dr Paweł Zawadzki

@article{Piernik2022,

title = {DBFE: distribution-based feature extraction from structural variants in whole-genome data},

author = {Maciej Piernik and Dariusz Brzezinski and Pawel Sztromwasser and Klaudia Pacewicz and Weronika Majer-Burman and Michal Gniot and Dawid Sielski and Oleksii Bryzghalov and Alicja Wozna and Paweł Zawadzki},

editor = {Pier Luigi Martelli},

url = {https://doi.org/10.1093/bioinformatics/btac513},

doi = {10.1093/bioinformatics/btac513},

year  = {2022},

date = {2022-08-01},

journal = {Bioinformatics},

volume = {38},

number = {19},

pages = {4466--4473},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kaja2022,

title = {The Thousand Polish Genomes—A Database of Polish Variant Allele Frequencies},

author = {Elżbieta Kaja and Adrian Lejman and Dawid Sielski and Mateusz Sypniewski and Tomasz Gambin and Mateusz Dawidziuk and Tomasz Suchocki and Paweł Golik and Marzena Wojtaszewska and Magdalena Mroczek and Maria Stępień and Joanna Szyda and Karolina Lisiak-Teodorczyk and Filip Wolbach and Daria Kołodziejska and Katarzyna Ferdyn and Maciej Dąbrowski and Alicja Woźna and Marcin Żytkiewicz and Anna Bodora-Troińska and Waldemar Elikowski and Zbigniew J. Król and Artur Zaczyński and Agnieszka Pawlak and Robert Gil and Waldemar Wierzba and Paula Dobosz and Katarzyna Zawadzka and Paweł Zawadzki and Paweł Sztromwasser},

url = {https://doi.org/10.3390/ijms23094532},

doi = {10.3390/ijms23094532},

year  = {2022},

date = {2022-04-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {9},

pages = {4532},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wojtaszewska2021,

title = {Validation of HER2 Status in Whole Genome Sequencing Data of Breast Cancers with the Ploidy-Corrected Copy Number Approach},

author = {Marzena Wojtaszewska and Rafał Stępień and Alicja Woźna and Maciej Piernik and Pawel Sztromwasser and Maciej Dąbrowski and Michał Gniot and Sławomir Szymański and Maciej Socha and Piotr Kasprzak and Rafał Matkowski and Paweł Zawadzki},

url = {https://doi.org/10.1007/s40291-021-00571-1},

doi = {10.1007/s40291-021-00571-1},

year  = {2021},

date = {2021-12-01},

journal = {Molecular Diagnosis &$mathsemicolon$ Therapy},

volume = {26},

number = {1},

pages = {105--116},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zawadzi_2021,

title = {Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths},

author = {Paul Bastard and Paweł Zawadzki},

url = {https://doi.org/10.1126/sciimmunol.abl4340},

doi = {10.1126/sciimmunol.abl4340},

year  = {2021},

date = {2021-08-01},

journal = {Science Immunology},

volume = {6},

number = {62},

pages = {1-26},

publisher = {science group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhang2020,

title = {Inborn errors of type I IFN immunity in patients with life-threatening COVID-19},

author = {Qian Zhang and Paul Bastard and Zhiyong Liu and Jér é and Marcela Moncada-Velez and Jie Chen and Masato Ogishi and Ira K D Sabli and Stephanie Hodeib and Cecilia Korol and Jeremie Rosain and Kaya Bilguvar and Junqiang Ye and Alexandre Bolze and Benedetta Bigio and Rui Yang and Andres Augusto Arias and Qinhua Zhou and Yu Zhang and Fanny Onodi and Sarantis Korniotis and Lea Karpf and Quentin Philippot and Marwa Chbihi and Lucie Bonnet-Madin and Karim Dorgham and Nikaïa Smith and William M Schneider and Brandon S Razooky and Hans-Heinrich Hoffmann and Eleftherios Michailidis and Leen Moens and Ji Eun Han and Lazaro Lorenzo and Lucy Bizien and Philip Meade and Anna-Lena Neehus and Aileen Camille Ugurbil and Aur é and Gaspard Kerner and Peng Zhang and Franck Rapaport and Yoann Seeleuthner and Jeremy Manry and Cecile Masson and Yohann Schmitt and Agatha Schlüter and Tom Le Voyer and Taushif Khan and Juan Li and Jacques Fellay and Lucie Roussel and Mohammad Shahrooei and Mohammed F Alosaimi and Davood Mansouri and Haya Al-Saud and Fahd Al-Mulla and Feras Almourfi and Saleh Zaid Al-Muhsen and Fahad Alsohime and Saeed Al Turki and Rana Hasanato and Diederik van de Beek and Andrea Biondi and Laura Rachele Bettini and Mariella DÁngio' and Paolo Bonfanti and Luisa Imberti and Alessandra Sottini and Simone Paghera and Eugenia Quiros-Roldan and Camillo Rossi and Andrew J Oler and Miranda F Tompkins and Camille Alba and Isabelle Vandernoot and Jean-Christophe Goffard and Guillaume Smits and Isabelle Migeotte and Filomeen Haerynck and Pere Soler-Palacin and Andrea Martin-Nalda and Roger Colobran and Pierre-Emmanuel Morange and Sevgi Keles and Fatma Colkesen and Tayfun Ozcelik and Kadriye Kart Yasar and Sevtap Senoglu and Semsi Nur Karabela and Carlos Rodr í and Giuseppe Novelli and Sami Hraiech and Yacine Tandjaoui-Lambiotte and Xavier Duval and Cedric Laouenan and Andrew L Snow and Clifton L Dalgard and Joshua D Milner and Donald C Vinh and Trine H Mogensen and Nico Marr and Andr á and Bertrand Boisson and Stephanie Boisson-Dupuis and Jacinta Bustamante and Anne Puel and Michael J Ciancanelli and Isabelle Meyts and Tom Maniatis and Vassili Soumelis and Ali Amara and Michel Nussenzweig and Adolfo Garcia-Sastre and Florian Krammer and Aurora Pujol and Darragh Duffy and Richard P Lifton and Shen-Ying Zhang and Guy Gorochov and Vivien Beziat and Emmanuelle Jouanguy and Vanessa Sancho-Shimizu and Charles M Rice and Laurent Abel and Luigi D Notarangelo and Aur é and Helen C Su and Jean-Laurent Casanova and Paweł Zawadzki and ...},

url = {https://doi.org/10.1126/science.abd4570},

doi = {10.1126/science.abd4570},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {370},

number = {6515},

pages = {eabd4570},

publisher = {American Association for the Advancement of Science (AAAS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bastard2020,

title = {Autoantibodies against type I IFNs in patients with life-threatening COVID-19},

author = {Paul Bastard and Lindsey B Rosen and Qian Zhang and Eleftherios Michailidis and Hans-Heinrich Hoffmann and Yu Zhang and Karim Dorgham and Quentin Philippot and Jérémie Rosain and Vivien Béziat and Jérémie Manry and Elana Shaw and Liis Haljasmägi and Pärt Peterson and Lazaro Lorenzo and Lucy Bizien and Sophie Trouillet-Assant and Kerry Dobbs and Adriana Almeida de Jesus and Alexandre Belot and Anne Kallaste and Emilie Catherinot and Yacine Tandjaoui-Lambiotte and Jeremie Le Pen and Gaspard Kerner and Benedetta Bigio and Yoann Seeleuthner and Rui Yang and Alexandre Bolze and Andr á and Ottavia M Delmonte and Michael S Abers and Alessandro Aiuti and Giorgio Casari and Vito Lampasona and Lorenzo Piemonti and Fabio Ciceri and Kaya Bilguvar and Richard P Lifton and Marc Vasse and David M Smadja and M é and J é and Benjamin Terrier and Darragh Duffy and Lluis Quintana-Murci and Diederik van de Beek and Lucie Roussel and Donald C Vinh and Stuart G Tangye and Filomeen Haerynck and David Dalmau and Javier Martinez-Picado and Petter Brodin and Michel C Nussenzweig and St é and Carlos Rodr í and Guillaume Vogt and Trine H Mogensen and Andrew J Oler and Jingwen Gu and Peter D Burbelo and Jeffrey I Cohen and Andrea Biondi and Laura Rachele Bettini and Mariella D textquotesingle and Paolo Bonfanti and Patrick Rossignol and Julien Mayaux and Fréd é and Eystein S Husebye and Francesca Fusco and Matilde Valeria Ursini and Luisa Imberti and Alessandra Sottini and Simone Paghera and Eugenia Quiros-Roldan and Camillo Rossi and Riccardo Castagnoli and Daniela Montagna and Amelia Licari and Gian Luigi Marseglia and Xavier Duval and Jade Ghosn and John S Tsang and Raphaela Goldbach-Mansky and Kai Kisand and Michail S Lionakis and Anne Puel and Shen-Ying Zhang and Steven M Holland and Guy Gorochov and Emmanuelle Jouanguy and Charles M Rice and Aur é and Luigi D Notarangelo and Laurent Abel and Helen C Su and Jean-Laurent Casanova and Paweł Zawadzki and ...},

url = {https://doi.org/10.1126/science.abd4585},

doi = {10.1126/science.abd4585},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {370},

number = {6515},

pages = {eabd4585},

publisher = {American Association for the Advancement of Science (AAAS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SowiskaSeidler2020,

title = {The First Report of Biallelic Missense Mutations in the SFRP4 Gene Causing Pyle Disease in Two Siblings},

author = {Anna Sowińska-Seidler and Paweł Sztromwasser and Katarzyna Zawadzka and Dawid Sielski and Ewelina Bukowska-Olech and Paweł Zawadzki and Kazimierz Kozłowski and Aleksander Jamsheer},

url = {https://doi.org/10.3389/fgene.2020.593407},

doi = {10.3389/fgene.2020.593407},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Genetics},

volume = {11},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Casanova2020,

title = {A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection},

author = {Jean-Laurent Casanova and Helen C Su and Laurent Abel and Alessandro Aiuti and Saleh Almuhsen and Andres Augusto Arias and Paul Bastard and Catherine Biggs and Dusan Bogunovic and Bertrand Boisson and Stephanie Boisson-Dupuis and Alexandre Bolze and Anastasia Bondarenko and Aziz Bousfiha and Petter Brodin and Jacinta Bustamante and Manish Butte and Giorgio Casari and Michael Ciancanelli and Aurelie Cobat and Antonio Condino-Neto and Megan Cooper and Clifton Dalgard and Sara Espinosa and Hagit Feldman and Jacques Fellay and Jose Luis Franco and David Hagin and Yuval Itan and Emmanuelle Jouanguy and Carrie Lucas and Davood Mansouri and Isabelle Meyts and Joshua Milner and Trine Mogensen and Tomohiro Morio and Lisa Ng and Luigi D Notarangelo and Satoshi Okada and Tayfun Ozcelik and Pere Soler Palacin and Anna Planas and Carolina Prando and Anne Puel and Aurora Pujol and Claire Redin and Laurent Renia and Jose Carlos Rodriguez Gallego and Lluis Quintana-Murci and Vanessa Sancho-Shimizu and Vijay Sankaran and Mikko R J Seppanen and Mohammad Shahrooei and Andrew Snow and Andras Spaan and Stuart Tangye and Jordi Perez Tur and Stuart Turvey and Donald C Vinh and Horst von Bernuth and Xiaochuan Wang and Paweł Zawadzki and Qian Zhang and Shenying Zhang},

url = {https://doi.org/10.1016/j.cell.2020.05.016},

doi = {10.1016/j.cell.2020.05.016},

year  = {2020},

date = {2020-01-01},

journal = {Cell},

volume = {181},

number = {6},

pages = {1194--1199},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1093/nar/gky1143,

title = {Single-molecule imaging of DNA gyrase activity in living Escherichia coli},

author = {Mathew Stracy and Adam JM Wollman and Elżbieta Kaja and Jacek Gapiński and Ji-Eun Lee and Victoria A Leek and Shannon J McKie and Lesley A Mitchenall and Anthony Maxwell and David J Sherratt and Mark C Leake and Paweł Zawadzki},

url = {http://dx.doi.org/10.1093/nar/gky1143},

doi = {10.1093/nar/gky1143},

year  = {2019},

date = {2019-01-10},

journal = {Nucleic Acids Research},

volume = {47},

number = {1},

pages = {210-220},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zawadzka2018,

title = {MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin},

author = {Katarzyna Zawadzka and Paweł Zawadzki and Rachel Baker and Karthik V Rajasekar and Florence Wagner and David J Sherratt and Lidia K Arciszewska},

url = {https://doi.org/10.7554/elife.31522},

doi = {10.7554/elife.31522},

year  = {2018},

date = {2018-01-01},

journal = {eLife},

volume = {7},

publisher = {eLife Sciences Organisation, Ltd.},

abstract = {The Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerisation domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head. We propose that this interaction leads to an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerisation is preserved during this interaction, MukF directs the formation of dimer of dimer MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate MukB ATPase independently and additively. We demonstrate that impairment of the MukF interaction with MukB in vivo leads to ATP hydrolysis-dependent release of MukBEF complexes from chromosomes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Stracy2016,

title = {Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli},

author = {Mathew Stracy and Marcin Jaciuk and Stephan Uphoff and Achillefs N Kapanidis and Marcin Nowotny and David J Sherratt and Paweł Zawadzki},

url = {http://www.nature.com/doifinder/10.1038/ncomms12568},

doi = {10.1038/ncomms12568},

issn = {2041-1723},

year  = {2016},

date = {2016-08-01},

journal = {Nature Communications},

volume = {7},

pages = {12568},

publisher = {Nature Publishing Group},

abstract = {Nucleotide excision repair is able to identify and remove a wide range of DNA helix distorting lesions from the genome. Here the authors use single molecule imaging of UvrA and UvrB molecules and suggest a two-step ‘scan and recruit' model for UvrA function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pinkney2012,

title = {Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence},

author = {J N M Pinkney and Paweł Zawadzki and Jarosław Mazuryk and L K Arciszewska and D J Sherratt and A N Kapanidis},

url = {http://www.ncbi.nlm.nih.gov/pubmed/23184986 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3529024 http://www.pnas.org/cgi/doi/10.1073/pnas.1211922109},

doi = {10.1073/pnas.1211922109},

issn = {0027-8424},

year  = {2012},

date = {2012-12-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {109},

number = {51},

pages = {20871--20876},

abstract = {Site-specific recombination plays key roles in microbe biology and is exploited extensively to manipulate the genomes of higher organisms. Cre is a well studied site-specific recombinase, responsible for establishment and maintenance of the P1 bacteriophage genome in bacteria. During recombination, Cre forms a synaptic complex between two 34-bp DNA sequences called loxP after which a pair of strand exchanges forms a Holliday junction (HJ) intermediate; HJ isomerization then allows a second pair of strand exchanges and thus formation of the final recombinant product. Despite extensive work on the Cre-loxP system, many of its mechanisms have remained unclear, mainly due to the transient nature of complexes formed and the ensemble averaging inherent to most biochemical work. Here, we address these limitations by introducing tethered fluorophore motion (TFM), a method that monitors large-scale DNA motions through reports of the diffusional freedom of a single fluorophore. We combine TFM with Foerster resonance energy transfer (FRET) and simultaneously observe both large- and small-scale conformational changes within single DNA molecules. Using TFM-FRET, we observed individual recombination reactions in real time and analyzed their kinetics. Recombination was initiated predominantly by exchange of the "bottom-strands" of the DNA substrate. In productive complexes we used FRET distributions to infer rapid isomerization of the HJ intermediates and that a rate-limiting step occurs after this isomerization. We also observed two nonproductive synaptic complexes, one of which was structurally distinct from conformations in crystals. After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zawadzki2010,

title = {A fluorescence correlation spectroscopy study of ligand interaction with cytokinin-specific binding protein from mung bean},

author = {Paweł Zawadzki and Genowefa Ślósarek and Jerzy Boryski and Przemysław Wojtaszek},

url = {http://www.ncbi.nlm.nih.gov/pubmed/19919180 https://www.degruyter.com/view/j/bchm.2010.391.issue-1/bc.2010.005/bc.2010.005.xml},

doi = {10.1515/bc.2010.005},

issn = {1437-4315},

year  = {2010},

date = {2010-01-01},

journal = {Biological Chemistry},

volume = {391},

number = {1},

pages = {43--53},

abstract = {Cytokinins are essential plant hormones that regulate numerous physiological processes. Recently, a protein was identified in mung bean (Vigna radiata) and characterized as a cytokinin-specific binding protein (VrCSBP). Fluorescence correlation spectroscopy was used to investigate the interaction between VrCSBP and its ligands. The synthetic cytokinin, N-phenyl-N'-(4-pyridyl) urea, was labeled with two fluorophores, 7-nitro-2,1,3-benzoxadiazole and rhodamine B. Protein-ligand binding was analyzed in an equilibrium saturation binding experiment and confirmed by the competition assay. Surprisingly, it was found that VrCSBP binds not only to cytokinins, but also to gibberellins. In addition, in the presence of natural cytokinins and gibberellins, two populations of VrCSBP that differ in their diffusion coefficients were detected. The diffusion coefficients of these two populations could be related to mono- and dimeric states, which suggests a new mode of operation in ligand binding by VrCSBP, in which dimerization induced by natural ligands enhances the ligand binding capacity of the protein.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}