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Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis.
Nature genetics, 2025
doi:10.1038/s41588-025-02081-w.
A senescent cluster in aged human hematopoietic stem cell compartment as target for senotherapy.
International journal of molecular sciences, 2025
doi:10.3390/ijms26020787.
HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling.
Genome biology, 2024
doi:10.1186/s13059-024-03450-0.
Integration of genetic and chromatin modification data pinpoints autoimmune-specific remodeling of enhancer landscape in CD4+ T cells.
Cell reports, 2024
doi:10.1016/j.celrep.2024.114810.
Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters.
Nature communications, 2024
doi:10.1038/s41467-024-51785-w.
Basis of gene-specific transcription regulation by the Integrator complex.
Molecular cell, 2024
doi:10.1016/j.molcel.2024.05.027.
APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation.
Proceedings of the National Academy of Sciences of the United States of America, 2024
doi:10.1073/pnas.2312330121.
Escape from X inactivation is directly modulated by levels of Xist non-coding RNA.
bioRxiv, 2024
doi:10.1101/2024.02.22.581559.
Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation.
Frontiers in immunology, 2024
doi:10.3389/fimmu.2024.1285798.
The remission status of AML patients post alloSCT is associated with a distinct single-cell bone marrow T cell signature.
Blood, 2024
doi:10.1182/blood.2023021815.
Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease.
bioRxiv, 2023
doi:10.1101/2023.12.26.573253.
A single-cell multi-omic and spatial atlas of B cell lymphomas reveals differentiation drives intratumor heterogeneity.
bioRxiv, 2023
doi:10.1101/2023.11.06.565756.
Transcriptional profiling unveils molecular subgroups of adaptive and maladaptive right ventricular remodeling in pulmonary hypertension.
Nature cardiovascular research, 2023
doi:10.1038/s44161-023-00338-3.
GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks.
Molecular systems biology, 2023
doi:10.15252/msb.202311627.
MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention.
Molecular psychiatry, 2023
doi:10.1038/s41380-023-01959-7.
Convolutional networks for supervised mining of molecular patterns within cellular context.
Nature methods, 2023
doi:10.1038/s41592-022-01746-2.
Current challenges in understanding the role of enhancers in disease.
Nature structural & molecular biology, 2022
doi:10.1038/s41594-022-00896-3.
Identifying a novel role for the master regulator Tal1 in the Endothelial to Hematopoietic Transition.
Scientific reports, 2022
doi:10.1038/s41598-022-20906-0.
Operation of a TCA cycle subnetwork in the mammalian nucleus.
Science advances, 2022
doi:10.1126/sciadv.abq5206.
Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL.
Molecular systems biology, 2022
doi:10.15252/msb.202110855.
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements.
Molecular systems biology, 2022
doi:10.15252/msb.202110473.
Glucose metabolism and aging of hematopoietic stem and progenitor cells.
International journal of molecular sciences, 2022
doi:10.3390/ijms23063028.
CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia.
EMBO molecular medicine, 2022
doi:10.15252/emmm.202114990.
Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting.
Nature protocols, 2021
doi:10.1038/s41596-021-00630-1.
Enhancers in disease: molecular basis and emerging treatment strategies.
Trends in molecular medicine, 2021
doi:10.1016/j.molmed.2021.07.012.
Transcription factors: bridge between cell signaling and gene regulation.
Proteomics, 2021
doi:10.1002/pmic.202000034.
Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response.
Nature cancer, 2021
doi:10.1038/s43018-021-00213-9.
Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype.
PLoS pathogens, 2021
doi:10.1371/journal.ppat.1009430.
Donor cell memory confers a metastable state of directly converted cells.
Cell stem cell, 2021
doi:10.1016/j.stem.2021.02.023.
Integrative single-cell RNA-Seq and ATAC-Seq analysis of human developmental hematopoiesis.
Cell stem cell, 2020
doi:10.1016/j.stem.2020.11.015.
Predictive features of gene expression variation reveal mechanistic link with differential expression.
Molecular systems biology, 2020
doi:10.15252/msb.20209539.
Landscape of cohesin-mediated chromatin loops in the human genome.
Nature, 2020
doi:10.1038/s41586-020-2151-x.
Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons.
Cell systems, 2020
doi:10.1016/j.cels.2020.05.003.
Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension.
Nature communications, 2020
doi:10.1038/s41467-020-15463-x.
Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy.
Nature genetics, 2020
doi:10.1038/s41588-020-0586-5.
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions.
Nature communications, 2020
doi:10.1038/s41467-019-13888-7.
Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTF.
Cell reports, 2019
doi:10.1016/j.celrep.2019.10.106.
Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML.
Blood, 2019
doi:10.1182/blood.2018862383.
TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells.
Genome research, 2019
doi:10.1101/gr.239277.118.
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline.
Nature communications, 2018
doi:10.1038/s41467-018-06353-4.
Structure meets function: How chromatin organisation conveys functionality.
2018
doi:10.1016/j.coisb.2017.01.003.
CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals.
Cell systems, 2017
doi:10.1016/j.cels.2017.10.018.
Co-expression networks reveal the tissue-specific regulation of transcription and splicing.
Genome research, 2017
doi:10.1101/gr.216721.116.
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
GENOME RESEARCH, 2017
doi:10.1101/gr.216754.116.
Haplotype-specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders.
Molecular neurodegeneration, 2017
doi:10.1186/s13024-017-0224-6.
Genetic effects on gene expression across human tissues
NATURE, 2017
doi:10.1038/nature24277.
The impact of rare variation on gene expression across tissues.
Nature, 2017
doi:10.1038/nature24267.
Dynamic landscape and regulation of RNA editing in mammals
NATURE, 2017
doi:10.1038/nature24041.
Landscape of X chromosome inactivation across human tissues.
Nature, 2017
doi:10.1038/nature24265.
Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation.
Nucleic acids research, 2016
doi:10.1093/nar/gkw683.
SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data.
Bioinformatics (Oxford, England), 2016
doi:10.1093/bioinformatics/btw127.
Data-driven hypothesis weighting increases detection power in genome-scale multiple testing.
Nature methods, 2016
doi:10.1038/nmeth.3885.
Influence of the bleaching interval on the luminosity of long-term discolored enamel-dentin discs.
Clinical oral investigations, 2016
doi:10.1007/s00784-015-1545-x.
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.
2015
doi:10.1016/j.cell.2015.07.048.
Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast.
Nucleic acids research, 2014
doi:10.1093/nar/gku100.
Extensive variation in chromatin states across humans
Science (New York, N.Y.), 2013
doi:10.1126/science.1242510.
Gene loops enhance transcriptional directionality
Science (New York, N.Y.), 2012
doi:10.1126/science.1224350.
A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast
Genome research, 2012
doi:10.1101/gr.124099.111.