Jens Lagergren

DisCell: Separating Spillover from Niche Response in Spatial Transcriptomics

DisCell identifies and separates spillover from niche responses in spatial transcriptomics data, confirming a previously reported finding about esophageal cancer cells.

Scalable and robust phylogenetic tree reconstruction from copy-number data with Sparse Rooted Neighbor Joining

This paper introduces SRNJ, a scalable rooted Neighbor Joining method for phylogenetic tree reconstruction from copy-number data, showing improved accuracy and efficiency over standard NJ.

LN's t-Test: A Principled Approach to t-Testing in Single-Cell RNA Sequencing

The paper introduces LNs t-test, a method for differential gene expression analysis in scRNA-seq that reduces bias and improves accuracy compared to existing approaches.

CopyMix: Mixture Model Based Single-Cell Clustering and Copy Number Profiling using Variational Inference

CopyMix jointly infers cell clusters and copy number profiles from single-cell DNA sequencing data, avoiding clustering artifacts and parameter tuning.

Scuphr: A probabilistic framework for cell lineage tree reconstruction

Scuphr reconstructs cell lineage trees using bulk and single-cell DNA sequencing data, addressing technical artifacts and improving accuracy over existing methods.

Clonally heritable gene expression imparts a layer of diversity within cell types

The paper identifies heritable transcriptional diversity within cell types by studying clonal human lymphocytes and mouse brain cells, showing clone-specific chromatin accessibility leads to distinct gene expression.

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

Celloscope deconvolves cell types in spatial transcriptomics data using marker genes, outperforming existing methods and accurately identifying brain structures and immune infiltrates.

C-ToMExO: Learning Cancer Progression Dynamics from Clonal Composition of Tumors

The paper introduces a method to infer cancer progression models from clone-level data, showing improved robustness and scalability using a novel MCMC algorithm.

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data

DeepMP detects DNA methylation from Nanopore sequencing data using a CNN that combines signals and basecalling errors, outperforming existing methods across multiple datasets.

PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data

PhylEx reconstructs clonal structure by integrating bulk DNA-seq and scRNA-seq data, outperforming existing methods in clonal-tree reconstruction and mutation clustering.

Charting Tissue Expression Anatomy by Spatial Transcriptome Decomposition

The paper introduces a probabilistic framework to analyze spatial transcriptomics data, identifying transcriptomic patterns corresponding to cell types and tissue components in mouse brain samples.

Species tree-aware simultaneous reconstruction of gene and domain evolution

The paper introduces a model for reconstructing gene and domain evolution using a species tree, showing it outperforms existing methods on synthetic and biological data.