Short bio
My Master’s research was conducted as part of the Antisense Peptide Nucleic Acids as Inhibitors of Bacterial Translation TEAM project, funded by the Foundation for Polish Science and supervised by Prof. Joanna Trylska at the University of Warsaw. My primary responsibility was to identify a specific region on the 16S rRNA of the bacterial ribosome suitable for targeting with an antisense Peptide Nucleic Acid (PNA) molecule. Additionally, I had the opportunity to participate in an internship with Prof. Andrew J. McCammon’s group in San Diego, where I advanced and expanded the Molecular Dynamics modeling required for the project.
During my PhD, I was a member of the Max Planck Research School, where I worked in Prof. Daniel Huson’s group, focusing on developing methodologies for analyzing human gut microbiome sequencing data. Alongside my research, I dedicated a significant portion of my PhD to teaching. I taught courses in Bioinformatics, Programming, and Scientific Data Visualization, among other topics, and supervised bachelor’s students throughout their thesis projects.
Over the past five years, I have been part of the Infectious Diseases research group led by Prof. Evelina Tacconelli, collaborating closely with clinicians and clinical scientists. This role has provided me with invaluable experience in translating research findings into patient care. My interdisciplinary collaborations have led to several first co-authorship publications with clinical partners, showcasing my ability to bridge the gap between scientific research and clinical application, as well as my strong communication skills in interdisciplinary settings. I joined the Infectious Diseases group in April 2019 as part of the Value-DX project, which aimed to enhance diagnostics for respiratory infections. However, the onset of the COVID-19 pandemic rapidly shifted our research priorities and transformed the field. During this time, I maintained close connections with infectious disease scientists across Europe, contributing to the adaptation of research strategies to address emerging challenges. In 2020, I played a pivotal role in designing the COVID-19-focused ORCHESTRA project, leading a multidisciplinary team from seven European institutions to investigate post-COVID sequelae.
Employment
since April 2019, Italy
Postdoctoral researcher in
Infectious Diseases group under a lead of Prof. Evelina Tacconelli, University of Verona.
Sep 2013 - Mar 2019, Germany
Ph.D. student in
Algorithms for Bioinformatics group supervised by Prof. Daniel Huson, Center for Bioinformatics Tübingen.
14 March - 20 April 2016, USA
Internship in
Prof. Mihai Pop’s group , Center for Bioinformatics and Computational Biology, University of Maryland.
July – September 2012, USA
Internship in
Prof. Andrew J. McCammon’s group, University of California San Diego.
June 2011 - September 2013, Poland
Graduate student fellowship in the TEAM project, co-founded by The Foundation for Polish Science at
Biomolecular Machines Laboratory, supervised by Prof. Joanna Trylska, Centre of New Technologies "Ochota", University of Warsaw
2009 - 2010, Poland
Internship in
Prof. Janusz Bujnicki’s group at Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, RNA structure modeling.
International projects
Management of the development of the Central Data Repository.
Development of the automated mapping of the cohort studies in Europe. Standardisation and harmonisation of the clinical data questionnaires.
Member of the coordination work package delegated to working with the data-management and statistical work-packages, and coordination of the analysis of the COVID-19 long-term-sequele cohort data.
Development of the clinical algorithm for diagnosis of the community acquired respiratory-tract infections.
Bloomy, 2021
Development of the machine-learning-based variable selection for prediction of sepsis in the hospitalized patients.
Saturn, 2015-2019
Development of the machine-learning methodology to measure impact of the antibiotic therapy on the carriage of the extended-spectrum beta-lactamases (ESBLs)
Education
Feb 2019, Germany
Ph.D. degree with
Summa cum laude in Bioinformatics,
Center for Bioinformatics, Faculty of Science, University of Tübingen.
Nov 2013, Poland
M.Sc. degree with Very Good in Macro-field of Study, Bioinformatics and Systems Biology, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw.
Sep 2011, Poland
B.Sc. degree in Macro-field of Study, Bioinformatics and Systems
Biology, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland.
Areas of specialization
developed in prof. Tacconelli group
Systematic review and meta-analysis
Medical data analysis
Natural language processing
Large language models
developed in prof. Huson group
Didactics
Human gut microbiome anlysis
Machine learning
Scientific data visualisation, static and interactive.
developed in prof. Trylska group
Antibiotic resistance mechanisms
Molecular dynamics
Selected training
Sep 2013 - Sep 2016, Germany
Ph.D. program
International Max Planck Research School From Molecules to Organisms, Max Planck Institute for Developmental Biology and University of Tübingen. IMPRS course provided a supervisorial structure Thesis-Advisory-Committee, scientific exchange opportunity during yearly symposia, and soft skills training on communication, presentation, scientific writing, and ethics in science.
During my time at the University of Tuebingen, I took courses on didactics in higher education, grant writing and networking.
22 – 27 November 2015, Belium
Biological Data Visualization Workshop, Leuven.
2 – 6 March 2015, Germany
Machine learning course by Prof. Michael Cummings