Alexander Hoffmann

Kinetics of local C3 production orchestrates neutrophil recruitment in lung injury

This study shows lung-derived C3 initiates neutrophil recruitment in pneumonia before systemic C3, highlighting local complement's role in mucosal immunity.

The metabolic cofactor Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling

This study shows Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling by providing a weak TLR4 signal.

SARS-CoV-2 nucleocapsid induces hyperinflammation and vascular leakage through the Toll-like receptor signaling axis in macrophages

This study shows the SARS-CoV-2 nucleocapsid protein drives hyperinflammation and vascular leakage in macrophages via Toll-like receptor signaling, contributing to severe COVID-19 complications.

Tensor-Based Integration of Time-Series Measurements Reveals Relationships Between Underlying Disease, Early Injury, and CD4+ Polarization in Liver Transplantation

This study integrates time-series cytokine and liver function data from liver transplant patients to identify immunological signatures linked to disease etiology, injury, and CD4+ T cell polarization affecting allograft survival.

A data-driven model of macrophage polarization states reveals an IFN macrophage signature in active Crohn's disease

The paper uses in vitro macrophage polarization data to identify an IFNγ signature in active Crohn's disease intestinal inflammation.

Reconstructing Noisy Gene Regulation Dynamics UsingExtrinsic-Noise-Driven Neural Stochastic Differential Equations

This paper introduces an END-nSDE framework to reconstruct noisy gene regulation dynamics from heterogeneous cell populations, outperforming RNNs and LSTMs in modeling extrinsic noise effects.

Distinct causes of three phenotypic hallmarks of hematopoietic aging

This study identifies distinct causes for three hematopoietic aging phenotypes using mouse models and single-cell analysis, showing HSC accumulation is NFκB-independent, functional impairment is HSC-autonomous NFκB-driven, and myeloid bias is driven by the NFκB-altered bone marrow environment.

Systems biology-enabled targeting of NF-κB and BCL2 overcomes microenvironment-mediated BH3-mimetic resistance in DLBCL.

This study identifies resistance mechanisms to BH3-mimetics in DLBCL and shows that combining BCL2 inhibition with non-canonical NF-κB inhibition overcomes microenvironment-mediated resistance.

Phased epigenetic fragility and stability accelerate the genetic evolution of B-cells

The paper shows that phased epigenetic fragility and stability in B-cells accelerate affinity maturation by modulating high-affinity outlier generation and removal during vaccine response.

IFNγ-induced memory in human macrophages is not sustained by epigenetic changes but the durability of the cytokine itself

This study shows that IFNγ-induced memory in macrophages relies on ongoing cytokine signaling, not epigenetic changes, as cytokine removal reverses enhancer formation and memory.

Synergy and antagonism in the integration of BCR and CD40 signals that control B-cell proliferation

The paper develops a mathematical model to study how BCR and CD40 signals integrate to control B-cell proliferation and selection, revealing synergistic and antagonistic interactions.

A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling

This study develops a computational workflow to assess drug effects on NFκB signaling dynamics, finding that temporal coding capacity is robust to pharmacological perturbations.

Macrophages maintain signaling fidelity in response to ligand mixtures

This paper shows macrophages maintain stimulus-response specificity through NFκB signaling even when exposed to multi-ligand mixtures, using mathematical modeling and live-cell experiments.

Temporal dose inversion properties of adaptive biomolecular circuits

The paper demonstrates temporal dose inversion in adaptive biomolecular circuits using synthetic gene circuits and identifies key parameters for this behavior.

Gene regulatory logic of the interferon-β enhancer contains multiple selectively deployed modes of transcription factor synergy

The paper identifies multiple synergy modes of transcription factors in the IFNβ enhancer that enable stimulus-specific regulation of IFNβ expression.

Examining NFκB Genomic Interactions by ChIP-seq and CUT&Tag

This study compares ChIP-seq and CUT&Tag for NFκB transcription factor genomic interactions, showing how experimental conditions affect detected interactions and their functional relevance.

Stimulus-Response signaling dynamics characterize macrophage polarization states

This study characterizes macrophage polarization states by analyzing NFκB signaling dynamics in response to different stimuli, revealing a multi-dimensional polarization landscape rather than a simple M1/M2 dichotomy.

Tracking of Lineage Mass via Quantitative Phase Imaging and Confinement in Low Refractive Index Microwells

This paper introduces a platform combining quantitative phase imaging and microwell confinement to improve lineage tracking by measuring cell mass.

Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression

The paper uses optogenetic control of RelA to show its nuclear translocation alone can activate downstream genes, revealing dynamic gene responses and the need for complex promoter models.

Distinct execution modes of a biochemical necroptosis model explain cell type-specific responses and variability to cell-death cues

As potential biomarkers, kinetic network features may be more predictive than molecule abundances

The paper shows that kinetic network features, not molecule abundances, are more predictive for drug response in a TRAIL cell death model using machine learning.

High dose IFN-β activates GAF to enhance expression of ISGF3 target genes in epithelial cells

The paper shows that high-dose IFN-β activates both ISGF3 and GAF in epithelial cells, with GAF enhancing ISGF3 target gene expression through co-localization and chromosome looping.

An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisions

The paper identifies an incoherent feedforward loop involving NFκB/RelA and A20 that determines TNF-induced necroptosis decisions based on dynamic signaling.

NFκB dynamics determine stimulus-responsive epigenomic reprogramming in macrophages

This study shows that NFκB activity dynamics determine stimulus-specific epigenomic reprogramming in macrophages by promoting de novo enhancer formation.

Input dose differentiation by NF-κB

The paper shows NF-κB differentiates cytokine input doses by using negative feedback loops to track changes in concentration rather than absolute levels.

Polypyrimidine Tract Binding Protein blocks microRNA-124 biogenesis to enforce its neuronal specific expression.

The paper shows PTBP1 inhibits miR-124 biogenesis in mESCs, creating a regulatory loop that reinforces neuronal differentiation.