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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
About me
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Posts
portfolio
Chromograph
Chromograph pipeline for analysis of scATAC-seq and multiome data. Available on github
fetal brain multiomics
Code to recreate figures in the 2023 fetal brain multiomics paper. Also contains deepNeuron, the CNN trained to recognize enhancers relevant to neuronal subtypes. Available on github.
publications
Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH
Published in Nature Biotechnology, 2023
Here we develop a method named Enhanced ELectric Fluorescence in situ Hybridization (EEL FISH) that can rapidly process large tissue samples without compromising spatial resolution. By electrophoretically transferring RNA from a tissue section onto a capture surface, EEL speeds up data acquisition by reducing the amount of imaging needed, while ensuring that RNA molecules move straight down toward the surface, preserving single-cell resolution. We apply EEL on eight entire sagittal sections of the mouse brain and measure the expression patterns of up to 440 genes to reveal complex tissue organization. Moreover, EEL can be used to study challenging human samples by removing autofluorescent lipofuscin, enabling the spatial transcriptome of the human visual cortex to be visualized.
Download paper here
Dynamics of chromatin accessibility during human first-trimester neurodevelopment
Published in Nature, 2024
Here, we focus on the chromatin landscape and paired gene expression across the developing human brain to provide a comprehensive single cell atlas during the first trimester (6 - 13 post-conceptional weeks). We identified 135 clusters across half a million cells and using the multiomic measurements linked candidate cis-regulatory elements (cCREs) to gene expression. We found an increase in the number of accessible regions driven both by age and neuronal differentiation. Using a convolutional neural network we identified putative functional TF-binding sites in enhancers characterizing neuronal subtypes and we applied this model to cCREs upstream of ESRRB to elucidate its activation mechanism. Finally, by linking disease-associated SNPs to cCREs we validated putative pathogenic mechanisms in several diseases and identified midbrain-derived GABAergic neurons as being the most vulnerable to major depressive disorder related mutations. Together, our findings provide a higher degree of detail to some key gene regulatory mechanisms underlying the emergence of cell types during the first trimester. We anticipate this resource to be a valuable reference for future studies related to human neurodevelopment, such as identifying cell type specific enhancers that can be used for highly specific targeting in in vitro models.
Download paper here
talks
10X Genomics webinar about applying single cell ATAC-seq in the developing human brain
Published:
In 2020 10X Genomics invited me to give a talk about our ongoing efforts to generate a comprehensive atlas of all cell types in the developing human brain. I had recently started to collect scATAC-seq and single cell paired ATAC:RNA-seq using the 10X chromium platform and presented some of our preliminary findings. The webinar can be seen in its entirety here.
teaching
Bioinformatics MSc. course
MSc. course, Karolinska Institute, Department of Biochemistry and Biophysics, 2019
From 2019 until 2021 I was involved as a teacher in the Bionformatics course for the MSc. Biomedical Sciences program. During this time I taught different subjects including sequence alignment, phylogeny, simple -omics analysis and protein visualization. During this time together with with Ian Hofecker I helped redesign the practical side of the course, introducing a python based introduction to programming and modern data analysis skills. In particular I designed the scRNA-seq analysis practical
Student supervision
MSc. course, Karolinska Institute, Department of Biochemistry and Biophysics, 2021
During the first half of 2021 Bas joined our lab for an MSc. internship. Together we analyzed the Glioblastoma scATAC-seq data I had previously collected and built a Convolutional Neural Network.