Selected publications

Publications that are part of the Web of Science database, possibly also other publications chosen by authors.

2021

• Krafcik, D; Istvankova, E; Dzatko, S; Viskova, P; Foldynova-Trantirkova, S; Trantirek, L, 2021: Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 22(11), doi: 10.3390/ijms22116042
• Cheng, MP; Qiu, DH; Tamon, L; Istvankova, E; Viskova, P; Amrane, S; Guedin, A; Chen, JL; Lacroix, L; Ju, HX; Trantirek, L; Sahakyan, AB; Zhou, J; Mergny, JL, 2021: Thermal and pH Stabilities of i-DNA: Confronting in vitro Experiments with Models and In-Cell NMR Data. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 60(18), p. 10286 - 10294, doi: 10.1002/anie.202016801
• Živković, ML; Gajarský, M; Beková, K; Stadlbauer, P; Vicherek, L; Petrová, M; Fiala, R; Rosenberg, I; Šponer, J; Plavec, J; Trantírek, L, 2021: Insight into formation propensity of pseudocircular DNA G-hairpins. NUCLEIC ACIDS RESEARCH 49(4), p. 2317 - 2332, doi: 10.1093/nar/gkab029
• Broft, P; Dzatko, S; Krafcikova, M; Hansel-Hertsch, R; Wacker, A; Doetsch, V; Trantirek, L; Schwalbe, H , 2021: In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 60(2), p. 865 - 872, doi: 10.1002/anie.202007184

2020

• Dzatko, S; Fiala, R; Hansel-Hertsch, R; Foldynova-Trantirkova, S; Trantirek, L, 2020: In-cell NMR Spectroscopy of Nucleic Acids. IN-CELL NMR SPECTROSCOPY: FROM MOLECULAR SCIENCES TO CELL BIOLOGY 21, p. 272 - 297
• Johard, H; Omelyanenko, A; Fei, G; Zilberter, M; Dave, Z; Abu-Youssef, R; Schmidt, L; Harisankar, A; Vincent, CT; Walfridsson, J; Nelander, S; Harkany, T; Blomgren, K; Andang, M, 2020: HCN Channel Activity Balances Quiescence and Proliferation in Neural Stem Cells and Is a Selective Target for Neuroprotection During Cancer Treatment. MOLECULAR CANCER RESEARCH 18(10), p. 1522 - 1533, doi: 10.1158/1541-7786.MCR-20-0292
• Zivkovic, ML; Rozman, J; Plavec, J, 2020: Structure of a DNA G-Quadruplex Related to Osteoporosis with a G-A Bulge Forming a Pseudo-loop. MOLECULES 25(20), doi: 10.3390/molecules25204867
• Peskova, L; Jurcikova, D; Vanova, T; Krivanek, J; Capandova, M; Sramkova, Z; Sebestikova, J; Kolouskova, M; Kotasova, H; Streit, L; Barta, T, 2020: miR-183/96/182 cluster is an important morphogenetic factor targetingPAX6expression in differentiating human retinal organoids. STEM CELLS 38(12), p. 1557 - 1567, doi: 10.1002/stem.3272
• PALUŠOVÁ, V.; RENZOVÁ, T.; VERLANDE, A.; VACLOVÁ, T.; MEDKOVÁ, M.; CETLOVÁ, L.; SEDLÁČKOVÁ, M.; HŘÍBKOVÁ, H.; SLANINOVÁ, I.; KRUTÁ, M.; ROTREKL, V.; UHLÍŘOVÁ, H.; KŘÍŽOVÁ, A.; CHMELÍK, R.; VESELÝ, P.; KRAFČÍKOVÁ, M.; TRANTÍREK, L.; SCHINK, K.; ULDRIJAN, S., 2020: Dual Targeting of BRAF and mTOR Signaling in Melanoma Cells with Pyridinyl Imidazole Compounds. CANCERS 12(6), p. 1 - 24, doi: 10.3390/cancers12061516; FULL TEXT
• Jurikova, K; Gajarsky, M; Hajikazemi, M; Nosek, J; Prochazkova, K; Paeschke, K; Trantirek, L; Tomaska, L, 2020: Role of folding kinetics of secondary structures in telomeric G-overhangs in the regulation of telomere maintenance inSaccharomyces cerevisiae. JOURNAL OF BIOLOGICAL CHEMISTRY 295(27), p. 8958 - 8971, doi: 10.1074/jbc.RA120.012914
• Giassa, IC; Vavrinska, A; Zelinka, J; Sebera, J; Sychrovsky, V; Boelens, R; Fiala, R; Trantirek, L, 2020: HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids. CHEMPLUSCHEM 85(9), p. 2177 - 2185, doi: 10.1002/cplu.202000505
• Skolakova, P; Badri, Z; Foldynova-Trantirkova, S; Rynes, J; Sponer, J; Fojtova, M; Fajkus, J; Marek, R; Vorlickova, M; Mergny, JL; Trantirek, L, 2020: Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 1864(9), doi: 10.1016/j.bbagen.2020.129651

2019

• Stadlbauer, P; Kuhrova, P; Vicherek, L; Banas, P; Otyepka, M; Trantirek, L; Sponer, J, 2019: Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. NUCLEIC ACIDS RESEARCH 47(14), p. 7276 - 7293, doi: 10.1093/nar/gkz610
• Krafcikova, M; Dzatko, S; Caron, C; Granzhan, A; Fiala, R; Loja, T; Teulade-Fichou, MP; Fessl, T; Hansel-Hertsch, R; Mergny, JL; Foldynova-Trantirkova, S; Trantirek, L, 2019: Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 141(34), p. 13281 - 13285, doi: 10.1021/jacs.9b03031
• Bosakova, MK; Nita, A; Gregor, T; Varecha, M; Gudernova, I; Fafilek, B; Barta, T; Basheer, N; Abraham, SP; Balek, L; Tomanova, M; Kucerova, JF; Bosak, J; Potesil, D; Zieba, J; Song, J; Konik, P; Park, S; Duran, I; Zdrahal, Z; Smajs, D; Jansen, G; Fu, Z; Ko, HW; Hampl, A; Trantirek, L; Krakow, D; Krejci, P, 2019: Fibroblast growth factor receptor influences primary cilium length through an interaction with intestinal cell kinase. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116(10), p. 4316 - 4325, doi: 10.1073/pnas.1800338116
• Harnos, J; Canizal, MCA; Jurasek, M; Kumar, J; Holler, C; Schambony, A; Hanakova, K; Bernatik, O; Zdrahal, Z; Gomoryova, K; Gybel, T; Radaszkiewicz, TW; Kravec, M; Trantirek, L; Rynes, J; Dave, Z; Fernandez-Llamazares, AI; Vacha, R; Tripsianes, K; Hoffmann, C; Bryja, V, 2019: Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. NATURE COMMUNICATIONS 10, doi: 10.1038/s41467-019-09651-7

2018

• Csukasi, F; Duran, I; Barad, M; Barta, T; Gudernova, I; Trantirek, L; Martin, JH; Kuo, CY; Woods, J; Lee, H; Cohn, DH; Krejci, P; Krakow, D, 2018: The PTH/PTHrP-SIK3 pathway affects skeletogenesis through altered mTOR signaling. SCIENCE TRANSLATIONAL MEDICINE 10(459), doi: 10.1126/scitranslmed.aat9356
• Fafilek, B; Balek, L; Bosakova, MK; Varecha, M; Nita, A; Gregor, T; Gudernova, I; Krenova, J; Ghosh, S; Piskacek, M; Jonatova, L; Cernohorsky, NH; Zieba, JT; Kostas, M; Haugsten, EM; Wesche, J; Erneux, C; Trantirek, L; Krakow, D; Krejci, P, 2018: The inositol phosphatase SHIP2 enables sustained ERK activation downstream of FGF receptors by recruiting Src kinases. SCIENCE SIGNALING 11(548), doi: 10.1126/scisignal.aap8608
• Balek, L; Buchtova, M; Bosakova, MK; Varecha, M; Foldynova-Trantirkova, S; Gudernova, I; Vesela, I; Havlik, J; Neburkova, J; Turner, S; Krzyscik, MA; Zakrzewska, M; Klimaschewski, L; Claus, P; Trantirek, L; Cigler, P; Krejci, P, 2018: Nanodiamonds as ´artificial proteins´: Regulation of a cell signalling system using low nanomolar solutions of inorganic nanocrystals. BIOMATERIALS 176, p. 106 - 121, doi: 10.1016/j.biomaterials.2018.05.030
• Dzatko, S; Krafcikova, M; Hansel-Hertsch, R; Fessl, T; Fiala, R; Loja, T; Krafcik, D; Mergny, JL; Foldynova-Trantirkova, S; Trantirek, L, 2018: Evaluation of the Stability of DNA i-Motifs in the Nuclei of Living Mammalian Cells. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 57(8), p. 2165 - 2169, doi: 10.1002/anie.201712284
• Harnos, J; Rynes, J; Viskova, P; Foldynova-Trantirkova, S; Bajard-Esner, L; Trantirek, L; Bryja, V, 2018: Analysis of binding interfaces of the human scaffold protein AXIN1 by peptide microarrays. JOURNAL OF BIOLOGICAL CHEMISTRY 293(42), p. 16337 - 16347, doi: 10.1074/jbc.RA118.005127
• Giassa, IC; Rynes, J; Fessl, T; Foldynova-Trantirkova, S; Trantirek, L, 2018: Advances in the cellular structural biology of nucleic acids. FEBS LETTERS 592(12), p. 1997 - 2011, doi: 10.1002/1873-3468.13054
• Verlande, A; Krafcikova, M; Potesil, D; Trantirek, L; Zdrahal, Z; Elkalaf, M; Trnka, J; Soucek, K; Rauch, N; Rauch, J; Kolch, W; Uldrijan, S, 2018: Metabolic stress regulates ERK activity by controlling KSR-RAF heterodimerization. EMBO REPORTS 19(2), p. 320 - 336, doi: 10.15252/embr.201744524

2017

• Gregor, T; Rynes, J; Foldynova-Trantirkova, S; Mayer, J; Krejci, P; Trantirek, L, 2017: Systematic analysis of BCR-ABL interactome in chronic myeloid leukemia. FEBS JOURNAL 284, p. 286 - 286
• Rynes, J; Fessl, T; Krafcikova, M; Trantirek, L; Foldynova-Trantirkova, S, 2017: Structure-activity relationships in polymorphic G-quadruplex forming segment of c-MYC promoter. FEBS JOURNAL 284, p. 274 - 275
• Gajarsky, M; Zivkovic, ML; Stadlbauer, P; Pagano, B; Fiala, R; Amato, J; Tomaska, L; Sponer, J; Plavec, J; Trantirek, L, 2017: Structure of a Stable G-Hairpin. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139(10), p. 3591 - 3594, doi: 10.1021/jacs.6b10786
• Gudernova, I; Foldynova-Trantirkova, S; El Ghannamova, B; Fafilek, B; Varecha, M; Balek, L; Hruba, E; Jonatova, L; Jelinkova, I; Kunova Bosakova, M; Trantirek, L; Mayer; J; Krejci, P, 2017: One reporter for in-cell activity profiling of majority of protein kinase oncogenes. ELIFE 6(14), doi: 10.7554/eLife.21536
• Renciuk, D; Rynes, J; Kejnovska, I; Foldynova-Trantirkova, S; Andang, M; Trantirek, L; Vorlickova, M, 2017: G-quadruplex formation in the Oct4 promoter positively regulates Oct4 expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2(1860), p. 175 - 183, doi: 10.1016/j.bbagrm.2016.11.002
• Linke, F; Harenberg, M; Nietert, M M; Zaunig, S; von Bonin, F; Arlt, A; Szczepanowski, M; Weich, H A; Lutz S; Dullin, C; Janovská, P; Krafčíková, M; Trantírek, L; Ovesná, P; Klapper, W; Beissbarth, T; Alves, F; Bryja, V; Trümper, L; Wilting, J, Kube, D, 2017: Microenvironmental interactions between endothelial and lymphoma cells: a role for the canonical WNT pathway in Hodgkin lymphoma. LEUKEMIA 31(2), p. 361 - 372, doi: 10.1038/leu.2016.232
• Niklasson, M; Maddalo, G; Sramkova, Z; Mutlu, E; Wee, S; Sekyrova, P; Schmidt, L; Fritz, N; Dehnisch, I; Kyriatzis, G; Krafcikova, M; Carson, BB; Feenstra, JM; Marinescu, VD; Segerman, A; Haraldsson, M; Gustavsson, AL; Hammarstrom, LGJ; Jensen, AJ; Uhrbom, L; Altelaar, AFM; Linnarsson, S; Uhlen, P; Trantirek, L; Vincent, CT; Nelander, S; Enger, PO; Andang, M, 2017: Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses. CANCER RESEARCH 77(7), p. 1741 - 1752, doi: 10.1158/0008-5472.CAN-16-2274
• Gudernova, I; Balek, L; Varecha, M; Kucerova, JF; Bosakova, MK; Fafilek, B; Palusova, V; Uldrijan, S; Trantirek, L; Krejci, P, 2017: Inhibitor repurposing reveals ALK, LTK, FGFR, RET and TRK kinases as the targets of AZD1480. ONCOTARGET 8(65), p. 109319 - 109331, doi: 10.18632/oncotarget.22674

2016

• Slaninova, V; Krafcikova, M; Perez-Gomez, R; Steffal, P; Trantirek, L; Bray, SJ; Krejci, A, 2016: Notch stimulates growth by direct regulation of genes involved in the control of glycolysis and the tricarboxylic acid cycle. OPEN BIOLOGY 6(2), doi: 10.1098/rsob.150155
• Taylor, SP; Bosakova, MK; Varecha, M; Balek, L; Barta, T; Trantirek, L; Jelinkova, I; Duran, I; Vesela, I; Forlenza, KN; Martin, JH; Hampl, A; Bamshad, M; Nickerson, D; Jaworski, ML; Song, J; Ko, HW; Cohn, DH; Krakow, D; Krejci, P, 2016: An inactivating mutation in intestinal cell kinase, ICK, impairs hedgehog signalling and causes short rib-polydactyly syndrome. HUMAN MOLECULAR GENETICS 25(18), p. 3998 - 4011, doi: 10.1093/hmg/ddw240
• Rynes, J; Harnos, J; Bryja, V; Krejci, P; Trantirkova, S; Trantirek, L, 2016: Modulation of cell signaling via interfering specific protein-protein interactions of a hub scaffold protein. FEBS JOURNAL 283, p. 229 - 229
• Vavrinska, A; Zelinka, J; Sebera, J; Sychrovsky, V; Fiala, R; Boelens, R; Sklenar, V; Trantirek, L, 2016: Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. JOURNAL OF BIOMOLECULAR NMR 64(1), p. 53 - 62, doi: 10.1007/s10858-015-0005-x
• Vavrinska, A; Zelinka, J; Sebera, J; Sychrovsky, V; Fiala, R; Boelens, R; Sklenar, V; Trantirek, L, 2016: Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions (vol 64, pg 53, 2016). JOURNAL OF BIOMOLECULAR NMR 65(1), p. 49 - 49, doi: 10.1007/s10858-016-0034-0

2015

• Skolakova, P; Foldynova-Trantirkova, S; Bednarova, K; Fiala, R; Vorlickova, M; Trantirek, L, 2015: Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA. NUCLEIC ACIDS RESEARCH 43(9), p. 4733 - 4745, doi: 10.1093/nar/gkv296
• Konvalinova, H; Dvorakova, Z; Renciuk, D; Bednarova, K; Kejnovska, I; Trantirek, L; Vorlickova, M; Sagi, J, 2015: Diverse effects of naturally occurring base lesions on the structure and stability of the human telomere DNA quadruplex. BIOCHIMIE 118, p. 15 - 25, doi: 10.1016/j.biochi.2015.07.013
• Stadlbauer, P; Kuhrova, P; Banas, P; Koca, J; Bussi, G; Trantirek, L; Otyepka, M; Sponer, J, 2015: Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. NUCLEIC ACIDS RESEARCH 43(20), p. 9626 - 9644, doi: 10.1093/nar/gkv994
• Buchtova, M; Chaloupkova, R; Zakrzewska, M; Vesela, I; Cela, P; Barathova, J; Gudernova, I; Zajickova, R; Trantirek, L; Martin, J; Kostas, M; Otlewski, J; Damborsky, J; Kozubik, A; Wiedlocha, A; Krejci, P, 2015: Instability restricts signaling of multiple fibroblast growth factors. CELLULAR AND MOLECULAR LIFE SCIENCES 72(12), p. 2445 - 2459, doi: 10.1007/s00018-015-1856-8
• Kant, SG; Cervenkova, I; Balek, L; Trantirek, L; Santen, GWE; de Vries, MC; van Duyvenvoorde, HA; van der Wielen, MJR; Verkerk, AJMH; Uitterlinden, AG; Hannema, SE; Wit, JM; Oostdijk, W; Krejci, P; Losekoot, M, 2015: A novel variant of FGFR3 causes proportionate short stature. EUROPEAN JOURNAL OF ENDOCRINOLOGY 172(6), p. 763 - 770, doi: 10.1530/EJE-14-0945

2014

• Sebera, J; Trantirek, L; Tanaka, Y; Nencka, R; Fukal, J; Sychrovsky, V, 2014: The activation of N-glycosidic bond cleavage performed by base-excision repair enzyme hOGG1; theoretical study of the role of Lys 249 residue in activation of G, OxoG and FapyG. RSC ADVANCES 4(83), p. 44043 - 44051, doi: 10.1039/c4ra08278h
• Stadlbauer, P; Trantirek, L; Cheatham, TE; Koca, J; Sponer, J, 2014: Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. BIOCHIMIE 105, p. 22 - 35, doi: 10.1016/j.biochi.2014.07.009
• Bernatik, O; Sedova, K; Schille, C; Ganji, RS; Cervenka, I; Trantirek, L; Schambony, A; Zdrahal, Z; Bryja, V, 2014: Functional Analysis of Dishevelled-3 Phosphorylation Identifies Distinct Mechanisms Driven by Casein Kinase 1 epsilon and Frizzled5. JOURNAL OF BIOLOGICAL CHEMISTRY 289(34), p. 23520 - 23533, doi: 10.1074/jbc.M114.590638
• Hansel, R; Luh, LM; Corbeski, I; Trantirek, L; Dotsch, V, 2014: In-Cell NMR and EPR Spectroscopy of Biomacromolecules. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 53(39), p. 10300 - 10314, doi: 10.1002/anie.201311320

2013

• Krejci, P; Kunova, M; Kubikova, I; Trantirek, L; Kozubik, A; Dvorak, P, 2013: Expression of FGF19 in Human Embryonic Stem Cells. STEM CELLS 31(11), p. 2582 - 2584, doi: 10.1002/stem.1493
• Krejci, P; Kunova, M; Kubikova, I; Trantirek, L; Kozubik, A; Dvorak, P, 2013: Expression of FGF19 in Human Embryonic Stem Cells. STEM CELLS 31(11), p. 2582 - 2584, doi: 10.1002/stem.1493
• Hansel, R; Lohr, F; Trantirek, L; Dotsch, V, 2013: High-Resolution Insight into G-Overhang Architecture. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135(7), p. 2816 - 2824, doi: 10.1021/ja312403b
• Hansel, R; Foldynova-Trantirkova, S; Dotsch, V; Trantirek, L, 2013: Investigation of Quadruplex Structure Under Physiological Conditions Using In-Cell NMR. QUADRUPLEX NUCLEIC ACIDS 330, p. 47 - 65, doi: 10.1007/128_2012_332
• Emmer, J; Vavrinska, A; Sychrovsky, V; Benda, L; Kriz, Z; Koca, J; Boelens, R; Sklenar, V; Trantirek, L, 2013: Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic N-15 chemical shielding anisotropy tensors. JOURNAL OF BIOMOLECULAR NMR 55(1), p. 59 - 70, doi: 10.1007/s10858-012-9686-6

2012

• Sebera, J; Trantirek, L; Tanaka, Y; Sychrovsky, V, 2012: Pyramidalization of the Glycosidic Nitrogen Provides the Way for Efficient Cleavage of the N-Glycosidic Bond of 8-OxoG with the hOGG1 DNA Repair Protein. JOURNAL OF PHYSICAL CHEMISTRY B 116(41), p. 12535 - 12544, doi: 10.1021/jp309098d
• Fessl, T; Adamec, F; Polivka, T; Foldynova-Trantirkova, S; Vacha, F; Trantirek, L, 2012: Towards characterization of DNA structure under physiological conditions in vivo at the single-molecule level using single-pair FRET. NUCLEIC ACIDS RESEARCH 40(16), doi: 10.1093/nar/gks333
• Sychrovsky, V; Vokacova, ZS; Trantirek, L, 2012: Guanine Bases in DNA G-Quadruplex Adopt Nonplanar Geometries Owing to Solvation and Base Pairing. JOURNAL OF PHYSICAL CHEMISTRY A 116(16), p. 4144 - 4151, doi: 10.1021/jp2110049

2011

• Hansel, R; Lohr, F; Foldynova-Trantirkova, S; Bamberg, E; Trantirek, L; Dotsch, V, 2011: The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions. NUCLEIC ACIDS RESEARCH 39(13), p. 5768 - 5775, doi: 10.1093/nar/gkr174
• Fiala, R; Spackova, N; Foldynova-Trantirkova, S; Sponer, J; Sklenar, V; Trantirek, L, 2011: NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 133(35), p. 13790 - 13793, doi: 10.1021/ja202397p