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 together with the Schwank lab investigate the …

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

KrauthammerLab is taking part at the SOLA-Stafette 2023

The SOLA-Stafette is a bit of an ‘institution’ in Zürich, and again this year the KrauthammerLab is taking part! We are …

Ivna Ivanković

Last updated on Apr 21, 2023 1 min read Fun

Lab Ski Trip

2 days in Davos

Mark McMahon

Last updated on Jun 19, 2023 2 min read Fun

AI to support the early diagnosis of Systemic Sclerosis (SSc)

We recently published a joint work with the Department of Rheumatology, University Hospital of Zurich, the Department of Quantitative …

Michael Krauthammer, Farhad Nooralahzadeh

Last updated on Dec 13, 2022 1 min read Research

Zoo visit and Christmas dinner

Last week, our Lab went to the Zoo of Zurich and had a nice Christmas dinner with Fondue at “Chäsalp”. First, we spent the afternoon …

Manuel Schürch

Last updated on Jun 19, 2023 1 min read Fun

Lab Outing: Küsnacht walk

A late autumn “hike”.

Zsolt Balázs

Last updated on Jun 19, 2023 1 min read Fun

Interpretable Machine Learning

How can we better understand what our models are telling us?

Cécile Trottet

Last updated on Apr 21, 2023 5 min read Research

Bio-informatics event

Last month, the Krauthammerlab and four other bio-informatics groups (Boeva, Menze, Rätsch and Vogt labs) from the ETH, UZH and USZ …

Cécile Trottet

Last updated on Dec 15, 2022 1 min read Talks

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 Dec 9, 2022 3 min read Research

Lab Hike: Adlisberg

Hiking through the May fog.

Nivitha Punniyamoorthy

Last updated on Sep 22, 2022 1 min read Fun

Genomics

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

Ivna Ivanković

Last updated on Sep 9, 2022 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

Alexandru Garaiman, Farhad Nooralahzadeh, Carina Mihai, Nicolas Perez, Nikitas Gkikopoulos, Mike Oliver Becker, Oliver Distler, Michael Krauthammer, Britta Maurer

December 2022 British Society for Rheumatology

Vision transformer assisting rheumatologists in screening for capillaroscopy changes in systemic sclerosis: an artificial intelligence model

The first objective of this study was to implement and assess the performance and reliability of a vision transformer (ViT)-based deep-learning model, an ‘off-the-shelf’ artificial intelligence solution, for identifying distinct signs of microangiopathy in nailfold capilloroscopy (NFC) images of patients with SSc. The second objective was to compare the ViT’s analysis performance with that of practising rheumatologists.

PDF DOI

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

Meet the Team

Principal Investigator

Michael Krauthammer

PI

Clinical Data Science, Translational Bioinformatics, Cancer Genetics

Senior Researchers and Postdocs

Farhad Nooralahzadeh

Senior Researcher

NLP, Machine Learning, Information Extraction, Domain Adaptation

Manuel Schürch

Postdoc

Machine Learning, Gaussian Processes, Time Series

Zsolt Balázs

Senior Researcher

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

Ahmed Allam

Senior Researcher

Machine Learning

Amina Mollaysa

Postdoc

Machine Learning

Morteza Rohanian

Postdoc

Natural Language Processing, Clinical Machine Learning, Spoken Dialogue Processing

Sonia Difrancesco

Postdoc

Digital Health, Chatbots & Wearable sensors, Machine Learning

Grad Students

Ivna Ivanković

PhD Student

Bioinformatics, Cancer Genomics

Cécile Trottet

PhD Student

Machine Learning, Clinical Decision Support Systems

Beatrice Zanchi

Affiliated PhD Student

Electrical heart disease, Biomedical signal processing, Machine Learning, Time Series

Xiaochen Zheng

PhD Student

Machine Learning, Longitudinal Data Analysis, Machine Perception

Research Software Engineers

Mark McMahon

Senior Research Software Engineer

Data Science Tooling, Statistics, Machine Learning

Todor Gitchev

Senior Research Software Engineer

Bioinformatics, Applied Mathematics, Genomics & Epigenetics, Algorithms

Research Assistants

Giulia Rathmes

Physician

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

Noah Wolford

Master’s student

Bioinformatics, Machine Learning, Systems Biology

Wadusan Sebastianpillai

MSc student

Bioinformatics, Cancer Genomics, Liquid biopsy

Xingyu Chen

Research Assistant

Contrastive Learning, Time-series analysis, Natural Language Processing

Administrators

Claudia Stenger

Administrative Assistant

Oindrila Chakraborty

Project Manager

Project Management, Information Technology, Data Science

Affiliated Researchers

Fabio Rinaldi

Research Group Leader

Jan Bartussek

Research Group Leader

Physiology and Pathophysiology, Nonlinear Dynamics, Mechanistic Modelling

Matthias Joos

Associated Data Engineer, USZ

Alumni

Nicolas Perez

Postdoc

Kyriakos Schwarz

PhD Student

Laura Kinkead

Senior Research Software Engineer

Nivitha Punniyamoorthy

BSc student

Matteo Berchier

Research Assistant

Matthias Dittberner

Data Scientist

Anna Sintsova

Postdoc

Aron Horvath

Postdoctoral Researcher

Daniel Trejo Banos

Postdoctoral researcher

Han Yuan

Visiting PhD Student

Leopold Franz

Research Assistant

Lukas Bachmann

Physician

Melissa Ensmenger

MSc Student

Richard Affolter

Master Thesis Student

Sanghwan Kim

Research Assistant

Sebastian

Mascot

Simon

Mascot

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 🧶🎨