Author

Bettina Sobottka

University Hospital ZurichORCID 0000-0002-0890-5248Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:human· 5 Research Focus:cell type annotation· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Approach:experimental assay· 2 Assay:proteomics· 2 Research Focus:batch correction / integration· 1 Research Focus:cell-cell communication· 1

Frequent Co-Authors

Marija BuljaniD· 3 shared Sònia TuguesiD· 3 shared Burkhard BecheriD· 2 shared Fabius WiesmanniD· 2 shared Holger MochiD· 2 shared Jonas BossartiD· 2 shared Katharina Hast-Sribike· 2 shared Markus RottmariD· 2 shared

Activity by Year

2020-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Marija BuljanORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Decoding molecular programs that define macrophage responses to tumor-derived cues

Katharina Hast-Sribike, Lukas Jonathan Haeuser, Ariadna Acedo-Terrades, Rafael Riudavets Puig, Julia Hau, Tiberiu Totu, Jonas Bossart, Angelica Brooke Patterson, Ekaterina Krymova, Vanesa Ayala‐Nunez, Markus Rottmar, Katharina Maniura‐Weber, Sònia Tugues, Marian Christoph Neidert, Bettina Sobottka, Marija Buljan

This study identifies molecular programs in macrophages stimulated by tumor-derived cues, linking them to clinically relevant TAM states and functions.

bioRxiv · Jun 9, 2026 · PreprintImmunology

RIPPLET: Mutation-Only Gene and Pathway Profiling for Precision Oncology

Fabius Wiesmann, Cassandra Litchfield, Maud Mayoux, Andreas N. WICKI, Burkhard Becher, Viktor Hendrik Koelzer, Holger Moch, Marija Buljan, Sònia Tugues, Bettina Sobottka

RIPPLET converts somatic DNA variants into gene-impact scores and pathway-perturbation profiles, outperforming multi-omic tools in identifying cancer drivers and predicting drug response without RNA data.

bioRxiv · Sep 17, 2025 · PreprintBioinformatics

Memory CD4 T cells orchestrate neoadjuvant-responsive niches in colorectal cancer liver metastases

Maud Mayoux, Gioana Litscher, Fabius Wiesmann, Marijne Vermeer, Pau Jorba Adolff, Elena Guido Vinzoni, Nicolás Gonzalo Núñez, Colin Sparano, Viola Katharina Vetter, Ekaterina Friebel, Tobias Wertheimer, Xenia Ficht, Samira Burr, Ariana Karimi, Stanislav Dergun, , Sònia Tugues

The paper identifies CD4 memory T cell networks that form therapy-responsive immune niches in colorectal cancer liver metastases, determining chemotherapy response.

bioRxiv · Aug 22, 2025 · PreprintImmunology

Delineation of signaling routes that underlie differences in macrophage phenotypic states

Tiberiu Totu, Jonas Bossart, Elana Caire, Katharina Hast-Sribike, Chen Li, Markus Rottmar, Bettina Sobottka, Guocan Yu, Vanesa Ayala‐Nunez, Marija Buljan

This study identifies key kinases and transcription factors regulating immunosuppressive macrophages and validates proteomic signatures for detecting pro-inflammatory macrophages in tumors.

NAR Molecular Medicine · Mar 29, 2025Peer-reviewedBioinformatics

SCIM: Universal Single-Cell Matching with Unpaired Feature Sets

Stefan G. Stark, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Ruedi H. Aebersold, Faisal Alquaddoomi, Jonas B. Albinus, Ilaria Alborelli, Sonali Andani, Per-Olof Attinger, Marina Bacac, Daniel Baumhoer, Beatrice Beck‐Schimmer, , Vipin T. Sreedharan

SCIM matches single-cell measurements across technologies by learning a technology-invariant latent space and applying bipartite matching, achieving high accuracy in real-world datasets.

Bioinformatics · Sep 14, 2020Peer-reviewedBioinformatics