Publications

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Lab-Affiliated Author, External Collaborator

2023

• Korwek Z, Czerkies M, Jaruszewicz-Błońska J, Prus W, Kosiuk I, Kochańczyk M, Lipniacki T. Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response (submitted) bioRxiv

• Grabowski F, Kochańczyk M, Korwek Z, Czerkies M, Prus W, Lipniacki T. Antagonism between viral infection and innate immunity at the single-cell level (submitted) bioRxiv Data

• Nałęcz-Jawecki P, Gagliardi PA, Kochańczyk M, Dessauges C, Pertz O, Lipniacki T. The rate of information transmission through the MAPK/ERK signaling pathway stimulated in a pulsatile manner (submitted) bioRxiv Data

• Jaruszewicz-Błońska J, Kosiuk I, Prus W, Lipniacki T. A plausible identifiable model of the canonical NF-κB signaling pathway (submitted) bioRxiv

• Rinoldi C, Ziai Y, Zargarian SS, Nakielski P, Zembrzycki K, Haghighat Bayan MA, Zakrzewska A, Fiorelli R, Lanzi M, Kostrzewska-Księżyk A, Czajkowski R, Kublik E, Kaczmarek L, Pierini F. In vivo chronic brain cortex signal recording based on a soft conductive hydrogel biointerface, ACS Appl Mater Interfaces (accepted) CrossRef

• Paradiso A, Volpi M, Rinoldi C, Celikkin N, Contessi Negrini N, Bilgen M, Dallera G, Pierini F, Costantini M, Święszkowski W, Farè S. In vitro functional models for human liver diseases and drug screening: beyond animal testing, Biomater Sci (accepted) CrossRef

• Wang M, Du J, Li M, Pierini F, Li X, Yu J, Ding B. In-situ forming double-crosslinked hydrogels with highly dispersed short fibers for treatment of irregular wounds, Biomater Sci (accepted) CrossRef

• Quadretti D, Marinelli M, Salatelli E, Pierini F, Zanelli A, Lanzi M. Effects of water/alcohol soluble cationic polythiophenes as cathode interlayers for eco-friendly solar cells, Macromol Chem Phys (accepted) CrossRef

2022

• Topolewski P, Zakrzewska KE, Walczak J, Nienałtowski K, Müller-Newen G, Singhand A, Komorowski M. Phenotypic variability, not noise, accounts for most of the cell-to-cell heterogeneity in IFN-γ and oncostatin M signaling responses, Sci Signal (2022) PubMed CrossRef

• Zaremba D, Błoński S, Korczyk PM. Concentration on demand – a microfluidic system for precise adjustment of the content of single droplets, Chem Eng J 430(3):132935 (2022) CrossRef | PDF

• Czerkies M, Kochańczyk M, Korwek Z, Prus W, Lipniacki T. Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons, J Virol 96:22 e01341-22 (2022) PubMed CrossRef bioRxiv

• Grabowski F, Kochańczyk M, Lipniacki T. The spread of SARS-CoV-2 variant Omicron with the doubling time of 2.0–3.3 days can be explained by immune evasion, Viruses 14(2):294 (2022) PubMed CrossRef medRxiv | PDF Correspondence

• Mines RC, Lipniacki T, Shen X. Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts, PLOS Comput Biol 18(2):e1009811 (2022) PubMed CrossRef

• Rabcuka J, Blonski S, Meli A, Sowemimo-Coker S, Zaremba D, Stephenson D, Dzieciatkowska M, Nerguizian D, Cardigan R, Korczyk PM, Smethurst PA, D'Alessandro A, Swietach P. Metabolic reprogramming under hypoxic storage preserves faster oxygen unloading from stored red blood cells, Blood Adv 6(18):5415–5428 (2022) PubMed CrossRef

• Banerjee M, Lipniacki T, d’Onofrio A, Volpert A. Epidemic model with strain-dependent transmission rate, Commun Nonlinear Sci Numer Simul 114:106641 (2022) CrossRef

• Zakrzewska A, Haghighat Bayan MA, Nakielski P, Petronella F, De Sio L, Pierini F. Nanotechnology transition roadmap toward multifunctional stimuli-responsive face masks, ACS Appl Mater Interfaces 14(41):46123–46144 (2022) PubMed CrossRef

• Marinelli M, Lanzi M, Pierini F, Ziai Y, Zanelli A, Quadretti D, Di Maria F, Salatelli E. Ionic push–pull polythiophenes: A further step towards eco-friendly BHJ organic solar cells, Polymers 14(19):3965 (2022) PubMed CrossRef

• Ziai Y, Petronella F, Rinoldi C, Nakielski P, Zakrzewska A Kowalewski TA, Augustyniak W, Li X, Calogero A, Sabała I, Ding B, De Sio L, Pierini F. Chameleon-inspired multifunctional plasmonic nanoplatforms for biosensing applications, NPG Asia Mater 14:18 (2022) CrossRef

• de Amorim Filho EC, Moreira RA, Santos FAN The Euler characteristic and topological phase transitions in complex systems, J Phys: Complexity 3:025003 (2022) CrossRef

• Nakielski P, Rinoldi C, Pruchniewski M, Pawłowska S, Gazińska M, Strojny B, Rybak D, Jezierska-Woźniak K, Urbanek O, Denis P, Sinderewicz E, Czelejewska W, Staszkiewicz-Chodor J, Grodzik M, Ziai Y, Barczewska M, Maksymowicz W, Pierini F. Laser-assisted fabrication of injectable nanofibrous cell carriers, Small 18(2):e2104971 (2022) PubMed CrossRef

• Liu Z, Moreira RA, Dujmović A, Liu H, Yang B, Poma AB, Nash MA. Mapping mechanostable pulling geometries of a therapeutic anticalin/CTLA-4 protein complex, Nano Lett 22(1):179–187 (2022) PubMed CrossRef

• Liu Y, Wang Q, Liu X, Nakielski P, Pierini F, Li X, Yu J, Ding B. Highly adhesive, stretchable and breathable gelatin methacryloyl-based nanofibrous hydrogels for wound dressings, ACS Appl Bio Mater 5(3):1047–1056 (2022) PubMed CrossRef

• Liguori A, Pandini S, Rinoldi C, Zaccheroni N, Pierini F, Focarete ML, Gualandi C. Thermo-active smart electrospun nanofibers, Macromol Rapid Commun 2100694 (2022) CrossRef | PDF

• Glaeser JD, Bao X, Kaneda G, Avalos P, Behrens P, Salehi K, Da X, Chen A, Castaneda C, Nakielski P, Jiang W, Tawackoli W, Sheyn D. iPSC-neural crest derived cells embedded in 3D printable bio-ink promote cranial bone defect repair, Sci Rep 12:18701 (2022) PubMed CrossRef

• Ziai Y, Rinoldi C, Nakielski P, De Sio L, Pierini F. Smart plasmonic hydrogels based on gold and silver nanoparticles for biosensing application, Curr Opin Biomed Eng 24:100413 (2022) CrossRef

• Mahiout LA, Kaźmierczak B, Volpert V. Viral infection spreading and mutation in cell culture, Mathematics 10(2):256 (2022) CrossRef | PDF

• La Monaca A, Girard G, Savoie S, Krachkovskiy S, Veillette R, Pierini F, Ashok V, Rosei F, Paolella A. Influence of Ti^IV substitution on the properties of a Li_1.5Al_0.5Ge_1.5(PO₄)₃ nanofiber-based solid electrolyte, Nanoscale 14:5094–5101 (2022) PubMed CrossRef

• Cantor D, Wojtacki K. Effects of friction and spacing on the collaborative behavior of domino toppling, Phys Rev Appl 17:064021 (2022) CrossRef

• Komorowski M. Making sense of BMP signaling complexity, Cell Syst 13(5):349–351 (2022) PubMed CrossRef

2021

• Błoński S, J Aureille, S Badawi, D Zaremba, L Pernet, A Grichine, S Fraboulet, PM Korczyk, P Recho, Ch Guilluy, ME Dolega. Direction of epithelial folding defines impact of mechanical forces on epithelial state, Dev Cell 56:3222–3234 (2021) [1] CrossRef

• M Koehler, A Ray, RA Moreira, B Juniku, AB Poma, D Alsteens. Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants, Nat Commun 12(1):6977 (2021) PubMed CrossRef

• Kochańczyk M & Lipniacki T. Pareto-based evaluation of national responses to COVID-19 pandemic shows that saving lives and protecting economy are non-trade-off objectives, Sci Rep 11:2425 (2021)  PubMed CrossRef medRxiv | PDF GitHub

• Grabowski F, Preibisch G, Giziński S, Kochańczyk M, Lipniacki T. SARS-CoV-2 Variant of Concern 202012/01 has about twofold replicative advantage and acquires concerning mutations, Viruses 13(3):392 (2021) PubMed CrossRef medRxiv | PDF

• Zaremba D, Błoński S, Korczyk PM. Integration of capillary–hydrodynamic logic circuitries for built-in control over multiple droplets in microfluidic networks, Lab Chip 21:1771 (2021) PubMed CrossRef

• Kaźmierczak B & Sneyd J. Speed of traveling waves for monotone reaction–diffusion systems as a function of diffusion coefficients, Physica D: Nonlin Phenom 424:132940 (2021) CrossRef

• Nienałtowski K, Rigby RE, Walczak J, Zakrzewska KE, Głów E, Rehwinkel J, Komorowski M. Fractional response analysis reveals logarithmic cytokine responses in cellular populations, Nat Commun 12:4175 (2021) PubMed CrossRef

• Topolewski P & Komorowski M. Information-theoretic analyses of cellular strategies for achieving high signaling capacity — dynamics, cross-wiring and heterogeneity of cellular states, Curr Opin Syst Biol 27:100352 (2021) CrossRef

• Fiebelkow J, Guendel A, Guendel B, Mehwald N, Jetka T, Komorowski M, Waldherr S, Schaper F, Dittrich A. The tyrosine phosphatase SHP2 increases robustness and information transfer within IL-6-induced JAK/STAT signalling, Cell Commun Signal 19:94 (2021) PubMed CrossRef

• Poma A, Thu TTM, Tu LA, Hu C-K, Li MS. Nanomechanical stability of Aβ tetramers and fibril-like structures: Molecular dynamics simulations, J Phys Chem B 125(28):7628−7637 (2021) PubMed CrossRef

• Piechocka IK, Keary S, Sosa-Costa A, Lau L, Mohan N, Stanisavljevic J, Borgman KJE, Lakadamyali M, Manzo C, Garcia-Parajo MF. Shear forces induce ICAM-1 nanoclustering onendothelial cells that impact on T-cell migration, Biophys J 120:2644–2656 (2021) PubMed CrossRef

• Rinoldi C, Lanzi M, Fiorelli R, Nakielski P, Zembrzycki K, Kowalewski T, Urbanek O, Grippo V, Jezierska-Woźniak  K, Maksymowicz W, Camposeo A, Bilewicz R, Pisignano D, Sanai N, Pierini F. Three-dimensional printable conductive semi-interpenetrating polymer network hydrogel for neural tissue applications, Biomacromolecules 22(7):3084–3098 (2021) PubMed CrossRef | PDF

• Rinoldi C, Zargarian SS, Nakielski P, Li X, Liguori A, Petronella G, Presutti D, Wang Q, Costantini M, De Sio L, Gualandi C, Ding B, Pierini F. Nanotechnology-assisted RNA delivery: From nucleic acid therapeutics to COVID-19 vaccines, Small Meth 5(9):2100402 (2021) PubMed CrossRef

• Haghighat Bayan MA, Taromi FA, Lanzi  M, Pierini F. Enhanced efficiency in hollow core electrospun nanofiber-based organic solar cells, Sci Rep 11:21144 (2021) PubMed CrossRef

• Lanzi M & Pierini F. Efficient and thermally stable BHJ solar cells based on a soluble hydroxy-functionalized regioregular polydodecylthiophene, React Funct Polym 158:104803 (2021) CrossRef

• De Sio L, Ding B, Focsan M, Kogermann K, Pascoal-Faria P, Petronella F, Mitchell G, Zussmann E, Pierini F. Personalized reusable face masks with smart nano‐assisted destruction of pathogens for COVID‐19: A visionary road, Chem Eur J 27(20):6112–6130 (2021) PubMed CrossRef

• Lanzi M, Quadretti D, Marinelli M, Ziai Y, Salatelli E, Pierini F. Influence of the active layer structure on the photovoltaic performance of water-soluble polythiophene-based solar cells, Polymers 13(10):1640 (2021) PubMed CrossRef

• Guglielmelli A, Pierini F, Tabiryan N, Umeton C, Bunning TJ, De Sio L. Thermoplasmonics with gold nanoparticles: A new weapon in modern optics and biomedicine, Adv Photonics Res 2000198 (2021) CrossRef

• Marinelli M, Candini A, Monti F, Boschi A, Zangoli M, Salatelli E, Pierini F, Lanzi M, Zanelli A, Gazzano M, Di Maria F. Push–pull thiophene-based small molecules with donor and acceptor units of varying strength for photovoltaic application: Beyond P3HT and PCBM, J Mater Chem C 9:11216–11228 (2021) CrossRef

• Cidonio G, Costantini M, Pierini F, Scognamiglio C, Agarwal T, Barbetta A. 3D printing of biphasic inks: Beyond single-scale architectural control, J Mater Chem C (2021) 9:12489–12508 CrossRef

• Urbanek O, Wysocka A, Nakielski P, Pierini F, Jagielska E, Sabała I. Staphylococcus aureus specific electrospun wound dressings: Influence of immobilization technique on antibacterial efficiency of novel enzybiotic, Pharmaceutics 13(5), 711 (2021) PubMed CrossRef

• La Monac A, Girard G, Savoie S, Bertoni G, Krachkovskiy S, Vijh A, Pierini F, Rosei F, Paolella A. Synthesis of electrospun NASICON Li_1.5Al_0.5Ge_1.5(PO₄)₃ solid electrolyte nanofibers by control of germanium hydrolysis, J Electrochem Soc 168(11):110512 (2021) CrossRef

• Mahmood MI, Poma AB, Okazaki K. Optimizing Gō-MARTINI coarse-grained model for F-BAR protein on lipid membrane, Front Mol Biosci, 8:619381 PubMed CrossRef

• Wencel A, Ciezkowska M, Wisniewska M, Zakrzewska KE, Pijanowska DG, Pluta KD. Effects of genetically modified human skin fibroblasts, stably overexpressing hepatocyte growth factor, on hepatic functions of cocultured C3A cells, Biotechnol Bioeng 118(1):72–81 (2021) PubMed CrossRef

• Janczewska M, Szkop M, Pikus G, Kopyra K, Świątkowska A, Brygoła K, Karczmarczyk U, Walczak J, Żuk MT, Duszak J, Ciach T. PSMA targeted conjugates based on dextran, Appl Radiat Isot 167:109439 (2021) CrossRef

• Boopathi S, Poma AB, Garduño-Juárez R. An overview of several inhibitors for Alzheimer’s disease: Characterization and failure, Int J Mol Sci 22:10798 (2021) PubMed CrossRef

• Dębska-Vielhaber G, Miller I, Peeva V, Zuschratter W, Walczak J, Schreiber S, Petri S, Machts J, Vogt S, Szczepanowska J, Gellerich FN, Hermann A, Vielhaber S, Kunz WS Impairment of mitochondrial oxidative phosphorylation in skin fibroblasts of SALS and FALS patients is rescued by in vitro treatment with ROS scavengers, Exp Neurol 339:113620 (2021) PubMed CrossRef

• Majkut M, Kwiecińska-Piróg J, Wszelaczyńska E, Pobereżny J, Gospodarek-Komkowska E, Wojtacki K, Barczak T. Antimicrobial activity of heat-treated Polish honeys, Food Chem 343:128561 (2020) PubMed CrossRef

2020

• Kochańczyk M, Grabowski F, Lipniacki T. Super-spreading events initiated the exponential growth phase of COVID-19 with R₀ higher than initially estimated, R Soc Open Sci 7:200786 (2020) PubMed CrossRef | PDF SuppInfo-PDF Correspondence

• Hat B, Jaruszewicz-Błońska J, Lipniacki T. Model-based optimization of combination protocols for irradiation-insensitive cancers, Sci Rep 10:12652 (2020) PubMed CrossRef | PDF

• Bialecki S, Nalecz-Jawecki P, Kazmierczak B, Lipniacki. Traveling and standing fronts on curved surfaces, Physica D 401:132215 (2020) CrossRef

• Kochańczyk M, Grabowski F, Lipniacki T. Dynamics of COVID-19 pandemic at constant and time-dependent contact rates, Math Model Nat Phenom 15:28 (2020) CrossRef | PDF SuppCode

• Chatterjee P, Glimm T, Kaźmierczak B. Mathematical modeling of chondrogenic pattern formation during limb development: Recent advances in continuous models, Math Biosci 322:108319 (2020) PubMed CrossRef

• Nakielski P, Pawłowska S, Rinoldi C, Ziai Y, De Sio L, Urbanek O, Zembrzycki K, Pruchniewski M, Lanzi M, Salatelli E, Calogero A, Kowalewski TA, Yarin AL, Pierini F. Multifunctional platform based on electrospun nanofibers and plasmonic hydrogel: A smart nanostructured pillow for near-infrared light-driven biomedical applications, ACS Appl Mater Interfaces 12(49):54328–54342 (2020) PubMed CrossRef

• Pierini F, Guglielmelli A, Urbanek O, Nakielski P, Pezzi L, Buda R, Lanzi M, Kowalewski TA, De Sio L. Thermoplasmonic-activated hydrogel based dynamic light attenuator, Adv Opt Mater 2000324 (2020) CrossRef | SuppInfo-PDF SuppMovie-AVI

• Pawłowska S, Rinoldi C, Nakielski P, Ziai Y, Urbanek O, Li X, Kowalewski TA, Ding B, Pierini F. Ultraviolet light-assisted electrospinning of core–shell fully cross-linked P(NIPAAm-co-NIPMAAm) hydrogel-based nanofibers for thermally-induced drug delivery self-regulation, Adv Mater Interfaces 2000247 (2020) CrossRef | SuppInfo-PDF SuppMovie-MP4 CoverPicture

• Blonski S, Zaremba D, Jachimek M, Jakiela S, Wacławczyk T, Korczyk PM. Impact of inertia and channel angles on flow distribution in microfluidic junctions, Microfluid Nanofluid 24:14 (2020) CrossRef

• Sankaran A, Pawłowska S, Pierini F, Kowalewski, Yarin AL. Dynamics of electrospun hydrogel filaments in oscillatory microchannel flows: A theoretical and experimental approach, Phys Fluids 32(7):072008 (2020) CrossRef | PDF

• Chen WC, Kaźmierczak B. Traveling waves in quadratic autocatalytic systems with complexing agent, Discrete Contin Dyn Syst–Ser B (2020) CrossRef

• Moreira RA, Chwastyk M, Baker JL, Guzman HV, Poma AB. Quantitative determination of mechanical stability in the novel coro-navirus spike protein, Nanoscale 12:16409 (2020) PubMed CrossRef

• Moreira RA, Guzman HV, Boopathi S, Baker JL, Poma AB. Characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein, Materials 13(23):5362 PubMed CrossRef

• Zalewska-Piątek B, Olszewski M, Lipniacki T, Błoński S, Wieczór M, Bruździak P, Skwarska A, Nowicki B, Nowicki S, Piątek R. A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin, PLOS Pathog 16(1): e1008247 (2020) PubMed CrossRef

• Białobrzeska W, Firganek D, Czerkies M, Lipniacki T, Skwarecka M, Dziąbowska K, Cebula Z, Malinowska N, Bigus D, Bięga E, Pyrć K, Pala K, Żołędowska S, Nidzworski D. Electrochemical immunosensors based on screen-printed gold and glassy carbon electrodes: Comparison of performance for respiratory syncytial virus detection, Biosensors 10(11):175 (2020) PubMed CrossRef

• Volpert V, Banerjee M, d’Onofrio A, Lipniacki T, Petrovskii S, Tran VC. Coronavirus – Scientific insights and societal aspects, Math Model Nat Phenom 15:E2 (2020) CrossRef

• Bartali R, Gaixia Z , Tong X, Speranza G, Micheli V, Gottardi G, Fedrizzi M, Pierini F, Sun S, Laidani N, Tavares AC. Graphene oxide/reduced graphene oxide films as protective barriers on lead against differential aeration corrosion induced by water drops, Nanoscale Adv 2:5421 (2020) PubMed CrossRef | PDF SuppInfo-PDF

• Wang L, Lv H, Liu L, Zhang Q, Nakielski P, Si Y, Cao J, Li X, Pierini F, Yu J, Ding B. Electrospun nanofiber reinforced three-dimensional chitosan matrices: Architectural, mechanical and biological properties, J Colloid Interface Sci 565(1):416–425 (2020) PubMed CrossRef

• Martinez M, Cooper CD, Poma AB, Guzman HV. Free energies of the disassembly of viral capsids from a multiscale molecular simulation approach, J Chem Inf Model 60(2):974–981 (2020) PubMed CrossRef

• Boopathi S, Poma AB, Kolandaivel P. Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment, J Biomol Struct Dyn (2020) PubMed CrossRef

• Ozen M, Lipniacki T, Levchenko A, Emamian ES, Abdi A. Modeling and measurement of signaling outcomes affecting decision making in noisy intracellular networks using machine learning methods, Itegr Biol 12(5):122–138 (2020) PubMed CrossRef |  PDF