Lightnews — Scholar-powered news

Reposted by Leo Lahti

Nordic Computational Biology @nordic-compbio.org · 2d

🎉 The Nordic CompBio Conference is coming soon to Tallinn, Estonia 🇪🇪
📅 Thursday-Friday 23-24th of October (10:30-17:15 EEST)
📢 Abstract submissions and registration are open
🔗 nordic-compbio.org/ncb-week

#NordicCompBio #ComputationalBiology #Bioinformatics #Nordics

2 3

Reposted by Leo Lahti

Hall Lab @halllab.bsky.social · 8d

Come join us 2-4th March 2026 for a cracking #microbiome conference in Hinxton UK! Speaker line up is AMAZING and lots of opportunities for ECRs for selected talks, flash talks and posters.

Bursaries are also available!

See details below 👇

Wellcome Connecting Science Learning and Training @eventswcs.bsky.social · 8d

Showcase your microbiome research at our 2026 conference! #Microbiome26

Demonstrate how #genomics tools and technologies are contributing to a deeper understanding of the microbiome.

🗓️ 2-4 March
Submit an abstract by 24 November ✍🏼

📎 bit.ly/4kttBOX
#MicrobiomeSky #AcademicSky

Wellcome Connecting Science hybrid conference
Microbiome Interactions in Health and Disease

Conference dates: 2-4 March 2026
Location: Hinxton Hall Conference Centre, Wellcome Genome Campus, UK and online

Bursary and abstract deadline: 24 November 2025
Registration deadline
In person: 2 February
Virtual: 14 February

9 17

Reposted by Leo Lahti

Zamin Iqbal @zaminiqbal.bsky.social · 13d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

14 150 300

Reposted by Leo Lahti

Craig MacLean @craigmaclean.bsky.social · 13d

New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...

Job Details

my.corehr.com

4 32 26

Reposted by Leo Lahti

Jukka Suomela @jukkasuomela.fi · 13d

New fun stuff for those applying for RCF funding:
www.aka.fi/en/research-...

Research security

All applicants must include an appendix with their application that contains a self-assessment of research security issues and, if necessary, a more detailed description of the risks and a risk manage...

www.aka.fi

2 1 1

Reposted by Leo Lahti

Mark Copelovitch @mcopelov.bsky.social · 18d

Nothing is inevitable. In either direction. Hope and work.

Scott L Greer @scottlgreer.bsky.social · 18d

“52% of all autocratization episodes become U-Turns, which increases to 73% when focusing on the last 30 years. The vast majority of U-Turns (90%) lead to restored or even improved levels of democracy”

V-Dem data

When autocratization is reversed: episodes of U-Turns since 1900

The world is in a “wave of autocratization.” Yet, recent events in Brazil, the Maldives, and Zambia demonstrate that autocratization can be halted and reversed. This article introduces “U-Turn” as ...

www.tandfonline.com

19 350 1K

Reposted by Leo Lahti

Physalia-courses@Online @physaliacourses.bsky.social · 22d

🌱 New course: Orchestrating Microbiome Analysis with @bioconductor.bsky.social (2–6 Feb 2026, online). Learn from @antagomir.bsky.social & Toumas Borman how to analyse microbiome & multi-omics data in R/Bioconductor.

www.physalia-courses.org/courses-work...

Orchestrating Microbiome Analysis with Bioconductor

2–6 February 2026

www.physalia-courses.org

2 4

Reposted by Leo Lahti

Sabina Leonelli @sabinaleonelli.bsky.social · 26d

A quick reminder to all those who care about open research to consider joining us for the FOR2026 Conference in the Future of Open Research at the Technical University of Munich in May 4-6, 2026! Deadline for paper and poster proposals: 30 September

opensciencestudies.eu/for-2026-con...

FOR 2026 Conference – A Philosophy of Open Science for Diverse Research Environments

opensciencestudies.eu

22 25

Reposted by Leo Lahti

Professoriliitto @professoriliitto.bsky.social · Aug 21

TIA Seed 2025 -rahoitushaku avautuu 15.9. Rahoitusta voivat hakea professorit, jotka ovat olleet palkattuna suomalaisessa korkeakoulussa tai tutkimuslaitoksessa enintään kolme vuotta ja jotka ovat asuneet vähintään viisi vuotta yhtäjaksoisesti Suomen ulkopuolella ennen Suomeen tuloaan.

TIA Seed 2025 -rahoitushaku avautuu 15.9. – ilmoittaudu info-webinaariin! - www.vaikuttavuussaatio.fi

Vaikuttavuussäätiö avaa tänä syksynä Tandem Industry Academia (TIA) Seed -rahoitushaun, joka on suunnattu hiljattain suomalaisen tutkimusrahoitusjärjestelmän piiriin tulleille professoritasoisille tut...

www.vaikuttavuussaatio.fi

1 1

Reposted by Leo Lahti

W. Joel Schneider @w-joel-schneider.bsky.social · Aug 20

Now on CRAN, ggdiagram is a #ggplot2 extension that draws diagrams programmatically in #Rstats. Allows for precise control in how objects, labels, and equations are placed in relation to each other.
wjschne.github.io/ggdiagram/ar...

Trigonometric functions and a unit circle

A bivariate change model with structured residuals

A hierarchical model of cognitive abilities

11 75 180

Reposted by Leo Lahti

Ákos T Kovács @evolvedbiofilm.bsky.social · Aug 17

Race by other names: critiquing population categories in microbiome research

#mSystems MiniReview by Marta Scaglioni

journals.asm.org/doi/10.1128/...

Race by other names: critiquing population categories in microbiome research | mSystems

Behind the façade of scientific objectivity, race continues to haunt modern science. Contemporary biomedical research often employs categories of human difference that have recently come under critici...

journals.asm.org

7 6

Leo Lahti @antagomir.bsky.social · Aug 10

Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis www.nature.com/articles/s42...

Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis - Communications Biology

An interpretable Transformer-based model accurately predicts chronological age across body site and identifies key microbial signatures of aging.

www.nature.com

1

Reposted by Leo Lahti

Evan Spotte-Smith (they/them) @ewcspottesmith.bsky.social · Aug 8

The Journal of Open Source Software (@joss-openjournals.bsky.social‬) is looking for editors. Come join our team!

I've only been an editor for a few months, but I love working with JOSS. Our peer review process is actually collaborative, and we're Diamond Open Access.

#AcademicSky 🧪 ⚗️ #CompChem

Call for editors | Journal of Open Source Software Blog

Blog for the Journal of Open Source Software • <a href='https://joss.theoj.org'>https://joss.theoj.org</a>

blog.joss.theoj.org

18 33

Reposted by Leo Lahti

Mike Inouye @mikeinouye.bsky.social · Aug 4

IMHO green computing & green software engineering are becoming even very important.

Check out our Green Algorithms Initiative for more tools and information www.green-algorithms.org

And the GREENER Principles which lay the foundation for a sustainability roadmap www.nature.com/articles/s43...

Green Algorithms

Towards environmentally sustainable computational science

www.green-algorithms.org

4 6

Reposted by Leo Lahti

Constantin Ahlmann-Eltze @const-ae.bsky.social · Aug 4

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

2 57 130

Reposted by Leo Lahti

Johannes B. Gruber @jbgruber.bsky.social · Aug 3

The next version of the #rstats 📦 {atrrr} will likely contain a function to stream from the Bluesky Firehose! Looking for people to test and comment now:

github.com/JBGruber/atr...

support firehose · Issue #23 · JBGruber/atrrr

See: https://docs.bsky.app/docs/advanced-guides/firehose I tried it at some point and the socket part works fine. However, decoding the CBOR event data is a bigger challenge. The Python package use...

github.com

2 7 16

Reposted by Leo Lahti

Sean Gibbons 🦠💩 @gibbological.bsky.social · Jul 31

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems

In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

journals.asm.org

7 50 94

Reposted by Leo Lahti

EurIPS Conference @euripsconf.bsky.social · Jul 16

EurIPS is coming! 📣 Mark your calendar for Dec. 2-7, 2025 in Copenhagen 📅

EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu

eurips.cc

2 70 140

Reposted by Leo Lahti

Elina Mäntylä @elinamantyla.bsky.social · Jul 18

"Long-term ecological research is not the only area that needs to maintain and update data for future use. Many researchers add to, revise or overhaul their data sets over the course of their projects or careers, all while continuing to publish articles." www.nature.com/articles/d41... #OpenData

Need to update your data? Follow these five tips

Researchers engaged in long-term projects often need to update their data sets over time. Here’s how to do it while maintaining reproducibility.

www.nature.com

2 2

Reposted by Leo Lahti

Bioconductor @bioconductor.bsky.social · Jul 17

🌟 Bioconductor 2025 CAB & TAB nominations are open!

Join our advisory boards to support community growth or guide technical strategy.

📅 Apply by Aug 31
CAB: forms.gle/8NYxRGhprfuN...
TAB: forms.gle/eqef9ThpUypc...

#Bioconductor #RStats

Bioconductor nominations graphic with CAB and TAB illustrations and www.bioconductor.org

13 13

Reposted by Leo Lahti

Nature Microbiology @natmicrobiol.nature.com · Jul 16

New RESOURCE!

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria

@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co

#microbiomesky #microsky

www.nature.com/articles/s41...

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria - Nature Microbiology

A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.

www.nature.com

22 39

Leo Lahti @antagomir.bsky.social · Jul 15

Interested in an international #PhD at the intersection of computational & environmental microbiome research (Finland + Australia)?

PM/email for more details.