Publications - Centre of New Technologies : Centre of New Technologies

Junctions and inflammation in the skin.
Kobielak A. and Boddupally K.
Cell Comm. and Adhesion, 21(3):141-7.

Defining the slow cycling stem cells of minor salivary glands: role in gland regeneration and tumor formation.
Zhang H., Boddupally K., Kandyba E., Kobielak K., Chen Y., Zu S., Krishnan R., Sinha U., Kobielak A.
Stem Cells. 32(8):2267-77;

Smad1&5 but not Smad8 establish stem cell quiescence which is critical to transform the premature hair follicle during morphogenesis towards the postnatal state.
Kandyba E, Hazen V, Kobielak A, Butler J.S, Kobielak K.
Stem Cells. 32(2):534-47

Microwave-assisted nonaqueous synthesis of WO3 nanoparticles for crystallographically oriented photoanodes for water splitting.
Hilaire, S., Süess, M. J., Kränzlin, N., Bieńkowski, K., Solarska, R., Augustyński, J., & Niederberger, M. (2014).
Journal of Materials Chemistry A, 2(48), 20530-20537.

Nanoporous WO3–Fe2O3 films; structural and photo-electrochemical characterization.
Solarska, R., Bieńkowski, K., Królikowska, A., Dolata, M., & Augustyński, J. (2014).
Functional Materials Letters, 7(06), 1440006.

Lone-pair interactions and photodissociation of compresssed nitrogen trifluoride
Kurzydłowski, D., Wang, H. B., Troyan, I. A., & Eremets, M. I. (2014)
The Journal of chemical physics, 141(6), 064706

Connecting termal and mechanical protein (un)folding landscapes
Sun, L., Noel, J. K., Sulkowska, J. I., Levine, H., & Onuchic, J. N. (2014).
Biophysical journal, 107(12), 2950-2961.

Ag[Fe(CO)5]2+: A Bare Silver Complex with Fe(CO)5 as a Ligand
Malinowski, P. J., & Krossing, I. (2014)
Chemie International Edition, 53(49), 13460-13462.

M(BH3NH2BH2NH2BH3) salts – the missing link in the mechanism of thermal decomposition of light alkali metal amidoboranes
Fijalkowski, K. J., Jaroń, T., Leszczyński, P. J., Magos-Palasyuk, E., Palasyuk, T., Cyrański, M. K., & Grochala, W. (2014).
Physical Chemistry Chemical Physics, 16(42), 23340-23346.

Trypanosoma brucei translation initiation factor homolog EIF4E6 forms a tripartite cytosolic complex with EIF4G5 and a capping enzyme homolog.
Freire, E. R., Malvezzi, A. M., Vashisht, A. A., Zuberek, J., Saada, E. A., Langousis, G., ... & de Melo Neto, O. P. (2014).
Eukaryotic cell, 13(7), 896-908.

Synthesis, properties, and biological activity of boranophosphate analogs of the mRNA cap: versatile tools for manipulation of therapeutically relevant cap-dependent processes.
Kowalska, J., Wypijewska del Nogal, A., Darzynkiewicz, Z. M., Buck, J., Nicola, C., Kuhn, A. N., ... & Maciejczyk, M. (2014).
Nucleic acids research, 42(16), 10245-10264.

Synthesis, properities and biological activity of boranophosphate analogs of the mRNA cap: versalite tools for manipulation of therapeutically relevant cap-dependent processes
Kowalska, J., Wypijewska del Nogal, A., Darzynkiewicz, Z. M., Buck, J., Nicola, C., Kuhn, A. N., ... & Maciejczyk, M. (2014)
Nucleic acids research, 42(16), 10245-10264

Inﬂuence of electrolyte composition and temperature on behaviour of AB5 hydrogen storage alloy used as negative electrode in Ni-MH batteries
Karwowska, M., Jaron, T., Fijalkowski, K. J., Leszczynski, P. J., Rogulski, Z., & Czerwinski, A. (2014)
Journal of Power Sources, 263, 304-309.

Cap analogs containing 6-thioguanosine – reagents for the synthesis of mRNAs selectively photo-crosslinkable with cap-binding biomolecules
Nowakowska, M., Kowalska, J., Martin, F., d'Orchymont, A., Zuberek, J., Lukaszewicz, M., ... & Jemielity, J. (2014).
Organic & biomolecular chemistry, 12(27), 4841-4847.

Two-dimensional NMR spectroscopy with temperature-sweep
Bermel, W., Dass, R., Neidig, K. P., & Kazimierczuk, K. (2014).
ChemPhysChem, 15(11), 2217-2220.

Accelerating diffusion-ordered NMR spectroscopy by joint sparse sampling of diffusion and time dimensions
Urbańczyk, M., Koźmiński, W., & Kazimierczuk, K. (2014).
Angewandte Chemie, 126(25), 6582-6585.

Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases
Szczepińska, T., Kutner, J., Kopczyński, M., Pawłowski, K., Dziembowski, A., Kudlicki, A., Ginalski K., ... & Rowicka, M. (2014).
PLoS computational biology, 10(3), e1003514.

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification
Majorek, K. A., Dunin-Horkawicz, S., Steczkiewicz, K., Muszewska, A., Nowotny, M., Ginalski, K., & Bujnicki, J. M. (2014).
Nucleic acids research, 42(7), 4160-4179

A PCR-RFLP based test for distinguishing European and Atlantic Sturgeons
Panagiotopoulou, H., Baca, M., Popovic, D., Weglenski, P., & Stankovic, A. (2014).
Journal of Applied Ichthyology, 30(1), 14-17.

Ensemble learning prediction of protein–protein interactions using proteins functional annotations.
Saha, I., Zubek, J., Klingström, T., Forsberg, S., Wikander, J., Kierczak, M., ... & Plewczynski, D. (2014).
Molecular BioSystems, 10(4), 820-830.

Next generation sequencing reveals microRNA isoforms in liver cirrhosis and hepatocellular carcinoma.
Wojcicka, A., Swierniak, M., Kornasiewicz, O., Gierlikowski, W., Maciag, M., Kolanowska, M., ... & Krawczyk, M. (2014).
The international journal of biochemistry & cell biology, 53, 208-217.

Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation.
Smietanski, M., Werner, M., Purta, E., Kaminska, K. H., Stepinski, J., Darzynkiewicz, E., ... & Bujnicki, J. M. (2014).
Nature communications, 5, 3004.

Modeling nucleic acids at the residue-level resolution.
Leonarski, F., & Trylska, J. (2014).
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes (pp. 109-149). Springer, Berlin, Heidelberg

Role of S-turn2 in the structure, dynamics, and function of mitochondrial ribosomal A-site. A bioinformatics and molecular dynamics simulation study.
Panecka, J., Havrila, M., Réblová, K., Šponer, J., & Trylska, J. (2014).
The Journal of Physical Chemistry B, 118(24), 6687-6701.

Polylactide conjugates of camptothecin with different drug release abilities.
Oledzka, E., Horeglad, P., Gruszczyńska, Z., Plichta, A., Nałęcz-Jawecki, G., & Sobczak, M. (2014).
Molecules, 19(12), 19460-19470.

Defining the slow cycling stem cells of minor salivary glands: role in gland regeneration and tumor formation.
Zhang H., Boddupally K., Kandyba E., Kobielak K., Chen Y., Zu S., Krishnan R., Sinha U., Kobielak A. , (2014)
Stem Cells. 32(8):2267-77

Junctions and inflammation in the skin.
Kobielak, A., & Boddupally, K. (2014).
Cell communication & adhesion, 21(3), 141-147.

A method for joint sparse sampling of time and gradient domains in diffusion-ordered NMR spectroscopy.
Kazimierczuk, K., Lafon, O., & Lesot, P. (2014).
Analyst, 139(11), 2702-2713.

MicroRNA-related sequence variations in human cancers.
Wojcicka, A., De La Chapelle, A., & Jazdzewski, K. (2014).
Human genetics, 133(4), 463-469.

HarmonyDOCK: the structural analysis of poses in protein-ligand docking.
Plewczynski, D., Philips, A., Grotthuss, M. V., Rychlewski, L., & Ginalski, K. (2014).
Journal of Computational Biology, 21(3), 247-256.

A PCR‐RFLP based test for distinguishing European and Atlantic sturgeons.
Panagiotopoulou, H., Baca, M., Popovic, D., Weglenski, P., & Stankovic, A. (2014).
Journal of Applied Ichthyology, 30(1), 14-17.

Variants in the ATM‐CHEK2‐BRCA1 axis determine genetic predisposition and clinical presentation of papillary thyroid carcinoma.
Wójcicka, A., Czetwertyńska, M., Świerniak, M., Długosińska, J., Maciąg, M., Czajka, A., ... & Chapelle, A. (2014).
Genes, Chromosomes and Cancer, 53(6), 516-523.

Diamond: the electronic ground state of carbon at temperatures approaching 0 k
Grochala, W. (2014)
Angewandte Chemie International Edition, 53(14), 3680-3683

Criteria for sensitivity enhancement by compressed sensing: practical application to anisotropic NAD 2D-NMR spectroscopy.
Kazimierczuk, K., Lafon, O., & Lesot, P. (2014).
Analyst, 139(11), 2702-2713.

The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast.
Yoshida, K., Bacal, J., Desmarais, D., Padioleau, I., Tsaponina, O., Chabes, A., ... & Ginalski, K. (2014).
Molecular cell, 54(4), 691-697.

Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies.
Dudek, M., Romanowska, J., Wituła, T., & Trylska, J. (2014).
Biochimie, 102, 188-202.

Two‐Dimensional NMR Spectroscopy with Temperature‐Sweep.
Bermel, W., Dass, R., Neidig, K. P., & Kazimierczuk, K. (2014).
ChemPhysChem, 15(11), 2217-2220.

Accelerating Diffusion‐Ordered NMR Spectroscopy by Joint Sparse Sampling of Diffusion and Time Dimensions.
Urbańczyk, M., Koźmiński, W., & Kazimierczuk, K. (2014).
Angewandte Chemie, 126(25), 6582-6585.

The history of sturgeon in the Baltic Sea.
Popović, D., Panagiotopoulou, H., Baca, M., Stefaniak, K., Mackiewicz, P., Makowiecki, D., ... & Stankovic, A. (2014).
Journal of biogeography, 41(8), 1590-1602.

Structures of late transition metal monoxides from Jahn-Teller instabilities in the rock salt lattice.
Derzsi, M., Piekarz, P., & Grochala, W. (2014).
Physical review letters, 113(2), 025505.

Cap analogs containing 6-thioguanosine–reagents for the synthesis of mRNAs selectively photo-crosslinkable with cap-binding biomolecules.
Nowakowska, M., Kowalska, J., Martin, F., d'Orchymont, A., Zuberek, J., Lukaszewicz, M., ... & Jemielity, J. (2014).
Organic & biomolecular chemistry, 12(27), 4841-4847.

“Plasmon–exciton interactions in a core–shell geometry: from enhanced absorption to strong coupling.”
Antosiewicz, Tomasz J., S. Peter Apell, and Timur Shegai
Acs Photonics 1, no. 5 (2014): 454-463

Locals, resettlers, and pilgrims: A genetic portrait of three pre‐Columbian Andean populations.
Baca, M., Molak, M., Sobczyk, M., Węgleński, P., & Stankovic, A. (2014)
American journal of physical anthropology, 154(3), 402-412.

Exploring structures and properties of new geodesic polyarenes.
Trzaskowski, B., Adamowicz, L., Beck, W., Muralidharan, K., & Deymier, P. A. (2014).
Chemical Physics Letters, 595, 6-12.

Synthesis, properties, and biological activity of boranophosphate analogs of the mRNA cap: versatile tools for manipulation of therapeutically relevant cap-dependent processes.
Kowalska, J., Wypijewska del Nogal, A., Darzynkiewicz, Z. M., Buck, J., Nicola, C., Kuhn, A. N., ... & Maciejczyk, M. (2014).
Nucleic acids research, 42(16), 10245-10264.

Ligand-and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor.
Abrol, R., Trzaskowski, B., Goddard, W. A., Nesterov, A., Olave, I., & Irons, C. (2014).
Proceedings of the National Academy of Sciences, 111(36), 13040-13045.

SuperBiHelix method for predicting the pleiotropic ensemble of G-protein–coupled receptor conformations.
Bray, J. K., Abrol, R., Goddard, W. A., Trzaskowski, B., & Scott, C. E. (2014).
Proceedings of the National Academy of Sciences, 111(1), E72-E78.

Towards novel efficient and stable nuclear import signals: synthesis and properties of trimethylguanosine cap analogs modified within the 5′, 5′-triphosphate bridge.
Zytek, M., Kowalska, J., Lukaszewicz, M., Wojtczak, B. A., Zuberek, J., Ferenc-Mrozek, A., ... & Jemielity, J. (2014).
Organic & biomolecular chemistry, 12(45), 9184-9199.

eIF4F-like complexes formed by cap-binding homolog TbEIF4E5 with TbEIF4G1 or TbEIF4G2 are implicated in post-transcriptional regulation in Trypanosoma brucei.
Freire, E. R., Vashisht, A. A., Malvezzi, A. M., Zuberek, J., Langousis, G., Saada, E. A., ... & Neto, O. P. D. M. (2014).
RNA, 20(8), 1272-1286.

Triazole-containing monophosphate mRNA cap analogs as effective translation inhibitors.
Piecyk, K., Lukaszewicz, M., Darzynkiewicz, E., & Jankowska-Anyszka, M. (2014).
RNA, 20(10), 1539-1547.

Trypanosoma brucei translation initiation factor homolog EIF4E6 forms a tripartite cytosolic complex with EIF4G5 and a capping enzyme homolog.
Freire, E. R., Malvezzi, A. M., Vashisht, A. A., Zuberek, J., Saada, E. A., Langousis, G., ... & de Melo Neto, O. P. (2014).
Eukaryotic cell, 13(7), 896-908.

KnotProt: a database of proteins with knots and slipknots.
Jamroz, M., Niemyska, W., Rawdon, E. J., Stasiak, A., Millett, K. C., Sułkowski, P., & Sulkowska, J. I. (2014).
Nucleic acids research, 43(D1), D306-D314.

mRNA and snRNA Cap Analogs: Synthesis and Applications.
Stepinski, J., & Darzynkiewicz, E. (2014).
Chemical Biology of Nucleic Acids (pp. 511-561). Springer, Berlin, Heidelberg.

Ancient DNA and dating of cave bear remains from Niedźwiedzia Cave suggest early appearance of Ursus ingressus in Sudetes.
Baca, M., Mackiewicz, P., Stankovic, A., Popović, D., Stefaniak, K., Czarnogórska, K., ... & Weglenski, P. (2014).
Quaternary International, 339, 217-223.

Inhibition of bacterial translation and growth by antisense peptide nucleic acids and their potential application in biotechnology
Markowska-Zagrajek, A., Rownicki, M., & Trylska, J. (2014)
POSTEPY MIKROBIOLOGII, 53(3), 255-263

The causality principle in the reconstruction of sparse NMR spectra.
Mayzel, M., Kazimierczuk, K., & Orekhov, V. Y. (2014).
Chemical Communications, 50(64), 8947-8950.

Most Probable Distance between the Nucleus and HOMO Electron: The Latent Meaning of Atomic Radius from the Product of Chemical Hardness and Polarizability.
Szarek, P., & Grochala, W. (2014).
The Journal of Physical Chemistry A, 118(44), 10281-10287.

M (BH 3 NH 2 BH 2 NH 2 BH 3)–the missing link in the mechanism of the thermal decomposition of light alkali metal amidoboranes.
Fijalkowski, K. J., Jaroń, T., Leszczyński, P. J., Magos-Palasyuk, E., Palasyuk, T., Cyrański, M. K., & Grochala, W. (2014).
Physical Chemistry Chemical Physics, 16(42), 23340-23346.

Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study.
Panecka, J., Mura, C., & Trylska, J. (2014).
PloS one, 9(11), e111811.

Microsatellite multiplex assay for the analysis of Atlantic sturgeon populations.
Panagiotopoulou, H., Popovic, D., Zalewska, K., Weglenski, P., & Stankovic, A. (2014).
Journal of applied genetics, 55(4), 505-510.

Polymorphism and hydrogen discharge from holmium borohydride, Ho (BH 4) 3, and KHo (BH 4) 4.
Wegner, W., Jaroń, T., & Grochala, W. (2014).
international journal of hydrogen energy, 39(35), 20024-20030.

“Quasi-isotropic surface plasmon polariton generation through near-field coupling to a penrose pattern of silver nanoparticles.”
Verre, Ruggero, Tomasz J. Antosiewicz, Mikael Svedendahl, Kristof Lodewijks, Timur Shegai, and Mikael Kall
ACS nano 8, no. 9 (2014): 9286-9294

Microwave-assisted nonaqueous synthesis of WO3 nanoparticles for crystallographically oriented photoanodes for water splitting.
Hilaire, S., Süess, M. J., Kränzlin, N., Bieńkowski, K., Solarska, R., Augustyński, J., & Niederberger, M. (2014)
Journal of Materials Chemistry A, 2(48), 20530-20537.

Enhanced water splitting at thin film tungsten trioxide photoanodes bearing plasmonic gold–polyoxometalate particles.
Solarska, R., Bienkowski, K., Zoladek, S., Majcher, A., Stefaniuk, T., Kulesza, P. J., & Augustynski, J. (2014).
Angewandte Chemie International Edition, 53(51), 14196-14200.

Ag [Fe (CO) 5] 2+: A Bare Silver Complex with Fe (CO) 5 as a Ligand.
Malinowski, P. J., & Krossing, I. (2014).
Angewandte Chemie International Edition, 53(49), 13460-13462.

Modified OMP algorithm for exponentially decaying signals.
Kazimierczuk, K., & Kasprzak, P. (2014).
Sensors, 15(1), 234-247.

Oxygenic photosynthesis: translation to solar fuel technologies.
Olmos, J. D. J., & Kargul, J. (2014)
Acta Societatis Botanicorum Poloniae, 83(4), 423.

Connecting thermal and mechanical protein (un) folding landscapes.
Sun, L., Noel, J. K., Sulkowska, J. I., Levine, H., & Onuchic, J. N. (2014).
Biophysical journal, 107(12), 2950-2961.

Analysis of complex reacting mixtures by time-resolved 2D NMR.
Dass, R., Kozminski, W., & Kazimierczuk, K. (2014).
Analytical chemistry, 87(2), 1337-1343.