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Gioele La Manno @gioelelamanno.bsky.social · Sep 4

I dedicate the achievement to my family, whose patience and support through every creative burst made this possible.

Gioele La Manno @gioelelamanno.bsky.social · Sep 4

I am deeply honoured to have been recognized by the European Research Council with a #StartingGrant. @erc.europa.eu

With this support, my team and I will launch #MOVIOLA. Our goal is to understand how human neural progenitors decide their fate during brain development.

Two life sciences ERC Starting Grants at EPFL

Milena Schuhmacher and Gioele La Manno at EPFL’s School of Life Sciences have received European Research Council (ERC) Starting Grants. Former EPFL researcher Can Aztekin (now at Max Planck), is also ...

actu.epfl.ch

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Reposted by Gioele La Manno

Nature Methods @natmethods.nature.com · Sep 3

uMAIA offers an analytical framework designed to enable construction of high-resolution metabolic atlases using mass spec imaging data. @gioelelamanno.bsky.social

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

Unified mass imaging maps the lipidome of vertebrate development - Nature Methods

uMAIA is an analytical framework designed to enable the construction of metabolic atlases at high resolution using mass spectrometry imaging data.

www.nature.com

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Gioele La Manno @gioelelamanno.bsky.social · Sep 3

Proud of these advances, achieved in great company @EPFL : @giodang.bsky.social (co-PI), with Halima Schede & Leila Alieh leading the project, and the Oates lab bringing their zebrafish expertise [2/2]

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Gioele La Manno @gioelelamanno.bsky.social · Sep 3

Excited to share #uMAIA, our method to create 4D lipidomic atlases, now published in @natmethods.nature.com

We demonstrate that with uMAIA, the field is ready for atlas-level analyses capable of uncovering histological metabolic heterogeneity in both space and time. [1/2]

Unified mass imaging maps the lipidome of vertebrate development - Nature Methods

uMAIA is an analytical framework designed to enable the construction of metabolic atlases at high resolution using mass spectrometry imaging data.

www.nature.com

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Gioele La Manno @gioelelamanno.bsky.social · Sep 3

Proud of these advances, achieved in great company @EPFL : @giodang.bsky.social(co-PI), with Halima Schede & Leila Alieh leading the project, and the Oates lab bringing their zebrafish expertise [2/2]

Gioele La Manno @gioelelamanno.bsky.social · Sep 3

In my view even “function” isn’t well-posed concept. Context, timing, cell type, and interactions matter. Genes products have conditional context-dependent effects which have retrospecrivelly contributed to fitness.

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Reposted by Gioele La Manno

Ignacio_Rubio-Somoza @ignaciorubiosomoza.bsky.social · Aug 20

And he made it again!...tour the force from JIa-Wei´s Wang lab using comparative sc-transcriptomes, and developing new analytical tools, to tackle evolutionary trajectories of plant cell types!. Amazing work as usual! www.cell.com/cell/abstrac...

A unified cell atlas of vascular plants reveals cell-type foundational genes and accelerates gene discovery

A cross-species single-cell atlas highlights a core subset of cell-type foundational genes associated with major vascular plant cell types, enabling the identification of hidden cell types and the dev...

www.cell.com

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Reposted by Gioele La Manno

Sten Linnarsson @sten.linnarsson.org · Aug 15

A little over two weeks to the deadline! 20 positions, generous startup funding, a great community and fantastic infrastructure. Come join us!

Sten Linnarsson @sten.linnarsson.org · Jun 25

A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)

Karolinska Institutet @ki.se · Jun 25

Applications are now open! We are recruiting 20 Assistant Professors in a wide range of subject areas. We're looking for early-career researchers with strong scientific merits and future potential.
🔗 All positions: ki.se/en/about-ki/...

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Reposted by Gioele La Manno

Gonçalo Castelo-Branco @gocastelobranco.bsky.social · Aug 12

Join us at the FENS Single-Cell & Spatial Omics Winter School with:

@sarabiz86.bsky.social
@rongfan8.bsky.social
@gokcegroup.bsky.social
@gioelelamanno.bsky.social
@sj-marzi.bsky.social
@jplopez-atalaya.bsky.social
Ana Falcão
Florian Rosenberger
Gabriel Baró
Bosiljka Tasic
Barbara Treutlein

Federation of European Neuroscience Societies - FENS @fens.org · Aug 5

🌟 Registration is now OPEN! 🌟

Join the 2025-2026 #FENS-Hertie #WinterSchool and explore this year's topic – Single-cell and Spatial Omics to Understand Brain Heterogeneity! 🔬

📍 Alicante, Spain
🗓️ 11-17 Jan 2026

🔗 https://loom.ly/RM55lFQ

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Reposted by Gioele La Manno

Nature Methods @natmethods.nature.com · Aug 4

An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social

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

Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods

The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...

www.nature.com

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Reposted by Gioele La Manno

Nicolas Chiaruttini @nkiaru.bsky.social · Jul 24

Hey, it's out!
doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:

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Reposted by Gioele La Manno

Rita Strack @ritastrack.bsky.social · Jul 16

Wowee! Super-resolution stimulated X-ray Raman spectroscopy | Nature share.google/Mdn4Z0ddIy2t...

Super-resolution stimulated X-ray Raman spectroscopy - Nature

A high-resolution spectroscopic tool is demonstrated using the stochastically fluctuating intensity spikes in time and energy domains of a self-amplified spontaneous emission X-ray free-electron laser...

share.google

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Reposted by Gioele La Manno

Anton Goloborodko @golobor.bsky.social · Jul 15

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/

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Reposted by Gioele La Manno

Oded Rechavi @odedrechavi.bsky.social · Jul 14

I love the idea of "micropublications" www.micropublication.org (preparing one now)

microPublication - Get Your Data Out, Be Cited

www.micropublication.org

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Gioele La Manno @gioelelamanno.bsky.social · Jul 12

Amazing contributions to the community!

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Reposted by Gioele La Manno

DeepLabCut @deeplabcut.bsky.social · Jul 1

Super thrilled to give a full day #DeepLabCut Workshop in Okinawa today!

We had a packed house and everyone got models trained 🚀 - even then used #CEBRA 🦓 and/or #DLC2Action on the outputs!

Thank you #OIST for hosting us!! 🥳

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Reposted by Gioele La Manno

Waggoner Lab @labwaggoner.bsky.social · Jun 30

A major step forward in organoid technology–producing liver tissue that grows its own internal blood vessels
#TakebeLab @cincyresearch.bsky.social @natbiomedeng.nature.com
scienceblog.cincinnatichildrens.org/liver-organo...
www.nature.com/articles/s41...

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Reposted by Gioele La Manno

Anshul Kundaje @anshulkundaje.bsky.social · Jun 28

There is absolutely no reason to think that such models are actually learning biology. So maximizing the perturbation prediction objective does not necessarily result in a "virtual cell". 3/

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Reposted by Gioele La Manno

Sten Linnarsson @sten.linnarsson.org · Jun 25

A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)

Karolinska Institutet @ki.se · Jun 25

Applications are now open! We are recruiting 20 Assistant Professors in a wide range of subject areas. We're looking for early-career researchers with strong scientific merits and future potential.
🔗 All positions: ki.se/en/about-ki/...

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Reposted by Gioele La Manno

Marc Robinson-Rechavi @marcrr.bsky.social · Jun 24

Call from 6 Swiss Fields Medal laureates to preserve science funding
science-under-threat.com

Swiss Science Under Threat

science-under-threat.com

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Reposted by Gioele La Manno

BWJones @bwjones.bsky.social · Jun 8

Almost all Nobel Prizes are awarded for work that is exploratory, or absolutely basic science with no obvious commercial or medical benefit.

You cannot predict where advancements come from, so you have to invest in science and scientists.

Targeted (corporate) science investment will never do this.

Ted Pavlic (he/him/his) @tedpavlic.bsky.social · Jun 8

Reminder: Nobel-prize winning PCR (1983), used in basically all genetic tech today, was only possible because of extremophile bacterium discovered in 1964 in Yellowstone funded by a small ~$80k NSF grant with no obvious application at the time. #science 🧪
www.richmondscientific.com/how-a-discov...

How a discovery in Yellowstone National Park led to the development of PCR - Richmond Scientific

A discovery in Yellowstone National Park led to the development of PCR, the gold-standard COVID-19 tests used to fight the global pandemic.

www.richmondscientific.com

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Gioele La Manno @gioelelamanno.bsky.social · Jun 7

Check out our Spotiflow to accurately identify any spot-like objects (and more)! First output of an amazing colaboration experience with @maweigert.bsky.social

Martin Weigert @maweigert.bsky.social · Jun 6

Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social
www.nature.com/articles/s41...
rdcu.be/epIB7

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Reposted by Gioele La Manno

Albert Dominguez Mantes @albertdm.bsky.social · Jun 6

Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression

Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...

rdcu.be

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Reposted by Gioele La Manno

Martin Weigert @maweigert.bsky.social · Jun 6

Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social
www.nature.com/articles/s41...
rdcu.be/epIB7

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