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Truncating <i>RELA</i> variants drive autoinflammation and autoimmunity by impairing the negative feedback control of NF-kB Open

Baerbel Keller, Özlem Şatırer, A.A. Desrochers, Timothy J.S. Ramnarine, Mohammad Mokhtari , et al. · 2025

The NF-κB signaling pathway coordinates inflammation, cell survival, and proliferation, while restraining excessive cell death to maintain immune homeostasis. Truncating mutations in RELA , encoding the NF-κB subunit p65, have been linked …

Sample-multiplexed FACS-preprocessing of PBMCs enables scalable scRNA-seq without compromising transcriptomic or cellular integrity Open

Mohammad Mokhtari, Timothy J.S. Ramnarine, Antonia Eicher, Alexander Braunsperger, Philipp Baumert , et al. · 2025

Efficient preprocessing of peripheral blood mononuclear cells (PBMCs) for single-cell RNA-Sequencing (scRNA-seq) is crucial to ensure high sample throughput while maintaining sample integrity. In particular, when enrichment of rare immune …

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics Open

Inbal Avraham‐Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada , et al. · 2025

While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single …

Author response: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics Open

Inbal Avraham‐Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada , et al. · 2025

SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data Open

Diane Zhang, Åsa Segerstolpe, Michal Slyper, Julia Waldman, Evan Murray , et al. · 2025

Solid tumors are spatially heterogeneous in their genetic, molecular, and cellular composition, but recent spatial profiling studies have mostly charted genetic and RNA variation in tumors separately. To leverage the potential of RNA to id…

Author Correction: A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features Open

Johanna Klughammer, Daniel L. Abravanel, Åsa Segerstolpe, Timothy R. Blosser, Yury Goltsev , et al. · 2025

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics Open

Inbal Avraham‐Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada , et al. · 2025

While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single …

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics Open

Inbal Avraham‐Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada , et al. · 2025

While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single …

Author response: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics Open

Inbal Avraham‐Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada , et al. · 2025

A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features Open

Johanna Klughammer, Daniel L. Abravanel, Åsa Segerstolpe, Timothy R. Blosser, Yury Goltsev , et al. · 2024

Although metastatic disease is the leading cause of cancer-related deaths, its tumor microenvironment remains poorly characterized due to technical and biospecimen limitations. In this study, we assembled a multi-modal spatial and cellular…

BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images Open

Jaspreet Ishar, Yee Man Tam, Simon Mages, Johanna Klughammer · 2024

Spatio-molecular data and microscopy images provide complementary information, essential to study structure and function of spatially organised multicellular systems such as healthy or diseased tissues. However, aligning these two types of…

P06.02 Spatio-functional characterization of tumor-infiltrating B cells in the tumor microenvironment of cutaneous T cell lymphoma Open

Sabine Oganesian, M Funk, Admir Hadžić, Martin Kirmaier, Guido Piontek , et al. · 2024

Background The majority cutaneous T cell lymphoma (CTCL) run an indolent clinical course. However, advanced stages (>=IIB) or certain CTCL subtypes such as folliculotropic Mycosis Fungoides (FMF) and Sézary Syndrome (SS) are associated wit…

Emergence of division of labor in tissues through cell interactions and spatial cues Open

Miri Adler, Noa Moriel, Aleksandrina Goeva, Inbal Avraham‐Davidi, Simon Mages , et al. · 2023

Most cell types in multicellular organisms can perform multiple functions. However, not all functions can be optimally performed simultaneously by the same cells. Functions incompatible at the level of individual cells can be performed at …

TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics Open

Simon Mages, Noa Moriel, Inbal Avraham‐Davidi, Evan Murray, Jan Watter , et al. · 2023

Transferring annotations of single-cell-, spatial- and multi-omics data is often challenging owing both to technical limitations, such as low spatial resolution or high dropout fraction, and to biological variations, such as continuous spe…

SlideCNA: Spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data Open

Diane Zhang, Åsa Segerstolpe, Michal Slyper, Julia Waldman, Evan Murray , et al. · 2022

Solid tumors are spatially heterogeneous in their genetic, molecular and cellular composition, and this variation can be meaningful for diagnosis, prognosis and therapy. Recent spatial profiling studies have mostly charted genetic and RNA …

Emergence of division of labor in tissues through cell interactions and spatial cues Open

Miri Adler, Noa Moriel, Aleksandrina Goeva, Inbal Avraham‐Davidi, Simon Mages , et al. · 2022

Most cell types in multicellular organisms can perform multiple functions. However, not all functions can be optimally performed simultaneously by the same cells. Functions incompatible at the level of individual cells can be performed at …

TACCO: Unified annotation transfer and decomposition of cell identities for single-cell and spatial omics Open

Simon Mages, Noa Moriel, Inbal Avraham‐Davidi, Evan Murray, Fei Chen , et al. · 2022

Rapid advances in single-cell-, spatial-, and multi-omics, allow us to profile cellular ecosystems in tissues at unprecedented resolution, scale, and depth. However, both technical limitations, such as low spatial resolution and biological…

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics Open

Inbal Avraham‐Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada , et al. · 2022

While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single …

SM-Omics is an automated platform for high-throughput spatial multi-omics Open

Sanja Vicković, Britta Lötstedt, Johanna Klughammer, Simon Mages, Åsa Segerstolpe , et al. · 2022

Lattice QCD thermodynamics up to the perturbative regime Open

R. Bellwied, Sz. Borsányi, Zoltán Fodor, Jana Günther, K.‐H. Kampert , et al. · 2017

We study the thermodynamics of the quark gluon plasma with lattice simulations in the continuum limit up to 1 GeV temperature where we show that a perturbative description already applies. We calculate the effect of the presence of charm q…

Lattice QCD on nonorientable manifolds Open

Simon Mages, Bálint Tóth, Szabolcs Borsányi, Zoltán Fodor, S. D. Katz , et al. · 2017

A common problem in lattice QCD simulations on the torus is the extremely\nlong autocorrelation time of the topological charge, when one approaches the\ncontinuum limit. The reason is the suppressed tunneling between topological\nsectors. …

Lattice QCD on non-orientable manifolds Open

Simon Mages, Bálint Tóth, Szabolcs Borsányi, Z. Fodor, S. D. Katz , et al. · 2017

A common problem in lattice QCD simulations on the torus is the extremely long autocorrelation time of the topological charge, when one approaches the continuum limit. The reason is the suppressed tunneling between topological sectors. The…

Viscosity of the pure SU(3) gauge theory revisited Open

Attila Pásztor, Szabolcs Borsányi, Zoltán Fodor, Matteo Giordano, S. D. Katz , et al. · 2017

We compute the Euclidean correlators of the energy-momentum tensor in Yang-Mills theory at finite temperature at zero and finite spatial momenta with lattice simulations. We perform continuum extrapolations of these quantities using Nt = 1…

Calculation of the axion mass based on high-temperature lattice quantum chromodynamics Open

Szabolcs Borsányi, Zoltán Fodor, Jana N. Guenther, K.‐H. Kampert, S. D. Katz , et al. · 2016

Pure SU(3) Topological Susceptibility at Finite Temperature with the Wilson Flow Open

Simon Mages, Szabolcs Borsányi, Zoltán Fodor, S. D. Katz, Dániel Nógrádi , et al. · 2016

We give a summary of our preliminary results on the finite temperature topological susceptibility χ from pure SU(3) theory.The simulations use a Symanzik improved action and a gluonic definition of the topological charge with cutoff effect…

Lattice QCD for Cosmology Open

Sz. Borsányi, Zoltán Fodor, K.‐H. Kampert, S. D. Katz, T. Kawanai , et al. · 2016

We present a full result for the equation of state (EoS) in 2+1+1 (up/down, strange and charm quarks are present) flavour lattice QCD. We extend this analysis and give the equation of state in 2+1+1+1 flavour QCD. In order to describe the …

Axion cosmology, lattice QCD and the dilute instanton gas Open

Sz. Borsányi, Markus Dierigl, Zoltán Fodor, S. D. Katz, Simon Mages , et al. · 2015

Shear Viscosity from Lattice QCD Open

Simon Mages, Szabolcs Borsányi, Zoltán Fodor, Andreas Schäfer, Kálman Szabó · 2015

Understanding of the transport properties of the the quark-gluon plasma is becoming increasingly important to describe current measurements at heavy ion collisions. This work reports on recent efforts to determine the shear viscosity h in …

QPACE 2 and Domain Decomposition on the Intel Xeon Phi Open

Tilo Wettig, Paul Arts, Jacques Bloch, Peter Georg, Benjamin Glaessle , et al. · 2015

We give an overview of QPACE 2, which is a custom-designed supercomputer based on Intel Xeon Phi processors, developed in a collaboration of Regensburg University and Eurotech.We give some general recommendations for how to write high-perf…

Charmonium spectral functions from 2+1 flavour lattice QCD Open

Attila Pásztor, Szabolcs Borsányi, Stephan Dürr, Zoltán Fodor, Christian Hoelbling , et al. · 2015

Finite temperature charmonium spectral functions in the \npseudoscalar(PS) and vector(V) channels are studied in lattice \nQCD with 2+1 flavours of dynamical Wilson quarks, on fine \nisotropic lattices (with a lattice spacing of 0.057fm), …

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