iiinova — where your digital self keeps evolving

Reposted by ToxicoloGee Whiz, PhD

Feringa Lab @feringalab.bsky.social · 12/03/2025

We would like to bring our EVOLVE consortium with its PhD positions to your attention again! Sharing is also much appreciated.

01110 11

Reposted by ToxicoloGee Whiz, PhD

David Fischer @davidsebfischer.bsky.social · 13/03/2025

Currently, there's a lot of interest in quantitative models that would help us understand and predict features of the complex cellular systems that underlie human health and disease - think about virtual cells, for example. On can trace some of these ideas back to the early days of systems biology.

1136 13

Reposted by ToxicoloGee Whiz, PhD

Ana Conesa @anaconesa.bsky.social · 13/03/2025

Kickking off the second day our @bcbhubcsic.bsky.social meeting with scientific sesions with Victor Sánchez Gaya, presenting POSTRE, a tool to predict the funcional impact of pstructural variants @hitseq.bsky.social @ibv-csic.bsky.social @csic-vaact.bsky.social

033 3

Reposted by ToxicoloGee Whiz, PhD

Ana Conesa @anaconesa.bsky.social · 13/03/2025

Next, Ana Martinez and Carmen Gil from @cib-csic.bsky.social presenting how to use a consortium of AI tools for drug design, with múltiple applicatons in the clínic @bcbhubcsic.bsky.social @csic-vaact.bsky.social #2AsambleaBCBHub

064 6

Reposted by ToxicoloGee Whiz, PhD

Yves Brun lab @brunlabcaulo.bsky.social · 12/03/2025

Please repost: Postdoc position in antibiotic discovery in a large multidisciplinary project combining high-throughput approaches, microscopy, AI, and hit-to-lead optimization at @umontreal.ca and @mila-quebec.bsky.social. Apply to ML.Antibiotics@gmail.com. See lnkd.in/dVVk4N3s. #microsky

179112 112

Reposted by ToxicoloGee Whiz, PhD

Tigem @tigem.bsky.social · 12/03/2025

🚨 The latest study from #NatureCommunications, led by Pasquale Piccolo, systematically evaluated AAV-mediated liver transduction across different fibrosis models.

174 7

Reposted by ToxicoloGee Whiz, PhD

Nextflow @nextflow.io · 10/03/2025

The #Nextflow #Training week has begun! 🎉 New to Nextflow or need a guided intro? Watch the brand new on-demand walkthrough videos for the "Hello Nextflow" course, and learn at your own pace! hubs.la/Q03b2-Rk0

hubs.la

Hello Nextflow: Intro and setup

Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

1106 10

Reposted by ToxicoloGee Whiz, PhD

Stephen Turner @stephenturner.us · 10/03/2025

Quantifying Metagenomic Strain Associations from Microbiomes with Anpan www.biorxiv.org/content/10.1... 🧬🖥️🧪 #Rstats 📦 github.com/biobakery/an...

085 8

Reposted by ToxicoloGee Whiz, PhD

Science News @scinews.bsky.social · 25/02/2025

Common gynaecological disorders linked to raised heart and cerebrovascular disease risk "They include polycystic ovary syndrome, endometriosis, heavy or irregular periods" heart.bmj.com/content/earl...

2269 26

Reposted by ToxicoloGee Whiz, PhD

PLOS Biology @plosbiology.org · 21/02/2025

PLOS has issued a statement on recent US Executive Orders and scientific integrity. We are determined to stand firmly behind our mission, our values and our principles, and against any attempt at censorship or undermining of the core principles of scientific inquiry. plos.io/3D4O8cH

plos.io

PLOS statement on recent US Executive Orders and scientific integrity - The Official PLOS Blog

Since its founding over twenty five years ago PLOS has been dedicated to advancing open science, ensuring that knowledge is accessible to…

291113436 1.1K

Reposted by ToxicoloGee Whiz, PhD

Hao Yin @haoyin.bsky.social · 21/02/2025

Is this real? I published it again on Brain @brain1878.bsky.social 😆 Truly appreciate the leadership of @rrust.bsky.social on this great project (>300 refs!)🫡👇 The blood–brain barrier: a help & a hindrance #Aging #Stroke #Neurodegeneration Crossing #BBB 😎 academic.oup.com/brain/advanc...

1237 23

Reposted by ToxicoloGee Whiz, PhD

Science Friday @scifri.bsky.social · 21/02/2025

In a small trial, nearly half of pancreatic cancer patients who received an mRNA vaccine had no signs of relapse after three years. Dr. Vinod Balachandran from @mskcancercenter.bsky.social joins us to discuss the results and what they could mean for cancer treatment.

buff.ly

A Vaccine For Pancreatic Cancer Continues To Show Promise

In a small trial, nearly half of pancreatic cancer patients who received an mRNA vaccine for the disease had no relapse three years later.

685240205574 24K

Reposted by ToxicoloGee Whiz, PhD

Nature Portfolio @natureportfolio.nature.com · 16/02/2025

A paper in Nature Methods presents Segment Anything for Microscopy, a tool for segmentation and tracking in multidimensional microscopy data. go.nature.com/3QiRonW

This is figure 1, which gives an overview of Segment Anything for Microscopy.

1458 45

Reposted by ToxicoloGee Whiz, PhD

Eric Topol @erictopol.bsky.social · 03/02/2025

Our gut microbiome and its metabolites have key interactions with our immune response to cancer and success from cancer immunotherapy. Nice perspective @jclinical-invest.bsky.social www.jci.org/articles/vie...

1647893 478

Reposted by ToxicoloGee Whiz, PhD

Ming Tommy Tang @tommytang.bsky.social · 04/02/2025

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted www.nature.com/articles/s4...

073 7

Reposted by ToxicoloGee Whiz, PhD

PLOS Biology @plosbiology.org · 04/02/2025

What is the mechanistic link between the NLRP3 #inflammasome, #autophagy & inflammatory #bowel disease (IBD)? This study shows that VANGL2 reduces #IBD progression by recruiting the ubiquitin ligase MARCH8 to regulate NLRP3 activation via OPTN-mediated autophagy 🧪 @plosbiology.org plos.io/42FTqFO

Top left: intestinal gross tissue was measured in the WT, Vangl2ΔM/ΔM, and MCC950 treated Vangl2ΔM/ΔM mice after DSS treatment (n = 7). Top right: HE staining was used to compare the colonic morphology between health control and IBD patients (upper panel). The expression of VANGL2 in colon of healthy control and IBD patients was detected by immunofluorescence staining (lower panel). Bottom: Schematic diagram of the action of VANGL2 in IBD.

1201 20

Reposted by ToxicoloGee Whiz, PhD

Samuel Kaski @samikaski.bsky.social · 04/02/2025

I have big news: @ellis.eu has launched its 2nd major research center, @ellisfinland.bsky.social! I have agreed to start as founding director & the first call for PI positions is open. This is a major opportunity for outstanding researchers, join us! ellisinstitute.fi/PI-recruit

ellisinstitute.fi

Principal Investigator positions at ELLIS Institute Finland | ELLIS Institute Finland

Now recruiting new PIs in artificial intelligence and machine learning

35826 58

Reposted by ToxicoloGee Whiz, PhD

Jenea Adams @jeneaia.bsky.social · 04/02/2025

📣

052 5

Reposted by ToxicoloGee Whiz, PhD

Anthony Mathelier @amathelier.bsky.social · 04/02/2025

🚨 PhD in Bioinformatics & Gene Regulation 🚨 Join the Bioinformatics in Life Science (BiLS) initiative through a multidisciplinary project to unravel gene regulation from DNA to proteins, co-supervised by E. Valen @jonnings.bsky.social and me! www.jobbnorge.no/en/available...

jobbnorge.no

PhD Research Fellow in Bioinformatics and Gene Regulation (274506) | University of Oslo

Job title: PhD Research Fellow in Bioinformatics and Gene Regulation (274506), Employer: University of Oslo, Deadline: Friday, February 28, 2025

076 7

Reposted by ToxicoloGee Whiz, PhD

Eric Topol @erictopol.bsky.social · 30/01/2025

In @science.org today, the discovery of the neuroimmune itch-scratch circuit. And why scratching can makes things worse www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...

731150 311

Reposted by ToxicoloGee Whiz, PhD

Eric Topol @erictopol.bsky.social · 29/01/2025

The feasibility of patching a severely damaged heart with stem cells as a bridge to transplant, actualized in a 46-year-old woman @nature.com www.nature.com/articles/s41... www.nature.com/articles/d41...

739271 392

Reposted by ToxicoloGee Whiz, PhD

PLOS Biology @plosbiology.org · 28/01/2025

#Liver #metabolism is divided between pericentral & periportal zones, but what are the broader consequences of this zonation? This study shows that proper liver zonation, regulated by R-spondin3, contributes to systemic glucose metabolism & body composition 🧪 @plosbiology.org plos.io/3PR0E2a

Schematic of a newly identified inter-organ communication system, showing that hepatic metabolic zonation mediated by Rspo3 plays an important role in maintaining metabolism in remote organs, such as adipose tissues and skeletal muscles, as well as locally in the liver through the inter-organ coordination consisting of neuronal and non-neuronal communication. However, in the setting of obesity, the impaired Rspo3 function in the liver leads to the disturbance of this Rspo3-mediated physiological inter-organ mechanism, paradoxically resulting in progression of pathophysiological features such as glucose intolerance, insulin resistance, fatty liver, and deterioration of organ quality. BAT, brown adipose tissue; Rspo3, R-spondin3; WAT, white adipose tissue.

031 3

Reposted by ToxicoloGee Whiz, PhD

What’s up with Downes? @gbdownes.bsky.social · 28/01/2025

We hope other labs find it as useful as we do! Given that it's free, we also hope it can be used in teaching labs, which are often low resourced. Congratulations to all authors! #zebrafish 🧠🧪🧬 bmcbioinformatics.biomedcentral.com/articles/10....

bmcbioinformatics.biomedcentral.com

Marigold: a machine learning-based web app for zebrafish pose tracking - BMC Bioinformatics

Background High-throughput behavioral analysis is important for drug discovery, toxicological studies, and the modeling of neurological disorders such as autism and epilepsy. Zebrafish embryos and lar...

0176 17

Reposted by ToxicoloGee Whiz, PhD

Jonathan Pritchard @jkpritch.bsky.social · 26/01/2025

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

6318118 318

Reposted by ToxicoloGee Whiz, PhD

Micha Sam Brickman Raredon @msbr89.bsky.social · 26/01/2025

We are hiring! We have a fully-funded 2-year T32 post-doc slot to study spatial biology in lung regeneration. Background in data visualization useful but not required. If you’re interested or know of anyone, please get in touch or pass along! RaredonLab.com Description & teasers attached:

063 6

Reposted by ToxicoloGee Whiz, PhD

Hao Yin @haoyin.bsky.social · 26/01/2025

Proximal Ascending aorta is made of #SmoothMuscleCell of dual lineage origins Luminal side: Wnt1+ #CardiacNeuralCrest Abluminal side: Mef2c+ #SecondHeartField Their transcript profiles by scRNAseq + snATACseq👇 #AortaEd #ATVB 2024 @ahajournals.bsky.social www.ahajournals.org/doi/10.1161/...

1217 21

Reposted by ToxicoloGee Whiz, PhD

Satoshi Yoshiji, MD, PhD @satoshiyoshiji.bsky.social · 26/01/2025

📣 We are hiring! Join Yoshiji Lab at McGill University Dept of Human Genetics in Montreal, Canada! yoshiji-lab.org/joinus ✅Fully Funded Positions • 2 MSc Students • 1 PhD Student • 1 Postdoc ✅Goal: Using human genetics and multi-omics for drug target discovery and precision medicine

194 9

Reposted by ToxicoloGee Whiz, PhD

bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 09/12/2024

Divalent siRNA for prion disease www.biorxiv.org/content/10.1101/202…

042 4

Reposted by ToxicoloGee Whiz, PhD

Science News @scinews.bsky.social · 21/01/2025

RNA gene therapies offer hope for millions with high cholesterol "Base editing, antisense oligonucleotides and siRNA therapies that target low-density lipoprotein and the genes encoding molecules that regulate it are being tested in several clinical trials." www.nature.com/articles/d41...

nature.com

RNA gene therapies offer hope for millions with high cholesterol

Base editing, antisense oligonucleotides and siRNA therapies that target low-density lipoprotein and the genes encoding molecules that regulate it are being tested in several clinical trials.

0287 28

Reposted by ToxicoloGee Whiz, PhD

Justine Debelius @jwoodelius.bsky.social · 24/01/2025

My research center is hiring a data analyst! If you've got a masters, a background in microbiome work, an interest in making life better for children going forward, come work with us! #microsky jobs.jhu.edu/job/Baltimor...

jobs.jhu.edu

Biostatistician

0106 10

Reposted by ToxicoloGee Whiz, PhD

Stephen Turner @stephenturner.us · 25/01/2025

Targeted decontamination of sequencing data with CLEAN www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪 Nextflow: github.com/rki-mf1/clean

02911 29

Reposted by ToxicoloGee Whiz, PhD

Gaspar Jekely @jekely.biologists.social.ap.brid.gy · 25/01/2025

I am preparing a talk on #OpenScience and looking for examples/studies quantifying non-openness, closed workflows, data code etc. Like this one on Excel errors in gene names per journal #science Can you recommend other good example?

4912 12

Reposted by ToxicoloGee Whiz, PhD

PastelBio @pastelbio.bsky.social · 25/01/2025

Cell Storage Conditions Impact Single-Cell Proteomic Landscapes pubs.acs.org/doi/10.... --- #proteomics #prot-paper

073 7

Reposted by ToxicoloGee Whiz, PhD

Max Kennerly @maxkennerly.bsky.social · 24/01/2025

Yup. Microsoft automatically switched me to the $99.99/year version with Spicy Autocomplete. You have to go all the way through "cancel subscription" to be presented these options and get the $69.99/year one you actually chose.

Graphic comparing Microsoft 365 "Personal" to "Personal Classic." The sole difference is $30 more a year for AI.

18637932223 3.8K

Reposted by ToxicoloGee Whiz, PhD

Marc Veldhoen @marcveld.bsky.social · 15/01/2025

Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning A technical paper on a newly developed method to follow the distribution of nanocarriers, such as LNPs, liposomes and adenoviruses, through the body of mice. www.nature.com/artic... 1/15

nature.com

Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning

Nature Biotechnology - An integrated experimental and deep learning pipeline reveals cell-level targeting of nanocarriers in whole bodies.

12110 21

Reposted by ToxicoloGee Whiz, PhD

Prisca Liberali @priscaliberali.bsky.social · 15/01/2025

A perfect start in the new year! 🌱 Regenerating tissues are just an amazing spatio temporal controlled process! Our new manuscript explores how cell heterogeneity and bistability orchestrate intestinal regeneration. 🧵 biorxiv.org/cgi/content/...

biorxiv.org

Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration

Tissue regeneration relies on the ability of cells to undergo de novo patterning. While tissue patterning has been viewed as the transition from initially identical un-patterned cells to an arrangemen...

614750 147

Reposted by ToxicoloGee Whiz, PhD

Li Song @mourisl.bsky.social · 15/01/2025

My PhD adviser Liliana Florea has developed a Coursera course "Bioinformatics Methods for Transcrptomics". A great resource to learn cutting-edge short- and long-read RNA-seq data analysis techniques: www.coursera.org/learn/bioinf...

coursera.org

Bioinformatics Methods for Transcriptomics

Offered by Johns Hopkins University. This course will cover bioinformatics methods for analyzing transcriptomic RNA sequencing data ... Enroll for free.

12713 27

Reposted by ToxicoloGee Whiz, PhD

Nature Portfolio @natureportfolio.nature.com · 14/01/2025

A Review in Nature Reviews Microbiology explores the pathways linking the gut and the brain and examines the microbial, endocrine and neural mechanisms involved in the gut microbiota-brain axis and their impact on gastrointestinal and neuropsychiatric health. go.nature.com/3DSeS0d 🔒

This is figure 1, which shows the gut microbiota–brain axis.

23411 34

Reposted by ToxicoloGee Whiz, PhD

Nicolas Minc @minclab.bsky.social · 14/01/2025

Our first paper on BlueSky!! Remarkable work published in @currentbiology.bsky.social from Jing Xie, Javad Najafi and others, on how cell shape affects mitotic spindle positioning forces in embryos, by impacting cytoplasm flows. @ijmonod.bsky.social www.sciencedirect.com/science/arti...

27824 78

Reposted by ToxicoloGee Whiz, PhD

Teif lab @teiflab.bsky.social · 14/01/2025

Here is a growing list of conferences and schools in gene regulation for 2025 generegulation.org/conferences-.... You can order/filter this list by the date, deadline, location. Please reply here to suggest new events* *should be specific to gene regulation

generegulation.org

Conferences & Schools – 2025 – Gene Regulation – Teif Lab

288548 85

Reposted by ToxicoloGee Whiz, PhD

Andrew Heiss @andrew.heiss.phd · 04/12/2024

The viridis palettes are great perceptually uniform color maps for #dataviz, but sometimes at the extremes they're too pale/dark. With ggplot and #rstats, though, you can truncate the palette to avoid the paler colors. I wrote a little guide for how datavizf24.classes.andrewheiss.com/news/2024-12...

When you use scale_fill_viridis_d() or scale_color_viridis_d(), ggplot chops the viridis color map into evenly spaced colors along the range of the gradient. For instance, if you have a plot with 4 categories, you’ll end up with these colors:

Figure showing 8 viridis palettes chopped at 0%, 33%, 66%, and 100%

R code for creating a bar chart four four continents, with one of the bars filled with a really really pale yellow from the viridis magma palette

Figure showing the 8 viridis palettes, but starting at 10% and ending at 80%, resulting in colors at at 10%, 33%, 57%, and 80%

R code for creating a bar chart four four continents, with the bars filled with colors from a truncated viridis magma palette because of scale_fill_viridis_d(option = "magma", begin = 0.1, end = 0.8)

819247 192

Reposted by ToxicoloGee Whiz, PhD

Nicola Rennie @nrennie.bsky.social · 10/01/2025

🚨 New blog post! 🚨 If you want to learn about: 🎨 How to define colours in R 📊 Choosing palettes for plots 🛠️ Generating your own colours Read this ➡️ nrennie.rbind.io/blog/colours... #DataViz #RStats #ggplot2 #RLadies

nrennie.rbind.io

Working with colours in R | Nicola Rennie

Whether you're building data visualisations or generative art, at some point you will likely need to consider which colours to use in R. This blog post describes different ways to define colours, how ...

520255 202

Reposted by ToxicoloGee Whiz, PhD

Tiago Peixoto @tiago.skewed.de · 08/01/2025

Bumping this once more. One of the benefits of IT:U is the very generous in-house base funding, consisting of recurrent positions for post-docs and PhDs, not just as a part of a startup package. Get in touch if you want to know more details.

02218 22

Reposted by ToxicoloGee Whiz, PhD

Francisco Rodriguez-Sanchez @frodsan.bsky.social · 08/01/2025

Eleven quick tips for properly handling tabular data doi.org/10.1371/jour...

An illustration of the 11 tips for tabular data.

56128 61

Reposted by ToxicoloGee Whiz, PhD

Ewan Birney @ewanbirney.bsky.social · 08/01/2025

It was good seeing this coming out in preprint and great to see it published. Excellent work by Antoni Beltran (not on bluesky?) @benlehner.bsky.social etc.

23912 39

Reposted by ToxicoloGee Whiz, PhD

Steven Sloan @sloanlab.bsky.social · 08/01/2025

First 🦋 post! Very excited to share our lab's latest work exploring the shared and divergent aspects of human astrocyte development and glioblastoma. This effort spans many fields from developmental #glial biology to #stem cells and #tumor biology. rdcu.be/d5ADz A 🧵

rdcu.be

Mapping the developmental trajectory of human astrocytes reveals divergence in glioblastoma

Nature Cell Biology - Sojka et al. analyse the transcriptomic and epigenomic landscape of human astrocyte maturation and identify an epigenetically regulated intermediate state associated with...

313240 132