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2015

Journal papers

Štěpka Karel, Matula Pavel, Matula Petr, Woerz Stefan, Rohr Karl, Kozubek Michal. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. Cytometry Part A, John Wiley & Sons, 2015, 87, 8, pp. 759-772. ISSN 1552-4930. 2015.

Ortiz-de-Solórzano Carlos, Muñoz-Barrutia Arrate, Meijering Erik, Kozubek Michal. Toward a Morphodynamic Model of the Cell. IEEE Signal Processing Magazine, New York: IEEE, 2015, 32, 1, pp. 20-29. ISSN 1053-5888. 2015.

Hnyluchová Zuzana, Bjalončíková Petra, Karas Pavel, Mravec Filip, Halásová Tereza, Pekař Miloslav, Kubala Lukáš, Víteček Jan. A simple microviscometric approach based on Brownian motion tracking. Review of Scientific Instruments, Melville (USA): American Institute of Physics, 2015, 2015, 2. ISSN 0034-6748. 2015.

Sorokin Dmitry, Stixová Lenka, Sehnalová Petra, Legartová Soňa, Suchánková Jana, Šimara Pavel, Kozubek Stanislav, Matula Pavel, Skalníková Magdalena, Raška Ivan, Bártová Eva. Localized movement and morphology of UBF1-positive nucleolar regions are changed by gamma-irradiation in G2 phase of the cell cycle. Nucleus, 2015, 6/2015, 4, pp. 301-313. ISSN 1949-1034. 2015.

Buchtová marcela, Oralová Veronika, Aklian Anie, Mašek Jan, Vesela Iva, Ouyang Zhufeng, Obadalová Tereza, Konečná Žaneta, Spoustová Tereza, Pospíšilová Tereza, Matula Petr, Vařecha Miroslav, Bálek Lukáš, Gudernová Iva, Jelínková Iva, Duran Ivan, Červenková Iveta, Murakami Shunichi, Kozubík Alois, Dvořák Petr, Bryja Vítězslav, Krejčí Pavel. Fibroblast growth factor and canonical WNT/beta-catenin signaling cooperate in suppression of chondrocyte differentiation in experimental models of FGFR signaling in cartilage. Biochimica et Biophysica Acta - Molecular Basis of Disease, Amsterdam: Elsevier Science BV, 2015, 1852, 5, pp. 839-850. ISSN 0925-4439. 2015.

Conference papers

Svoboda David, Ulman Vladimír, Peterlík Igor. On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy. In IEEE International Symposium on Biomedical Imaging: From Nano to Macro. Stoughton (WI, USA): Engineering in Medicine and Biology Society, 2015. pp. 712-716, 5 pages. ISBN 978-1-4799-2375-5.

Stoklasa Roman, Bálek Lukáš, Krejčí Pavel, Matula Petr. Automated Cell Segmentation in Phase-Contrast Images based on Classification and Region Growing. In IEEE International Symposium on Biomedical Imaging: From Nano to Macro. Stoughton (WI, USA): Engineering in Medicine and Biology Society, 2015. pp. 1447-1451, 5 pages. ISBN 978-1-4799-2375-5.

Maška Martin, Ederra Cristina, Fernández-Marqués Javier, Muñoz-Barrutia Arrate, Kozubek Michal, Ortiz-de-Solórzano Carlos. Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy. In 22nd IEEE International Conference on Image Processing. Québec City: IEEE, 2015. 4 pages, ISBN 978-1-4799-8338-4.

Anguiano María, Castilla Carlos, Maška Martin, Ederra Cristina, Fernández-Marqués Javier, Peláez Rafael, Rouzaut Ana, Muñoz-Barrutia Arrate, Kozubek Michal, Ortiz-de-Solórzano Carlos. Characterization of the Role of Collagen Network Structure and Composition in Cancer Cell Migration. In 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Milano: IEEE, 2015. in press.

Ulman Vladimír, Orémuš Zoltán, Svoboda David. TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells. In Proceedings of 18th International Conference on Image Analysis and Processing. Germany: Springer, 2015. pp. 623-634, 12 pages. ISBN 978-3-319-23230-0.

2014

Journal papers

Šalingová Barbara, Madarásová Martina, Stejskal Stanislav, Tesařová Lenka, Šimara Pavel, Koutná Irena. From Endothelial Progenitor Cells to Tissue Engineering: How Far Have We Come? Journal of Stem Cell Research & Therapy, USA: OMICS group, 2014, 4, 3, pp. 185-195. ISSN 2157-7633. 2014.

Chenouard Nicolas, Smal Ihor, de Chaumont Fabrice, Maška Martin, Sbalzarini Ivo F, Gong Yuanhao, Cardinale Janick, Carthel Craig, Coraluppi Stefano, Winter Mark, Cohen Andrew R, Godinez William J, Rohr Karl, Kalaidzidis Yannis, Liang Liang, Duncan James, Shen Hongying, Xu Yingke, Magnusson Klas E G, Jaldén Joakim, Blau Helen M, Paul-Gilloteaux Perrine, Roudot Philippe, Kervrann Charles, Waharte François, Tinevez Jean-Yves, Shorte Spencer L, Willemse Joost, Celler Katherine, van Wezel Gilles P, Dan Han-Wei, Tsai Yuh-Show, Ortiz-de-Solórzano Carlos, Olivo-Marin Jean-Christophe, Meijering Erik. Objective Comparison of Particle Tracking Methods. Nature Methods, 2014, 11, 3, pp. 281-289. ISSN 1548-7091. 2014.

Tesařová Lenka, Stejskal Stanislav, Koutná Irena. Driven hematopoietic differentiation of embryonic stem cells: Epigenetic perspectives. Current Pharmaceutical Design, Sharjah: Bentham Science Publ. Ltd., 2014, 20, 11, pp. 1674-1686. ISSN 1381-6128. 2014.

Stoklasa Roman, Majtner Tomáš, Svoboda David. Efficient k-NN based HEp-2 cells classifier. Pattern Recognition, Oxford: Pergamon-Elsevier Science Ltd., 2014, 47, 7, pp. 2409-2418. ISSN 0031-3203. 2014.

Jiang Yan, Habibollah Saba, Tilgner Katarzyna, Collin Joseph, Bárta Tomáš, Al-Aama Jumana Yousuf, Tesařová Lenka, Hussain Rafiqul, Trafford Andrew, Kirkwood Graham, Sernagor Evelyne, Eleftheriou Cyril, Przyborski Stefan, Stojkovic Miodrag, Lako Majlinda, Keavney Bernard, Armstrong Lyle. An induced pluripotent stem cell model of hypoplastic left heart syndrome (HLHS) reveals multiple expression and functional differences in HLHS derived cardiac myocytes. Stem cells translational medicine, 2014, 3, 4, pp. 416-423. ISSN 2157-6564. 2014.

Maška Martin, Ulman Vladimír, Svoboda David, Matula Pavel, Matula Petr, Ederra Cristina, Urbiola Ainhoa, España Tomás, Venkatesan Subramanian, Balak Deepak M W, Karas Pavel, Bolcková Tereza, Štreitová Markéta, Carthel Craig, Coraluppi Stefano, Harder Nathalie, Rohr Karl, Magnusson Klas E G, Jaldén Joakim, Blau Helen M, Dzyubachyk Oleh, Křížek Pavel, Hagen Guy M, Pastor-Escuredo David, Jimenez-Carretero Daniel, Ledesma-Carbayo Maria J, Muñoz-Barrutia Arrate, Meijering Erik, Kozubek Michal, Ortiz-de-Solorzano Carlos. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics, 2014, 30, 11, pp. 1609-1617. ISSN 1460-2059. 2014.

Kováčik Lubomír, Kereïche Sami, Höög Johanna, Jůda Pavel, Matula Pavel, Raška Ivan. A simple Fourier filter for suppression of the missing wedge ray artefacts in single-axis electron tomographic reconstructions. Journal of Structural Biology, Academic Press, 2014. ISSN 1047-8477. 2014.

Williams Ian, Bowring Nicholas, Svoboda David. A performance evaluation of statistical tests for edge detection in textured images. Computer Vision and Image Understanding, Elsevier, 2014, 122, May 2014, pp. 115-130. ISSN 1077-3142. 2014.

Suchánková Jana, Legartová Soňa, Sehnalová Petra, Kozubek Stanislav, Valente Sergio, Labella Donatella, Mai Antonello, Eckerich Carmen, O. Frank Fackelmayer, Dmitry Sorokin, Eva Bártová. PRMT1 arginine methyltransferase accumulates in cytoplasmic bodies that respond to selective inhibition and DNA damage. European Journal of Histochemistry, Italy: PAGEPress, 2014, 58/2014, 2, pp. 139-151. ISSN 1121-760X. 2014.

Bártová Eva, Foltánková Veronika, Legartová Soňa, Sehnalová Petra, Sorokin Dmitry, Suchánková Jana, Kozubek Stanislav. Coilin is rapidly recruited to UVA-induced DNA lesions and gamma-radiation affects localized movement of Cajal bodies. Nucleus, Landes Bioscience, 2014, 5/2014, 3, pp. 1-9. ISSN 1949-1034. 2014.

Potěšil David, Stejskal Stanislav, Borský Marek, Šimara Pavel, Havelková Martina, Rázga Filip, Koutná Irena, Dvořáková Dana, Mayer Jiří, Ráčil Zdeněk, Zdráhal Zbyněk. Determination of Imatinib in the Blood Cells of Chronic Myelogenous Leukemia Patients by Ion-Trap Mass Spectrometry. Analytical Letters, Philadelphia: Taylor & Francis Inc., 2014, 47, 6, pp. 944-957. ISSN 0003-2719. 2014.

Sorokin Dmitry, Suchánková Jana, Bártová Eva, Matula Pavel. Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation. Folia biologica, Praha, 2014, 60, (Suppl 1), pp. 45-49. ISSN 0015-5500. 2014.

Tesařová Lenka, Šimara Pavel, Stejskal Stanislav, Koutná Irena. Hematopoietic developmental potential of human pluripotent stem cell lines. Folia biologica, Praha, 2014, 60, (Suppl 1), pp. 90-94. ISSN 0015-5500. 2014.

Ručka Zdeněk, Koutná Irena, Tesařová Lenka, Potěšilová Michaela, Stejskal Stanislav, Šimara Pavel, Vaňhara Petr, Doležel Jan, Zvoníček Václav, Coufal Oldřich, Čapov Ivan. Intravenous insulin therapy during lung resection does not affect lung function or surfactant proteins. BMC Pulmonary Medicine, United Kingdom, 2014, 14, 1, pp. 155-163. ISSN 1471-2466. 2014.

Šimara Pavel, Tesařová Lenka, Paďourová Stanislava, Koutná Irena. Generation of Human Induced Pluripotent Stem Cells Using Genome Integrating or Non-integrating Methods. Folia Biologica, Praha, 2014, 60, (Suppl 1), pp. 85-89. ISSN 0015-5500. 2014.

Stejskal Stanislav, Tesařová Lenka, Koutná Irena. Mysterious Role of H3K56ac in Embryonic Stem Cells. Folia biologica, Praha, 2014, 60, (Suppl 1), 2014, pp. 71-75. ISSN 0015-5500. 2014.

Stixová Lenka, Sehnalová Petra, Legartová Soňa, Suchánková Jana, Hrušková Tereza, Kozubek Stanislav, Sorokin Dmitry, Matula Pavel, Raška Ivan, Kovařík Aleš, Fulneček Jaroslav, Bártová Eva. HP1B-dependent recruitment of UBF1 to irradiated chromatin occurs simultaneously with CPDs. Epigenetics & Chromatin, BioMed Central, 2014, 7, 39, pp. 1-17. ISSN 1756-8935.

Kovacik Lubomír, Kereiche Sami, Matula Pavel, Raška Ivan. Sub-Volume Averaging of Repetitive Structural Features in Angularly Filtered Electron Tomographic Reconstructions. Folia biologica, Praha, 2014, 60, Suppl. 1, pp. 66-70. ISSN 0015-5500.

Conference papers

Sorokin Dmitry, Tektonidis Marco, Rohr Karl, Matula Pavel. Non-rigid Contour-based Temporal Registration of 2D Cell Nuclei Images Using the Navier Equation. In IEEE International Symposium on Biomedical Imaging: From Nano to Macro. Beijing: IEEE, 2014. pp. 746-749, 4 pages. ISBN 978-1-4673-1959-1.

Majtner Tomáš, Stoklasa Roman, Svoboda David. RSurf - the Efficient Texture-Based Descriptor for Fluorescence Microscopy Images of HEp-2 Cells. In 22nd International Conference on Pattern Recognition. Los Alamitos, California: IEEE Computer Society, 2014. pp. 1194-1199, 6 pages. ISBN 978-1-4799-5208-3.

Majtner Tomáš, Svoboda David. Comparison of 3D Texture-based Image Descriptors in Fluorescence Microscopy. In 16th International Workshop on Combinatorial Image Analysis. Switzerland: Springer International Publishing, 2014. pp. 186-195, 10 pages. ISBN 978-3-319-07147-3.

Svoboda David, Ulman Vladimír, Matyska Luděk, Maška Martin, Bella Ján, Stejskal Stanislav. On Proper Simulation of Phenomena Influencing Image Formation in Fluorescence Microscopy. In 2014 IEEE International Conference on Image Processing. IEEE Signal Processing Society, 2014. pp. 3944-3948, 5 pages. ISBN 978-1-4799-5750-7.

Majtner Tomáš, Svoboda David. Texture Analysis Using 3D Gabor Features and 3D MPEG-7 Edge Histogram Descriptor in Fluorescence Microscopy. In 4th International Conference on 3D Imaging. Los Alamitos, California: IEEE Computer Society, 2014. pp. 1-7, 7 pages. ISBN 978-1-4799-8023-9.

2013

Book chapters

Karas Pavel, Svoboda David. Algorithms for Efficient Computation of Convolution. In Design and Architectures for Digital Signal Processing. 1st ed. Rijeka (CRO): InTech, 2013. pp. 179-208, 30 pages. ISBN 978-953-51-0874-0.

Journal papers

Foltánková Veronika, Matula Pavel, Sorokin Dmitry, Kozubek Stanislav, Bártová Eva. Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body co-localization in DNA lesions. Microscopy and Microanalysis, Saarbrücken: Cambridge University Press, 2013, Volume 19, Issue 2, pp. 360-369. ISSN 1431-9276. 2013.

Šimara Pavel, Motl Jason, Kaufman Dan. Pluripotent stem cells and gene therapy. Translational Research, 2013, 161, 4, pp. 284-292. ISSN 1931-5244. 2013.

Šimara Pavel, Stejskal Stanislav, Koutná Irena, Potěšil David, Tesařová Lenka, Potěšilová Michaela, Zdráhal Zbyněk, Mayer Jiří. Apoptosis in chronic myeloid leukemia cells transiently treated with imatinib or dasatinib is caused by residual BCR-ABL kinase inhibition. American Journal of Hematology, United States: John Wiley & Sons, 2013, 88, 5, pp. 385-393. ISSN 0361-8609. 2013.

Maška Martin, Daněk Ondřej, Garasa Saray, Rouzaut Ana, Muñoz-Barrutia Arrate, Ortiz-de-Solórzano Carlos. Segmentation and Shape Tracking of Whole Fluorescent Cells Based on the Chan-Vese Model. IEEE Transactions on Medical Imaging, 2013, 32, 6, pp. 995-1006. ISSN 0278-0062. 2013.

Ručka Zdeněk, Vaňhara Petr, Koutná Irena, Tesařová Lenka, Potěšilová Michaela, Stejskal Stanislav, Šimara Pavel, Doležel Jan, Zvoníček Václav, Coufal Oldřich, Čapov Ivan. Differential effects of insulin and dexamethasone on pulmonary surfactant-associated genes and proteins in A549 and H441 cells and lung tissue. International Journal of Molecular Medicine, United States: Spandidos Publ. Ltd., 2013, 32, 1, pp. 211-218. ISSN 1107-3756. 2013.

Conference papers

Maška Martin, Morales Xabier, Muñoz-Barrutia Arrate, Rouzaut Ana, Ortiz-de-Solórzano Carlos. Automatic Quantification of Filopodia-Based Cell Migration. In 10th IEEE International Symposium on Biomedical Imaging. San Francisco: IEEE, 2013. pp. 668-671, 4 pages. ISBN 978-1-4673-6454-6.

Štěpka Karel. Automated Cell Counting in Bürker Chamber. In 18th Scandinavian Conference on Image Analysis, SCIA 2013. Espoo (Finland): Springer, 2013. pp. 236-245, 10 pages. ISBN 978-3-642-38885-9.

Svoboda David, Ulman Vladimír. Towards a Realistic Distribution of Cells in Synthetically Generated 3D Cell Populations. In 17th International Conference on Image Analysis and Processing, ICIAP 2013. LNCS 8157, Part II. Berlin, Heidelberg: Springer-Verlag, 2013. pp. 429-438, 10 pages. ISBN 978-3-642-41183-0.

Karas Pavel, Kuderjavý Michal, Svoboda David. Deconvolution of huge 3-D images: Parallelization strategies on a multi-GPU system. In 13th International Conference on Algorithms and Architectures for Parallel Processing. Springer International Publishing, 2013. pp. 279-290, 12 pages. ISBN 978-3-319-03858-2.

2012

Book chapters

Koutná Irena, Šimara Pavel, Ondráčková Petra, Tesařová Lenka. Flow Cytometry Analysis of Intracellular Protein. In Flow Cytometry - Recent Perspectives. Rijeka, Croatia: InTech, 2012. pp. 421-438, 18 pages. ISBN 978-953-51-0626-5.

Journal papers

Daněk Ondřej, Matula Pavel, Maška Martin, Kozubek Michal. Smooth Chan-Vese Segmentation via Graph Cuts. Pattern Recognition Letters, Amsterdam: Elsevier, 2012, 33, 10, pp. 1405-1410. ISSN 0167-8655. 2012.

Lisauskas Tautvydas, Matula Petr, Claas Christoph, Reusing Susanne, Wiemann Stefan, Erfle Holger, Lehmann Lars, Fischer Peter, Eils Roland, Rohr Karl, Storrie Brian, Starkuviene Vytaute. Live cell assays to identify regulators of ER to Golgi trafficking. Traffic, John Wiley & Sons, 13, 3, pp. 416–432. ISSN 1398-9219. 2012.

Karas Pavel, Morard Vincent, Bartovský Jan, Grandpierre Thierry, Dokládalová Eva, Matula Petr, Dokládal Petr. GPU Implementation of Linear Morphological Openings with Arbitrary Angle. Journal of Real-Time Image Processing, Springer-Verlag, 2012, online, pp. 1-15. ISSN 1861-8200. 2012.

Šustáčková Gabriela, Kozubek Stanislav, Stixová Lenka, Legartová Soňa, Matula Pavel, Orlova Darya Yurevna, Bártová Eva. Acetylation-dependent nuclear arrangement and recruitment of BMI1 protein to UV-damaged chromatin. Journal of cellular physiology, United States: Wiley-Liss, 227, 5, pp. 1838-1850, 13 pages. ISSN 0021-9541. 2012.

Vařecha Miroslav, Potěšilová Michaela, Matula Pavel, Kozubek Michal. Endonuclease G interacts with histone H2B and DNA topoisomerase II alpha during apoptosis. Mol Cell Biochem, 363, 1-2, pp. 301-307, 7 pages. ISSN 0300-8177. 2012.

Stixová Lenka, Matula Pavel, Kozubek Stanislav, Cmarko Dušan, Gombitová Adriana, Raška Ivan, Bártová Eva. Trajectories and nuclear arrangement of PML bodies are influenced by A-type lamin deficiency. Biology of the Cell, 2012, 104, 7, pp. 418-432. ISSN 1768-322X. 2012.

Šimara Pavel, Peterková Martina, Stejskal Stanislav, Potěšilová Michaela, Koutná Irena, Ráčil Zdeněk, Rázga Filip, Jurček Tomáš, Dvořáková Dana, Mayer Jiří. BCR-ABL activity measured by 50% inhibitory concentration for imatinib, p-CrkL/CrkL ratio or p-CrkL ratio in CD34+ cells of patients with chronic myeloid leukemia does not predict treatment response. Leukemia & lymphoma, England: Informa Healthcare, 2012, 00, pp. 1-3, 3 pages. ISSN 1042-8194. 2012.

Tesařová Lenka, Koutná Irena, Dvořáková Magdaléna, Klabusay Martin. Relative expression of gammadelta T-cell receptor gene families detected by RT–PCR and capillary electrophoresis. International Journal of immunogenetics, Blackwell Publishing Ltd, Epub, 2012 Apr10, pp. 1-8, 8 pages. ISSN 1744-3121. 2012.

Orlova Darya Yurevna, Stixová Lenka, Kozubek Stanislav, Gierman Hinco, Šustáčková Gabriela, Chernyshev Andrei, Medvedev Ruslan, Legartová Soňa, Versteeg Rogier, Matula Pavel, Stoklasa Roman, Bártová Eva. Arrangement of nuclear structures is not transmitted through mitosis but is identical in sister cells. Journal of Cellular Biochemistry, 2012, 113, 11, pp. 3313-3329. ISSN 0730-2312. 2012.

Vařecha Miroslav, Páclová Daniela, Procházková Jiřina, Matula Pavel, Cmarko Dušan, Kozubek Michal. Knockdown of apoptosis-inducing factor disrupts function of respiratory complex I. BIOCELL, Argentina: National Council of Scientific and Techn, 2012, 36, 3, pp. 121-126. ISSN 0327-9545. 2012.

Serva Andrius, Knapp Bettina, Tsai Yueh-Tso, Class Christoph, Lisauskas Tautvydas, Matula Petr, Harder Nathalie, Kaderali Lars, Rohr Karl, Erfle Holger, Eils Roland, Braga Vania, Starkuviene Vytaute. miR-17-5p Regulates Endocytic Trafficking through Targeting TBC1D2/Armus. PLoS One, 2012, 7, 12: e52555. ISSN 1932-6203. 2012.

Conference papers

Svoboda David, Ulman Vladimír. Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy. In Proceedings of 9th International Conference on Image Analysis and Recognition. LNCS 7325, Part II. Heidelberg: Springer-Verlag, 2012. pp. 473-482, 10 pages. ISBN 978-3-642-31297-7.

Karas Pavel, Svoboda David, Zemčík Pavel. GPU Optimization of Convolution for Large 3-D Real Images. In Proceedings of the International Conference on Advanced Concepts for Intelligent Vision Systems (ACIVS’12). Springer Berlin / Heidelberg, 2012. pp. 59-71, 13 pages. ISBN 978-3-642-33139-8.

Majtner Tomáš, Svoboda David. Extension of Tamura Texture Features for 3D Fluorescence Microscopy. In 2012 Second Joint 3DIM/3DPVT Conference: 3D Imaging, Modeling, Processing, Visualization & Transmission. Los Alamitos, CA, USA: IEEE Computer Society, 2012. pp. 301-307, 7 pages. ISBN 978-0-7695-4873-9.

2011

Journal papers

Brázdilová Silvie Luisa, Kozubek Michal. Image Division Technique in Pre-acquisition Analysis of Information Content for Automated Microscopy. Journal of Microscopy, Oxford: Blackwell Science, 242, 3, pp. 279-289, 11 pages. ISSN 0022-2720. 2011.

Ulman Vladimír. Boundary Treatment for Young-van Vliet Recursive Zero-Mean Gabor Filtering. EURASIP Journal on Advances in Signal Processing, New York (USA): Hindawi Publishing Corporation, 2011, ID 234090, pp. 1-9, 9 pages. ISSN 1687-6172. 2011.

Tesařová Lenka, Koutná Irena, Kořístek Zdeněk, Klabusay Martin. Multiple myeloma patients at peripheral blood stem cell harvest: restricted usage of TCR beta variable families. Clinical Immunology, Elsevier, 2011, 138, pp. 67-76, 10 pages. ISSN 1521-6616. 2011.

Koutná Irena, Peterková Martina, Šimara Pavel, Stejskal Stanislav, Tesařová Lenka, Kozubek Michal. Proliferation and differentiation potential of CD133+ and CD34+ populations from the bone marrow and mobilized peripheral blood. Annals of hematology, Germany: Springer, 90, (2), pp. 127-137, 11 pages. ISSN 0939-5555. 2011.

Holubcová Zuzana, Matula Pavel, Sedláčková Miroslava, Vinarský Vladimír, Doležalová Dáša, Bárta Tomáš, Dvořák Petr, Hampl Aleš. Human embryonic stem cells suffer from centrosomal amplification. Stem Cells, 29, 1, pp. 46-56, 11 pages. ISSN 1066-5099. 2011.

Reiss S., Rebhan Ilka, Backes P., Romero-Brey I., Erfle Holger, Matula Petr, Kaderali Lars, Poenisch Marion, Blankenburg H., Hiet M.S., Longerich T., Diehl S., Ramirez F., Balla T., Rohr Karl, Kaul A., Bühler S., Pepperkok Rainer, Lengauer T., Albrecht M., Eils Roland, Schirmacher P., Lohmann V., Bartenschlager Ralf. Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host & Microbe, 9, 1, pp. 32-45, 13 pages. ISSN 1931-3128. 2011.

Stixová Lenka, Bártová Eva, Matula Pavel, Daněk Ondřej, Legartová Soňa, Kozubek Stanislav. Heterogeneity in the kinetics of nuclear proteins and trajectories of substructures associated with heterochromatin. Epigenetics & Chromatin, 4, 5, 17 pages. ISSN 1756-8935. 2011.

Pellicano Francesca, Šimara Pavel, Sinclair Amy, Helgason Gudmundur Vignir, Copland Mhairi, Grant Steven, Holyoake Tessa. The MEK inhibitor PD184352 enhances BMS-214662-induced apoptosis in CD34+ CML stem/progenitor cells. Leukemia, London: Nature Publishing Group, 2011, 25, pp. 1159-1167, 9 pages. ISSN 0887-6924. 2011.

Karas Pavel, Svoboda David. Convolution of Large 3D Images on GPU and its Decomposition. EURASIP Journal on Advances in Signal Processing, New York (USA): Hindawi Publishing Corporation, 2011, 120, pp. 1-12, 12 pages. ISSN 1687-6172. 2011.

Staier Florian, Eipel Heinz, Matula Petr, Evsikov Alexei V, Kozubek Michal, Cremer Christoph, Hausmann Michael. Micro axial tomography: A miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy. Rev. Sci. Instrum., USA: American Institute of Physica, 82, 9, 8 pages s. ISSN 0034-6748. 2011.

Šustáčková Gabriela, Kozubek Stanislav, Stixová Lenka, Legartová Soňa, Matula Pavel, Orlova Darya Yurevna, Bártová Eva. Acetylation-dependent nuclear arrangement and recruitment of BMI1 protein to UV-damaged chromatin. Journal of cellular physiology, United States: Wiley-Liss. ISSN 0021-9541. 2011.

Knapp Bettina, Rebhan Ilka, Kumar Anil, Matula Petr, Kiani Narsis A, Binder Marco, Erfle Hoger, Rohr Karl, Eils Roland, Bartenschlager Ralf, Kaderali Lars. Normalizing for Individual Cell Population Context in the Analysis of High-Content Cellular Screens. BMC Bioinformatics, BioMed Central, 2011, 12, 485, pp. 1-14. ISSN 1471-2105. 2011.

Conference papers

Daněk Ondřej, Matula Pavel. An Improved Riemannian Metric Approximation for Graph Cuts. In 16th International Conference on Discrete Geometry for Computer Imagery. Berlin, Heidelberg: Springer-Verlag, 2011. pp. 71-82, 12 pages. LNCS 6607. ISBN 978-3-642-19866-3.

Daněk Ondřej, Matula Pavel. On Euclidean Metric Approximation via Graph Cuts. In Computer Vision, Imaging and Computer Graphics. Theory and Applications. Berlin, Heidelberg: Springer-Verlag, 2011. pp. 125-134, 11 pages. ISBN 978-3-642-25381-2.

Daněk Ondřej, Maška Martin. A Simple Topology Preserving Max-Flow Algorithm for Graph Cut Based Image Segmentation. In Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (Selected Papers). Saarbrücken, Warden: Schloss Dagstuhl Publishing, 2011. pp. 19-25, 7 pages. OASIcs: Open Access Series in Informatics. ISBN 978-3-939897-22-4.

Maška Martin, Matula Pavel, Kozubek Michal. Simultaneous Tracking of Multiple Objects Using Fast Level Set-Like Algorithm. In Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (Selected Papers). Saarbrücken, Wadern: Schloss Dagstuhl Publishing, 2011. pp. 69-76, 8 pages. ISBN 978-3-939897-22-4.

Karas Pavel. Efficient Computation of Morphological Greyscale Reconstruction. In Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (Selected Papers). Saarbrücken, Warden: Schloss Dagstuhl Publishing, 2011. pp. 54-61, 8 pages. ISBN 978-3-939897-22-4.

Svoboda David, Homola Ondřej, Stejskal Stanislav. Generation of 3D Digital Phantoms of Colon Tissue. In Proceedings of 8th International Conference on Image Analysis and Recognition. LNCS 6754, Part II. Berlin, Heidelberg: Springer-Verlag, 2011. pp. 31-39, 9 pages. ISBN 978-3-642-21595-7.

Svoboda David. Efficient Computation of Convolution of Huge Images. In Image Analysys and Processing - ICIAP 2011. LNCS 6978, Part I. Berlin, Heidelberg: Springer-Verlag, 2011. pp. 453-462, 10 pages. ISBN 978-3-642-24084-3.

Stoklasa Roman, Matula Petr. Road Detection Using Similarity Search. In 2nd International Conference on Robotics in Education. Vienna: 2011. pp. 95-102, 8 pages. ISBN 978-3-200-02273-7.

Matula Petr, Lisauskas Tautvydas, Starkuviene Vytaute, Rohr Karl. Quantification of Golgi Complex Assembly and Disassembly in LiveCell Fluorescence Microscopy Images. In Proceedings of Workshop on Microscopic Image Analysis with Applications in Biology. 2011. 4 pages.

2010

Journal papers

Harničarová Andrea, Bártová Eva, Galiová Gabriela, Uhlířová Radka, Matula Pavel, Kozubek Stanislav. SUV39h-independent association of HP1b with fibrillarin-positive nucleolar regions. Chromosoma, Springer, 119, 3, pp. 227-241, 15 pages. ISSN 0009-5915. 2010.

Uhlířová Radka, Harničarová Andrea, Galiová Gabriela, Legartová Soňa, Matula Pavel, Fojtová Miloslava, Vařecha Miroslav, Amrichová Jana, Vondráček Jan, Kozubek Stanislav, Bártová Eva. SUV39h- and A-type Lamin-Dependent Telomere Nuclear Rearrangement. Journal of Cellular Biochemistry, 2010, 109, pp. 915-926, 11 pages. ISSN 0730-2312. 2010.

Harničarová Andrea, Galiová Gabriela, Legartová Soňa, Kozubek Stanislav, Matula Pavel, Bártová Eva. Chromocentre integrity and epigenetic marks. Journal of Structural Biology, United States: Academic Press, Elsevier Inc., 169, 1, pp. 124-133, 10 pages. ISSN 1047-8477. 2010.

Stejskal Stanislav, Koutná Irena, Matula Pavel, Ručka Zdeněk, Daněk Ondřej, Maška Martin, Kozubek Michal. The role of chromatin condensation during granulopoiesis in the regulation of gene cluster expression. Epigenetics, USA: Landes Bioscience, 5, 8, pp. 759-767, 9 pages. ISSN 1559-2294. 2010.

Suratanee Apichat, Rebhan Ilka, Matula Petr, Kumar Anil, Kaderali Lars, Rohr Karl, Bartenschlager Ralf, Eils Roland, König Rainer. Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images. Bioinformatics, 26, 18, pp. i653-i658, 6 pages. ISSN 1367-4803. 2010.

Stejskal Stanislav, Koutná Irena, Ručka Zdeněk. Isolation of granulocytes: Which transcriptome do we analyze neutrophils or eosinophils? Folia Biol., 56, pp. 252 - 255, 4 pages. ISSN 0015-5500. 2010.

Conference papers

Matula Petr, Verissimo Fatima, Wörz Stefan, Eils Roland, Pepperkok Rainer, Rohr Karl. Quantification of Fluorescent Spots in Time Series of 3D Confocal Microscopy Images of Endoplasmic Reticulum Exit Sites Based on the HMAX Transform. In Proceedings of SPIE Medical Imaging. 2010. 7 pages. Vol. 7626. ISBN 978-0-8194-8027-9.

Ulman Vladimír. Filtering with Anisotropic 3D Gabor Filter Bank Efficiently Computed with 1D Convolutions without Interpolation. In Proceedings of the Seventh IASTED International Conference on Signal Processing, Pattern Recognition and Applications. Calgary: ACTA Press, 2010. pp. 33-42, 10 pages. ISBN 978-0-88986-823-6.

Daněk Ondřej, Matula Pavel. Graph Cuts and Approximation of the Euclidean Metric on Anisotropic Grids. In VISAPP International Conference on Computer Vision Theory and Applications. Portugal: Institute for Systems and Technologies of Information, Control and Communication, 2010. pp. 68-73, 6 pages. ISBN 978-989-674-029-0.
BEST STUDENT PAPER AWARD

Ulman Vladimír. Improving Accuracy of Optical Flow of Heeger's Original Method on Biomedical Images. In Proceedings of the 7th International Conference on Image Analysis and Recognition, ICIAR 2010. Povoa de Varzim (Portugal): Springer, 2010. pp. 263-273, 11 pages. LNCS 6111. ISBN 978-3-642-13771-6.

Maška Martin, Matula Pavel, Daněk Ondřej, Kozubek Michal. A Fast Level Set-Like Algorithm for Region-Based Active Contours. In 6th International Symposium on Visual Computing. Berlin, Heidelberg: Springer-Verlag, 2010. pp. 387-396, 10 pages. LNCS 6455. ISBN 978-3-642-17276-2.

Brázdilová Silvie Luisa, Kozubek Michal. Image Division Technique in Automated Fluorescence Microscopy with Complex Content. In Proceedings of the IADIS International Conference on Computer Graphics, Visualization, Computer Vision and Image Processing 2010. 2010. Freiburg, Germany: International Association for Development of the Information Society, 2010. pp. 176-183, 8 pages. ISBN 978-972-8939-15-1.

Maška Martin, Matula Pavel, Kozubek Michal. Simultaneous Tracking of Multiple Objects Using Fast Level Set-Like Algorithm. In 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, 2010. pp. 117-125, 9 pages. ISBN 978-80-87342-10-7.

Daněk Ondřej, Maška Martin. A Simple Topology Preserving Max-Flow Algorithm for Graph Cut Based Image Segmentation. In 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, 2010. pp. 45-52, 8 pages. ISBN 978-80-87342-10-7.

Karas Pavel. Efficient Computation of Morphological Greyscale Reconstruction. In 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, 2010. pp. 92-100, 9 pages. ISBN 978-80-87342-10-7.
BEST PAPER AWARD

Williams Ian, Svoboda David, Bowring Nicholas. A Novel Performance Metric For Grey-Scale Edge Detection. In Proceedings of the International Conference on Computer Vision Theory and Applications. Vol. 1. Portugal: Institute for Systems and Technologies of Information, Control and Communication, 2010. pp. 91-97, 7 pages. ISBN 978-989-674-028-3.

Tesařová Lenka, Peterková Martina, Stejskal Stanislav, Potěšilová Michaela, Koutná Irena. Application of reverse transcription PCR and capillary electrophoresis in the analysis of T-cell receptor beta variable repertoire. In Advances in Molecular and Cancer Biology, 2010. Brno: muni PRESS, 2010. pp. 46-51, 6 pages. ISBN 978-80-210-5312-0.

Potěšilová Michaela, Vařecha Miroslav, Tesařová Lenka, Koutná Irena. Time lapse living cells microscopy for studying CML: Preparation of Abl1- and Bcr/Abl - fluorescent protein vectors using Gateway technology. In Advances in Molecular and Cancer Biology, 2010. Brno: muni PRESS, 2010. pp. 31-35, 5 pages. ISBN 978-80-210-5312-0.

Stejskal Stanislav, Matula Pavel, Daněk Ondřej, Maška Martin, Koutná Irena, Kozubek Michal. A novel approach to evaluation of the spatial relationship of fluorescent signals in ImunnoFISH analysis of different kind. In Advances in Molecular and Cancer Biology, 2010. Brno: muni PRESS, 2010. pp. 39-41, 3 pages. ISBN 978-80-210-5312-0.

Šimara Pavel, Stejskal Stanislav, Peterková Martina, Koutná Irena, Ráčil Zdeněk, Mayer Jiří. Determination of pCrkL level in chronic myeloid leukaemia cells using flow cytometry. In Advances in Molecular and Cancer Biology, 2010. Brno: muni PRESS, 2010. pp. 43-45, 3 pages. ISBN 978-80-210-5312-0.

Ručka Zdeněk, Tesařová Lenka, Potěšilová Michaela, Stejskal Stanislav, Koutná Irena, Vaňhara Petr, Doležel Jan. Dexamethasone and Insulin Affecting SFTPA1 and SFTPA2 mRNA Levels. In Advances in Molecular and Cancer Biology, 2010. Brno: muni PRESS, 2010. pp. 36-38, 3 pages. ISBN 978-80-210-5312-0.

Koutná Irena, Potěšilová Michaela, Peterková Martina, Tesařová Lenka, Ručka Zdeněk. Comparison of gene expression profiling between amplified clinical samples using cDNA microarrays. In Advances in Molecular and Cancer Biology, 2010. Brno: muni PRESS, 2010. pp. 26-30, 5 pages. ISBN 978-80-210-5312-0.

2009

Journal papers

Matula Petr, Kumar Anil, Wörz Ilka, Erfle Holger, Bartenschlager Ralf, Eils Roland, Rohr Karl. Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infection. Cytometry Part A, UNITED STATES: John Wiley & Sons, Inc., 75A, 4, pp. 309-318, 10 pages. ISSN 1552-4922. 2009.

Vařecha Miroslav, Zimmermann Michal, Amrichová Jana, Ulman Vladimír, Matula Pavel, Kozubek Michal. Prediction of localization and interactions of apoptotic proteins. Journal of Biomedical Science, BioMed website: BioMed Central, London, England, 16, 59, pp. 1-14, 14 pages. ISSN 1021-7770. 2009.

Šimara Pavel, Koutná Irena, Stejskal Stanislav, Krontorád Petr, Ručka Zdeněk, Peterková Martina, Kozubek Michal. Combination of mRNA and protein microarray analysis in complex cell profiling. Neoplasma, Bratislava, Slovensko: AEPress, s.r.o., 2/2009, 56, pp. 141-149, 9 pages. ISSN 0028-2685. 2009.

Peterková Martina, Koutná Irena, Tesařová Lenka, Potěšilová Michaela, Kozubek Michal, Hrabčáková Viera, Klabusay Martin, Doubek Michael, Mayer Jiří. Microarray analysis using limited amount of cells. Folia Biologica (Praha), 2009, 55, pp. 53-60, 8 pages. ISSN 0015-5500. 2009.

Svoboda David, Kozubek Michal, Stejskal Stanislav. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry. Cytometry Part A, John Wiley & Sons, Inc., 75A, 6, pp. 494-509, 16 pages. ISSN 1552-4922. 2009.

Brázdilová Silvie Luisa, Kozubek Michal. Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions. Journal of Microscopy, Oxford: Blackwell Science, 236, 3, pp. 194-202, 9 pages. ISSN 0022-2720. 2009.

Conference papers

Maška Martin, Matula Pavel. A Fast Level Set-Like Algorithm with Topology Preserving Constraint. In 13th International Conference on Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2009. pp. 930-938, 9 pages. LNCS 5702. ISBN 978-3-642-03766-5.

Daněk Ondřej, Matula Pavel, Ortiz-de-Solórzano Carlos, Muñoz-Barrutia Arrate, Maška Martin, Kozubek Michal. Segmentation of Touching Cell Nuclei using a Two-Stage Graph Cut Model. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009. pp. 410-419, 10 pages. LNCS 5575. ISBN 978-3-642-02229-6.

Maška Martin, Daněk Ondřej, Ortiz-de-Solórzano Carlos, Muñoz-Barrutia Arrate, Kozubek Michal, García Ignacio Fernández. A Two-Phase Segmentation of Cell Nuclei Using Fast Level Set-Like Algorithms. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009. pp. 390-399, 10 pages. LNCS 5575. ISBN 978-3-642-02229-6.

Matula Pavel, Maška Martin, Daněk Ondřej, Matula Petr, Kozubek Michal. Acquiarium: Free Software for the Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy. In IEEE International Symposium on Biomedical Imaging. Boston: IEEE, 2009. pp. 1138-1141, 4 pages. ISBN 978-1-4244-3932-4.

2008

Journal papers

Ondřej Vladan, Lukášová Emilie, Krejčí Jana, Matula Pavel, Kozubek Stanislav. Lamin A/C and polymeric actin in genome organization. Molecules and Cells, 26, 4, pp. 356-361, 6 pages. ISSN 1016-8478. 2008.

Conference papers

Williams Ian, Svoboda David, Bowring Nicholas, Guest Elizabeth. Statistical Edge Detection of Concealed Weapons Using Artificial Neural Networks. In Proceedings of SPIE-IS&T Electronic Imaging. Vol. 6812. Bellingham, Washington: SPIE, 2008. pp. 68121J-1-12, 12 pages. ISSN 0277-786X.

Brázdilová Silvie Luisa, Kozubek Michal. An Adaptive Algorithm for Multimodal Focus Functions in Automated Fluorescence Microscopy. In Medical Imaging Conference. Dresden: IEEE, 2008. pp. 1-5. M06-291. ISBN 978-1-4244-2714-7.

Vladimír Ulman. Arbitrarily-Oriented Anisotropic 3D Gaussian Filtering Computed with 1D Convolutions without Interpolation. In Proceedings of 8th WSEAS International Conference on Signal Processing, Computational Geometry and Artificial Vision. Ateny: WSEAS, 2008. pp. 56-62, 7 pages. ISBN 978-960-6766-95-4.

Matula Petr, Kumar Anil, Wörz Ilka, Harder Nathalie, Erfle Holger, Bartenschlager Ralf, Eils Roland, Rohr Karl. Automated analysis of siRNA screens of cells infected by hepatitis C and dengue viruses based on immunofluorescence microscopy images. In Proceedings of SPIE. Vol. 6916. 2008. ISSN 0277-786X.

Matula Petr, Kumar Anil, Wörz Ilka, Erfle Holger, Bartenschlager Ralf, Eils Roland, Rohr Karl. Evaluation of siRNA Screens of Cells Infected by Hepatitis C and Dengue Viruses based on Immunofluorescence Microscopy. In Proceedings of 3rd Workshop on Microscopic Image Analysis with Applications in Biology. 2008. 6 pages.

Matula Petr, Kumar Anil, Wörz Ilka, Harder Nathalie, Erfle Holger, Bartenschlager Ralf, Eils Roland, Rohr Karl. Automated Analysis of siRNA Screens of Virus Infected Cells Based on Immunofluorescence Microscopy Images. In Proc. Workshop Bildverarbeitung für die Medizin 2008 - Algorithmen, Systeme, Anwendungen. Berlin Heidelberg: Springer-Verlag, 2008. pp. 453-457, 5 pages.

2007

Journal papers

Vařecha Miroslav, Amrichová Jana, Zimmermann Michal, Ulman Vladimír, Lukášová Emilie, Kozubek Michal. Bioinformatic and image analyses of the cellular localization of the apoptotic proteins endonuclease G, AIF, and AMID during apoptosis in human cells. Apoptosis, USA: Springer Science, 12, 7, pp. 1155-1171, 17 pages. ISSN 1360-8185. 2007.

Koutná Irena, Krontorád Petr, Svoboda Zbyněk, Bártová Eva, Kozubek Michal, Kozubek Stanislav. New insights into gene positional clustering and its properties supported by large-scale analysis of various differentiation pathways. Genomics, United States: Elsevier Science Inc, 89, 1, pp. 81-88, 8 pages. ISSN 0888-7543. 2007.

Skalníková Magdalena, Bártová Eva, Ulman Vladimír, Matula Petr, Svoboda David, Harničarová Andrea, Kozubek Michal, Kozubek Stanislav. Distinct patterns of histone methylation and acetylation in human interphase nuclei. Physiological Research, Prague: Czech Academy of Sciences, 56, 6, pp. 797-806, 10 pages. ISSN 0862-8408. 2007.

Conference papers

Hubený Jan, Ulman Vladimír, Matula Pavel. Estimating Large Local Motion in Live-Cell Imaging Using Variational Optical Flow. In VISAPP 2007 Second International Conference On Computer Vision Theory And Applications, Proceedings. Portugal: INSTICC PRESS, 2007. pp. 542-548, 7 pages. ISBN 978-972-8865-74-0.

Svoboda David, Kašík Marek, Maška Martin, Hubený Jan, Stejskal Stanislav, Zimmermann Michal. On Simulating 3D Fluorescent Microscope Images. In Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2007. pp. 309-316, 8 pages. LNCS 4673. ISBN 978-3-540-74271-5.

Maška Martin, Hubený Jan, Svoboda David, Kozubek Michal. A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy. In 3rd International Symposium on Visual Computing. Berlin, Heidelberg: Spinger-Verlag, 2007. pp. 571-581, 11 pages. LNCS 4842. ISBN 978-3-540-76855-5.

Silvie Luisa Brázdilová. Towards Reliable Autofocusing in Automated Microscopy. In Proceedings of the 4th International Conference on Informatics in Control, Automation and Robotics. Portugal: Insticc Press, 2007. pp. 440-448, 8 pages. ISBN 978-972-8865-82-5.

Vladimír Ulman, Jan Hubený. Pseudo-real Image Sequence Generator for Optical Flow Computations. In Proceedings of 15th Scandinavian Conference on Image Analysis. LNCS 4522. Heidelberg: Springer, 2007. pp. 976-985, 10 pages. ISBN 978-3-540-73039-2.

Vladimír Ulman, Jan Hubený. On Generating Ground-truth Time-lapse Image Sequences and Flow Fields. In Proceedings of the 4th International Conference on Informatics in Control, Automation and Robotics. RA-1. Angers: INSTICC, 2007. pp. 234-239, 6 pages. ISBN 978-972-8865-83-2.

2006

Journal papers

Matula Petr, Matula Pavel, Kozubek Michal, Dvořák Vladimír. Fast Point-Based 3D Alignment of Live Cells. IEEE Transactions on Image Processing, 15, 8, pp. 2388-2396, 9 pages. ISSN 1057-7149. 2006.

Jansová Eva, Koutná Irena, Krontorád Petr, Svoboda Zbyněk, Křivánková Silvie, Žaloudík Jan, Kozubek Michal, Kozubek Stanislav. Comparative transcriptome maps: a new approach to the diagnosis of colorectal carcinoma patients using cDNA microarrays. Clinical Genetics, Denmark: Blackwell Munksgaard, 69, 3, pp. 218-227, 10 pages. ISSN 0009-9163. 2006.

Koutná Irena, Klabusay Martin, Hrabčáková Viera, Krontorád Petr, Svoboda Zbyněk, Kozubek Michal, Mayer Jiří. Evaluation of CD34+ - and Lin- -selected cells from peripheral blood stem cell grafts of patients with lymphoma during differentiation in culture ex vivo using a cDNA microarray technique. Experimental hematology, Netherlands: Elsevier Science Inc, 34, 7, pp. 832-840, 10 pages. ISSN 0301-472X. 2006.

Taslerová Renata, Kozubek Stanislav, Bártová Eva, Gajdušková Pavla, Kodet Roman, Kozubek Michal. Localization of genetic elements of intact and derivative chromosome 11 and 22 territories in nuclei of Ewing sarcoma cells. Journal of Structural Biology, San Diego,USA: Academic Press, 155, 3, pp. 493-504, 12 pages. ISSN 1047-8477. 2006.

Vladimír Ulman. Automatic Detection of Histones on Chromosome X in Images of Cell Nuclei. Clinician and Technology, Praha: Czech Medical Association J.E.Purkyne, roč. 36, 2, pp. 160-164, 5 pages. ISSN 0301-5491. 2006.

Ondřej Vladan, Kozubek Stanislav, Lukášová Emilie, Falk Martin, Matula Pavel, Matula Petr, Kozubek Michal. Directional motion of foreign plasmid DNA to nuclear HP1 foci. Chromosome Research, Dordrecht: Springer, 14, 5, pp. 505-514, 10 pages. ISSN 0967-3849. 2006.

Conference papers

Hubený Jan, Matula Pavel, Matula Petr, Kozubek Michal. Improved 3D Reconstruction of Interphase Chromosomes Based on Nonlinear Diffusion Filtering. In Proceedings of PDE-Based Image Processing and Related Inverse Problems. Berlin: Springer-Verlag, 2006. pp. 163-173, 10 pages. Mathematics and Visualization serie. ISBN 3-540-33266-9.

Svoboda David, Williams Ian, Bowring Nicholas, Guest Elizabeth. Statistical techniques for edge detection in histological images. In First International Conference on Computer Vision Theory and Applications. Portugalsko: INSTICC Press, 2006. pp. 457-462, 6 pages. ISBN 972-8865-40-6.

Ježek Jan, Vařecha Miroslav, Amrichová Jana, Kozubek Michal, Čižmár Tomáš, Zemánek Pavel. Optical tracking of microobjects within living cells. In Proceedings of SPIE. Vol. 6180. Bellingham, USA: International Society for Optical Engineering, 2006. pp. 618025-1, 6 pages. ISBN 0-8194-6236-5.

Williams Ian, Svoboda David, Bowring Nicholas, Guest Elizabeth. Improved statistical edge detection through neural networks. In 10th Conference on Medical Image Understanding and Analysis. Manchester: BMVA, 2006. pp. 56-60, 5 pages. ISBN 1-901727-31-9.

Hubený Jan, Matula Pavel. Fast and Robust Segmentation of Low Contrast Biomedical Images. In Visualization Imaging and Image Processing. Anaheim, Calgary, Zurich: ACTA Press, 2006. pp. 189-196, 8 pages. ISBN 0-88986-598-1.

Kozubek Michal. Automated analysis of multi-dimensional biomedical image data acquired using optical microscopy. Ed. R. Lechnerová, I. Saxl, V. Beneš. In Proceedings of the 6th International Conference on Stereology, Spatial Statistics and Stochastic Geometry. Prague: Union of Czech Mathematicians and Physicists, 2006. pp. 465-476. ISBN 80-7015-037-8.

Brázdilová Silvie Luisa. Focus Function for Biomedical Images as a Result of Genetic Programming. In 2nd Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS). Brno: Brno University of Technology, 2006. pp. 24-31, 8 pages. ISBN 80-214-3287-X.

2005

Book chapters

Kozubek Michal. Image acquisition and its automation in fluorescence microscopy. In From cells to proteins: Imaging nature across dimensions. Dordrecht: Springer, 2005. pp. 227-270, 44 pages. NATO Science Series. ISBN 1-4020-3615-9.

Journal papers

Lukášová Emilie, Kořístek Zdeněk, Falk Martin, Kozubek Stanislav, Grigoryev Sergei, Kozubek Michal, Ondřej Vladan, Kroupová Iva. Methylation of histones in myeloid leukemias as a potential marker of granulocyte abnormalities. Journal of Leukocyte Biology, 77, 1, pages 100-111, 2005. ISSN: 0741-5400.

Bártová Eva, Pacherník J., Harničarová Andrea, Kovařík A., Kovaříková M., Hofmanová Jiřina, Skalníková Magdalena, Kozubek Michal, Kozubek Stanislav. Nuclear levels and patterns of histone H3 modification and HP1 proteins after inhibition of histone deacetylases. Journal of Cell Science, 118, 21, pages 5035-5046, 2005. ISSN: 0021-9533.

Conference papers

Kozubek Michal, Matula Pavel, Matula Petr, Svoboda David. Analysis of biomedical image data acquired using optical microscopy. In Proceedings of the 1st International Summer School on Computational Biology, pages 21-28. Brno : Masaryk University, 2005. ISBN: 80-210-3907-8.

Kozubek Michal, Matula Pavel, Matula Petr, Svoboda David. Analysis of biomedical image data acquired using optical microscopy. In Prague Post Genome Technology Workshop, pages 24-27. Prague, Czech Republic : Czech Pattern Recognition Society, 2005. ISBN: 80-01-03239-6.

Koutná Irena, Jansová Eva, Krontorád Petr, Svoboda Zbyněk, Kozubek Michal, Kozubek Stanislav. cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases. In Prague Post Genome Technology Workshop, pages 69-72. Prague, Czech Republic : Czech Pattern Recognition Society, 2005. ISBN: 80-01-03239-6.

Hubený Jan. Enhancement of Images Acquired using Optical Microscope. In Proceedings of the 1st International Summer School on Computational Biology, pages 29-38. Brno (Česká republika) : Masarykova universita, 2005. ISBN: 80-210-3907-8.

Ulman Vladimír. Mosaicking of High-resolution Biomedical Images Acquired from Wide-field Optical Microscope. In Proceedings of the 3rd European Medical and Biological Engineering Conference EMBEC'05, pages 1-5. Praha : IFMBE Proceedings Series, 2005. ISSN: 1727-1983.

Ulman Vladimír. Quantitative Analysis of Intracellular Processes in Living Cells. In Proceedings of the 1st International Summer School on Computational Biology, pages 84-94. Brno : Masarykova universita, 2005. ISBN: 80-210-3907-8.

2004

Journal papers

Kozubek Michal, Matula Petr, Matula Pavel, Kozubek Stanislav. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. Microscopy research and technique, 64, 2, pages 164-175, 2004. ISSN: 1059-910X.

Jansová Eva, Krontorád Petr, Svoboda Zbyněk, Pavlík Tomáš, Koutná Irena, Kozubek Michal, Žaloudík Jan, Kozubek Stanislav. Nové možnosti v diagnostice kolorektálního karcinomu s využitím technologie cDNA mikročipů. Klinická onkologie, 17, 6, pages 203-207, 2004. ISSN: 0862-495X.

Feit Josef, Ulman Vladimír, Kempf Werner, Jedličková Hana. Pořizování obrazů o velmi vysokém rozlišení metodou skládání. Čes-slov. Patologie, 40, 2, pages 78-82, 2004. ISSN: 1210-7875.

Lukášová Emilie, Kozubek Stanislav, Falk Martin, Kozubek Michal, Žaloudík Jan, Vagunda Václav, Pavlovský Zdeněk. Topography of genetic loci in the nuclei of cells of colorectal carcinoma and adjacent tissue of colonic epithelium. Chromosoma, 112, pages 221-230, 2004. ISSN: 0009-5915.

Conference papers

Matula Petr, Kozubek Michal, Matula Pavel. Applications of Image Registration in Human Genome Research. In Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, pages 376-384. Berlin : Springer-Verlag, 2004. LNCS 3117. ISBN: 3-540-22675-3.

Kozubek Michal, Matula Petr, Matula Pavel. Automated confocal microscopy: The way of achieving both quality and quantity in 3D image cytometry. In International Symposium on Biomedical Imaging, pages 69-72. Arlington, USA : IEEE, 2004. ISBN: 0-7803-8389-3.

Kozubek Michal, Matula Petr, Matula Pavel, Svoboda David, Hubený Jan, Krontorád Petr. Automated image analysis in fluorescence microscopy: From isolated cells to tissues and microarray images. In Biophysics of the Genome, pages 44-46. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Koutná Irena, Jansová Eva, Krontorád Petr, Svoboda Zbyněk, Pavlík Tomáš, Bártová Eva, Kozubek Michal, Kozubek Stanislav. Clustering of genes with similar regulation patterns during monocyte and granulocyte differentiation of HL-60 cells. In Biophysics of the Genome, pages 38-43. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Falk Martin, Lukášová Emilie, Faretta Mario, Dellino Ivan, Kozubek Stanislav, Pelicci Giuseppe, Kozubek Michal, Rochi Mariano. Colocalization of PML bodies and PML/RARalpha microspeckles with up- and down-regulated loci and changes of chromatin structure in APL leukemia cells. In Biophysics of the Genome, pages 8-23. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Skalníková Magdalena, Bártová Eva, Kozubek Stanislav, Kozubek Michal. Cytological study of DNA methylation and histone methylation patterns in human cell lines. In Biophysics of the Genome, pages 72-75. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Ondřej Vladan, Kozubek Stanislav, Lukášová Emilie, Matula Pavel, Matula Petr, Kozubek Michal. Dynamics of HP1 transgene loci movement and silencing in living cells. In Biophysics of the Genome, pages 66-71. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Matula Pavel, Hubený Jan, Kozubek Michal. Fast Marching 3D Reconstruction of Interphase Chromosomes. In Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, pages 385-394. Berlin : Springer-Verlag, 2004. LNCS 3117. ISBN: 3-540-22675-3.

Kozubek Stanislav, Kozubek Michal. From Jenalumar to Ultrafast Microscopy of Living Cells. In Biophysics of the Genome, pages 47-52. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Jansová Eva, Krontorád Petr, Svoboda Zbyněk, Koutná Irena, Pavlík Tomáš, Kozubek Michal, Jarošová Marie, Žaloudík Jan, Kozubek Stanislav. Gene expression in colorectal carcinoma determined by cDNA microarrays using a combination of several evaluation approaches. In Biophysics of the Genome, pages 29-37. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Matula Pavel, Matula Petr, Kozubek Michal, Mejzlík Petr. High-Resolution Cytometry Network Project: Client/Server System for 3D Optical Microscope Data Storage and Analysis. In 2nd International Symposium on 3D Data Processing, Visualization, and Transmission, pages 580-583. Los Alamitos : IEEE Computer Society, 2004. ISBN: 0-7695-2223-8.

Matula Petr, Ondřej Vladan, Kozubek Stanislav. Image analysis of the movement of sub-cellular structures. In Biophysics of the Genome, pages 62-65. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Vařecha Miroslav, Amrichová Jana, Ondřej Vladan, Lukášová Emilie, Kozubek Stanislav, Matula Pavel, Matula Petr, Kozubek Michal. In vivo imaging of cell interior using automated high-resolution cytometry. In Biophysics of the Genome, pages 76-82. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Lukášová Emilie, Falk Martin, Kořistek Zdeněk, Kozubek Stanislav, Grigoryev Sergei, Kozubek Michal, Ondřej Vladan, Kroupová Iva. Methylation of histone H3K9 in human blood cells and in granulocytes of patients with myeloid leukemia. In Biophysics of the Genome, pages 53-57. Brno : Masaryk University, 2004. ISBN: 80-210-3560-9.

Matula Pavel, Kozubek Michal, Kozubek Stanislav, Ondřej Vladan. Rapid Image Acquisition of Living Cells and its Limits. In Biophysics of the Genome, pages 58-61. Brno, Czech Republic : Masaryk University, 2004. ISBN: 80-210-3560-9.

Svoboda David. Towards a Fully Automated Tissue Cell Segmentation Method. In Visualization, Imaging, and Image Processing, pages 430-434. Anaheim, Calgary, Zurich : ACTA Press, 2004. ISBN: 0-88986-454-3.

2003

Journal papers

Taslerová Renata, Kozubek Stanislav, Lukášová Emilie, Jirsová Pavla, Bártová Eva, Kozubek Michal. Arrangement of chromosome 11 and 22 territories, EWSR1 and FLI-1 genes, and other genetic elements of these chromosomes in human lymphocytes and Ewing sarcoma cells. Human Genetics, 112, pages 143-155, 2003. ISSN: 0340-6717.

Bártová Eva, Kozubek Stanislav, Gajová Hana, Jirsová Pavla, Žlůvová Jitka, Taslerová Renata, Koutná Irena, Kozubek Michal. Cytogenetics and cytology of retinoblastomas. J Cancer Res. Clin.Oncol., 129, 2, pages 89-99, 2003. ISSN: 0171-5216.

Amrichová Jana, Lukášová Emilie, Kozubek Stanislav, Kozubek Michal. Nuclear and territorial topography of chromosome telomeres in human lymphocytes. Experimental Cell Research, 289, 1, pages 11-26, 2003. ISSN: 0014-4827.

Matula Petr, Kozubek Michal, Staier Florian, Hausmann Michael. Precise 3D image alignment in micro-axial tomography. Journal of Microscopy, 209, pages 126-142, 2003. ISSN: 0022-2720.

Conference papers

Kozubek Michal, Matula Petr, Matula Pavel, Mejzlík Petr. A network solution for high-resolution image cytometry. In Biophysics of the Genome, pages 30-36. Brno : Masaryk University, 2003. ISBN: 80-210-3226-X.

Skalníková Magdalena, Bártová Eva, Gajdušková Pavla, Kozubek Stanislav, Kozubek Michal. Analysis of DNA methylation status of cell nuclei using high-resolution. In Biophysics of the Genome, pages 59-61. Brno : Masaryk University, 2003. ISBN: 80-210-3226-X.

Bártová Eva, Fojtová Miloslava, Souček Karel, Matula Pavel, Palša Stanislav, Kozubek Stanislav. Architecture of chromosomal territories in apoptotic cells. In Biophysics of the Genome, pages 13-22. Brno : Masaryk University, 2003. ISBN: 80-210-3226-X.

Kozubek Stanislav, Lukášová Emilie, Bártová Eva, Kozubek Michal, Katsuzumi Okumura. Detailed studies of the human genome 3D structure. In Biophysics of the Genome, pages 37-41. Brno : Masaryk University, 2003. ISBN: 80-210-3226-X.

Matula Petr, Skalníková Magdalena, Kozubek Michal, Hausmann Michael. Improving measurement precision using automated micro-axial tomography. In Biophysics of the Genome, pages 51-53. Brno : Masaryk University, 2003. ISBN: 80-210-3226-X.

Svoboda David, Matula Pavel. Multilevel Adaptive Thresholding and Dual Simplex Mesh Deformation as a Tool for Tissue Reconstruction. In Visualization, Imaging, and Image Processing, pages 499-503. Anaheim, Calgary, Zurich : ACTA Press, 2003. ISBN: 0-88986-382-2.

Matula Pavel, Svoboda David. Spherical Object Reconstruction Using Simplex Meshes from Sparse Data. In Discrete Geometry for Computer Imagery, pages 524-533. Berlin Heidelberg New York : Springer-Verlag, 2003. LNCS 2886. ISBN: 3-540-20499-7.

Vařecha Miroslav, Jaburek Martin, Dvorak Lubomi, Jezek Petr, Pauček Petr, Garlid Keith, Kozubek Stanislav, Kozubek Michal. Structural and functional characterization of uncoupling proteins: Alkylsulfonates as probes of UCP transport mechanism. In Biophysics of the Genome, pages 74-81. Brno : Masaryk University, 2003. ISBN: 80-210-3226-X.

Svoboda David, Matula Pavel. Tissue image reconstruction: Localization of nuclei markers and segmentation based on deformable models. In Biophysics of the Genome, pages 67-70. Brno : Masaryk University, 2003. ISBN: 80-210-3226-X.

Svoboda David, Matula Pavel. Tissue Reconstruction Based on Deformation of Dual Simplex Meshes. In Discrete Geometry for Computer Imagery, pages 514-523. Berlin, Heidelberg, New York : Springer, 2003. LNCS 2886. ISBN: 3-540-20499-7.

Amrichová Jana, Kozubek Stanislav, Lukášová Emilie, Kozubek Michal. Topography of telomeres and structure of chromosome territories in human lymphocytes. In Biophysics of the Genome, pages 1-11. Brno : Masaryk University, 2003. ISBN: 80-210-3226-X.

2002

Journal papers

Kozubek Michal, Skalníková Magdalena, Matula Petr, Bártová Eva, Rauch Joachim, Neuhaus Friedrich, Eipel Heinz, Hausmann Michael. Automated micro axial tomography of cell nuclei after specific labelling by fluorescence in situ hybridisation. Micron, 33, pages 655-665, 2002. ISSN: 0968-4328.

Bártová Eva, Kozubek Stanislav, Jirsová Pavla, Kozubek Michal, Gajová Hana, Lukášová Emilie, Skalníková Magdalena, Gaňová Alena, Koutná Irena, Hausmann Michael. Nuclear structure and gene activity in human differentiated cells. Journal of Structural Biology, 139, pages 76-89, 2002. ISSN: 1047-8477.

Kozubek Michal, Matula Petr, Matula Pavel. The power of computerized light microscopy. Imaging & Microscopy, 4, pages 25-28, 2002. ISSN: 1439-4243.

Lukášová Emilie, Kozubek Stanislav, Kozubek Michal, Falk Martin, Amrichová Jana. The 3D structure of human chromosomes in cell nuclei. Chromosome Research, 10, pages 535-548, 2002. ISSN: 0967-3849.

Falk Martin, Lukášová Emilie, Kozubek Stanislav, Kozubek Michal. Topography of genetic elements of X-chromosome relative to the cell nucleus and to the chromosome X territory determined for human lymphocytes. Gene, 292, pages 13-24, 2002. ISSN: 0378-1119.

Kozubek Stanislav, Lukášová Emilie, Jirsová Pavla, Koutná Irena, Kozubek Michal, Gaňová Alena, Bártová Eva, Falk Martin, Taslerová Renata. 3D Structure of the human genome: Order in randomness. Chromosoma, 111, pages 321-331, 2002. ISSN: 0009-5915.

Conference papers

Kozubek Michal, Matula Petr, Eipel Heinz, Hausmann Michael. Automated multi-view 3D image acquisition in human genome research. In 3D data processing, visualization and transmission, pages 91-98. Los Alamitos : IEEE Computer Society, 2002. ISBN: 0-7695-1521-5.

Matula Pavel, Svoboda David. Cell Nuclei Segmentation Using Star-Shaped Simplex Meshes. In Biophysics of the Genome and Its Interactions, pages 74-76. Brno : Masaryk University, 2002. ISBN: 80-210-2853-X.

Bártová Eva, Kozubek Stanislav, Gajová Hana, Jirsová Pavla, Autrata Rudolf, Kozubek Michal. Cytogenetics of Retinoblastoma. In Biophysics of the genome and its interactions, pages 7-11. Brno : Masaryk University, 2002. ISBN: 80-210-2853-X.

Kozubek Michal, Skalníková Magdalena, Matula Petr, Bártová Eva, Eipel Heinz, Hausmann Michael. Development of software for automated micro-axialtomography. In Biophysics of the genome and its interactions, pages 45-53. Brno : Masaryk University, 2002. ISBN: 80-210-2853-X.

Matula Pavel. Effectivity of Spherical Object Reconstruction Using Star-Shaped Simplex Meshes. In 1st International Symposium on 3D Data Processing Visualization and Transmission, pages 794-799. Los Alamitos : IEEE Computer Society, 2002. ISBN: 0-7695-7521-5.

Matula Petr, Matula Pavel, Mejzlík Petr, Kozubek Michal. FISH 3.0 client-server system for 3D optical microscope data storage and analysis. In Biophysics of the genome and its interactions, pages 77-79. Brno : Masaryk University, 2002. ISBN: 80-210-2853-X.

Kozubek Michal, Matula Petr, Matula Pavel, Mejzlík Petr. High-resolution cytometry network project: Towards remote and distributed acquisition, processing and visualisation of 3D image data in human genome research. In 3D data processing, visualization and transmission, pages 99-106. Los Alamitos : IEEE Computer Society, 2002. ISBN: 0-7695-1521-5.

Bártová Eva, Kozubek Stanislav, Jirsová Pavla, Kozubek Michal, Lukášová Emilie, Skalníková Magdalena, Gaňová Alena, Koutná Irena, Paseková Renata. Nuclear topography and gene activity. In Biophysics of the genome and its interactions, pages 13-17. Brno : Masaryk University, 2002. ISBN: 80-210-2853-X.

Skalníková Magdalena, Kozubek Michal, Matula Petr, Bártová Eva, Eipel Heinz, Hausmann Michael. Optimisation of FISH Methodology for the Study of 3D Structure of Cell Nuclei Using Micro Axial Tomography. In Biophysics of the Genome and Its Interactions, pages 82-85. Brno : Masaryk University, 2002. ISBN: 80-210-2853-X.

Amrichová Jana, Lukášová Emilie, Kozubek Stanislav, Jirsová Pavla, Kozubek Michal. Spatial distribution of centromeric and subtelomeric DNA sequences in interphase nuclei of human Go and stimulated lymphocytes. In Biophysics of the genome and its interactions, pages 1-6. Brno : Masaryk University, 2002. ISBN: 80-210-2853-X.

Kozubek Stanislav, Lukášová Emilie, Bártová Eva, Koutná Irena, Jirsová Pavla, Kozubek Michal, Gaňová Alena, Paseková Renata, Amrichová Jana, Falk Martin, Hložek Pavel. Structure of the human genome: Experimental results and models. In Biophysics of the genome and its interactions, pages 54-67. Brno : Masaryk University, 2002. ISBN: 80-210-2853-X.

2001

Book chapters

Kozubek Michal. FISH Imaging. In Confocal and two-photon microscopy: Foundations, applications, and advances. New York: Wiley-Liss, 2001. pp. 389-429. ISBN 0-471-40920-0.

Journal papers

Jabůrek M., Vařecha M., Ježek P., Garlid K.D. Alkylsulfonates as probes of uncoupling protein transport mechanism: ion pair transport demonstrates that H+ translocation by UCP1 is not necessary for uncoupling. Journal of Biological Chemistry, 276, 34, pages 31897-31905, 2001. ISSN: 0021-9258.

Kozubek Michal, Kozubek Stanislav, Lukášová Emilie, Bártová Eva, Skalníková Magdalena, Matula Pavel, Matula Petr, Jirsová Pavla, Gaňová Alena, Koutná Irena. Combined confocal and wide-field high-resolution cytometry of FISH-stained cells. Cytometry, 45, pages 1-12, 2001. ISSN: 0196-4763.

Gaňová Alena, Lukášová Emilie, Kozubek Stanislav, Kozubek Michal, Govorun Raisa, Koutná Irena, Bártová Eva, Skalníková Magdalena, Jirsová Pavla, Paseková Renata, Krasavin Evgenij. Exchange aberrations among 11 chromosomes of human lymphocytes induced by gamma-rays. International Journal of Radiation Biology, 77, pages 419-429, 2001. ISSN: 0955-3002.

Bártová Eva, Kozubek Stanislav, Jirsová Pavla, Kozubek Michal, Lukášová Emilie, Skalníková Magdalena, Gaňová Alena, Koutná Irena, Paseková Renata. Higher-order chromatin structure of human granulocytes. Chromosoma, 110, pages 360-370, 2001. ISSN: 0009-5915.

Jirsová Pavla, Kozubek Stanislav, Bártová Eva, Kozubek Michal, Lukášová Emilie, Gaňová Alena, Koutná Irena, Skalníková Magdalena. Spatial distribution of selected genetic loci in nuclei of human leukemia cells after irradiation. Radiation Research, 155, pages 311-319, 2001. ISSN: 0033-7587.

Kozubek Michal. Theoretical versus experimental resolution in optical microscopy. Microscopy research and technique, 53, pages 157-166, 2001. ISSN: 1059-910X.

Conference papers

Voráček Jan, Kozubek Michal, Bártová Eva, Mannio Markus. Deterministic modeling of the chromatin organization in human cell nuclei. In Shaping future with simulation, pages 1-7. Delft : TU Delft, 2001. ISBN: 90-806441-1-0.

Matula Pavel, Svoboda David. Spherical Object Reconstruction Using Star-Shaped Simplex Meshes. In Energy Minimization Methods in Computer Vision and Pattern Recognition, pages 608-620. Berlin, Heidelberg, New York : Springer-Verlag, 2001. LNCS 2134. ISBN: 3-540-42523-3.

2000

Journal papers

Kozubek Michal, Matula Petr. An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy. Journal of Microscopy, 200, pages 206-217, 2000. ISSN: 0022-2720.

Garlid K.D., Jabůrek M., Ježek P., Vařecha M.. How do uncoupling proteins uncouple?. Biochimica et Biophysica Acta, 3, pages 383-389, 2000. ISSN: 0005-2728.

Kozubek Stanislav, Lukášová Emilie, Amrichová Jana, Kozubek Michal, Lišková Andrea, Šlotová Jana. Influence of cell fixation on chromatin topography. Analytical Biochemistry, 282, pages 29-38, 2000. ISSN: 0003-2697.

Bártová Eva, Kozubek Stanislav, Kozubek Michal, Jirsová Pavla, Lukášová Emilie, Skalníková Magdalena, Cafourková Alena, Koutná Irena. Nuclear topography of the c-myc gene in human leukemic cells. Gene, 244, pages 1-11, 2000. ISSN: 0378-1119.

Skalníková Magdalena, Kozubek Stanislav, Lukášová Emilie, Bártová Eva, Jirsová Pavla, Cafourková Alena, Koutná Irena, Kozubek Michal. Spatial arrangement of genes, centromeres and chromosomes in human blood cell nuclei and its changes during the cell cycle, differentiation and after irradiation. Chromosome Research, 8, pages 487-499, 2000. ISSN: 0967-3849.

Bártová Eva, Kozubek Stanislav, Kozubek Michal, Jirsová Pavla, Lukášová Emilie, Skalníková Magdalena, Buchníčková Kateřina. The influence of the cell cycle, differentiation and irradiation on the nuclear location of the ABL, BCR and C-MYC genes in human leukemic cells. Leukemia Research, 24, pages 233-241, 2000. ISSN: 0145-2126.

Koutná Irena, Kozubek Stanislav, Žaloudík Jan, Kozubek Michal, Lukášová Emilie, Matula Pavel, Bártová Eva, Skalníková Magdalena, Cafourková Alena, Jirsová Pavla. Topography of genetic loci in tissue samples: towards new diagnostic tool using interphase FISH and high-resolution image analysis techniques. Analytical Cellular Pathology, 20, pages 173-185, 2000. ISSN: 0921-8912.

1999

Journal papers

Kozubek Michal, Kozubek Stanislav, Lukášová Emilie, Marečková Andrea, Bártová Eva, Skalníková Magdalena, Jergová Adriana. High-resolution cytometry of FISH dots in interphase cell nuclei. Cytometry, 36, pages 279-293, 1999. ISSN: 0196-4763.

Lukášová Emilie, Kozubek Stanislav, Kozubek Michal, Kroha Václav, Marečková Andrea, Skalníková Magdalena, Bártová Eva, Šlotová Jana. Chromosomes participating in translocations typical of malignant hemoblastoses are also involved in exchange aberrations induced by fast neutrons. Radiation Research, 151, pages 375-384, 1999. ISSN: 0033-7587.

Kozubek Stanislav, Lukášová Emilie, Marečková Andrea, Skalníková Magdalena, Kozubek Michal, Bártová Eva, Kroha Václav, Krahulcová Eva, Šlotová Jana. The topological organization of chromosomes 9 and 22 in cell nuclei has a determinative role in the induction of t(9,22) translocations and in the pathogenesis of t(9,22) leukemias. Chromosoma, 108, pages 426-435, 1999. ISSN: 0009-5915.

Jabůrek M., Vařecha M., Gimeno R.E., Dembski M., Ježek P., Zhang M., Burn P., Tartaglia L.A., Garlid K.D. Transport function and regulation of mitochondrial uncoupling proteins 2 and 3. Journal of Biological Chemistry, 274, 37, pages 26003-26007, 1999. ISSN: 0021-9258.

Conference papers

Lukášová Emilie, Kozubek Stanislav, Govorun Raisa, Repin Michail, Rýznar Leonard, Krasavin Evgenij, Kozubek Michal, Kroha Václav. Aberrations induced in chromosome 1, 2 and Y of human lymphocytes by three types of radiation of different LET value as detected by FISH. In Fundamentals for the assesment of risks from environmental radiation, pages 195-202. Dordrecht : Kluwer Academic Publishers, 1999. ISBN: 0-7923-5667-5.

Kozubek Michal, Kozubek Stanislav, Lukášová Emilie, Rýznar Leonard, Lišková Andrea, Amrichová Jana, Horneck Gerda. Advances in computer analysis of radiation-induced changes in human genome. In Fundamentals for the assesment of risks from environmental radiation, pages 243-248. Dordrecht : Kluwer Academic Publishers, 1999. ISBN: 0-7923-5667-5.

Kozubek Stanislav, Lukášová Emilie, Rýznar Leonard, Kozubek Michal, Lišková Andrea, Kroha Václav. Chromatin structure and its cell cycle kinetics in intact and irradiated cell nuclei. In Fundamentals for the assesment of risks from environmental radiation, pages 231-242. Dordrecht : Kluwer Academic Publishers, 1999. ISBN: 0-7923-5667-5.

Bártová Eva, Kozubek Stanislav, Durm Markus, Hausmann Michael, Kozubek Michal, Lukášová Emilie, Skalníková Magdalena, Jirsová Pavla, Cafourková Alena, Buchníčková Kateřina. The position of centromeres in interphase nuclei of human leukemic cells during myeloid differentiation and after gamma-irradiation. In Fluorescence microscopy and fluorescent probes, pages 347-354. Ústí nad Labem : Espero Publishing, 1999. ISBN: 80-238-4668-X.

Skalníková Magdalena, Kozubek Stanislav, Lukášová Emilie, Kozubek Michal, Bártová Eva, Marečková Andrea, Jirsová Pavla, Cafourková Alena. Topography of some genes and chromosomes in interphase nuclei of human cells. In Fluorescence microscopy and fluorescent probes, pages 259-266. Ústí nad Labem : Espero Publishing, 1999. ISBN: 80-238-4668-X.

1998

Conference papers

Kozubek Michal, Kozubek Stanislav, Lukášová Emilie, Amrichová Jana, Rýznar Leonard, Lišková Andrea. Semi-automated FISH-stained interphase nuclei analysis in human genome studies. In Fluorescence Microscopy and Fluorescent Probes, pages 173-179. New York : Plenum, 1998. ISBN: 0-306-46021-1.

1997

Journal papers

Lukášová Emilie, Kozubek Stanislav, Kozubek Michal, Kjeronská Jana, Rýznar Leonard, Horáková Jana, Krahulcová Eva, Horneck Gerda. Localisation and distance between ABL and BCR genes in interphase nuclei of bone marrow cells of control donors and patients with chronic myeloid leukemia. Human Genetics, pages 525-535, 1997. ISSN: 0340-6717.

Kozubek Stanislav, Lukášová Emilie, Rýznar Leonard, Kozubek Michal, Govorun Raisa, Krasavin Evgenij, Horneck Gerda. Distribution of ABL and BCR genes in cell nuclei of normal and irradiated lymphocytes. Blood, 89, pages 4537-4545, 1997. ISSN: 0006-4971.

Schrader Martin, Kozubek Michal, Hell Stefan, Wilson Tony. Optical transfer functions of 4Pi confocal microscopes : theory and experiment. Optics Letters, 22, pages 436-438, 1997. ISSN: 0146-9592.

Conference papers

Wilson Tony, Juškaitis Rimas, Neil Mark, Kozubek Michal. An aperture correlation approach to confocal microscopy. In Three-Dimensional Microscopy: Image Acquisition and Processing IV, pages 21-24. Bellingham : SPIE, 1997. ISBN: 0-8194-2395-5.

1996

Journal papers

Wilson Tony, Juškaitis Rimas, Neil Mark, Kozubek Michal. Confocal microscopy by aperture correlation. Optics Letters, 21, pages 1879-1881, 1996. ISSN: 0146-9592.

Juškaitis Rimas, Wilson Tony, Neil Mark, Kozubek Michal. Efficient real-time confocal microscopy with white light sources. Nature, 383, pages 804-806, 1996. ISSN: 0028-0836.