Research Project Results
Determination of markers, screening and early diagnostics of cancer diseases using highly automated processing of multidimensional biomedical images (Biomarker)
| Project Identification: | 2B06052 | ||||||
| MU Investigator: | Prof. RNDr. Michal Kozubek, Ph.D. | ||||||
| MU Faculty/Unit: | Faculty of Informatics | ||||||
| Project Period: | 7/2006 - 6/2011 | ||||||
| Investor/Programme: | Ministry of Education, Youth and Sports of the CR - | ||||||
| Cooperating Organization: |
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Brno University of Technology Results: (Czech only)
Cílem projektu je vyvinout nové postupy zpracování obrazových dat z fluorescenční mikroskopie a microarrays, které v kombinaci s výzkumem genomických a proteomických technik pomohou s vytipováním markerů, screeningu a diagnostice nádorových onemocnění.
Publications:
ŠIMARA, Pavel - PETERKOVÁ, Martina - STEJSKAL, Stanislav - POTĚŠILOVÁ, Michaela - KRONTORÁD 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, Great Britain. ISSN 1042-8194, 2012, vol. 53, no. 8, pp. 1627-1629.
VAŘECHA, Miroslav - POTĚŠILOVÁ, Michaela - MATULA, Pavel - KOZUBEK, Michal.
Endonuclease G interacts with histone H2B and DNA topoisomerase II alpha during apoptosis. Mol Cell Biochem, , , The Nederlands. ISSN 0300-8177, 2012, vol. 363, no. 1-2, pp. 301-307.
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). Neuveden : Springer Berlin / Heidelberg, 2012. ISBN 978-3-642-33139-8, pp. 59-71. 2012, Brno.
VAŘECHA, Miroslav - PÁCLOVÁ, Daniela - PROCHÁZKOVÁ, Jiřina - MATULA, Pavel - CMARKO, Dušan - KOZUBEK, Michal.
Knockdown of apoptosis-inducing factor increases mitochondrial superoxide level in telomerasepositive cancer cells. BIOCELL, Argentina, National Council of Scientific and Techn, Argentina. ISSN 0327-9545, 2012, vol. 36, no. 3, pp. 121-126.
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, USA. ISSN 1398-9219, 2012, vol. 13, no. 3, 416–432-17 pp.
DANĚK, Ondřej - MATULA, Pavel - MAŠKA, Martin - KOZUBEK, Michal.
Smooth Chan-Vese Segmentation via Graph Cuts. Pattern Recognition Letters, Amsterdam, Elsevier, The Nederlands. ISSN 0167-8655, 2012, vol. 33, no. 10, pp. 1405-1410.
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. ISBN 978-3-939897-22-4, pp. 19-25. 22.10.2010, MikulovOASIcs: Open Access Series in Informatics.
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. ISBN 978-3-642-19866-3, pp. 71-82. 2011, NancyLNCS 6607.
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, USA. ISSN 1687-6172, 2011, vol. 2011, no. ID 234090, pp. 1-9.
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, USA. ISSN 1687-6172, 2011, vol. 2011, no. 120, pp. 1-12.
SVOBODA, David.
Efficient Computation of Convolution of Huge Images. In Image Analysys and Processing - ICIAP 2011. Vyd. LNCS 6978, Part I. Berlin, Heidelberg : Springer-Verlag, 2011. ISBN 978-3-642-24084-3, pp. 453-462. 13.9.2011, Ravenna, Italy.
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. ISBN 978-3-939897-22-4, pp. 54-61. 22.10.2010, Mikulov.
VAŘECHA, Miroslav - POTĚŠILOVÁ, Michaela - MATULA, Pavel - KOZUBEK, Michal.
Endonuclease G interacts with histone H2B, AIF, and DNA topoisomerase II alpha during apoptosis as revealed by FRET analysis of living cells. 2011.
ULMAN, Vladimír.
Fast Anisotropic Filtering and Performance Evaluation Tool for Optical Flow in Biomedical Image Analysis. 2011.
MAŠKA, Martin - MATULA, Pavel - MUNOZ-BARRUTIA, Arrate - ORTIZ-DE-SOLÓRZANO, Carlos.
Fast Tracking Algorithm of GFP-Transfected Living Cells Based on the Chan-Vese Model. 2011.
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. Vyd. LNCS 6754, Part II. Berlin, Heidelberg : Springer-Verlag, 2011. ISBN 978-3-642-21595-7, pp. 31-39. 22.6.2011, Burnaby, BC, Canada.
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, , , USA. ISSN 1066-5099, 2011, vol. 29, no. 1, pp. 46-56.
BRÁZDILOVÁ, Silvie Luisa - KOZUBEK, Michal.
Image Division Technique in Pre-acquisition Analysis of Information Content for Automated Microscopy. Journal of Microscopy, Oxford, Blackwell Science, Great Britain. ISSN 0022-2720, 2011, vol. 242, no. 3, pp. 279-289.
VAŘECHA, Miroslav - POTĚŠILOVÁ, Michaela - MATULA, Pavel - KOZUBEK, Michal.
Interaction of endonuclease G with histone H2B, AIF, and DNA topoisomerase II alpha during apoptosis as revealed by FRET imaging of living cells. 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, USA. ISSN 0034-6748, 2011, vol. 82, no. 9, pp. "093701-1"-"093701-8".
TESAŘOVÁ, Lenka - KRONTORÁD 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, USA. ISSN 1521-6616, 2011, vol. 138, no. 1, pp. 67-76.
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, Great Britain. ISSN 1471-2105, 2011, vol. 12, no. 485, pp. 1-14.
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. ISBN 978-3-642-25381-2, pp. 125-134. 2010, Angers.
KRONTORÁD 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, Germany. ISSN 0939-5555, 2011, vol. 90, no. (2), pp. 127-137.
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. Neuveden : Neuveden, 2011. 4 p. 2.9.2011, Heidelberg.
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, , , USA. ISSN 1931-3128, 2011, vol. 9, no. 1, pp. 32-45.
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. ISBN 978-3-939897-22-4, pp. 69-76. 22.10.2010, Mikulov.
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, Great Britain. ISSN 0887-6924, 2011, vol. 25, no. 7, pp. 1159-1167.
ULMAN, Vladimír - SVOBODA, David.
Tool for Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy. 2011.
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. ISBN 978-3-642-17276-2, pp. 387-396. 27.11.2010, Las VegasLNCS 6455.
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. ISBN 978-80-210-5312-0, pp. 39-41. 11.11.2010, Brno, Česká Republika.
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. ISBN 978-80-87342-10-7, pp. 45-52. 22.10.2010, Mikulov.
MATULA, Pavel - DANĚK, Ondřej - MAŠKA, Martin - VINKLER, Marek - KOZUBEK, Michal.
Acquiarium: Free Software For Image Acquisition And Image Analysis In Cytometry. 2010.
VAŘECHA, Miroslav.
AIFM2 (apoptosis-inducing factor, mitochondrion-associated, 2). Atlas of Genetics and Cytogenetics in Oncology and Haematology, Francie, INIST-CNRS, France. ISSN 1768-3262, 2010, vol. 5, no. 14, pp. 435-436.
Alteration in mitochondrial superoxide production by shRNA gene silencing of AIF in various cell line. 2010.
VAŘECHA, Miroslav - PÁCLOVÁ, Daniela - PROCHÁZKOVÁ, Jiřina - MATULA, Pavel - KOZUBEK, Michal.
Alteration in mitochondrial superoxide production by shRNA gene silencing of AIF in various cell lines. 2010.
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, Česká republika : muni PRESS, 2010. ISBN 978-80-210-5312-0, pp. 46-51. 11.11.2010, Brno, Česká Republika.
VAŘECHA, Miroslav - MATULA, Pavel - KOZUBEK, Michal.
Automated spinning disk confocal microscopy in 3D live cell imaging. 2010.
KOZUBEK, Michal - SVOBODA, David - STEJSKAL, Stanislav.
CytoPacq: A web-based toolbox for simulation of 3D cell imaging and quality control of related image analysis. 2010. Československá mikroskopická společnost.
ŠIMARA, Pavel - STEJSKAL, Stanislav - PETERKOVÁ, Martina - KRONTORÁD KOUTNÁ, Irena - RÁČIL, Zdeněk - MAYER, Jiří.
Dasatinib Promotes BIM Dependent Apoptosis Via MEK/ERK without Need for Permanent BCR-ABL Inhibition. 2010.
ŠIMARA, Pavel - STEJSKAL, Stanislav - PETERKOVÁ, Martina - MAYER, Jiří - RÁČIL, Zdeněk - KRONTORÁD KOUTNÁ, Irena - KOZUBEK, Michal.
Dasatinib suppresses MEK/ERK pathway activity without sustained BCR-ABL inhibition and promotes BIM dependent apoptosis in chronic myeloid leukaemia cells. 2010.
Determination of pCrkL level in chronic myeloid leukaemia cells using flow cytometry. In Advances in Molecular and Cancer Biology, 2010. Brno, Česká Republika : muni PRESS, 2010. ISBN 978-80-210-5312-0, pp. 43-45. 11.11.2010, Brno, Česká Republika.
KOZUBEK, Michal.
Digital phantoms of cell nuclei and the use of simulations in nuclear studies. 2010.
KARAS, Pavel.
Efficient Computation of Morphological Greyscale Reconstruction. In 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno : NOVPRESS, 2010. ISBN 978-80-87342-10-7, pp. 92-100. 22.10.2010, Mikulov.
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. ISBN 978-0-88986-823-6, pp. 33-42. 17.2.2010, Innsbruck.
KOZUBEK, Michal - BRÁZDILOVÁ, Silvie Luisa.
From autofocusing to automatic 3D information content analysis. 2010. Faculty of Informatics, Masaryk University, Brno, Czech republic.
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. ISBN 978-989-674-029-0, pp. 68-73. 17.5.2010, AngersUděleno ocenění Best Student Paper Award.
BRÁZDILOVÁ, Silvie Luisa - KOZUBEK, Michal.
Image Division Technique in Automated Fluorescence Microscopy. 2010.
BRÁZDILOVÁ, Silvie Luisa - KOZUBEK, Michal.
Image Division Technique in Automated Fluorescence Microscopy with Complex Content. In PROCEEDINGS OF THE IADIS INTERNATIONAL CONFERENCE COMPUTER GRAPHICS, VISUALIZATION, COMPUTER VISION AND IMAGE PROCESSING 2010. Vyd. 2010. Freiburg, Germany : International Association for Development of the Information Society, 2010. ISBN 978-972-8939-15-1, pp. 176-183. 26.7.2010, Freiburg.
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. ISBN 978-3-642-13771-6, pp. 263-273. 21.6.2010, Povoa de Varzim (Portugal)LNCS 6111.
BRÁZDILOVÁ, Silvie Luisa.
Information Content Analysis in Automated Fluorescence Microscopy. 2010.
BRÁZDILOVÁ, Silvie Luisa - KOZUBEK, Michal.
Information content analysis in automated microscopy imaging using modified autofocusing approach. 2010. p. 40.
STEJSKAL, Stanislav - KRONTORÁD KOUTNÁ, Irena - RUČKA, Zdeněk.
Isolation of granulocytes: Which transcriptome do we analyze neutrophils or eosinophils?. Folia Biol. ISSN 0015-5500, 2010, vol. Neuveden, no. 56, pp. 252 - 255.
MATULA, Petr - VERISSIMO, Fatima - WÖRZ, Stefan - EILS, Roland - PEPPERKOK, Rainer - ROHR, Karl.
Quantification of Fluorescent Spots in Time Series of 3-D Confocal Microscopy Images Based on the HMAX Transform. 2010. 15. Leipziger Workshop, Cytomics and Stem Cells Incorporating: 8th International Workshop, Slide-Based Cytometry, Biotechnological-Biomedical Centre, Bio-City Leipzig.
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. Neuveden : Neuveden, 2010. ISBN 978-0-8194-8027-9, 7 p. 2010, San DiegoVol. 7626.
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. ISBN 978-80-87342-10-7, pp. 117-125. 22.10.2010, Mikulov.
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, , , USA. ISSN 0730-2312, 2010, vol. 109, no. 5, pp. 915-926.
HARNIČAROVÁ, Andrea - BÁRTOVÁ, Eva - GALIOVÁ, Gabriela - UHLÍŘOVÁ, Radka - MATULA, Pavel - KOZUBEK, Stanislav.
SUV39h-independent association of HP1b with fibrillarin-positive nucleolar regions. Chromosoma, , Springer, Germany. ISSN 0009-5915, 2010, vol. 119, no. 3, pp. 227-241.
STEJSKAL, Stanislav - KRONTORÁD 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, USA. ISSN 1559-2294, 2010, vol. 5, no. 8, pp. 759-767.
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. ISBN 978-80-210-5312-0, pp. 31-35. 11.11.2010, Brno.
HOLUBCOVÁ, Zuzana - MATULA, Pavel - SEDLÁČKOVÁ, Miroslava - BÁRTA, Tomáš - DOLEŽALOVÁ, Dáša - DVOŘÁK, Petr - HAMPL, Aleš.
To divide or not to divide? How human embryonic stem cells deal with extra chromosomes?. 2010.
Too much of a good thing can harm: deregulation of centrosome number in human embryonic stem cells. 2010.
KOZUBEK, Michal.
Využití laseru ve světelné mikroskopii při studiu prostorového uspořádání a dynamiky buněčných struktur. 2010.
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. ISBN 978-3-642-03766-5, pp. 930-938. 2.9.2009, MuensterLNCS 5702.
MAŠKA, Martin - DANĚK, Ondřej - ORTIZ-DE-SOLÓRZANO, Carlos - MUNOZ-BARRUTIA, Arrate - KOZUBEK, Michal - FERNÁNDEZ GARCÍA, Ignacio.
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. ISBN 978-3-642-02229-6, pp. 390-399. 15.6.2009, OsloLNCS 5575.
MATULA, Pavel - MAŠKA, Martin - DANĚK, Ondřej - VINKLER, Marek.
Acquiarium 2009. 2009.
MATULA, Pavel - DANĚK, Ondřej - MAŠKA, Martin - VINKLER, Marek - KOZUBEK, Michal.
Acquiarium: Free image acquisition and analysis software for image cytometry. 2009.
MATULA, Pavel - DANĚK, Ondřej - MAŠKA, Martin - VINKLER, Marek - KOZUBEK, Michal.
Acquiarium: Free Software For Image Acquisition And 3D Analysis Of Fluorescently Labeled Cells. 2009.
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. ISBN 978-1-4244-3932-4, pp. 1138-1141. 28.6.2009, Boston.
BRÁZDILOVÁ, Silvie Luisa - KOZUBEK, Michal.
Autofocusing software issues in automated fluorescence microscopy. 2009.
BRÁZDILOVÁ, Silvie Luisa - KOZUBEK, Michal.
Automated search for information content in fluorescence microscopy images using modified autofocusing approach. 2009.
VAŘECHA, Miroslav - AMRICHOVÁ, Jana - MATULA, Pavel - KOZUBEK, Michal.
Automated spinning disk confocal microscopy in 3D live cell imaging. 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., Slovakia. ISSN 0028-2685, 2009, vol. 2/2009, no. 56, pp. 141-149.
SVOBODA, David - KOZUBEK, Michal - COUFAL, Jaromír.
CytoPacq. 2009.
KOZUBEK, Michal.
Free tools for automated cell image acquisition and analysis. 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., USA. ISSN 1552-4922, 2009, vol. 75A, no. 6, pp. 494-509.
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, Great Britain. ISSN 0022-2720, 2009, vol. 236, no. 3, pp. 194-202.
RUČKA, Zdeněk - VAŇHARA, Petr - TESAŘOVÁ, Lenka - POTĚŠILOVÁ, Michaela - STEJSKAL, Stanislav - DOLEŽEL, Jan - KOUTNÁ, Irena.
Insulin Decreases Transcription of Three Proteins Associated with Lung Surfactant. Vyd. 2009. Posters@Technologynetworks.net, 2009. The Online Journal of Scientific Posters.
ŠIMARA, Pavel - GRANT, Steven - HOLYOAKE, Tessa - PELLICANO, Francesca.
MEK inhibition enhances BMS-214662-induced apoptosis in primitive CD34+ CML stem/progenitor cells. 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). ISSN 0015-5500, 2009, vol. 2009, no. 55, pp. 53-60.
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, Great Britain. ISSN 1021-7770, 2009, vol. 16, no. 59, pp. 1-14.
VAŘECHA, Miroslav - ULMAN, Vladimír - MATULA, Pavel - KOZUBEK, Michal.
Prediction of localization and interactions of apoptotic proteins. 2009.
VAŘECHA, Miroslav - PÁCLOVÁ, Daniela - PROCHÁZKOVÁ, Jiřina - MATULA, Pavel - KOZUBEK, Michal.
Prediction of localization and interactions of proteins involved in caspase-independent apoptosis. 2009.
TESAŘOVÁ, Lenka - KOUTNÁ, Irena - PETERKOVÁ, Martina - POTĚŠILOVÁ, Michaela - DVOŘÁKOVÁ, Magdaléna - STEJSKAL, Stanislav.
Representation of T-cell receptor V beta families detected by reverse transcription PCR and capillary electrophoresis. In Experimental Hematology, Volume 37, Number 9. University of Nevada, USA : Elsevier, 2009. p. 72-72. 2009, Athens, Greece.
DANĚK, Ondřej - MATULA, Pavel - ORTIZ-DE-SOLÓRZANO, Carlos - MUNOZ-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. ISBN 978-3-642-02229-6, pp. 410-419. 15.6.2009, OsloLNCS 5575.
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., USA. ISSN 1552-4922, 2009, vol. 75A, no. 4, pp. 309-318.
PETERKOVÁ, Martina - KOUTNÁ, Irena - ŠIMARA, Pavel - STEJSKAL, Stanislav - TESAŘOVÁ, Lenka.
The in vitro proliferation potential and proportion of CD133+ versus CD34+ hematopoietic stem cells. In Experimental Hematology, Volume 37, Number 9. University of Nevada, USA : Elsevier, 2009. pp. 35-36. 2009, Athens, Greece.
POTĚŠILOVÁ, Michaela - VAŘECHA, Miroslav - STEJSKAL, Stanislav - KOUTNÁ, Irena - KOZUBEK, Michal.
Time-lapse living cells microscopy of cell line K562 for study of CML-associated proteins dynamics - immobilization of suspension cultured cells. 2009.
SVOBODA, David - KOZUBEK, Michal - STEJSKAL, Stanislav.
Towards Proper Evaluation of Image Analysis Methods Used in Biomedical Research. 2009.
SVOBODA, David - MAŠKA, Martin - SKALICKÝ, Jan - KOZUBEK, Michal - STEJSKAL, Stanislav.
3D AcquiGen 0.2. 2008.
SVOBODA, David - MAŠKA, Martin - SKALICKÝ, Jan - KOZUBEK, Michal - STEJSKAL, Stanislav.
3D CytoGen 0.2. 2008.
SVOBODA, David - MAŠKA, Martin - SKALICKÝ, Jan - KOZUBEK, Michal - STEJSKAL, Stanislav.
3D OptiGen 0.2. 2008.
MATULA, Pavel - DANĚK, Ondřej - MAŠKA, Martin - VINKLER, Marek.
Acquiarium version 1.6. 2008.
BRÁZDILOVÁ, Silvie Luisa - KOZUBEK, Michal.
An Adaptive Algorithm for Multimodal Focus Functions in Automated Fluorescence Microscopy. In Medical Imaging Conference. Dresden : IEEE, 2008. ISBN 978-1-4244-2714-7, pp. 1-5. 22.10.2008, DresdenM06-291.
ULMAN, Vladimír.
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. ISBN 978-960-6766-95-4, pp. 56-62. 20.8.2008, Rhodes, Greece.
PETERKOVÁ, Martina - KOUTNÁ, Irena - TESAŘOVÁ, Lenka - POTĚŠILOVÁ, Michaela - RUČKA, Zdeněk - HRABČÁKOVÁ, Viera - KLABUSAY, Martin.
cDNA Microarray: Gene Expression Profiling of Small Cell Populations. 2008.
KOUTNÁ, IrenaKOUTNÁ, IrenaKLABUSAY, MartinPETERKOVÁ, MartinaPOTĚŠILOVÁ, MichaelaKOZUBEK, Michal.
Gene Expression differences in bone marrow hematoietic stem cell subpopulation. 2008.
TESAŘOVÁ, Lenka - KOUTNÁ, Irena - KLABUSAY, Martin - HRABČÁKOVÁ, Viera - KRONTORÁD, Petr.
Gene Expression Profiling During Ex Vivo Granulopoiesis: a Possible Tool for Quality Assessment of CD34+ Cells from Lymphoma Patients. 2008.
MATULA, Pavel - MAŠKA, Martin - DANĚK, Ondřej - MATULA, Petr - STEJSKAL, Stanislav - ONDŘEJ, Vladan - KOZUBEK, Michal.
High-Resolution Image Cytometry of a Large Number of 3D Confocal FISH and Immunofluorescence Stained Cells. 2008.
VAŘECHA, Miroslav - ZIMMERMANN, Michal - AMRICHOVÁ, Jana - ULMAN, Vladimír - KOZUBEK, Michal.
Interactions of apoptotic proteins AIF and endonuclease G analyzed by bioinformatic predictions, molecular docking, and fluorescent microscopy. 2008.
VAŘECHA, Miroslav - MATULA, Pavel - KOZUBEK, Michal.
New approaches to automated cell image acquisition and analysis using fluorescence microscopy. 2008. Invited talk.
MATULA, Pavel - MAŠKA, Martin - DANĚK, Ondřej - MATULA, Petr - KOZUBEK, Michal.
Processing of a Large Number of FISH and Immunofluorescence Stained Cells on Confocal Spinning Disk Systems. 2008.
KOZUBEK, Michal - SVOBODA, David - KAŠÍK, Marek - MAŠKA, Martin - HUBENÝ, Jan - STEJSKAL, Stanislav - SEEMAN, Michal - ZEMČÍK, Pavel.
Simulation of fluorescence image formation in 3D image cytometry. 2008.
KOZUBEK, Michal - SVOBODA, David - KAŠÍK, Marek - MAŠKA, Martin - HUBENÝ, Jan - STEJSKAL, Stanislav - SEEMAN, Michal - ZEMČÍK, Pavel.
Simulation of fluorescence image formation in 3D light microscopy. 2008.
STEJSKAL, Stanislav - MATULA, Pavel - KOUTNÁ, Irena - DANĚK, Ondřej - MAŠKA, Martin - KOZUBEK, Michal.
The Use of RNA Polymerase II in Epigenetic Analysis. 2008.
SVOBODA, David - MAŠKA, Martin - KAŠÍK, Marek - HUBENÝ, Jan - KOZUBEK, Michal - ZIMMERMANN, Michal - STEJSKAL, Stanislav.
3D AcquiGen 0.1. 2007.
SVOBODA, David - MAŠKA, Martin - KAŠÍK, Marek - HUBENÝ, Jan - KOZUBEK, Michal - ZIMMERMANN, Michal - STEJSKAL, Stanislav.
3D CytoGen 0.1. 2007.
SVOBODA, David - MAŠKA, Martin - KAŠÍK, Marek - HUBENÝ, Jan - KOZUBEK, Michal - ZIMMERMANN, Michal - STEJSKAL, Stanislav.
3D OptiGen 0.1. 2007.
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. ISBN 978-3-540-76855-5, pp. 571-581. 26.11.2007, Lake Tahoe, Nevada/CaliforniaLNCS 4842.
MATULA, Pavel - MAŠKA, Martin - DANĚK, Ondřej - MATULA, Petr - KOZUBEK, Michal - KRONTORÁD, Petr.
Acquiarium 1.0. 2007.
KOZUBEK, Michal.
Automation of biomedical image acquisition and analysis in optical microscopy. 2007. Uppsala University, Sweden, Invited talk.
KOUTNÁ, Irena - TESAŘOVÁ, Lenka - KLABUSAY, Martin - KROTORÁD, Petr - STREHOVSKÝ, Michal - PETERKOVÁ, Martina - HRABČÁKOVÁ, Viera.
Expression Profiling of CD34+ of Peripheral Blood of Patients with Lymphoma During ex vivo Granulocytic Differentiation. 2007.
KRONTORÁD, Petr - KOUTNÁ, Irena - STREHOVSKÝ, Michal.
Interactive Transcription Maps Over Microarray Data. 2007.
KRONTORÁD, Petr.
JABS-I. 2007.
ŠIMARA, Pavel - KOUTNÁ, Irena - STEJSKAL, Stanislav - PETERKOVÁ, Martina - KRONTORÁD, Petr - RUČKA, Zdeněk.
Large-scale Microarray Analysis of Protein and mRNA Level Changes in HL-60 Cells. 2007.
ULMAN, Vladimír - HUBENÝ, Jan.
On Generating Ground-truth Time-lapse Image Sequences and Flow Fields. In Proceedings of the Fourth International Conference on Informatics in Control, Automation and Robotics. Vyd. RA-1. Angers : INSTICC, 2007. ISBN 978-972-8865-83-2, pp. 234-239. 9.5.2007, Angers, France.
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. ISBN 978-3-540-74271-5, pp. 309-316. 2007, ViennaLNCS 4673.
KOZUBEK, Michal.
Precise simulation of 3D fluorescence microscope image formation. 2007. Center for Machine Perception, Czech Technical University, Prague, Invited talk.
ULMAN, Vladimír - HUBENÝ, Jan.
Pseudo-real Image Sequence Generator for Optical Flow Computations. In Proceedings of 15th Scandinavian Conference on Image Analysis. Vyd. LNCS 4522. Heidelberg : Springer, 2007. ISBN 978-3-540-73039-2, pp. 976-985. 10.6.2007, Aalborg, Denmark.
KOZUBEK, Michal.
Simulace degradace obrazu v optické mikroskopii. 2007. FI MU, Brno, Invited talk.
BRÁZDILOVÁ, Silvie Luisa.
Towards Reliable Autofocusing in Automated Microscopy. In Proceedings of the 4th International Conference on Informatics in Control, Automation and Robotics. Portugal : Insticc Press, 2007. ISBN 978-972-8865-82-5, pp. 440-448. 9.5.2007, Angers, France.
STREHOVSKÝ, Michal.
TransMap Viewer. 2007.
KOZUBEK, Michal.
Automation of biomedical image acquisition and processing in optical microscopy: Exploring the structure and function of human genome. 2006. University of Navarra, Pamplona, Spain, Invited talk.
