Michał Burdukiewicz

Research profile and academic CV of Michał Burdukiewicz: publications, experience, education and BioGenies news.

Biography

Hi! My name is Michał Burdukiewicz and I am passionate about bioinformatics and R.

I am currently leading the Laboratory of Bioinformatics and Multi-omics Analysis at the Medical University of Białystok. Contact me if you want to collaborate with us!

My current projects:

AmyloGraph, a comprehensive database of amyloid-amyloid interactions (doi:10.1093/nar/gkac882).
HaDeX, an integrated analytical tool for HDX-MS (maintainer Weronika Puchała).
Negative data sampling, where we show that benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data (doi:10.1093/bib/bbac343).

I am also maintaining the list of machine learning models for prediction of peptide properties (see also our article on that).

I ❤️ R!

Contact

Email GitHub ORCID LinkedIn X

Research stays

2022-05-01 – ongoing

Protein Folding and Conformational Diseases

Institute of Biotechnology and Biomedicine · Universitat Autònoma de Barcelona · Barcelona · Spain

Barcelona, Spain

2018-05-01 – 2018-05-31

Chapman Lab

Molecular, Cellular and Developmental Biology · University of Michigan · Michigan · USA

Michigan, USA

2017-10-01 – 2018-03-31

Protein Sorting

Department of Bio and Health Informatics · Denmark Technical University · Copenhagen · Denmark

Copenhagen, Denmark

Earlier records (5)

2017 1

2017-02-01 – 2017-02-28

Center for Biological Sequence Analysis

Department of Systems Biology · Denmark Technical University · Copenhagen · Denmark

Copenhagen, Denmark

2016 1

2016-03-01 – 2014-04-30

InnoProfile Research Group

Institute of Biotechnology · Brandenburg University of Technology Cottbus-Senftenberg · Senftenberg · Germany

Senftenberg, Germany

2015 1

2015-07-01 – 2015-08-30

InnoProfile Research Group

Institute of Biotechnology · Brandenburg University of Technology Cottbus-Senftenberg · Senftenberg · Germany

Senftenberg, Germany

2014 1

2014-06-01 – 2014-09-30

Institute for Medical Informatics and Biometry

Technical University Dresden · Dresden · Germany

Dresden, Germany

2013 1

2013-07-01 – 2013-09-30

InnoProfile Research Group

Institute of Biotechnology · Brandenburg University of Technology Cottbus-Senftenberg · Senftenberg · Germany

Senftenberg, Germany

Experience

2024-09-01 – ongoing

Senior researcher

Amyloid research sector · Life Sciences Centre · Vilnius University

Vilnius, Lithuania

2024-05-01 – ongoing

Assistant professor | Group leader

Bioinformatics and Multiomics Analysis Laboratory · Clinical Research Centre · Medical University of Białystok

Białystok, Poland

2022-05-01 – ongoing

Post-doc (Maria Zambrano)

Protein Folding and Conformational Diseases · Institute of Biotechnology and Biomedicine · Autonomous University of Barcelona

Barcelona, Spain

Earlier records (6)

2021 1

2021-11-01 – 2022-09-30

Senior bioinformatician

National Institute of Public Heath NIH National Research Institute

Warsaw, Poland

2020 2

2020-12-14 – 2024-04-30

Assistant professor

Metabolomics Laboratory · Clinical Research Centre · Medical University of Białystok

Białystok, Poland

2020-10-01 – 2021-06-30

Post-doc

Laboratory of Mass Spectrometry · Institute of Biochemistry and Biophysics

Warsaw, Poland

2019 1

2019-06-01 – 2021-09-30

Founder and CEO

.prot

Warsaw, Poland

2018 2

2018-10-01 – 2020-10-30

Adjunct professor

Warsaw University of Technology

Warsaw, Poland

2018-02-01 – 2023-10-30

Founder and board member

Why R? Foundation

Warsaw, Poland

Education

2015 – 2019

University of Wrocław PhD

Wrocław, Poland

Molecular biology

Thesis: n-gram analysis of biological sequences

2015-10-01 – 2019-01-15 · Wrocław, Poland

2011 – 2013

University of Wrocław MSc

Wrocław, Poland

Bioinformatics and systems biology

Thesis: Machine learning algorithms in prediction of signal peptides of heterokonts

2011-10-01 – 2013-06-15 · Wrocław, Poland

Conferences, workshops and training

55 conference and training events

2026-09-16 – 2026-09-18

Symposium of the Polish Bioinformatics Society

Poznań, Poland

Talks, posters & participation (1)

Talk
European AI Act and biomedical data: more paperwork or more governance?

Event

2025-09-24 – 2025-09-26

Functional Amyloid Meeting

Hamburg, Germany

Talks, posters & participation (1)

Poster
Aggregating amyloid resources

2025-09-15 – 2025-09-17

Symposium of the Polish Bioinformatics Society

Białystok, Poland

Talks, posters & participation (1)

Talk
DeepSkim: Towards Automated Assessment of Publication Content

Earlier activities (52)

2025 2

2025-06-22 – 2025-06-26

Metabolomics

Prague, Czech Republic

Talks, posters & participation (1)

Poster
MetaboCrates: An open-source pipeline for quality-aware analysis of targeted metabolomics data

2025-05-20 – 2025-05-23

Meeting on Non-globular proteins in the era of Machine Learning

Vilnius, Lithuania

Talks, posters & participation (1)

Poster
Comprehensive protein datasets and benchmarking for liquid-liquid phase separation

2024 3

2024-10-20 – 2024-10-24

Human Proteome Organisation World Congress

Dresden, Germany

Talks, posters & participation (1)

Poster
Confident protein datasets for liquid-liquid phase separation studies

2024-09-11 – 2024-09-13

Symposium of the Polish Bioinformatics Society

Warsaw, Poland

Talks, posters & participation (1)

Poster
Confident datasets of client, driver and negative proteins in liquid-liquid phase separation

2024-05-14 – 2024-05-17

Meeting on Non-globular proteins in the era of Machine Learning

Thessaloniki, Greece

Talks, posters & participation (1)

Poster
Confident dataset generation for the specific prediction and benchmarking of client, driver and negative proteins in liquid-liquid phase separation

2023 2

IBID

2023-10-17 – 2023-10-19

International Biotech Innovation Days

Senftenberg, Germany

Talks, posters & participation (1)

Keynote
AmyloGraph: mapping the landscape of amyloid-amyloid interactions

2023-07-05 – 2023-07-07

Meeting on Non-globular proteins in the era of Machine Learning

Bratislava, Slovakia

Talks, posters & participation (1)

Talk
AmyloGraph: A comprehensive database of amyloid-amyloid interactions

2022 5

DAaC

2022-11-24

Hasso Plattner Institute, University of Potsdam

Potsdam, Germany

Talks, posters & participation (1)

Keynote
Sampling of negative datasets

CBaB

2022-11-16

Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw

Warsaw, Poland

Talks, posters & participation (1)

Keynote
The impact of negative data sampling on antimicrobial peptide prediction

ARgs

2022-11-11

Institute of Biotechnology, Vilnius University

Vilnius, Lithuania

Talks, posters & participation (1)

Keynote
Pitfalls of machine learning for peptide analysis

Ptas

2022-10-27

Faculty of Mathematics and Computer Science, University of Wrocław

Wrocław, Poland

Talks, posters & participation (1)

Keynote
Pułapki w analizie danych peptydowych

CASUSCON

2022-07-11 – 2022-07-15

UWr-HZDR-CASUS International Conference on Advanced Systems Research CASUSCON

Wrocław, Poland

Talks, posters & participation (1)

Poster
Differentation anticancer from antimicrobial pepides using Cancergram

2021 4

EYSF

2021-10-21 – 2021-10-22

EMBO Young Scientists' Forum (EYSF)

Warsaw, Poland

Talks, posters & participation (1)

Poster
The impact of negative data sampling on antimicrobial peptides prediction

GCB

2021-09-06 – 2021-09-09

German Conference on Bioinformatics

online, Online

Talks, posters & participation (1)

Talk
The impact of negative data sampling on antimicrobial peptide prediction

PCBBE

2021-05-19 – 2021-05-21

Polish Conference on Biocybernetics and Biomedical Engineering

Warsaw, Poland

Talks, posters & participation (1)

Poster
Negative data set sampling as the source of bias in prediction of antimicrobial peptides

GfV

2021-03-24 – 2021-03-26

Meeting of the Society for Virology

online, Online

Talks, posters & participation (1)

Poster
AntiViroGram - proteome-wide prediction of antiviral peptide precursors

2019 6

SSP

2019-11-03 – 2019-11-06

Symposium on Structural Proteomics

Gottingen, Germany

Talks, posters & participation (1)

Poster
Just give me a p-value: statistical analysis of deuterium uptake curves in HDX-MS

2019-09-19 – 2019-09-21

Symposium of the Polish Bioinformatics Society

Krakow, Poland

Talks, posters & participation (1)

Talk
HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments

2019-09-19 – 2019-09-21

Symposium of the Polish Bioinformatics Society

Cracow, Poland

Talks, posters & participation (1)

Talk
Did the targeting signals for mitochondria and plastids evolve from antimicrobial peptides?

GCB

2019-09-17 – 2019-09-19

German Conference on Bioinformatics

Heidelberg, Germany

Talks, posters & participation (1)

Poster
autobiogramML: towards automated machine learning in protein function prediction

SMBE

2019-07-21 – 2019-07-25

Meeting of the Society for Molecular Biology and Evolution

Manchester, United Kingdom

Talks, posters & participation (1)

Poster
Did the targeting signals for mitochondria and plastids evolve from ancient antimicrobial peptides?

SatRday

2019-05-17 – 2019-05-18

Conference for users of the R Language

Gdańsk, Poland

Talks, posters & participation (1)

Talk
predPCR: an automated classification of qPCR curves

2018 5

PL in ML

2018-12-14 – 2018-12-17

Polish View on Machine Learning

Warsaw, Poland

Talks, posters & participation (2)

Poster
PCRedux: machine learning helper tool for sigmoid curves
Poster
PCRedux: machine learning helper tool for sigmoid curves

2018-09-05 – 2018-09-07

Symposium of the Polish Bioinformatics Society

Wrocław, Poland

Talks, posters & participation (1)

Talk
predPCR: automated classification of sigmoid curves

IBID

2018-05-23 – 2018-05-25

International Biotech Innovation Days

Senftenberg, Germany

Talks, posters & participation (1)

Workshops
Introduction to basic R

MRCL

2018-05-01

University of Michigan

Michigan, USA

Talks, posters & participation (1)

Keynote
Amyloid stretches in proteinous scaffolds of biofilms

SiL

2018-01-24

Interdisciplinary Nanoscience Center & Department of Molecular Biology and Genetics, Aarhus University

Aarhus, Denmark

Talks, posters & participation (1)

Keynote
Challenges in the computational prediction of peptide amyloidogenicity

2017 6

WBS

2017-10-09 – 2017-10-10

Wrocław Biofilm Symposium

Wrocław, Poland

Talks, posters & participation (1)

Talk
Predicting properties of biological sequences using n-gram analysis

NGP-Net

2017-08-28 – 2017-09-01

NGP-Net Symposium on non-globular proteins

Košice, Slovakia

Talks, posters & participation (1)

Talk
Challenges in the computational prediction of peptide amyloidogenicity

2017-07-21 – 2017-07-25

Intelligent Systems For Molecular Biology and the European Conference on Computational Biology

Prague, Czech Republic

Talks, posters & participation (1)

Poster
Computational and experimental validation of amyloid databases

useR!

2017-07-04 – 2017-07-07

useR!

Brussels, Belgium

Talks, posters & participation (2)

Poster
AmyloGram: prediction of amyloid sequences in R
Poster
Integrated analysis of digital PCR experiments in R

IA„A

2017-05-25

Brandenburg University of Technology Cottbus-Senftenberg

Senftenberg, Germany

Talks, posters & participation (1)

Keynote
Modelling amyloidogenic scaffolds of biofilms

qPCR dPCR & NGS

2017-04-03 – 2017-04-05

qPCR dPCR & NGS

Freising, Germany

Talks, posters & participation (1)

Talk
dpcReport: web server and software suite for unified analysis of digital PCRs and digital assays

2016 9

eRum

2016-10-12 – 2016-10-14

European R Users Meeting

Poznań, Poland

Talks, posters & participation (1)

Poster
N-gram analysis of biological sequences in R

2016-09-28 – 2016-09-30

Symposium of the Polish Bioinformatics Society

Białystok, Poland

Talks, posters & participation (1)

Talk
SignalHsmm: prediction of malarial signal peptides

BIO

2016-09-13 – 2016-09-16

Congress of the Polish Biochemistry, Cell Biology, Biophysics and Bioinformatics

Wrocław, Poland

Talks, posters & participation (1)

Poster
AmyloGram: analysis and prediction of amyloids using n-grams

GCB

2016-09-12 – 2016-09-15

German Conference on Bioinformatics

Berlin, Germany

Talks, posters & participation (1)

Talk
Prediction of malarial signal peptides

ECCB

2016-09-03 – 2016-09-07

European Conference on Computational Biology

Hague, Netherlands

Talks, posters & participation (1)

Talk
AmyloGram: a novel predictor of amyloidogenicity

ESCS

2016-09-03

European Student Council Symposium

Hague, Netherlands

Talks, posters & participation (1)

Poster
AmyloGram: a novel predictor of amyloidogenicity

CHARME

2016-06-21 – 2016-06-22

CHARME of standardisation in life sciences

Warsaw, Poland

Talks, posters & participation (1)

Poster
Biogram: standardization of biological n-gram analysis in R

BIT

2016-06-16 – 2016-06-18

BioInformatics in Toruń

Toruń, Poland

Talks, posters & participation (1)

Poster
AmyloGram: n-gram analysis of amyloids

IBID

2016-06-01 – 2016-06-02

Innovation Forum Senftenberg

Senftenberg, Germany

Talks, posters & participation (2)

Poster
dpcR: web server and R package for analysis of digital PCR experiments
Talk
biogram: a toolkit for biological n-gram analysis

2015 5

Potsdam Days

2015-11-01 – 2015-11-02

Potsdam Days on Bioanalysis

Potsdam, Germany

Talks, posters & participation (1)

Poster
dpcReport -- Mobile-Health analysis framework

GCB

2015-09-27 – 2015-09-30

German Conference on Bioinformatics

Dortmund, Germany

Talks, posters & participation (1)

Poster
N-gram analysis of amyloid data

2015-09-17 – 2015-09-19

Symposium of the Polish Bioinformatics Society

Lublin, Poland

Talks, posters & participation (1)

Poster
biogram: a toolkit for n-gram analysis

RECOMB

2015-04-12 – 2015-04-15

International Conference on Research in Computational Molecular Biology

Warsaw, Poland

Talks, posters & participation (1)

Poster
Predicting eukaryotic signal peptides using hidden Markov models

qPCR dPCR & NGS

2015-03-23 – 2015-03-27

qPCR dPCR & NGS

Freising-Weihenstephan, Germany

Talks, posters & participation (2)

Poster
The dpcR Package – a Framework for Analysis and Visualization of Digital PCR Experiments
Poster
Methods of Comparing Digital PCR Experiments

2014 4

IMB - Seminar

2014-10-09

Technical University Dresden

Dresden, Germany

Talks, posters & participation (1)

Keynote
Prediction of eukaryotic signal peptides using hidden semi-Markov models

DGHM & VAAM

2014-10-05 – 2014-10-08

Joint Microbiology & Infection Conference of the German Society for Hygiene and Microbiology and the Association of General and Applied Microbiology

Dresden, Germany

Talks, posters & participation (1)

Poster
Prevalence of Shiga toxin-producing, enterohemorrhagic and enteropathogenic Escherichia coli – a systematic review

BIO

2014-09-09 – 2014-09-12

Congress of the Polish Biochemistry, Cell Biology, Biophysics and Bioinformatics

Warsaw, Poland

Talks, posters & participation (1)

Talk
Signal peptide prediction using hidden Markov models

qPCR dPCR & NGS

2014-09-09 – 2014-09-10

qPCR dPCR & NGS

Lyon, France

Talks, posters & participation (1)

Poster
dpcR: an R package for the analysis of digital PCR

Undated 1

Event

ongoing

BioHackaton

Berlin, Germany

Talks, posters & participation (1)

Workshops

Publications

69 publications listed · most recent first

Databases of liquid–liquid phase separation proteins and condensates

Current Opinion in Structural Biology · 2026-07-21

Authors & citation details

Carlos Pintado‐Grima, Michał Jan Burdukiewicz, Salvador Ventura

Authorship: coauthor

https://doi.org/10.1016/j.sbi.2026.103341

Application of class–balancing algorithms to diverse plasma metabolomics datasets using brain tumor as an example

bioRxiv (Cold Spring Harbor Laboratory) · 2026-07-07

Authors & citation details

Adrian Godlewski, Krzysztof Sołowiej, Patrycja Mojsak, Joanna Godzień, Julia Siemińska, Adam Jacek Kretowski, Tomasz Łysoń, Michał Jan Burdukiewicz, Karol Adam Kamiński, Michał Ciborowski

Authorship: coauthor

https://doi.org/10.64898/2026.07.02.735756

Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium

Microbiome · 2026-03-28

Authors & citation details

Rafał Kolenda, Marwa M. Hassan, Ainhoa Arrieta-Gisasola, Rebecca Ansorge, Katarzyna Sidorczuk, Luke Acton, Gaetan J. A. Thilliez, Dave Baker, Michał Jan Burdukiewicz, Mark D. Stares, Hilary P. Browne, Gwénaëlle Le Gall, Mark P. Stevens, Trevor D. Lawley, Andreas J. Bäumler, Roberto La Ragione, Falk Hildebrand, Robert A. Kingsley

Authorship: coauthor

https://doi.org/10.1186/s40168-025-02322-4

Earlier publications (66)

2026 4

Additional file 3 of Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium

Figshare · 2026-03-28

Authors & citation details

Rafał Kolenda, Marwa M. Hassan, Ainhoa Arrieta-Gisasola, Rebecca Ansorge, Katarzyna Sidorczuk, Luke Acton, Gaetan J. A. Thilliez, Dave Baker, Michał Jan Burdukiewicz, Mark D. Stares, Hilary P. Browne, Gwenaelle Le Gall, Mark P. Stevens, Trevor D. Lawley, Andreas J. Bäumler, Roberto La Ragione, Falk Hildebrand, Robert A. Kingsley

Authorship: coauthor

https://doi.org/10.6084/m9.figshare.31969200

HaDeX2: multi-dimensional analysis of hydrogen–deuterium exchange mass spectrometry data

Bioinformatics · 2026-02-28

Authors & citation details

Weronika Puchała, Krystyna Grzesiak, Dominik Rafacz, Michał Kistowski, Jochem H. Smit, Julien Marcoux, Michał Dadlez, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.1093/bioinformatics/btag128

hadexversum/HRaDeX: HRaDeX 1.0 release

Zenodo (CERN European Organization for Nuclear Research) · 2026-02-20

Authors & citation details

Weronika Puchała, Michał Jan Burdukiewicz

Authorship: last

https://doi.org/10.5281/zenodo.18718114

HaDeX2 1.0: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Zenodo (CERN European Organization for Nuclear Research) · 2026-02-09

Authors & citation details

Michał Jan Burdukiewicz, Weronika Puchała

Authorship: first

https://doi.org/10.5281/zenodo.18543702

2025 4

Comprehensive protein datasets and benchmarking for liquid–liquid phase separation studies

Genome biology · 2025-07-08

Authors & citation details

Carlos Pintado‐Grima, Oriol Bárcenas, Valentín Iglesias, Michał Jan Burdukiewicz, Salvador Ventura

Authorship: coauthor, corresponding

https://doi.org/10.1186/s13059-025-03668-6

Experimental methods for studying amyloid cross‐interactions

Protein Science · 2025-05-19

Authors & citation details

Aleksandra A. Kalitnik, Anna Lassota, Oliwia Polańska, Marlena Gąsior‐Głogowska, Monika Szefczyk, Agnieszka Barbach, Jarosław Chilimoniuk, Izabela Jęśkowiak, Alicja W. Wojciechowska, Jakub Wiktor Wojciechowski, Natalia Szulc, Małgorzata Kotulska, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.1002/pro.70151

HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX–MS Data

Journal of Proteome Research · 2025-03-19

Authors & citation details

Weronika Puchała, Michał Kistowski, Lilia Zhukova, Michał Jan Burdukiewicz, Michał Dadlez

Authorship: coauthor

https://doi.org/10.1021/acs.jproteome.4c00700

Comparative analysis of anticoagulant influence on PMI estimation based on porcine blood metabolomics profile measured using GC-MS

Frontiers in Molecular Biosciences · 2025-01-07

Authors & citation details

Patrycja Mojsak, Paulina Samczuk, Michał Jan Burdukiewicz, Jarosław Chilimoniuk, Krystyna Grzesiak, Karolina Pietrowska, Anna Niemcunowicz‐Janica, Adam Jacek Kretowski, Michał Ciborowski, Michał Szeremeta

Authorship: coauthor

https://doi.org/10.3389/fmolb.2024.1400622

2024 9

Scientific reasoning driven by influential data: resuscitate dfstat !

bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-30

Authors & citation details

Andrej‐Nikolai Spiess, Stefan Rödiger, Matthias Schaks, Michał Jan Burdukiewicz, Joel Tellinghuisen

Authorship: coauthor

https://doi.org/10.1101/2024.10.30.621016

Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation

Computational and Structural Biotechnology Journal · 2024-10-29

Authors & citation details

Valentín Iglesias, Jarosław Chilimoniuk, Carlos Pintado‐Grima, Oriol Bárcenas, Salvador Ventura, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.1016/j.csbj.2024.10.047

ML-based clinical decision support models based on metabolomics data

TrAC Trends in Analytical Chemistry · 2024-06-18

Authors & citation details

Michał Jan Burdukiewicz, Jarosław Chilimoniuk, Krystyna Grzesiak, Adam Jacek Kretowski, Michał Ciborowski

Authorship: first

https://doi.org/10.1016/j.trac.2024.117819

adhesiomeR: a tool for Escherichia coli adhesin classification and analysis

BMC Genomics · 2024-06-17

Authors & citation details

Katarzyna Sidorczuk, Michał Jan Burdukiewicz, Joachim Fritscher, Robert A. Kingsley, Peter Schierack, Falk Hildebrand, Rafał Kolenda

Authorship: coauthor

https://doi.org/10.1186/s12864-024-10525-6

Structural information in therapeutic peptides: Emerging applications in biomedicine

FEBS Open Bio · 2024-06-14

Authors & citation details

Valentín Iglesias, Oriol Bárcenas, Carlos Pintado‐Grima, Michał Jan Burdukiewicz, Salvador Ventura

Authorship: coauthor, corresponding

https://doi.org/10.1002/2211-5463.13847

Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation

Nucleic Acids Research · 2024-05-13

Authors & citation details

Oriol Bárcenas, Mateusz Zalewski, Valentín Iglesias, Carlos Pintado‐Grima, Grzegorz Firlik, Michał Jan Burdukiewicz, Sebastian Kmiecik, Salvador Ventura

Authorship: coauthor

https://doi.org/10.1093/nar/gkae382

Challenges and opportunities in processing NanoString nCounter data

Computational and Structural Biotechnology Journal · 2024-04-30

Authors & citation details

Jarosław Chilimoniuk, Anna Erol, Stefan Rödiger, Michał Jan Burdukiewicz

Authorship: last

https://doi.org/10.1016/j.csbj.2024.04.061

Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · 2024-03-06

Authors & citation details

Natalia Szulc, Marlena Gąsior‐Głogowska, P. Żyłka, Monika Szefczyk, Jakub Wiktor Wojciechowski, Andrzej Marek Żak, Witold Dyrka, Aleksandra Kaczorowska, Michał Jan Burdukiewicz, Mounir Tarek, Małgorzata Kotulska

Authorship: coauthor

https://doi.org/10.1016/j.saa.2024.124094

imputomics: web server and R package for missing values imputation in metabolomics data

Bioinformatics · 2024-02-19

Authors & citation details

Jarosław Chilimoniuk, Krystyna Grzesiak, Jakub Kała, Dominik Nowakowski, Adam Jacek Kretowski, Rafał Kolenda, Michał Ciborowski, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.1093/bioinformatics/btae098

2023 6

A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms

Nucleic Acids Research · 2023-10-28

Authors & citation details

Aleksandra Elzbieta Badaczewska-Dawid, Carlos Pintado‐Grima, Javier García‐Pardo, Michał Jan Burdukiewicz, Valentín Iglesias, Sebastian Kmiecik, Salvador Ventura

Authorship: coauthor

https://doi.org/10.1093/nar/gkad942

Prediction of protein subplastid localization and origin with PlastoGram

Scientific Reports · 2023-05-24

Authors & citation details

Katarzyna Sidorczuk, Przemysław Gagat, Jakub Kała, Henrik Nielsen, Filip Pietluch, Paweł Mackiewicz, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.1038/s41598-023-35296-0

Genomic characterization of enterohaemolysin-encoding haemolytic Escherichia coli of animal and human origin

Microbial Genomics · 2023-04-27

Authors & citation details

Katarzyna Sidorczuk, Adrianna Aleksandrowicz, Michał Jan Burdukiewicz, Robert A. Kingsley, Rafał Kolenda

Authorship: coauthor

https://doi.org/10.1099/mgen.0.000999

VisQualdex: a Comprehensive Guide to Good Data Visualization

Scientific Visualization · 2023-04-01

Authors & citation details

Jan Sawicki, Michał Jan Burdukiewicz

Authorship: last

https://doi.org/10.26583/sv.15.1.11

Testing Antimicrobial Properties of Selected Short Amyloids

International Journal of Molecular Sciences · 2023-01-02

Authors & citation details

Przemysław Gagat, Anna Duda-Madej, Michał Ostrówka, Filip Pietluch, Paweł Mackiewicz, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.3390/ijms24010804

aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation

Database · 2023-01-01

Authors & citation details

Carlos Pintado‐Grima, Oriol Bárcenas, Valentín Iglesias, Jaime Santos, Zoe Manglano-Artuñedo, Irantzu Pallarès, Michał Jan Burdukiewicz, Salvador Ventura

Authorship: coauthor, corresponding

https://doi.org/10.1093/database/baad084

2022 6

AmyloGraph: a comprehensive database of amyloid–amyloid interactions

Nucleic Acids Research · 2022-10-16

Authors & citation details

Michał Jan Burdukiewicz, Dominik Rafacz, Agnieszka Barbach, Laura Bąkała, Anna Lassota, Jakub Stecko, Natalia Szymańska, Natalia Szymańska, Natalia Szymańska, Jakub Wiktor Wojciechowski, Dominika Kozakiewicz, Natalia Szulc, Jarosław Chilimoniuk, Izabela Jęśkowiak, Marlena Gąsior‐Głogowska, Małgorzata Kotulska

Authorship: first, corresponding

https://doi.org/10.1093/nar/gkac882

Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data

Briefings in Bioinformatics · 2022-08-21

Authors & citation details

Katarzyna Sidorczuk, Przemysław Gagat, Filip Pietluch, Jakub Kała, Dominik Rafacz, Laura Bąkała, Jadwiga Słowik, Rafał Kolenda, Stefan Rödiger, Legana C H W Fingerhut, Ira Cooke, Paweł Mackiewicz, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.1093/bib/bbac343

PCRedux: A Quantitative PCR Machine Learning Toolkit

The Journal of Open Source Software · 2022-08-21

Authors & citation details

Michał Jan Burdukiewicz, Andrej‐Nikolai Spiess, Dominik Rafacz, Благодатских Константин Александрович, Stefan Rödiger

Authorship: first

https://doi.org/10.21105/joss.04407

Intracellular Protein S-Nitrosylation—A Cells Response to Extracellular S100B and RAGE Receptor

Biomolecules · 2022-04-20

Authors & citation details

Monika Zaręba-Kozioł, Michał Jan Burdukiewicz, Aleksandra Wysłouch‐Cieszyńska

Authorship: coauthor

https://doi.org/10.3390/biom12050613

VisQualdex -- the comprehensive guide to good data visualization

arXiv (Cornell University) · 2022-01-21

Authors & citation details

Michał Jan Burdukiewicz

Authorship: last

https://doi.org/10.48550/arxiv.2201.08684

The dynamic landscape of peptide activity prediction

Computational and Structural Biotechnology Journal · 2022-01-01

Authors & citation details

Oriol Bárcenas, Carlos Pintado‐Grima, Katarzyna Sidorczuk, Felix Teufel, Henrik Nielsen, Salvador Ventura, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.1016/j.csbj.2022.11.043

2021 8

Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of Escherichia coli

Microbial Genomics · 2021-12-23

Authors & citation details

Rafał Kolenda, Katarzyna Sidorczuk, Mateusz Noszka, Adrianna Aleksandrowicz, Muhammad Moman Khan, Michał Jan Burdukiewicz, Peter Schierack

Authorship: coauthor

https://doi.org/10.1099/mgen.0.000743

Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild‐type rats

Protein Science · 2021-06-02

Authors & citation details

Line Friis Bakmann Christensen, Michał Jan Burdukiewicz, Florian‐Alexander Herbst, Henrik Kjeldal, Morten Simonsen Dueholm, Daniel E. Otzen

Authorship: coauthor

https://doi.org/10.1002/pro.4137

Variability of Amyloid Propensity in Imperfect Repeats of CsgA Protein of Salmonella enterica and Escherichia coli

International Journal of Molecular Sciences · 2021-05-12

Authors & citation details

Natalia Szulc, Marlena Gąsior‐Głogowska, Jakub Wiktor Wojciechowski, Monika Szefczyk, Andrzej Marek Żak, Michał Jan Burdukiewicz, Małgorzata Kotulska

Authorship: coauthor, corresponding

https://doi.org/10.3390/ijms22105127

Bioinformatics methods for identification of amyloidogenic peptides show robustness to misannotated training data

Scientific Reports · 2021-04-26

Authors & citation details

Natalia Szulc, Michał Jan Burdukiewicz, Marlena Gąsior‐Głogowska, Jakub Wiktor Wojciechowski, Jarosław Chilimoniuk, Paweł Mackiewicz, Tomas Šneideris, Vytautas Smirnovas, Małgorzata Kotulska

Authorship: coauthor, corresponding

https://doi.org/10.1038/s41598-021-86530-6

Functional amyloids in the microbiomes of a rat Parkinson’s disease model and wild-type rats

bioRxiv (Cold Spring Harbor Laboratory) · 2021-04-05

Authors & citation details

Line Friis Bakmann Christensen, Michał Jan Burdukiewicz, Florian‐Alexander Herbst, Henrik Kjeldal, Morten Simonsen Dueholm, Daniel E. Otzen

Authorship: coauthor

https://doi.org/10.1101/2021.03.31.438001

countfitteR: efficient selection of count distributions to assess DNA damage

Annals of Translational Medicine · 2021-04-01

Authors & citation details

Jarosław Chilimoniuk, Alicja Gosiewska, Jadwiga Słowik, Romano Weiss, Peter Markus Deckert, Stefan Rödiger, Michał Jan Burdukiewicz

Authorship: last, corresponding

https://doi.org/10.21037/atm-20-6363

PCRedux: A Data Mining and Machine Learning Toolkit for qPCR Experiments

bioRxiv (Cold Spring Harbor Laboratory) · 2021-04-01

Authors & citation details

Michał Jan Burdukiewicz, Andrej‐Nikolai Spiess, Dominik Rafacz, Благодатских Константин Александрович, Jim F. Huggett, Matthew N. McCall, Peter Schierack, Stefan Rödiger

Authorship: first

https://doi.org/10.1101/2021.03.31.437921

MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets

Journal of Proteome Research · 2021-03-04

Authors & citation details

Pieter Verschaffelt, Tim Van Den Bossche, Wassim Gabriel, Michał Jan Burdukiewicz, Alessio Soggiù, Lennart Martens, Lennart Martens, Bernhard Y. Renard, Henning Schiebenhoefer, Bart Mesuere

Authorship: coauthor

https://doi.org/10.1021/acs.jproteome.0c00926

2020 7

MIRRAGGE – Minimum Information Required for Reproducible AGGregation Experiments

Frontiers in Molecular Neuroscience · 2020-11-27

Authors & citation details

Pedro Miguel Martins, Susanna Navarro, Alexandra Silva, Maria Filipa Pinto, Zsuzsa Sárkány, Francisco Figueiredo, Pedro José Barbosa Pereira, Francisca Pinheiro, Zuzana Bednáriková, Michał Jan Burdukiewicz, Oxana V. Galzitskaya, Zuzana Gažová, Cláudio M. Gomes, Annalisa Pastore, Louise C. Serpell, Rostislav Škrabana, Vytautas Smirnovas, Mantas Žiaunys, Daniel E. Otzen, Salvador Ventura, Sandra Macedo‐Ribeiro

Authorship: coauthor

https://doi.org/10.3389/fnmol.2020.582488

Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens

Applied and Environmental Microbiology · 2020-11-02

Authors & citation details

Rafał Kolenda, Michał Jan Burdukiewicz, Adrianna Aleksandrowicz, Aamir Ali, István Szabó, Karsten Tedin, Josefin Bartholdson Scott, Peter Schierack

Authorship: coauthor

https://doi.org/10.1128/aem.02177-20

CancerGram: An Effective Classifier for Differentiating Anticancer from Antimicrobial Peptides

Pharmaceutics · 2020-10-31

Authors & citation details

Michał Jan Burdukiewicz, Katarzyna Sidorczuk, Dominik Rafacz, Filip Pietluch, Laura Bąkała, Jadwiga Słowik, Przemysław Gagat

Authorship: first

https://doi.org/10.3390/pharmaceutics12111045

Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram

International Journal of Molecular Sciences · 2020-06-17

Authors & citation details

Michał Jan Burdukiewicz, Katarzyna Sidorczuk, Dominik Rafacz, Filip Pietluch, Jarosław Chilimoniuk, Stefan Rödiger, Przemysław Gagat

Authorship: first

https://doi.org/10.3390/ijms21124310

HaDeX: an R package and web-server for analysis of data from hydrogen–deuterium exchange mass spectrometry experiments

Bioinformatics · 2020-06-16

Authors & citation details

Weronika Puchała, Michał Jan Burdukiewicz, Michał Kistowski, Katarzyna Dąbrowska, Aleksandra Elzbieta Badaczewska-Dawid, Dominik Cysewski, Michał Dadlez

Authorship: coauthor

https://doi.org/10.1093/bioinformatics/btaa587

Classification of dead and living microalgae Chlorella vulgaris by bioimage informatics and machine learning

Algal Research · 2020-04-28

Authors & citation details

Ronny Reimann, Michał Jan Burdukiewicz, Peter Schierack, Stefan Rödiger

Authorship: coauthor

https://doi.org/10.1016/j.algal.2020.101908

Modeling Amyloid Aggregates using Machine Learning and Structural Predictions

Biophysical Journal · 2020-02-01

Authors & citation details

Małgorzata Kotulska, Jakub Wiktor Wojciechowski, Michał Jan Burdukiewicz

Authorship: last

https://doi.org/10.1016/j.bpj.2019.11.225

2019 3

Simultaneous detection and quantification of DNA and protein biomarkers in spectrum of cardiovascular diseases in a microfluidic microbead chip

Analytical and Bioanalytical Chemistry · 2019-11-01

Authors & citation details

Franziska Dinter, Michał Jan Burdukiewicz, Peter Schierack, Gregory Dame, Stefan Rödiger

Authorship: coauthor

https://doi.org/10.1007/s00216-019-02199-x

Phylogenetic grouping and biofilm formation of multidrug resistant Escherichia coli isolates from humans, animals and food products in South-West Nigeria

Scientific African · 2019-09-12

Authors & citation details

Olugbenga Adekunle Olowe, Olusolabomi Jose Adefioye, Titilayo Adenike Ajayeoba, Aamir Ali, Michał Jan Burdukiewicz, Stefan Rödiger, Peter Schierack

Authorship: coauthor

https://doi.org/10.1016/j.sciaf.2019.e00158

HaDeX – an R package and web-server for analysis of data from hydrogen-deuterium exchange-mass spectrometry experiments

2019-08-30

Authors & citation details

Weronika Puchała, Michał Jan Burdukiewicz, Michał Kistowski, Katarzyna Dąbrowska, Aleksandra Elzbieta Badaczewska-Dawid, Dominik Cysewski, Michał Dadlez

Authorship: coauthor

https://doi.org/10.7490/f1000research.1117436.1

2018 5

Prediction of Signal Peptides in Proteins from Malaria Parasites

International Journal of Molecular Sciences · 2018-11-22

Authors & citation details

Michał Jan Burdukiewicz, Piotr Sobczyk, Jarosław Chilimoniuk, Przemysław Gagat, Paweł Mackiewicz

Authorship: first

https://doi.org/10.3390/ijms19123709

Algorithms for automated detection of hook effect-bearing amplification curves

Biomolecular Detection and Quantification · 2018-10-16

Authors & citation details

Michał Jan Burdukiewicz, Andrej‐Nikolai Spiess, Благодатских Константин Александрович, Peter Schierack, Stefan Rödiger

Authorship: first

https://doi.org/10.1016/j.bdq.2018.08.001

Adhesion of Salmonella to Pancreatic Secretory Granule Membrane Major Glycoprotein GP2 of Human and Porcine Origin Depends on FimH Sequence Variation

Frontiers in Microbiology · 2018-08-22

Authors & citation details

Rafał Kolenda, Michał Jan Burdukiewicz, Stefan Rödiger, István Szabó, Alexander Böhm, Ulrike Gerber, Dirk Roggenbuck, Peter Schierack

Authorship: coauthor

https://doi.org/10.3389/fmicb.2018.01905

Role of recombination and faithfulness to partner in sex chromosome degeneration

Scientific Reports · 2018-06-06

Authors & citation details

Dorota Mackiewicz, Michał Jan Burdukiewicz, Paweł Błażej

Authorship: coauthor

https://doi.org/10.1038/s41598-018-27219-1

PhyMet 2 : a database and toolkit for phylogenetic and metabolic analyses of methanogens

Environmental Microbiology Reports · 2018-04-06

Authors & citation details

Michał Jan Burdukiewicz, Przemysław Gagat, Sławomir Jan Jabłoński, Jarosław Chilimoniuk, Michał Gaworski, Paweł Mackiewicz, Marcin Łukaszewicz

Authorship: first

https://doi.org/10.1111/1758-2229.12648

2017 3

Genotypic and Phenotypic Characteristics Associated with Biofilm Formation by Human Clinical Escherichia coli Isolates of Different Pathotypes

Applied and Environmental Microbiology · 2017-10-06

Authors & citation details

Alexander Böhm, Michał Jan Burdukiewicz, Aamir Ali, Dirk Roggenbuck, Stefan Rödiger, Peter Schierack

Authorship: coauthor

https://doi.org/10.1128/aem.01660-17

Amyloidogenic motifs revealed by n-gram analysis

Scientific Reports · 2017-10-05

Authors & citation details

Michał Jan Burdukiewicz, Piotr Sobczyk, Stefan Rödiger, Anna Duda-Madej, Paweł Mackiewicz, Małgorzata Kotulska

Authorship: first

https://doi.org/10.1038/s41598-017-13210-9

Enabling reproducible real-time quantitative PCR research: the RDML package

Bioinformatics · 2017-08-24

Authors & citation details

Stefan Rödiger, Michał Jan Burdukiewicz, Andrej‐Nikolai Spiess, Благодатских Константин Александрович

Authorship: coauthor

https://doi.org/10.1093/bioinformatics/btx528

2016 7

System-specific periodicity in quantitative real-time polymerase chain reaction data questions threshold-based quantitation

Scientific Reports · 2016-12-13

Authors & citation details

Andrej‐Nikolai Spiess, Stefan Rödiger, Michał Jan Burdukiewicz, Joel Tellinghuisen

Authorship: coauthor

https://doi.org/10.1038/srep38951

AmyloGram: a novel predictor of amyloidogenicity

2016-09-01

Authors & citation details

Michał Jan Burdukiewicz, Piotr Sobczyk, Stefan Rödiger, Paweł Mackiewicz, Małgorzata Kotulska

Authorship: first, corresponding

https://doi.org/10.7490/f1000research.1112970.1

Prediction of amyloidogenicity based on the n-gram analysis

2016-08-24

Authors & citation details

Michał Jan Burdukiewicz, Piotr Sobczyk, Stefan Rödiger, Anna Duda-Madej, Paweł Mackiewicz, Małgorzata Kotulska

Authorship: first

https://doi.org/10.7287/peerj.preprints.2390v1

Prediction of amyloidogenicity based on the n-gram analysis

2016-08-24

Authors & citation details

Michał Jan Burdukiewicz, Piotr Sobczyk, Stefan Rödiger, Anna Duda-Madej, Paweł Mackiewicz, Małgorzata Kotulska

Authorship: first

https://doi.org/10.7287/peerj.preprints.2390

Methods for comparing multiple digital PCR experiments

Biomolecular Detection and Quantification · 2016-08-10

Authors & citation details

Michał Jan Burdukiewicz, Stefan Rödiger, Piotr Sobczyk, Mario Menschikowski, Peter Schierack, Paweł Mackiewicz

Authorship: first, corresponding

https://doi.org/10.1016/j.bdq.2016.06.004

Multiparameter analysis of double strand breaks and associated biomarkers during genome editing

2016-03-08

Authors & citation details

Michał Jan Burdukiewicz, Annika Reddig, Dirk Reinhold, Peter Schierack, Dirk Roggenbuck, Stefan Rödiger

Authorship: coauthor

https://doi.org/10.7490/f1000research.1111392.1

dpcR: an R package for the analysis of digital PCR

2016-02-25

Authors & citation details

Michał Jan Burdukiewicz, Andrej‐Nikolai Spiess, Peter Schierack, Stefan Rödiger

Authorship: first

https://doi.org/10.7490/f1000research.1111325.1

2015 3

chipPCR: an R package to pre-process raw data of amplification curves

Bioinformatics · 2015-04-24

Authors & citation details

Stefan Rödiger, Michał Jan Burdukiewicz, Peter Schierack

Authorship: coauthor

https://doi.org/10.1093/bioinformatics/btv205

A systematic review and meta-analysis of the epidemiology of pathogenic Escherichia coli of calves and the role of calves as reservoirs for human pathogenic E. coli

Frontiers in Cellular and Infection Microbiology · 2015-03-12

Authors & citation details

Rafał Kolenda, Michał Jan Burdukiewicz, Peter Schierack

Authorship: coauthor

https://doi.org/10.3389/fcimb.2015.00023

R as an Environment for Reproducible Analysis of DNA Amplification Experiments

The R Journal · 2015-01-01

Authors & citation details

Stefan Rödiger, Michał Jan Burdukiewicz, Благодатских Константин Александрович, Michael Jahn, Peter Schierack

Authorship: coauthor

https://doi.org/10.32614/rj-2015-011

2014 1

Impact of Smoothing on Parameter Estimation in Quantitative DNA Amplification Experiments

Clinical Chemistry · 2014-12-05

Authors & citation details

Andrej‐Nikolai Spiess, Claudia Deutschmann, Michał Jan Burdukiewicz, Peter Schierack, Stefan Rödiger

Authorship: coauthor

https://doi.org/10.1373/clinchem.2014.230656

Other activities

Special issue guest editor (Analysis of Amplification Curve Data), Life
Special issue guest editor (Cross-Interactions in Amyloid Aggregation), Frontiers in Molecular Biosciences.
Reviewer (ACS Omega, Analytical Chemistry, Antibiotics, Bioinformatics, BMC Biology, Briefings in Bioinformatics, Computational and Structural Biotechnology Journal, FEBS Open Bio, Frontiers in Molecular Biosciences, International Journal of Molecular Sciences, Journal of Molecular Biology, Journal of Personalized Medicine, Journal of Statistical Software, Journal of Functional Biomaterials, Pharmaceutics, PLOS One, PLOS Computational Biology, Scientific Reports, Theory in Biosciences).
Chair of the Organizing Committee (Wrocław Biofilm Symposium, 9-10 October 2017, Wrocław, Poland).
Chair of the Organizing Committee (Why R? - Polish-German Conference of R Users, 2-5 July 2018, Wrocław, Poland).
Member of the Scientific Committee (International Biotech Innovation Days, 23-25 May 2018, Senftenberg, Germany).
Member of the Organizing Committee (Why R? - International Conference of R Users, 26-29 September 2020, Warsaw, Poland).
Member of the Organizing Committee (Barcelona Protein Aggregation Training School, 12-16 September 2022, Barcelona).
Member of the Organizing Committee (Iberian Prion Conference, 11-12 May 2023, Barcelona).
Member of the Organizing Committee (Iberian Prion Conference, 23-24 May 2025, Santiago de Compostela).
ML4NGP COST Action Management Committee Member.
Secretary of the Board of the Genomics Platform at Warsaw University of Technology.
Founder and board member of Why R? Foundation.
Founder of Wrocław R User Group (STWUR).
Founder of Student Bioinformatics Club (University of Wrocław).