Lars Velten
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View article: Emergence of activation or repression in transcriptional control under a fixed molecular context
Emergence of activation or repression in transcriptional control under a fixed molecular context Open
Transcription factors (TFs) can be both activators and repressors of gene transcription. This can manifest as “duality,” where the transcriptional response increases (activation) with TF concentration in one context but decreases (repressi…
View article: Clonal tracing with somatic epimutations reveals dynamics of blood ageing
Clonal tracing with somatic epimutations reveals dynamics of blood ageing Open
Current approaches used to track stem cell clones through differentiation require genetic engineering1,2 or rely on sparse somatic DNA variants3,4, which limits their wide application. Here we discover that DNA methylation of a subset of C…
View article: Clonal hematopoiesis landscape in frequent blood donors
Clonal hematopoiesis landscape in frequent blood donors Open
Donor blood saves lives, yet the potential impact of recurrent large-volume phlebotomy on donor health and hematopoietic stem cells (HSCs) remains largely unexplored. In our study, we conducted a comprehensive screening of 217 older male v…
View article: EPI-clone:Clonal tracing with somatic epimutations v1
EPI-clone:Clonal tracing with somatic epimutations v1 Open
This protocol describes the EPI-Clone method for single-cell lineage tracing using somatic epimutations (Scherer et al., 2025). This method is based on targeted single cell DNA-methylation profiling with scTAM-seq. We here provide targetin…
View article: Synthetic enhancers reveal design principles of cell state specific regulatory elements in hematopoiesis
Synthetic enhancers reveal design principles of cell state specific regulatory elements in hematopoiesis Open
During cellular differentiation, enhancers transform overlapping gradients of transcription factors (TFs) to highly specific gene expression patterns. However, the vast complexity of regulatory DNA impedes the identification of the underly…
View article: Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data
Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data Open
Motivation Single-cell RNA sequencing (scRNA-seq) data are widely used to study cancer cell states and their heterogeneity. However, the tumour microenvironment is usually a mixture of healthy and cancerous cells and it can be difficult to…
View article: Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants
Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants Open
Clonal cell population dynamics play a critical role in both disease and development. Due to high mitochondrial mutation rates under both healthy and diseased conditions, mitochondrial genomic variability is a particularly useful resource …
View article: Emergence of activation or repression in transcriptional control under a fixed molecular context
Emergence of activation or repression in transcriptional control under a fixed molecular context Open
For decades, studies have noted that transcription factors (TFs) can behave as either activators or repressors of different target genes. More recently, evidence suggests TFs can act on transcription simultaneously in positive and negative…
View article: Late-onset <i>NPM1</i> mutation in a MYC-amplified relapsed / refractory acute myeloid leukemia patient treated with gemtuzumab ozogamicin and glasdegib
Late-onset <i>NPM1</i> mutation in a MYC-amplified relapsed / refractory acute myeloid leukemia patient treated with gemtuzumab ozogamicin and glasdegib Open
Not available.
View article: Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan
Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan Open
Summary Current approaches to lineage tracing of stem cell clones require genetic engineering or rely on sparse somatic DNA variants, which are difficult to capture at single-cell resolution. Here, we show that targeted single-cell measure…
View article: Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data
Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data Open
Single cell RNA sequencing (scRNA-seq) data is widely used to study cancer cell states and their heterogeneity. However, the tumour microenvironment is usually a mixture of healthy and cancerous cells and it can be difficult to fully separ…
View article: Integrative single‐cell expression and functional studies unravels a sensitization to cytarabine‐based chemotherapy through HIF pathway inhibition in AML leukemia stem cells
Integrative single‐cell expression and functional studies unravels a sensitization to cytarabine‐based chemotherapy through HIF pathway inhibition in AML leukemia stem cells Open
Relapse remains a major challenge in the clinical management of acute myeloid leukemia (AML) and is driven by rare therapy‐resistant leukemia stem cells (LSCs) that reside in specific bone marrow niches. Hypoxia signaling maintains cells i…
View article: EPI-Clone datasets M.1-M.3: Single cell targeted DNA methylation profiling of hematopoietic stem and progenitor cells
EPI-Clone datasets M.1-M.3: Single cell targeted DNA methylation profiling of hematopoietic stem and progenitor cells Open
This is the dataset supporting the EPI-Clone manuscript: Targeted single cell methylation profiling of hematopoietic stem and progenitor cells (HSPCs) was performed with the scTAMseq method. Three experiments are included: In M.1 and M.2 H…
View article: Expression of 197 surface markers and 462 mRNAs in 15281 cells from blood and bone marrow from a young healthy donor
Expression of 197 surface markers and 462 mRNAs in 15281 cells from blood and bone marrow from a young healthy donor Open
seurat v3 objectASSAYS:AB: Antibody expression dataRNA: mRNA expression dataBOTH: Antibody and mRNA expression matrices concatenatedDIMENSIONALITY REDUCTIONProjected: Data was projected on the reference dataset MOFAUMAP coordinates.METADAT…
View article: P323: UNCOVERING SUBCLONAL METABOLIC VULNERABILITIES IN ACUTE LYMPHOBLASTIC LEUKEMIA AT SINGLE CELL RESOLUTION
P323: UNCOVERING SUBCLONAL METABOLIC VULNERABILITIES IN ACUTE LYMPHOBLASTIC LEUKEMIA AT SINGLE CELL RESOLUTION Open
Background: Despite improvements of therapy regimens for acute lymphoblastic leukemia (ALL), a significant number of patients experience relapse or do not respond to treatment, highlighting the need for continued research into the underlyi…
View article: P470: SINGLE-CELL METABOLIC MULTIOMICS TO IDENTIFY VULNERABILITIES IN ACUTE MYELOID LEUKEMIA STEM CELLS
P470: SINGLE-CELL METABOLIC MULTIOMICS TO IDENTIFY VULNERABILITIES IN ACUTE MYELOID LEUKEMIA STEM CELLS Open
Background: Acute myeloid leukemia (AML) is an aggressive myeloid malignancy, which is characterized by substantial inter and intra-patient heterogeneity. While treatment regimens lead to remission in most patients, relapse rates are high …
View article: Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia
Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia Open
Inter-patient variability and the similarity of healthy and leukemic stem cells (LSCs) have impeded the characterization of LSCs in acute myeloid leukemia (AML) and their differentiation landscape. Here, we introduce CloneTracer, a novel m…
View article: Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung
Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung Open
Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of new therapeutic approaches for lung diseases. We combined new mouse models that allow diphtheria toxin (DTA)-mediated d…
View article: Seurat SmartSeq A.10-12
Seurat SmartSeq A.10-12 Open
seurat v3 object ASSAYS: RNA: mRNA expression data DIMENSIONALITY REDUCTION projected: Data was projected on the main AML dataset from Cohorts A and B. scanorama: Data was integrated with Scanorama, using the patient as Batch key umap: u…
View article: Seurat more cells A.2
Seurat more cells A.2 Open
seurat v3 object ASSAYS: ADT: Antibody expression data RNA: mRNA expression data DIMENSIONALITY REDUCTION projAML: Data was projected on the main AML dataset from Cohorts A and B. pca: pca computed on the 2000 most variable features umap…
View article: Expression of 97 surface markers and 462 mRNAs in 31586 cells from 15 leukemic human bone marrow
Expression of 97 surface markers and 462 mRNAs in 31586 cells from 15 leukemic human bone marrow Open
Seurat v3 object ASSAYS: AB: Antibody expression data RNA: mRNA expression data integrated: Antibody and mRNA expression matrices were concatenated and data was integrated across patients using scanorama DIMENSIONALITY REDUCTION MOFA: Mu…
View article: MAIN DATASET: Seurat CloneTracer Cohort
MAIN DATASET: Seurat CloneTracer Cohort Open
seurat v3 object ASSAYS: AB: Antibody expression data RNA: mRNA expression data DIMENSIONALITY REDUCTION Projected: Data was projected on the reference dataset MOFAUMAP coordinates (Triana et al., 2021) scanorama: Data was integrated wit…
View article: REFERENCE DATASET: Expression of 97 surface markers and 462 mRNAs in 49057 cells from healthy young and healthy old bone marrow
REFERENCE DATASET: Expression of 97 surface markers and 462 mRNAs in 49057 cells from healthy young and healthy old bone marrow Open
Seurat v3 object ASSAYS: AB: Antibody expression data RNA: mRNA expression data BOTH: mRNA and Antibody expression data, concatenated integrated: Antibody and mRNA expression matrices were concatenated and data was integrated across patie…
View article: CloneTracer output
CloneTracer output Open
CloneTracer outputs tar.gz file which contains for each patient a list with the following items: patient: patient name M: matrix with mutant counts (mutationsxcells) N: matrix with reference counts (mutationsxcells) mutations_matrix: col…
View article: Seurat more cells A.9
Seurat more cells A.9 Open
seurat v3 object ASSAYS: ADT: Antibody expression data RNA: mRNA expression data DIMENSIONALITY REDUCTION projAML: Data was projected on the main AML dataset from Cohorts A and B. pca: pca computed on the 2000 most variable features uma…
View article: Expression of 97 surface markers and RNA (transcriptome wide) in 13165 cells from a healthy young bone marrow donor
Expression of 97 surface markers and RNA (transcriptome wide) in 13165 cells from a healthy young bone marrow donor Open
Seurat v3 object ASSAYS: AB: Antibody expression data RNA: mRNA expression data BOTH: Concatenated mRNA and antbody expression matrices DIMENSIONALITY REDUCTION MOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA served …