KrauthammerLab

University of Zurich & University Hospital Zurich

Our Research

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Clinical Data Science

Translational Bioinformatics

Projects

Federated Learning

Today, in every aspect of our lives, everything we do leaves a digital footprint. Health-care institutions are also increasingly …

Human Reproduction Reloaded

We are proud to be part of the UZH University Research Priority Programs (URPP) where we with the Schwank lab investigate the use of AI …

Patient Similarity Analysis

Since the early days of computing, healthcare professionals have dreamt of using the vast storage and processing powers of computers to …

Long-read sequencing - Part I

An introduction to long-read sequencing.

MRIdle

Helping reduce idle time in the USZ Radiology department

30 days All-Cause Readmission

Comparing neural-networks versus logistic regression for predicting readmission.

autoDISCERN

Assessing the quality of online health information with AI.

Drug-Drug Interactions

Novel computational method for drug-drug interaction predictions which are an important consideration for patient treatment.

Automated Reports from Xrays

Using deep learning for automatically generated medical reports describing radiological images.

Featured Publications

View All Publications

Kim F. Marquart, Ahmed Allam, Sharan Janjuha, Anna Sintsova, Lukas Villiger, Nina Frey, Michael Krauthammer, Gerald Schwank

August 2021 Nature Communications

Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens

Here we perform an extensive analysis of adenine- and cytosine base editors on a library of 28,294 lentivirally integrated genetic sequences and establish BE-DICT, an attention-based deep learning algorithm capable of predicting base editing outcomes with high accuracy.

PDF DOI

Kyriakos Schwarz, Ahmed Allam, Nicolas Perez, Michael Krauthammer

August 2021 BMC Bioinformatics

AttentionDDI: Siamese Attention-based Deep Learning method for drug-drug interaction predictions

We propose a Siamese self-attention multi-modal neural network for Drug-drug interaction (DDI) prediction that integrates multiple drug similarity measures that have been derived from a comparison of drug characteristics including drug targets, pathways and gene expression profiles.

PDF

Egle Ramelyte, Aizhan Tastanova, Zsolt Balázs, Patrick Turko, Ulrike Menzel, Emmanuella Guenova, Christian Beisel, Michael Krauthammer, Mitchell Paul Levesque, Reinhard Dummer

March 2021 Cancer Cell

Oncolytic Virotherapy Mediated Anti-Tumor Response: A Single-Cell Perspective

We investigated Talimogene laherparepvec (T-VEC) and its effect on the clinical, histological, single-cell transcriptomic and immune repertoire level using repeated fine-needle aspirates (FNAs) of injected and noninjected lesions in primary cutaneous B-cell lymphoma (pCBCL).

Project DOI

Laura Kinkead, Ahmed Allam, Michael Krauthammer

June 2020 BMC Medical Informatics and Decision Making

AutoDiscern: Rating the Quality of Online Health Information with Hierarchical Encoder Attention-based Neural Networks

To help patients find high quality health information online, we developed a Deep Learning system that evaluates the quality of online health articles. The system implements the DISCERN criteria, which checks for references, balanced writing, and more.

PDF Project DOI

Ahmed Allam, Matthias Dittberner, Anna Sintsova, Dominique Brodbeck, Michael Krauthammer

May 2020 arXiv preprint

Patient Similarity Analysis with Longitudinal Health Data

In this review, we provide a comprehensive overview of the tools and methods that are used in patient similarity analysis with longitudinal data and discuss its potential for improving clinical decision making.

PDF

Meet the Team

Principal Investigator

Michael Krauthammer

PI

Clinical Data Science, Translational Bioinformatics, Cancer Genetics

Senior Researchers and Postdocs

Ahmed Allam

Senior Researcher

Machine Learning

Zsolt Balázs

Postdoc

Bioinformatics, Cancer Genomics, Long-read sequencing, cfDNA sequencing

Farhad Nooralahzadeh

Postdoc

NLP, Machine Learning, Information Extraction, Domain Adaptation

Aron Horvath

Postdoctoral Researcher

Finding solutions for biology motivated problems from an engineering point of view, Leveraging ICT for medicine, IoT & Smart Sensors

Daniel Trejo Banos

Postdoctoral researcher

Time series analysis, Bayesian inference, Machine learning, Decision support systems for healthcare

Grad Students

Kyriakos Schwarz

PhD Student

Bioinformatics, Computational Pharmacology, Deep Learning

Ivna Ivanković

PhD Student

Bioinformatics, Cancer Genomics

Research Software Engineers

Laura Kinkead

Senior Research Software Engineer

Data Science Tooling, Reproducibility, Machine Learning

Mark McMahon

Junior Research Software Engineer

Data Science Tooling, Statistics, Machine Learning

Research Assistants

Matteo Berchier

Research Assistant

Data Science, Human Disease Monitoring, IoT & Smart Sensors

Giulia Rathmes

Physician

Epidemiology, Biostatistics, Machine Learning for Health Care, Internal Medicine

Lukas Bachmann

Physician

Internal Medicine, Health Economics, Machine Learning in Health Care

Todor Gitchev

Senior Research Assistant

Bioinformatics, Applied Mathematics, Genomics & Epigenetics, Algorithms

Administrators

Claudia Stenger

Administrative Assistant

Affiliated Researchers

Fabio Rinaldi

Research Group Leader

Jan Bartussek

Research Group Leader

Physiology and Pathophysiology, Nonlinear Dynamics, Mechanistic Modelling

Alumni

Nicolas Perez

Postdoc

Machine Learning, NLP, Image Processing

Nivitha Punniyamoorthy

BSc student

Bioinformatics, Molecular biology

Matthias Dittberner

Data Scientist

Artificial Intelligence, Causal Inference

Anna Sintsova

Postdoc

Bioinformatics, Microbiome

Leopold Franz

Research Assistant

Machine Learning for Health Care

Siyuan Luo

MSc student

Bioinformatics, Machine learning

Mascots

Globi

Senior Data Masseuse

Sleeping, Hunting birds and mice, Scratching trees

Oscar

The Last Airbender

Jumping all over the place 🦘, Knocking over Chess pieces ♟️♕, remote control 📺 and everything in front of him, Playing soccer ⚽ and chasing butterflies 🦋, Sleeping 😴 in front of laptops 💻, Participating in origami 📄🏮 and crafting activities 🧶🎨

Sebastian

Director of Box Exploration

Kinematics of toy mice, Hiding in cardboard boxes

Simon

Chief Napping Officer

Fluid dynamics, Burrowing under blankets

Teuta

Bird Flight Coordinator

Belly rubs, Staying at home, Hanging around with her dog

Job Opportunities

Ph.D. Position in A.I. for healthcare

The Krauthammer lab is looking for a motivated PhD candidate to work on projects in the intersection of healthcare, data science and …

Ahmed Allam, Michael Krauthammer

Last updated on Oct 1, 2021 Data Science, Bioinformatics

We are looking for Masters Students!

We are currently looking for Master’s students in the field of bioinformatics for the following topics Data integration in Cancer …

Michael Krauthammer, Zsolt Balázs, Daniel Trejo Banos

Last updated on Oct 1, 2021 Data Science, Bioinformatics

Our Research

Clinical Data Science

Translational Bioinformatics

Projects

Recent Posts

Featured Publications

Meet the Team

Principal Investigator

PI

Senior Researchers and Postdocs

Senior Researcher

Postdoc

Postdoc

Postdoctoral Researcher

Postdoctoral researcher

Grad Students

PhD Student

PhD Student

Research Software Engineers

Senior Research Software Engineer

Junior Research Software Engineer

Research Assistants

Research Assistant

Physician

Physician

Senior Research Assistant

Administrators

Administrative Assistant

Affiliated Researchers

Research Group Leader

Research Group Leader

Alumni

Postdoc

BSc student

Data Scientist

Postdoc

Research Assistant

MSc student

Mascots

Senior Data Masseuse

The Last Airbender

Director of Box Exploration

Chief Napping Officer

Bird Flight Coordinator

Job Opportunities

Contact