The Bodenmiller group, in collaboration with the Krishnaswamy group, publishes a method to uncover axes of variation among single-cell cancer specimens
Uncovering axes of variation among single-cell cancer specimens
-
- Phenotypic-Earth-Mover’s-Distance
- Fig. 1: The PhEMD approach. https://doi.org/10.1038/s41592-019-0689-z
This work results from a collaboration between the Bodenmiller group and the Krishnaswamy group at Yale School of Medicine.
William S. Chen and Nevena Zivanovic contributed equally to this work.
This work was co-supervised by Bernd Bodenmiller and Smita Krishnaswamy.
See Chen, Zivanovic et al, Nature Methods
More news
- 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
- DQBM's roundup of 2019
- 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!