5 months ago
A few more
#SingleCell
and
#SpatialBiology
methods have been published recently, making it a total of 362 in the table I compiled over the years.
lookerstudio.google.com/reporting/c3...
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Yolanda Perez
5 months ago
😱 “A researcher recalled wondering about the level of 6 LIN tanks used to maintain samples “going back to the 80s” and checked on them to find that “all of them were bone dry. Then they checked with their business office and learned that “our lab hadn’t purchased any liquid nitrogen since 2016.”
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Exclusive: How a researcher faked data and gaslit a labmate for years
Ryan Evanoff Sometime in early 2019, a postdoc in a veterinary microbiology lab at Washington State University (WSU) in Pullman came to suspect that a research assistant in her lab was fabricating …
https://retractionwatch.com/2022/01/13/exclusive-how-a-researcher-faked-data-and-gaslit-a-labmate-for-years/
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Marc Stadler
5 months ago
www.ingentaconnect.com/content/wfbi...
In our new paper we have described several new species of Hypoxylaceae and found that the genus Rostrohypoxylon is obsolete because it is nested in Annulohypoxylon in the multi-locus phylogeny. Secondary metabolite profiles of all taxa are also reported.
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bioRxiv Neuroscience
5 months ago
Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease
https://www.biorxiv.org/content/10.1101/2025.08.25.672093v1
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bioRxivpreprint
5 months ago
Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease
https://www.biorxiv.org/content/10.1101/2025.08.25.672093v1
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Elisabeth Bik
5 months ago
Making Your Research Free May Cost You * With federal funding exceptionally unreliable, scientists say they are stressed about spending thousands of grant dollars on unexpected and questionable open-access charges. By
@stephaniemlee.bsky.social
for
@chronicle.com
www.chronicle.com/article/maki...
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Making Your Research Free May Cost You
Under a new requirement that NIH-funded research be freely, immediately available, some journals are forcing researchers to pay to publish.
https://www.chronicle.com/article/making-your-research-free-may-cost-you
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eLife
5 months ago
Exercise can reduce pain, but you don’t have to work out harder to feel the benefit. New research suggests that fitness level and sex may play a bigger role than exercise intensity in how we experience exercise-induced pain relief.
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Painkiller exercise
High-intensity exercise relieves pain more than low-intensity activity – but only in males with high fitness levels.
https://buff.ly/ILoFgpu
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Philipp Flotho
5 months ago
If you want to try it out, the plugin can be installed from pip: pip install napari[all] napari-pyflowreg and allows motion correction as well as basic motion analysis and visualization functionality.
#napari
#2P
#microscopy
#neuroimaging
#motioncorrection
add a skeleton here at some point
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CRAN Updates
5 months ago
New on CRAN: ggdiceplot (0.1.0). View at
https://CRAN.R-project.org/package=ggdiceplot
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ggdiceplot: Dice Plot Visualization for 'ggplot2'
Provides 'ggplot2' extensions for creating dice-based visualizations where each dot position represents a specific categorical variable. The package includes geom_dice() for displaying presence/absence of categorical variables using traditional dice patterns. Each dice position (1-6) represents a different category, with dots shown only when that category is present. This allows intuitive visualization of up to 6 categorical variables simultaneously.
https://CRAN.R-project.org/package=ggdiceplot
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Just released: PyFlowReg and napari-FlowReg are now online and on pip. Python bindings and a Napari plugin for Flow-Registration – variational optical-flow motion correction for 2-photon microscopy.
github.com/FlowRegSuite
#pip
#openscience
#2PImaging
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5 months ago
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Matthias Flotho
Altmetric
5 months ago
This is the definition of a failed social media platform.
add a skeleton here at some point
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#NeuroDegeneration preprints
6 months ago
ROSMAP-Compass: A data-harmonised, AI-ready atlas of 22 million single nuclei from the ROSMAP cohort #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.1101/2025.08.11.668964v1
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bioRxiv Bioinfo
6 months ago
PBMCpedia: A Harmonized PBMC scRNA-seq Database With Unified Mapping and Enhanced Celltype Annotation
https://www.biorxiv.org/content/10.1101/2025.08.06.668843v1
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#SingleCell preprints
6 months ago
PBMCpedia: A Harmonized PBMC scRNA-seq Database With Unified Mapping and Enhanced Celltype Annotation #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.08.06.668843v1
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Matthias Flotho
6 months ago
Agreed, papermills are for people with a small PNAS! Thanks for getting this big one out!
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The title speaks for itself: The entities enabling scientific fraud at scale are large, resilient, and growing rapidly
doi.org/10.1073/pnas...
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PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
https://doi.org/10.1073/pnas.2420092122
6 months ago
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