KrauthammerLab

University of Zurich & University Hospital Zurich

Our Research

$ health = f(data) $

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.

Recent Posts

Data Traffic Control - make your data files human-friendly

Data files are the building materials we work with every day, all day. Working with them should be effortless.

Laura Kinkead

Last updated on Nov 16, 2021 3 min read Research

Lab Hike: Adlisberg

Hiking through the May fog.

Nivitha Punniyamoorthy

Last updated on Nov 16, 2021 1 min read Fun

Genomics

Genomics has and continues to transform our world and our society.

Ivna Ivanković

Last updated on Nov 16, 2021 7 min read Genomics

Lab Hike: Mount Rigi

This is how our lab gatherings look like during the pandemic.

Ivna Ivanković

Last updated on Nov 6, 2020 2 min read Fun

A Quest for Reproducible Data Science

Have you ever tried to reproduce someone else’s analysis and got different results?

Ivna Ivanković

Last updated on Nov 16, 2021 3 min read Research

Book Review: Causality, Probability and Medicine by Donald Gillies

I read Donald Gillies’ book “Causality, Probability and Medicine” a while ago and wanted to give a brief comment and overview of the …

Matthias Dittberner

Last updated on Nov 16, 2021 6 min read

Biobanking at USZ

The USZ is building a centralized biobank infracture primarily for liquid samples together with standardized processed regarding sample …

Laura Kinkead

Last updated on Mar 3, 2020 2 min read Talks

Cat videos and retrotransposons

Rambling about memes and junk DNA

Zsolt Balázs

Last updated on Nov 16, 2021 5 min read Genetics

DQBM opening

The newly formed department of Quantitative Biomedicine, which the Krauthammer lab is part of, celebrated a kick-off meeting in October …

Nicolas Perez

Last updated on Nov 16, 2021 1 min read Fun

3rd Brown Bag Lunch

Last week’s Brown Bag Lunch was hosted by the Medical Informatics Group of University of Zurich. Prof. Krauthammer provided an …

Matthias Dittberner

Last updated on Jan 7, 2020 1 min read Talks

Secure Data Exchange Using Distributed Ledger Technologies

Secure data exchange and integration is essential in medical informatics as it enables and accelerates evidence based medicine. …

Matthias Dittberner

Last updated on Dec 2, 2019 2 min read Talks

Outing Around the Lake

Whereas our first Lab outing toured the old city center, our second excursion explored Zurich’s lake. Our day began at the head …

Laura Kinkead

Last updated on Dec 2, 2019 2 min read Fun

Lab Outing: City Tour

The first group activity of our newly founded group was to take a walk in the city we all work in and get acquainted with its history …

Zsolt Balázs

Last updated on Dec 2, 2019 2 min read Fun

2nd Brown Bag Lunch

Last week, the Research Data Service Center (RDSC) of UniSpital Zürich (USZ) hosted the 2nd event of our jointly conducted series of …

Matthias Dittberner

Last updated on Dec 2, 2019 1 min read Talks

Mobile Health – Eine Technologie wird erwachsen

Michael Krauthammer

Last updated on Feb 3, 2020 1 min read

Von der Forschung profitieren auch die Patientinnen und Patienten

Das UniversitätsSpital Zürich (USZ) engagiert sich stark im Bereich Forschung und Lehre. Im Jahre 2017 standen verschiedene Projekte im …

Michael Krauthammer

Last updated on Feb 3, 2020 1 min read

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

Grad Students

Kyriakos Schwarz

PhD Student

Bioinformatics, Computational Pharmacology, Deep Learning

Ivna Ivanković

PhD Student

Bioinformatics, Cancer Genomics

Cécile Trottet

PhD Student

Machine Learning, Clinical Decision Support Systems

Xiaochen Zheng

PhD Student

Machine Learning, Longitudinal Data Analysis, Machine Perception

Research Software Engineers

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

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

Laura Kinkead

Senior Research Software Engineer

Nivitha Punniyamoorthy

BSc student

Matthias Dittberner

Data Scientist

Anna Sintsova

Postdoc

Daniel Trejo Banos

Postdoctoral researcher

Han Yuan

Visiting PhD Student

Leopold Franz

Research Assistant

Lukas Bachmann

Physician

Siyuan Luo

MSc student

Mascots

Globi

Senior Data Masseuse

Sleeping, Hunting birds and mice, Scratching trees

Iskra

Feel-good and Security Officer

Being the fastest dog in the neighborhood, Maintaining owner’s physical and mental health, Living the best day of her life every day

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 🧶🎨