Publications

BioGenies research publications in bioinformatics, amyloids, antimicrobial peptides and multiomics, with full citations and links to original papers.

Our publications connect computational methods with biological questions. Meet the researchers behind this work, explore our software and databases, and discover research and impact.

Research stories

• AmyloGraph: a database of amyloid–amyloid interactions
• imputomics: missing data imputation for omics research
• HaDeX: analysing hydrogen–deuterium exchange data

Publication catalogue

Full publication bibliography

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

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

A closely related pair of superoxide dismutase isozymes from Staphylococcus aureus show distinct stabilities and proton-exchange dynamics

Journal of Biological Chemistry · 2026-06-05

Authors & citation details

Mariam Esmaeeli, Lorna Nikolic, Rafał Mazgaj, Lilia Zhukova, Weronika Puchała, Michał Dadlez, Kevin John Waldron

https://doi.org/10.1016/j.jbc.2026.113226

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

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

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

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

DisProt in 2026: enhancing intrinsically disordered proteins accessibility, deposition, and annotation

Nucleic Acids Research · 2025-11-17

Authors & citation details

María Victoria Nugnes, Kamel Eddine Adel Bouhraoua, Mehdi Zoubiri, Rita Pancsa, Erzsébet Fichó, Alexander Miguel Monzón, Ana M. Melo, Edoardo Salladini, Emanuela Leonardi, Federica Quaglia, Hamidreza Ghafouri, Emilie Pasche, Patrick Ruch, László Dobson, Marco Schiavina, Trinidad de los Ángeles Cordero Gil, Zsófia E. Kálmán, Ximena Aixa Castro, Valentín Iglesias, István Reményi, Mahta Mehdiabadi, Zsuzsanna Dosztányi, Péter Tompa, Damiano Piovesan, Silvio C. E. Tosatto, Maria Cristina Aspromonte

https://doi.org/10.1093/nar/gkaf1175

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

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

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

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

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

The dual nature of amyloids: From pathogenic aggregates to functional biostructures

The Biochemist · 2024-12-19

Authors & citation details

Valentín Iglesias, Javier García‐Pardo, Salvador Ventura

https://doi.org/10.1042/bio_2024_928

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

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

Leveraging the Aggregated Protein Dye YAT2150 for Malaria Chemotherapy

Pharmaceutics · 2024-09-30

Authors & citation details

Claudia Camarero-Hoyos, Yunuen Avalos‐Padilla, Antonino Nicolò Fallica, Lucía Román-Álamo, Miriam Ramírez, Marc Orozco-Quer, Inga Sidén‐Kiamos, Valentín Iglesias, Benigno Crespo, Sara Viera, David Andreu, Elena Sulleiro, Francesc Zarzuela, Nerea Urtasun, Sandra Pérez‐Torras, Marçal Pastor‐Anglada, Elsa M. Arce, Diego Muñoz‐Torrero, Xavier Fernàndez‐Busquets, Xavier Fernàndez‐Busquets

https://doi.org/10.3390/pharmaceutics16101290

Aggrescan4D: A comprehensive tool for pH‐dependent analysis and engineering of protein aggregation propensity

Protein Science · 2024-09-26

Authors & citation details

Mateusz Zalewski, Valentín Iglesias, Oriol Bárcenas, Salvador Ventura, Sebastian Kmiecik

https://doi.org/10.1002/pro.5180

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

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

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

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

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

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

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

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

Effect of the aggregated protein dye YAT2150 on Leishmania parasite viability

Antimicrobial Agents and Chemotherapy · 2024-02-13

Authors & citation details

Lucía Román-Álamo, Yunuen Avalos‐Padilla, Valentín Iglesias, Luís Rivas, Roser Fisa, Cristina Riera, David Andreu, Carlos Pintado‐Grima, Salvador Ventura, Elsa M. Arce, Diego Muñoz‐Torrero, Xavier Fernàndez‐Busquets, Xavier Fernàndez‐Busquets

https://doi.org/10.1128/aac.01127-23

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

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

A3DyDB: exploring structural aggregation propensities in the yeast proteome

Microbial Cell Factories · 2023-09-16

Authors & citation details

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

https://doi.org/10.1186/s12934-023-02182-3

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

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

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

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

A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation

Biophysica · 2023-01-18

Authors & citation details

Carlos Pintado‐Grima, Oriol Bárcenas, Andrea Bartolomé-Nafría, Marc Fornt‐Suñé, Valentín Iglesias, Javier García‐Pardo, Salvador Ventura

https://doi.org/10.3390/biophysica3010001

Exploring cryptic amyloidogenic regions in prion-like proteins from plants

Frontiers in Plant Science · 2023-01-16

Authors & citation details

Carlos Pintado‐Grima, Jaime Santos, Valentín Iglesias, Zoe Manglano-Artuñedo, Irantzu Pallarès, Salvador Ventura

https://doi.org/10.3389/fpls.2022.1060410

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

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

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

Selection of an Aptamer against the Enzyme 1-deoxy-D-xylulose-5-phosphate Reductoisomerase from Plasmodium falciparum

Pharmaceutics · 2022-11-19

Authors & citation details

Carlota Roca, Yunuen Avalos‐Padilla, Beatriz Prieto‐Simón, Valentín Iglesias, Miriam Ramírez, Santıago Imperial, Xavier Fernàndez‐Busquets, Xavier Fernàndez‐Busquets

https://doi.org/10.3390/pharmaceutics14112515

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

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

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

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

Characterization of Domiphen Bromide as a New Fast-Acting Antiplasmodial Agent Inhibiting the Apicoplastidic Methyl Erythritol Phosphate Pathway

Pharmaceutics · 2022-06-22

Authors & citation details

Arnau Biosca, Miriam Ramírez, Àlex Gomez‐Gómez, Aritz Lafuente, Valentín Iglesias, Óscar J. Pozo, Santıago Imperial, Xavier Fernàndez‐Busquets, Xavier Fernàndez‐Busquets

https://doi.org/10.3390/pharmaceutics14071320

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

https://doi.org/10.3390/biom12050613

Adhesion of Enteropathogenic, Enterotoxigenic, and Commensal Escherichia coli to the Major Zymogen Granule Membrane Glycoprotein 2

Applied and Environmental Microbiology · 2022-01-12

Authors & citation details

Rafał Kolenda, Jarosław Chilimoniuk, Krzysztof Grzymajło, Stefan Rödiger, Aamir Ali, Veronika L Tchesnokova, Dirk Roggenbuck, Peter Schierack

https://doi.org/10.1128/aem.02279-21

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

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

A3D 2.0 Update for the Prediction and Optimization of Protein Solubility

Methods in molecular biology · 2022-01-01

Authors & citation details

Jordi Pujols, Valentín Iglesias, Jaime Santos, Sebastian Kmiecik, Salvador Ventura

https://doi.org/10.1007/978-1-0716-1859-2_3

Prediction of the Effect of pH on the Aggregation and Conditional Folding of Intrinsically Disordered Proteins with SolupHred and DispHred

Methods in molecular biology · 2022-01-01

Authors & citation details

Valentín Iglesias, Carlos Pintado‐Grima, Jaime Santos, Marc Fornt‐Suñé, Salvador Ventura

https://doi.org/10.1007/978-1-0716-2095-3_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

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

DispHScan: A Multi-Sequence Web Tool for Predicting Protein Disorder as a Function of pH

Biomolecules · 2021-10-28

Authors & citation details

Carlos Pintado‐Grima, Valentín Iglesias, Jaime Santos, Vladimir Nikolaevich Uversky, Salvador Ventura

https://doi.org/10.3390/biom11111596

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

Nucleic Acids Research · 2021-10-20

Authors & citation details

Federica Quaglia, Bálint Mészáros, Edoardo Salladini, András Hatos, Rita Pancsa, Lucia Beatriz Chemes, Mátyás Pajkos, Tamás Lázár, Samuel Peña‐Díaz, Jaime Santos, Veronika Ács, Nazanin Farahi, Erzsébet Fichó, Maria Cristina Aspromonte, Claudio Bassot, Anastasia Chasapi, Norman E. Davey, Radoslav S. Davidović, László Dobson, Arne Elofsson, Gábor Erdős, Pascale Gaudet, Michelle Gwinn Giglio, Juliana Glavina, Javier Iserte, Valentín Iglesias, Zsófia E. Kálmán, Matteo Lambrughi, Emanuela Leonardi, Sonia Longhi, Sandra Macedo‐Ribeiro, Emiliano Maiani, Julia Marchetti, Cristina Marino‐Buslje, Attila Mészáros, Alexander Miguel Monzón, Giovanni Minervini, Suvarna Nadendla, Juliet F. Nilsson, Marián Novotný, Christos A. Ouzounis, Nicolás Palópoli, Elena Papaleo, Pedro José Barbosa Pereira, Gabriele Pozzati, Vasilis J. Promponas, Jordi Pujols, Alma Carolina Sánchez-Rocha, Martin Salas, Luciana Rodriguez Sawicki, Éva Schád, Aditi Shenoy, Tamás Szaniszló, Konstantinos D. Tsirigos, Nevena Veljković, Gustavo D. Parisi, Salvador Ventura, Zsuzsanna Dosztányi, Péter Tompa, Silvio C. E. Tosatto, Damiano Piovesan

https://doi.org/10.1093/nar/gkab1082

SGnn: A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress

Frontiers in Molecular Biosciences · 2021-08-18

Authors & citation details

Valentín Iglesias, Jaime Santos, Juan Santos-Suárez, Carlos Pintado‐Grima, Salvador Ventura

https://doi.org/10.3389/fmolb.2021.718301

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

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

Prion‐like proteins: from computational approaches to proteome‐wide analysis

FEBS Open Bio · 2021-05-31

Authors & citation details

Marcos Gil-García, Valentín Iglesias, Irantzu Pallarès, Salvador Ventura

https://doi.org/10.1002/2211-5463.13213

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

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

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

Critical assessment of protein intrinsic disorder prediction

Nature Methods · 2021-04-19

Authors & citation details

Marco Necci, Damiano Piovesan, Md Tamjidul Hoque, Ian Walsh, Sumaiya Iqbal, Michele Vendruscolo, Pietro Sormanni, Chen Wang, Daniele Raimondi, Ronesh Sharma, Yaoqi Zhou, Thomas Litfin, Oxana V. Galzitskaya, Wim Vranken, Björn Wallner, Claudio Mirabello, Nawar Malhis, Zsuzsanna Dosztányi, Bálint Mészáros, Jianzhao Gao, Kui Wang, Gang Hu, Zhonghua Wu, Zhonghua Wu, Alok K. Sharma, Alok K. Sharma, Jack Hanson, Kuldip K. Paliwal, Isabelle Callebaut, Tristan Bitard‐Feildel, Gabriele Orlando, Zhenling Peng, Jinbo Xu, Sheng Wang, Sheng Wang, Sheng Wang, David T. Jones, David T. Jones, Domenico Cozzetto, Jing Ru Yan, Jing Ru Yan, Jörg A. Gsponer, Jianlin Jack Cheng, Tianqi Wu, Tianqi Wu, Lukasz Kurgan, Vasilis J. Promponas, Stella Tamana, Cristina Marino‐Buslje, Elizabeth Martínez‐Pérez, Anastasia Chasapi, Christos A. Ouzounis, A. Keith Dunker, Andrey V. Kajava, Jeremy Y. Leclercq, Burcu Aykaç Fas, Matteo Lambrughi, Emiliano Maiani, Elena Papaleo, Lucia Beatriz Chemes, Nicolás S. González Foutel, Valentín Iglesias, Jordi Pujols, Salvador Ventura, Nicolás Palópoli, Gustavo D. Parisi, Claudio Bassot, Arne Elofsson, John Lamb, Marco Salvatore, András Hatos, Alexander Miguel Monzón, Martina Bevilacqua, Ivan Mičetić, Giovanni Minervini, Lisanna Paladin, Federica Quaglia, Emanuela Leonardi, Norman E. Davey, Tamás Horváth, Nikoletta Murvai, Rita Pancsa, Éva Schád, Beáta Szabó, Ágnes Tantos, Sandra Macedo‐Ribeiro, José A. Manso, Pedro José Barbosa Pereira, Radoslav S. Davidović, Nevena Veljković, Mátyás Pajkos, Tamás Szaniszló, Mainak Guharoy, Tamás Lázár, Péter Tompa, Silvio C. E. Tosatto

https://doi.org/10.1038/s41592-021-01117-3

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

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

MED15 prion-like domain forms a coiled-coil responsible for its amyloid conversion and propagation

Communications Biology · 2021-03-26

Authors & citation details

Cristina Batlle, Isabel Calvo, Valentín Iglesias, Cian J. Lynch, Marcos Gil-García, Manuel Serrano, Salvador Ventura

https://doi.org/10.1038/s42003-021-01930-8

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

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

Cryptic amyloidogenic regions in intrinsically disordered proteins: Function and disease association

Computational and Structural Biotechnology Journal · 2021-01-01

Authors & citation details

Jaime Santos, Irantzu Pallarès, Valentín Iglesias, Salvador Ventura

https://doi.org/10.1016/j.csbj.2021.07.019

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

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

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

https://doi.org/10.3390/pharmaceutics12111045

SolupHred: a server to predict the pH-dependent aggregation of intrinsically disordered proteins

Bioinformatics · 2020-10-09

Authors & citation details

Carlos Pintado‐Grima, Jaime Santos, Valentín Iglesias, Salvador Ventura

https://doi.org/10.1093/bioinformatics/btaa909

DispHred: A Server to Predict pH-Dependent Order–Disorder Transitions in Intrinsically Disordered Proteins

International Journal of Molecular Sciences · 2020-08-13

Authors & citation details

Jaime Santos, Valentín Iglesias, Carlos Pintado‐Grima, Juan Santos-Suárez, Salvador Ventura

https://doi.org/10.3390/ijms21165814

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

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

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

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

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

Detection of Protein Aggregation in Live Plasmodium Parasites

Antimicrobial Agents and Chemotherapy · 2020-04-11

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Arnau Biosca, Inga Sidén‐Kiamos, Valentín Iglesias, Salvador Ventura, Xavier Fernàndez‐Busquets, Xavier Fernàndez‐Busquets

https://doi.org/10.1128/aac.02135-19

Modeling Amyloid Aggregates using Machine Learning and Structural Predictions

Biophysical Journal · 2020-02-01

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Małgorzata Kotulska, Jakub Wiktor Wojciechowski, Michał Jan Burdukiewicz

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

pH-Dependent Aggregation in Intrinsically Disordered Proteins Is Determined by Charge and Lipophilicity

Cells · 2020-01-08

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Jaime Santos, Valentín Iglesias, Juan Santos-Suárez, Marco Mangiagalli, Stefania Brocca, Irantzu Pallarès, Salvador Ventura

https://doi.org/10.3390/cells9010145

Computational prediction of protein aggregation: Advances in proteomics, conformation-specific algorithms and biotechnological applications

Computational and Structural Biotechnology Journal · 2020-01-01

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Jaime Santos, Jordi Pujols, Irantzu Pallarès, Valentín Iglesias, Salvador Ventura

https://doi.org/10.1016/j.csbj.2020.05.026

Computational prediction and redesign of aberrant protein oligomerization

Progress in molecular biology and translational science · 2019-12-20

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Jaime Santos, Valentín Iglesias, Salvador Ventura

https://doi.org/10.1016/bs.pmbts.2019.11.002

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

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

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

DisProt: intrinsic protein disorder annotation in 2020

Nucleic Acids Research · 2019-10-12

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András Hatos, Alexander Miguel Monzón, Nicolás Palópoli, Lucı́a Álvarez, Burcu Aykaç Fas, Claudio Bassot, Martina Bevilacqua, Anastasia Chasapi, Lucia Beatriz Chemes, Norman E. Davey, Radoslav S. Davidović, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Mainak Guharoy, Tamás Horváth, Valentín Iglesias, Andrey V. Kajava, John Lamb, Matteo Lambrughi, Tamás Lázár, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo‐Ribeiro, Emiliano Maiani, José A. Manso, Cristina Marino‐Buslje, Elizabeth Martínez‐Pérez, Bálint Mészáros, Ivan Mičetić, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljković, Salvador Ventura, Wim Vranken, Zsuzsanna Dosztányi, Péter Tompa, Silvio C. E. Tosatto, Damiano Piovesan

https://doi.org/10.1093/nar/gkz975

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

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

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

Computational Assessment of Bacterial Protein Structures Indicates a Selection Against Aggregation

Cells · 2019-08-08

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Anita Čarija, Francisca Pinheiro, Valentín Iglesias, Salvador Ventura

https://doi.org/10.3390/cells8080856

Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility

Nucleic Acids Research · 2019-04-21

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Valentín Iglesias, Jordi Pujols, Mateusz Kurciński, Sebastian Kmiecik, Salvador Ventura

https://doi.org/10.1093/nar/gkz321

In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases

Frontiers in Physiology · 2019-03-27

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Valentín Iglesias, Lisanna Paladin, Teresa Juan-Blanco, Irantzu Pallarès, Patrick Aloy, Silvio C. E. Tosatto, Salvador Ventura

https://doi.org/10.3389/fphys.2019.00314

Aggrescan3D standalone package for structure-based prediction of protein aggregation properties

Bioinformatics · 2019-02-27

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Valentín Iglesias, Mateusz Kurciński, Salvador Ventura, Sebastian Kmiecik

https://doi.org/10.1093/bioinformatics/btz143

AMYCO: evaluation of mutational impact on prion-like proteins aggregation propensity

BMC Bioinformatics · 2019-01-14

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Valentín Iglesias, Oscar Conchillo‐Solé, Cristina Batlle, Salvador Ventura

https://doi.org/10.1186/s12859-019-2601-3

Formation of Cross-Beta Supersecondary Structure by Soft-Amyloid Cores: Strategies for Their Prediction and Characterization

Methods in molecular biology · 2019-01-01

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M. Rosario Fernández, Irantzu Pallarès, Valentín Iglesias, Jaime Santos, Salvador Ventura

https://doi.org/10.1007/978-1-4939-9161-7_12

Prediction of Signal Peptides in Proteins from Malaria Parasites

International Journal of Molecular Sciences · 2018-11-22

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

https://doi.org/10.3390/ijms19123709

Algorithms for automated detection of hook effect-bearing amplification curves

Biomolecular Detection and Quantification · 2018-10-16

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

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

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

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

Discovering Putative Prion-Like Proteins in Plasmodium falciparum: A Computational and Experimental Analysis

Frontiers in Microbiology · 2018-08-07

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Irantzu Pallarès, Natalia Sánchez de Groot, Valentín Iglesias, Ricardo Sant’Anna, Arnau Biosca, Xavier Fernàndez‐Busquets, Xavier Fernàndez‐Busquets, Salvador Ventura

https://doi.org/10.3389/fmicb.2018.01737

Role of recombination and faithfulness to partner in sex chromosome degeneration

Scientific Reports · 2018-06-06

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Dorota Mackiewicz, Michał Jan Burdukiewicz, Paweł Błażej

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

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

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

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

Applied and Environmental Microbiology · 2017-10-06

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

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

Amyloidogenic motifs revealed by n-gram analysis

Scientific Reports · 2017-10-05

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

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

Characterization of Soft Amyloid Cores in Human Prion-Like Proteins

Scientific Reports · 2017-09-15

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Cristina Batlle, Natalia Sánchez de Groot, Valentín Iglesias, Susanna Navarro, Salvador Ventura

https://doi.org/10.1038/s41598-017-09714-z

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

Bioinformatics · 2017-08-24

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

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

Perfecting prediction of mutational impact on the aggregation propensity of the ALS ‐associated hn RNPA 2 prion‐like protein

FEBS Letters · 2017-05-25

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Cristina Batlle, M. Rosario Fernández, Valentín Iglesias, Salvador Ventura

https://doi.org/10.1002/1873-3468.12698

Prion-like proteins and their computational identification in proteomes

Expert Review of Proteomics · 2017-03-08

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Cristina Batlle, Valentín Iglesias, Susanna Navarro, Salvador Ventura

https://doi.org/10.1080/14789450.2017.1304214

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

Scientific Reports · 2016-12-13

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

https://doi.org/10.1038/srep38951

Methods for comparing multiple digital PCR experiments

Biomolecular Detection and Quantification · 2016-08-10

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

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

The Rho Termination Factor of Clostridium botulinum Contains a Prion-Like Domain with a Highly Amyloidogenic Core

Frontiers in Microbiology · 2016-01-07

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Irantzu Pallarès, Valentín Iglesias, Salvador Ventura

https://doi.org/10.3389/fmicb.2015.01516

Computational analysis of candidate prion-like proteins in bacteria and their role

Frontiers in Microbiology · 2015-10-15

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Valentín Iglesias, Natalia Sánchez de Groot, Salvador Ventura

https://doi.org/10.3389/fmicb.2015.01123

PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores

Nucleic Acids Research · 2015-05-14

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Oscar Conchillo‐Solé, Valentín Iglesias, Frédéric Rousseau, Joost W. H. Schymkowitz, Raimon Sabaté, Xavier Daura, Salvador Ventura

https://doi.org/10.1093/nar/gkv490

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

Bioinformatics · 2015-04-24

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Stefan Rödiger, Michał Jan Burdukiewicz, Peter Schierack

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

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Rafał Kolenda, Michał Jan Burdukiewicz, Peter Schierack

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

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

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

Impact of Smoothing on Parameter Estimation in Quantitative DNA Amplification Experiments

Clinical Chemistry · 2014-12-05

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

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

Explore the research topics

Amyloids · Antimicrobial peptides · Phase separation · Missing data · HDX-MS