DQBM's roundup of 2019
We are UZH's Department of Quantitative Biomedicine (DQBM)
DQBM was founded on 1.1.2019. Our joint mission is to foster research and education at the interface of biomedical research, biotechnology, and computational biology, to develop the foundations of next generation precision medicine. Ultimately, our goal is to advance precision medicine for the benefit of patients.
We aim to strengthen quantitative biomedicine in Zurich
To achieve this, we take on the challenge of bridging the gap between basic research, data science and translational / clinical research groups. Specifically, we aim to strengthen quantitative biomedicine in Zurich by combining basic research and the development of novel quantitative methods for the molecular analysis of patient samples, with translational research and the development of medical informatics (Figure 1).
Ambitious goals require excellent science
To fulfil our mission, we rely on excellent science done by outstanding scientists. Below, we highlight the academic achievements of DQBM's members in 2019.
The following professorships were established at DQBM in 2019:
- Bernd Bodenmiller was appointed Associate Professor for Quantitative Cell Biology, as of 1 March 2019.
- Magdalini Polymenidou was appointed Associate Professor for Biomedicine,
in particular Molecular Pathogenesis of Neurodegeneration, as of 1 October 2019.
Grants and Fellowships
2019 was a great fundraising year for DQBM's scientists. Notably:
- Bernd Bodenmiller received a coveted ERC Consolidator Grant to analyze functional tissue motifs for precision medicine in metastatic breast cancer.
- Bernd Bodenmiller received a IMI2 Human Tumour Microenvironment Immunoprofiling Grant.
- Rolf Kümmerli received a Novartis Foundation grant for medical-biological research.
- Michael Krauthammer became project partner on the Infectious Disease Biobank Zurich Project, funded by SNF.
- Magdalini Polymenidou received an FTD Biomarker Initiative grant from AFTD to develop biomarkers for FTD patients.
DQBM's junior scientists also did a fantastic job in securing research funds:
- Hartland Jackson (Bodenmiller lab) received a Scholarship for the Next Generation of Scientists from the Cancer Research Society.
- Merrick Strotton (Bodenmiller lab) was awarded an SNF SPARK grant to develop new multiplex imaging approaches.
- Nils Eling (Bodenmiller lab) received an EMBO Postdoctoral Fellowship to analyze heterogeneity formation in breast cancer organoids.
- Özhan Özkaya (Kümmerli lab) received an UZH Forschungskredit Postdoc grant to study the ecological and evolutionary consequences of cell death on public goods cooperation in bacteria using single-cell tracking.
- Xiaokang Lun (Bodenmiller lab) received an SNF Early Postdoc.Mobility Fellowship.
Awards and Prizes
A number of DQBM members were honored for their scientific excellence:
- Bernd Bodenmiller received the Friedrich-Miescher-Award for outstanding research in the field of biochemistry.
- Bernd Bodenmiller was selected for the Analytical Scientist’s 2019 Power List Top 100.
- Julien Weber (Polymenidou lab) was voted Best Lab Manager of 2019 by Proteintech.
- Selina Niggli (Kümmerli lab) won the best oral presentation award on the topic Environmental Microbiology at the Annual Swiss Society for Microbiology Meeting 2019.
The following bright minds completed their PhD thesis in 2019:
- Chiara Rezzoagli (Kümmerli lab): 'Bacterial cooperation and the design of evolutionary robust antimicrobials'.
- Johanna Wagner *with distinction* (Bodenmiller lab): 'Single-Cell Proteomic Characterization of the Tumor and Immune Ecosystem of Human Breast Cancer with Focus on Metastatic Potential'.
- Marco Tognetti (Bodenmiller lab): 'Deciphering the signaling network landscape of breast cancer supports personalized medicine'.
- Mélanie Jambeau (Polymenidou lab): 'Understanding and Targeting Dipeptide Repeat Protein Toxicity by Immunotherapy in ALS and FTD'.
- Vito Zanotelli (Bodenmiller lab): 'Investigation of Intra- and Intercellular Signaling through Mass Cytometry Based Single Cell Methods'.
- Xiaokang Lun *with distinction* (Bodenmiller lab): 'Single-cell analysis reveals protein abundance-dependent signaling network modulations'.
Furthermore, the following MSc students graduated in 2019 with a DQBM MSc thesis:
- Martina Archetti (Kümmerli lab): 'Combining antibiotics and antivirulence compounds against Pseudomonas aeruginosa PAO1'.
- Nadine Koch (Kümmerli lab): 'Polymicrobial interactions in human serum and in the insect host Galleria mellonella'.
Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy.
Klufa J, Bauer T, Hanson B, Herbold C, Starkl P, Lichtenberger B, Srutkova D, Schulz D, Vujic I, Mohr T, Rappersberger K, Bodenmiller B, Kozakova H, Knapp S, Loy A, Sibilia M. Sci Transl Med. 2019 Dec 11;11(522). pii: eaax2693.
Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.
Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O.
Cell Rep. 2019 Oct 1;29(1):202-211.e6.
Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.
Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B.
Mol Cell. 2019 Jun 6;74(5):1086-1102.e5.
A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.
Wagner J, Rapsomaniki MA, Chevrier S, Anzeneder T, Langwieder C, Dykgers A, Rees M, Ramaswamy A, Muenst S, Soysal SD, Jacobs A, Windhager J, Silina K, van den Broek M, Dedes KJ, Rodríguez Martínez M, Weber WP, Bodenmiller B.
Cell. 2019 May 16;177(5):1330-1345.e18.
IL-8 and CXCR1 expression is associated with cancer stem cell-like properties of clear cell renal cancer.
Corrò C, Healy ME, Engler S, Bodenmiller B, Li Z, Schraml P, Weber A, Frew IJ, Rechsteiner M, Moch H. J Pathol. 2019 Jul;248(3):377-389.
In-Depth Characterization of Monocyte-Derived Macrophages using a Mass Cytometry-Based Phagocytosis Assay.
Schulz D, Severin Y, Zanotelli VRT, Bodenmiller B.
Sci Rep. 2019 Feb 13;9(1):1925.
A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry.
Damond N, Engler S, Zanotelli VRT, Schapiro D, Wasserfall CH, Kusmartseva I, Nick HS, Thorel F, Herrera PL, Atkinson MA, Bodenmiller B.
Cell Metab. 2019 Mar 5;29(3):755-768.e5.
Neural networks versus Logistic regression for 30 days all-cause readmission prediction.
Allam A, Nagy M, Thoma G, Krauthammer M.
Sci Rep. 2019 Jun 26;9(1):9277.
A novel anti-melanoma SRC-family kinase inhibitor.
Halaban R, Bacchiocchi A, Straub R, Cao J, Sznol M, Narayan D, Allam A, Krauthammer M, Mansour TS.
Oncotarget. 2019 Mar 19;10(23):2237-2251.
Positive linkage between bacterial social traits reveals that homogeneous rather than specialized behavioral repertoires prevail in natural Pseudomonas communities.
Kramer J, López Carrasco MÁ, Kümmerli R.
FEMS Microbiol Ecol. 2019 Nov 26. pii: fiz185.
Bacterial siderophores in community and host interactions.
Kramer J, Özkaya Ö, Kümmerli R.
Nat Rev Microbiol. 2019 Nov 20.
Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations.
O'Brien S, Kümmerli R, Paterson S, Winstanley C, Brockhurst MA.
Proc Biol Sci. 2019 Oct 9;286(1912):20191794.
Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia.
Sathe S, Mathew A, Agnoli K, Eberl L, Kümmerli R. Evolution Letters.
In-vivo microscopy reveals the impact of Pseudomonas aeruginosa social interactions on host colonization.
Rezzoagli C, Granato ET, Kümmerli R.
ISME J. 2019 Oct;13(10):2403-2414.
Individual- versus group-optimality in the production of secreted bacterial compounds.
Schiessl KT, Ross-Gillespie A, Cornforth DM, Weigert M, Bigosch C, Brown SP, Ackermann M, Kümmerli R.
Evolution. 2019 Apr;73(4):675-688.
Understanding policing as a mechanism of cheater control in cooperating bacteria.
Wechsler T, Kümmerli R, Dobay A.
J Evol Biol. 2019 May;32(5):412-424.
SarkoSpin: A Technique for Biochemical Isolation and Characterization of Pathological TDP-43 Aggregates.
Pérez-Berlanga M, Laferrière F, Polymenidou M. Bio-protocol.
Structural Transition, Function and Dysfunction of TDP-43 in Neurodegenerative Diseases.
Afroz T, Pérez-Berlanga M, Polymenidou M. Chimia (Aarau). 2019 May 29;73(6):380-390.
The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity.
Loughlin FE, Lukavsky PJ, Kazeeva T, Reber S, Hock EM, Colombo M, Von Schroetter C, Pauli P, Cléry A, Mühlemann O, Polymenidou M, Ruepp MD, Allain FH. Mol Cell. 2019 Feb 7;73(3):490-504.e6.
TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies and neurotoxic effects reflecting disease progression rates.
Laferrière F, Maniecka Z, Pérez-Berlanga M, Hruska-Plochan M, Gilhespy L, Hock EM, Wagner U, Afroz T, Boersema PJ, Barmettler G, Foti SC, Asi YT, Isaacs AM, Al-Amoudi A, Lewis A, Stahlberg H, Ravits J, De Giorgi F, Ichas F, Bezard E, Picotti P, Lashley T, Polymenidou M. Nat Neurosci. 2019 Jan;22(1):65-77.
Memory Decline and Its Reversal in Aging and Neurodegeneration Involve miR-183/96/182 Biogenesis.
Jawaid A, Woldemichael BT, Kremer EA, Laferriere F, Gaur N, Afroz T, Polymenidou M, Mansuy IM. Mol Neurobiol. 2019 May;56(5):3451-3462.
It is safe to say that DQBM is off to a great start. Our prognosis is that 2020 will be even more exciting, as i) we aim to expand our Faculty with a Professorship for Machine Learning in Precision Medicine, ii) we will proclaim our founding with a celebratory DQBM Founding Symposium on 19 October 2020, and iii) we will be doing more excellent science. Please stay tuned!
- The Bodenmiller group identifies prognostic single-cell populations in breast cancer lymph node metastases
- The Menze group publishes a deep learning approach to predict collateral flow in stroke patients
- The Menze group publishes Focused Decoder: a novel Detection Transformer for 3D anatomical structure detection
- Michael Krauthammer co-manages the establishment of the LOOP Zurich's new BioMedical Informatics Platform
- The Krauthammer lab and collaborators publish PRIDICT: An attention-based bidirectional recurrent neural network to predict prime editing efficiency and product purity
- The Bodenmiller group publishes a single-cell map of T cell exhaustion-associated immune environments in breast cancer
- The Menze group and collaborators publish the liver tumor segmentation benchmark
- The Bodenmiller group develops a strategy that estimates tissue spatial segregation to optimise multiplexed imaging experimental design
- DQBM's roundup of 2022
- The Polymenidou group's research is featured in EU GrantsAccess' Science Stories
- The Polymenidou group and collaborators systematically evaluate human-derived anti-poly-GA antibodies in C9orf72 disease models
- The Kümmerli group shows that collective decision-making in P. aeruginosa involves transient segregation of quorum-sensing activities across cells
- Michael Krauthammer and collaborators publish a perspective paper on the use and ethics of Digital Twins in medicine
- The Menze group publishes a new way of solving the inverse problem for brain tumor modeling
- The Kümmerli group shows that loss-of-function and regulon modulation drives diversification in quorum sensing activity patterns in P. aeruginosa
- The Menze group improves deep learning based super-resolution of 4D-flow MRI data
- Magdalini Polymenidou granted a Target ALS and Alzheimer’s Drug Discovery Foundation Award for Biomarker Research
- The Krauthammer lab is part of the newly funded DIZH innovation structure "Zurich Applied Digital Health Center"
- The Kümmerli group shows coordination of siderophore gene expression in clonal P. aeruginosa cells
- The Bodenmiller group's research is featured in EU GrantsAccess' Science Stories
- The Joller group publishes a review on the interplay between regulatory T cells and peripheral tissues
- The Menze group develops a convolutional neural network for residual motion correction in fast whole-brain MRI
- The Kümmerli group shows that enforced specialization fosters mutual cheating, but not division of labour, in P. aeruginosa
- The Bodenmiller group characterises chemokine expression and function in melanoma
- Magdalini Polymenidou receives an ERC Consolidator Grant
- The Menze group develops a deep neural network to reconstruct the 3D standing spine posture from 2D Radiographs
- The Polymenidou group publishes a protocol for the identification of RNA–RBP interactions in subcellular compartments by CLIP-Seq
- Zsolt Balázs (Krauthammer group) wins the Pfizer Research Prize 2022
- Watch Bernd Bodenmiller's video on innovative research at the Comprehensive Cancer Center Zurich (german only)
- The Kümmerli group and collaborators publish a high-throughput method to elucidate siderophores from natural Pseudomonas
- The Bodenmiller group develops a 3D IMC approach for multiplexed 3D tissue analysis at single-cell resolution
- The Menze group publishes a geometry-aware neural solver for fast Bayesian calibration of brain tumor models
- DQBM's roundup of 2021
- Michael Krauthammer's team is part of the new Innosuisse Flagship Project 'Smart Hospital'
- Prof. Dr. Nicole Joller and her team join the DQBM
- Rolf Kümmerli appointed Associate Professor for Evolution of Human Microbiomes and Pathogens
- The Krauthammer group and collaborators publish a perspective paper on analyzing patient trajectories with AI
- The Polymenidou group is awarded an SNSF Sinergia Grant together with collaborators at UZH and ETHZ
- "Bridging the Gap to Patients"
- The Polymenidou group shows that patient-derived pathological TDP-43 triggers de novo aggregation of physiological TDP-43 in host cells
- Johanna Wagner (Alumnus Bodenmiller group) wins the 2021 Ida de Pottère-Leupold and Dr. iur. Erik de Pottère Cancer Research Award
- The Kümmerli group identifies a dual role for siderophores in driving invasion dynamics in bacterial communities
- Johanna Furrer (Polymenidou group) wins the Faculty of Science's Semester Prize
- The Polymenidou group publishes a 'Spotlight' on benefits of distributing protein aggregates among microglial networks
- The Menze group publishes a deep learning-based approach to segment the claustrum in human brain MRI scans
- DQBM's wet lab groups are moving into UZI5
- The Kümmerli group uses single-cell imaging to show that S. aureus is highly competitive against P. aeruginosa on surfaces
- The Krauthammer group publishes BE-DICT: An attention-based deep learning algorithm to predict base editing outcomes
- The Krauthammer group publishes AttentionDDI: Siamese attention-based deep learning method for drug-drug interaction predictions
- The Kümmerli group shows that ecology drives evolution of social strategies in P. aeruginosa
- The Polymenidou group and collaborators show that LAG3 does not modulate α-synucleinopathies
- The Menze group and collaborators publish VerSe: A vertebrae labelling and segmentation benchmark for multi-detector CT images
- Bjoern Menze and Ender Konukoglu (ETHZ) organise 'MIDL 2022 - Medical Imaging with Deep Learning' in Zurich
- Watch the #NCCRWomen feature on Magdalini Polymenidou
- The Kümmerli group publishes their work on drivers of siderophore-mediated social interactions in natural bacterial communities
- The Polymenidou group shows that synaptic FUS accumulation triggers early misregulation of synaptic RNAs in an ALS mouse model
- Watch Michael Krauthammer's Inaugural Lecture 'Wie Daten und künstliche Intelligenz die Medizin von morgen prägen'
- The Bodenmiller group shows that mapping the breast cancer signaling network improves drug sensitivity prediction
- Watch Michael Krauthammer's 'Clinics meets Bioinformatics' Keynote on AI Support in the Clinic
- The Bodenmiller group publishes their collaborative work on dysregulation of T cell homeostasis and function in severe COVID-19
- The Krauthammer group publishes their collaborative work on AI support for ethical decision-making around resuscitation
- Watch Michael Krauthammer's NGW talk on AI in Medicine
- The Menze group publishes their review on deep learning for medical image analysis
- The Krauthammer group publishes their collaborative work on oncolytic virotherapy-mediated anti-tumor response
- The Tumor Profiler Consortium publishes their study on integrated, multi-omic, functional tumor profiling for clinical decision support
- The Bodenmiller group publishes the cytomapper package, a tool to visualise highly multiplexed imaging data in R
- The Bodenmiller group publishes their collaborative work on innate immune responses in COVID-19
- The Polymenidou group publishes their collaborative work on direct binding of importins to arginine-rich dipeptide repeat proteins
- DQBM's roundup of 2020
- The Bodenmiller group publishes their work on spatial phenotypic variability in 3D spheroids
- The Kümmerli group publishes their collaborative work on population invasion through exploitation of Pseudomonas aeruginosa public goods
- The Menze group publishes DeepVesselNet, a deep learning approach to perform vessel segmentation, centerline prediction, and bifurcation detection tasks
- The Menze group publishes a Deep Learning-enabled tool for segmentation of organs in whole-body mouse scans
- The Polymenidou group publishes their review on liquid-liquid phase separation in neurodegeneration
- The Polymenidou group receives competitive EU Consortium Grant
- Bernd Bodenmiller appointed as Dual Professor for Quantitative Biomedicine at UZH and ETH Zurich
- The Kümmerli group shows the potential of combining antivirulence drugs with antibiotics against an opportunistic human pathogen
- The Bodenmiller group receives SNF support to study primary immune response & memory in COVID-19 patients
- The Bodenmiller group publishes their collaborative work on CD4+ T Helper Cell response heterogeneity
- Prof. Dr. Bjoern Menze and his team join the DQBM
- The Kümmerli group shows how biotic and abiotic factors affect competitive dynamics between co-infecting human pathogens
- The Kümmerli group shows that competition overrides inter-species cooperation in bacteria
- The Krauthammer group publishes their work on deep learning-based multimodal fusion techniques to reduce annotation burden
- The Krauthammer Group publishes their work on machine learning models for assessing the quality of online health information.
- The Kümmerli group publishes their collaborative work on iron-driven phytopathogen control by natural rhizosphere microbiomes
- Magdalini Polymenidou awarded Franco Regli Prize 2018/2019
- The Krauthammer group publishes a data anonymization reference classification merging legal and technical considerations
- Johanna Wagner-Albrecht (Bodenmiller group) wins the 2020 Faculty of Science's Annual Thesis Award
- Michael Krauthammer shares his vision on using AI to generate medical evidence from real world health data in UZH magazine
- The Bodenmiller group publishes their review on profiling cell signaling networks at single-cell resolution
- The Bodenmiller group publishes their work linking imaging mass cytometry to breast cancer genomics
- The Kümmerli group publishes their review on harnessing bacterial interactions to manage infections
- The Bodenmiller group publishes their work on the single-cell pathology landscape of breast cancer
- The Bodenmiller group, in collaboration with the Krishnaswamy group, publishes a method to uncover axes of variation among single-cell cancer specimens
- Bernd Bodenmiller awarded ERC Consolidator Grant
- Julien Weber (Polymenidou group) wins Best Lab Manager Award 2019
- The Kümmerli group shows that homogeneous rather than specialised bacterial behavioral repertoires prevail in natural Pseudomonas communities
- The Kümmerli group publishes their review on bacterial siderophores in community and host interactions
- Bernd Bodenmiller selected for the Analytical Scientist's 2019 Power List Top 100
- The Kümmerli group publishes their work on genetic constraints of siderophore cooperation exploitation in Burkholderia cenocepacia
- Magdalini Polymenidou appointed Associate Professor for Biomedicine, in particular Molecular Pathogenesis of Neurodegeneration
- The Krauthammer group publishes their work on neural network-based models versus logistic regression for predicting readmission
- The Bodenmiller group publishes a human kinome- and phosphatome-wide screen revealing overexpression-induced effects on cancer-related signaling
- The Kümmerli group publishes their work on the impact of Pseudomonas aeruginosa social interactions on host colonization
- The Bodenmiller group finds that breast cancer ecosystems are linked to poor prognosis and immunosuppression.
- The Polymenidou group publishes their work on RNA binding of FUS
- The Polymenidou group publishes their work on TDP-43 strains
- Bernd Bodenmiller receives Friedrich Miescher Award
- The Department of Quantitative Biomedicine has been founded!