I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

chatomics! Bioinformatics is NOT Just Statistics! 🚨 The p-value is small in this example, but is it biologically meaningful?

Fig. 1 a–c, Intact whole brains immunolabeled, cleared and imaged with LSFM were used as input to the ACE pipeline. a, Whole-brain LSFM data are passed to ACE’s segmentation module, consisting of ViT- and CNN-based DL models, to generate binary segmentation maps in addition to a voxel-wise uncertainty map for estimation of model confidence. b, The autofluorescence channel of data is passed to the registration module, consisting of MIRACL registration algorithms, to register to a template brain such as the Allen Mouse Brain Reference Atlas (ARA). High-resolution segmentation maps are then voxelized using a convolution filter and warped to the ARA (10 µm) using deformations obtained from registration. c, Voxelized and warped segmentation maps are passed to ACE’s statistics module. Group-wise heatmaps of neuronal density are obtained by subtracting the average of warped and voxelized segmentation maps in each group to identify neural activity hotspots. To identify significant localized group-wise differences in neuronal activity in an atlas-agnostic manner, a cluster-wise, threshold-free cluster enhancement permutation analysis (using group-wise ANOVA) is conducted. The resulting P value map represents clusters showing significant differences between groups. Correspondingly, ACE outputs a table summarizing these clusters, including their volumes and the portion of each brain region included in each cluster.

New deep-learning cell detection pipeline for light-sheet mouse brain image stacks, with an interesting cell-coordinate clustering statistics approach:

A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel […]

[Original post on mstdn.science]

JOBS ALERT! PhD position & 3-y postdoc position in statistics within my research group at @ocbe.bsky.social @uio.no
Both are linked to a project funded from the Research Council of Norway on Integrative Bayesian clustering for high-dim data in omics

Deadline: 13 June 2025

More info & links below!

Just got back from the 2nd Pertomics Retreat with my colleagues @shawangela.bsky.social and @thorohde.bsky.social — Great to reconnect with the Pertomics community, share work across different scales.

Special thanks to @manuelkaulich.bsky.social ’s fantastic team for organizing this great event.

BaCoN (Balanced Correlation Network) improves prediction of gene buffering | Molecular Systems Biology imageimageFunctional buffering between pairs of genes can be predicted by correlating the knockout fitness effect of one with the expression of another gene across cell lines. BaCoN (Balanced Cor...

I am excited to announce the publication of our paper in @molsystbiol.org!
I am incredibly grateful for this wonderful collaboration with the team of @manuelkaulich.bsky.social. A big thank you to @yasirde.bsky.social, @shawangela.bsky.social and to @maxbillmann.bsky.social!
doi.org/10.1038/s443...

Anyone interested in #lipids #genetics and #MentalHealth ? Then come join us in @UniBonn in Germany for a #postdoc that combines all of that in a cutting-edge and innovative way ! Application deadline is April 30th.

Just back from the CRISPR and Beyond — Loved being back in Cambridge with the CRISPR community.

It was great to see familiar faces from last year and catch up on the latest developments.(especially members of @manuelkaulich.bsky.social, @leopoldparts.bsky.social 's group).

#WellcomeGenomeCampus

If a team wished to include combinatorial gene perturbation and bioinformatics in their program, please reach out.

Treemap chart showing the fragmented landscape of psychological measures.

Want to make nice graphs with me, starting this summer? I am hiring for two PhD positions at the University of Witten/Herdecke.

Genome-wide Association Studies of Missing Metabolite Measures: Results From Two Population-based Studies

www.medrxiv.org/content/10.1...

I wonder what a GWAS with imputing missing to zero would yield in comparison.