Selected Publications

Czernilofsky F et al (2026). Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma. Nature Cancer 7, 538-552.

Prummel KD et al (2025). Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia. Nature Communications 16, 10042.

Lobato-Moreno S et al (2025). Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics. Nature Methods 22, 1213-1225.

Mathioudaki A et al (2024). The remission status of AML patients after allo-HCT is associated with a distinct single-cell bone marrow T cell signature. Blood 143, 1269-1281.

Kamal et al (2023). GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks. Molecular Systems Biology 19, e11627.

Ibarra IL et al (2022). Comparative chromatin accessibility upon BDNF-induced neuronal activity delineates neuronal regulatory elements. Molecular Systems Biology 18, e10473.

De Teresa et al (2023). Convolutional networks for supervised mining of molecular patterns within cellular context. Nature Methods 20, 284–294.

Ranzoni AM et al (2021). Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell Stem Cell 28, 472-487.e7.

Reyes-Palomares et al (2020). Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. Nature Communications 11, 1673.

Sigalova OM et al (2020). Predictive features of gene expression variation reveal mechanistic link with differential expression. Molecular Systems Biology 16, e9539.

Berest et al (2019). Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Cell Reports 29, 3147–3159.e12.

Garg S et al (2019). Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML. Blood 134, 263–276.

Rasmussen KD et al (2019). TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Research 29, 564–575.

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