Výpis publikací

EFTIMIU, Nikomidisz Jorgosz a Michal KOZUBEK. Gravitational cell detection and tracking in fluorescence microscopy data. In IEEE International Symposium on Biomedical Imaging 2024. IEEE, 2024.

MAŠKA, Martin, Vladimír ULMAN, Pablo DELGADO-RODRIGUEZ, Estibaliz GÓMEZ-DE-MARISCAL, Tereza NEČASOVÁ, Fidel A Guerrero PEÑA, Tsang Ing REN, Elliot M MEYEROWITZ, Tim SCHERR, Katharina LÖFFLER, Ralf MIKUT, Tianqi GUO, Yin WANG, Jan P ALLEBACH, Rina BAO, Noor M AL-SHAKARJI, Gani RAHMON, Imad Eddine TOUBAL, Kannappan PALANIAPPAN, Filip LUX, Petr MATULA, Ko SUGAWARA, Klas E G MAGNUSSON, Layton AHO, Andrew R COHEN, Assaf ARBELLE, Tal BEN-HAIM, Tammy Riklin RAVIV, Fabian ISENSEE, Paul F JÄGER, Klaus H MAIER-HEIN, Yanming ZHU, Cristina EDERRA, Ainhoa URBIOLA, Erik MEIJERING, Alexandre CUNHA, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. The Cell Tracking Challenge: 10 years of objective benchmarking. Nature Methods. 2023, roč. 20, č. 7, s. 1010-1020. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/s41592-023-01879-y.

EISENMANN, M., A. REINKE, V. WERU, M. D. TIZABI, F. ISENSEE, T. J. ADLER, S. ALI, V. ANDREARCZYK, M. AUBREVILLE, U. BAID, S. BAKAS, N. BALU, S. BANO, J. BERNAL, S. BODENSTEDT, A. CASELLA, V. CHEPLYGINA, M. DAUM, M. DE BRUIJNE, A. DEPEURSINGE, R. DORENT, J. EGGER, D. G. ELLIS, S. ENGELHARDT, M. GANZ, N. GHATWARY, G. GIRARD, P. GODAU, A. GUPTA, L. HANSEN, K. HARADA, M. HEINRICH, N. HELLER, A. HERING, A. HUAULME, P. JANNIN, A. E. KAVUR, O. KODYM, Michal KOZUBEK, J. LI, H. LI, J. MA, C. MARTIN-ISLA, B. MENZE, A. NOBLE, V. OREILLER, N. PADOY, S. PATI, K. PAYETTE, T. RAEDSCH, J. RAFAEL-PATINO, V. Singh BAWA, S. SPEIDEL, C. H. SUDRE, K. VAN WIJNEN, M. WAGNER, D. WEI, A. YAMLAHI, M. H. YAP, C. YUAN, M. ZENK, A. ZIA, D. ZIMMERER, D. AYDOGAN, B. BHATTARAI, L. BLOCH, R. BRUENGEL, J. CHO, C. CHOI, Q. DOU, I. EZHOV, C. M. FRIEDRICH, C. FULLER, R. R. GAIRE, A. GALDRAN, A. Garcia FAURA, M. GRAMMATIKOPOULOU, S. HONG, M. JAHANIFAR, I. JANG, A. KADKHODAMOHAMMADI, I. KANG, F. KOFLER, S. KONDO, H. KUIJF, M. LI, M. LUU, T. MARTINCIC, P. MORAIS, M. A. NASER, B. OLIVEIRA, D. OWEN, S. PANG, J. PARK, S. PARK, S. PLOTKA, E. PUYBAREAU, N. RAJPOOT, K. RYU, N. SAEED, A. SHEPHARD, P. SHI, D. STEPEC, R. SUBEDI, G. TOCHON, H. R. TORRES, H. URIEN, J. L. VILACA, K. A. WAHID, H. WANG, J. WANG, L. WANG, X. WANG, B. WIESTLER, M. WODZINSKI, F. XIA, J. XIE, Z. XIONG, S. YANG, Y. YANG, Z. ZHAO, K. MAIER-HEIN, P. F. JAEGER, A. KOPP-SCHNEIDER a L. MAIER-HEIN. Why is the winner the best?. Online. In 979-8-3503-0129-8. 2023 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR). Vancouver: IEEE COMPUTER SOC, 2023, s. 19955-19966. ISBN 979-8-3503-0129-8. Dostupné z: https://dx.doi.org/10.1109/CVPR52729.2023.01911.

KEŘKOVSKÝ, Miloš, Marek DOSTÁL, Tereza KOPŘIVOVÁ, Tomáš JŮZA, Václav VYBÍHAL, Eduard NEUMAN, Petr MATULA a Michal KOZUBEK. Differentiation of high grade glioma and brain metastasis using intravoxel incoherent motion MRI. In 45th ESNR Annual Meeting. 2022.

PATI, Sarthak, Ujjwal BAID, Brandon EDWARDS, Micah SHELLER, Shih-Han WANG, G Anthony REINA, Patrick FOLEY, Alexey GRUZDEV, Deepthi KARKADA, Christos DAVATZIKOS, Chiharu SAKO, Satyam GHODASARA, Michel BILELLO, Suyash MOHAN, Philipp VOLLMUTH, Gianluca BRUGNARA, Chandrakanth J PREETHA, Felix SAHM, Klaus MAIER-HEIN, Maximilian ZENK, Martin BENDSZUS, Wolfgang WICK, Evan CALABRESE, Jeffrey RUDIE, Javier VILLANUEVA-MEYER, Soonmee CHA, Madhura INGALHALIKAR, Manali JADHAV, Umang PANDEY, Jitender SAINI, John GARRETT, Matthew LARSON, Robert JERAJ, Stuart CURRIE, Russell FROOD, Kavi FATANIA, Raymond Y HUANG, Ken CHANG, Carmen Balaña QUINTERO, Jaume CAPELLADES, Josep PUIG, Johannes TRENKLER, Josef PICHLER, Georg NECKER, Andreas HAUNSCHMIDT, Stephan MECKEL, Gaurav SHUKLA, Spencer LIEM, Gregory S ALEXANDER, Joseph LOMBARDO, Joshua D PALMER, Adam E FLANDERS, Adam P DICKER, Haris I SAIR, Craig K JONES, Archana VENKATARAMAN, Meirui JIANG, Tiffany Y SO, Cheng CHEN, Pheng Ann HENG, Qi DOU, Michal KOZUBEK, Filip LUX, Jan MICHÁLEK, Petr MATULA, Miloš KEŘKOVSKÝ, Tereza KOPŘIVOVÁ, Marek DOSTÁL, Václav VYBÍHAL, Michael A VOGELBAUM, J Ross MITCHELL, Joaquim FARINHAS, Joseph A MALDJIAN, Chandan Ganesh Bangalore YOGANANDA, Marco C PINHO, Divya REDDY, James HOLCOMB, Benjamin C WAGNER, Benjamin M ELLINGSON, Timothy F CLOUGHESY, Catalina RAYMOND, Talia OUGHOURLIAN, Akifumi HAGIWARA, Chencai WANG, Minh-Son TO, Sargam BHARDWAJ, Chee CHONG, Marc AGZARIAN, Alexandre Xavier FALCÃO, Samuel B MARTINS, Bernardo C A TEIXEIRA, Flávia SPRENGER, David MENOTTI, Diego R LUCIO, Pamela LAMONTAGNE, Daniel MARCUS, Benedikt WIESTLER, Florian KOFLER, Ivan EZHOV, Marie METZ, Rajan JAIN, Matthew LEE, Yvonne W LUI, Richard MCKINLEY, Johannes SLOTBOOM, Piotr RADOJEWSKI, Raphael MEIER, Roland WIEST, Derrick MURCIA, Eric FU, Rourke HAAS, John THOMPSON, David Ryan ORMOND, Chaitra BADVE, Andrew E SLOAN, Vachan VADMAL, Kristin WAITE, Rivka R COLEN, Linmin PEI, Murat AK, Ashok SRINIVASAN, J Rajiv BAPURAJ, Arvind RAO, Nicholas WANG, Ota YOSHIAKI, Toshio MORITANI, Sevcan TURK, Joonsang LEE, Snehal PRABHUDESAI, Fanny MORÓN, Jacob MANDEL, Konstantinos KAMNITSAS, Ben GLOCKER, Luke V M DIXON, Matthew WILLIAMS, Peter ZAMPAKIS, Vasileios PANAGIOTOPOULOS, Panagiotis TSIGANOS, Sotiris ALEXIOU, Ilias HALIASSOS, Evangelia I ZACHARAKI, Konstantinos MOUSTAKAS, Christina KALOGEROPOULOU, Dimitrios M KARDAMAKIS, Yoon Seong CHOI, Seung-Koo LEE, Jong Hee CHANG, Sung Soo AHN, Bing LUO, Laila POISSON, Ning WEN, Pallavi TIWARI, Ruchika VERMA, Rohan BAREJA, Ipsa YADAV, Jonathan CHEN, Neeraj KUMAR, Marion SMITS, Sebastian R VAN DER VOORT, Ahmed ALAFANDI, Fatih INCEKARA, Maarten M J WIJNENGA, Georgios KAPSAS, Renske GAHRMANN, Joost W SCHOUTEN, Hendrikus J DUBBINK, Arnaud J P E VINCENT, Martin J VAN DEN BENT, Pim J FRENCH, Stefan KLEIN, Yading YUAN, Sonam SHARMA, Tzu-Chi TSENG, Saba ADABI, Simone P NICLOU, Olivier KEUNEN, Ann-Christin HAU, Martin VALLIÈRES, David FORTIN, Martin LEPAGE, Bennett LANDMAN, Karthik RAMADASS, Kaiwen XU, Silky CHOTAI, Lola B CHAMBLESS, Akshitkumar MISTRY, Reid C THOMPSON, Yuriy GUSEV, Krithika BHUVANESHWAR, Anousheh SAYAH, Camelia BENCHEQROUN, Anas BELOUALI, Subha MADHAVAN, Thomas C BOOTH, Alysha CHELLIAH, Marc MODAT, Haris SHUAIB, Carmen DRAGOS, Aly ABAYAZEED, Kenneth KOLODZIEJ, Michael HILL, Ahmed ABBASSY, Shady GAMAL, Mahmoud MEKHAIMAR, Mohamed QAYATI, Mauricio REYES, Ji Eun PARK, Jihye YUN, Ho Sung KIM, Abhishek MAHAJAN, Mark MUZI, Sean BENSON, Regina G H BEETS-TAN, Jonas TEUWEN, Alejandro HERRERA-TRUJILLO, Maria TRUJILLO, William ESCOBAR, Ana ABELLO, Jose BERNAL, Jhon GÓMEZ, Joseph CHOI, Stephen BAEK, Yusung KIM, Heba ISMAEL, Bryan ALLEN, John M BUATTI, Aikaterini KOTROTSOU, Hongwei LI, Tobias WEISS, Michael WELLER, Andrea BINK, Bertrand POUYMAYOU, Hassan F SHAYKH, Joel SALTZ, Prateek PRASANNA, Sampurna SHRESTHA, Kartik M MANI, David PAYNE, Tahsin KURC, Enrique PELAEZ, Heydy FRANCO-MALDONADO, Francis LOAYZA, Sebastian QUEVEDO, Pamela GUEVARA, Esteban TORCHE, Cristobal MENDOZA, Vera FRANCO, Elvis RÍOS, Eduardo LÓPEZ, Sergio A VELASTIN, Godwin OGBOLE, Mayowa SONEYE, Dotun OYEKUNLE, Olubunmi ODAFE-OYIBOTHA, Babatunde OSOBU, Mustapha SHU'AIBU, Adeleye DORCAS, Farouk DAKO, Amber L SIMPSON, Mohammad HAMGHALAM, Jacob J PEOPLES, Ricky HU, Anh TRAN, Danielle CUTLER, Fabio Y MORAES, Michael A BOSS, James GIMPEL, Deepak Kattil VEETTIL, Kendall SCHMIDT, Brian BIALECKI, Sailaja MARELLA, Cynthia PRICE, Lisa CIMINO, Charles APGAR, Prashant SHAH, Bjoern MENZE, Jill S BARNHOLTZ-SLOAN, Jason MARTIN a Spyridon BAKAS. Federated learning enables big data for rare cancer boundary detection. Nature Communications. London: Nature Publishing Group, 2022, roč. 13, č. 7346, s. 1-17. ISSN 2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-022-33407-5.

PREISLER, Jan, Markéta MACHÁLKOVÁ, Barbora ADAMOVÁ, Jarmila NAVRÁTILOVÁ, Marek STIBOREK, Stanislava MELIORISOVÁ, Jiří KROUPA, Pavel HOUŠKA, Jan MICHÁLEK, Karel ŠTĚPKA, Katarzyna Anna RADASZKIEWICZ, Adam PRUŠKA, Viktor KANICKÝ, Michal KOZUBEK a Jan ŠMARDA. Multimodal Imaging of 3D Cell Aggregates. In MSB 2021. 2021.

MAIER-HEIN, Lena, Annika REINKE, Michal KOZUBEK, Anne L. MARTEL, Tal ARBEL, Matthias EISENMANN, Allan HANBURY, Pierre JANNIN, Henning MÜLLER, Sinan ONOGUR, Julio SAEZ-RODRIGUEZ, Bram VAN GINNEKEN, Annette KOPP-SCHNEIDER a Bennett A. LANDMAN. BIAS: Transparent reporting of biomedical image analysis challenges. Medical Image Analysis. Elsevier, 2020, roč. 66, č. 101796, s. 1-7. ISSN 1361-8415. Dostupné z: https://dx.doi.org/10.1016/j.media.2020.101796.

AKBAS, Cem Emre a Michal KOZUBEK. Condensed U-Net (CU-Net): An Improved U-Net Architecture for Cell Segmentation Powered by 4x4 Max-Pooling Layers. Online. In IEEE 17th International Symposium on Biomedical Imaging. Iowa: IEEE, 2020, s. 446-450. ISBN 978-1-5386-9330-8. Dostupné z: https://dx.doi.org/10.1109/ISBI45749.2020.9098351.

PAVLATOVSKÁ, Barbora, Markéta MACHÁLKOVÁ, Petra BRISUDOVÁ, Adam PRUŠKA, Karel ŠTĚPKA, Jan MICHÁLEK, Tereza NEČASOVÁ, Petr BENEŠ, Jan ŠMARDA, Jan PREISLER, Michal KOZUBEK a Jarmila NAVRÁTILOVÁ. Lactic Acidosis Interferes With Toxicity of Perifosine to Colorectal Cancer Spheroids: Multimodal Imaging Analysis. Frontiers in Oncology. Lausanne: Frontiers Media S.A., 2020, roč. 10, December, s. 1-18. ISSN 2234-943X. Dostupné z: https://dx.doi.org/10.3389/fonc.2020.581365.

KOZUBEK, Michal. When Deep Learning Meets Cell Image Synthesis. Cytometry Part A. John Wiley & Sons, 2020, roč. 97, č. 3, s. 222-225. ISSN 1552-4922. Dostupné z: https://dx.doi.org/10.1002/cyto.a.23957.

AKBAŞ, Cem Emre, Vladimír ULMAN, Martin MAŠKA, Florian JUG a Michal KOZUBEK. Automatic Fusion of Segmentation and Tracking Labels. In Laura Leal-Taixé, Stefan Roth. Computer Vision – ECCV 2018 Workshops. LNCS 11134. Switzerland: Springer Nature, 2019, s. 446-454. ISBN 978-3-030-11023-9. Dostupné z: https://dx.doi.org/10.1007/978-3-030-11024-6_34.

PAVLATOVSKÁ, Barbora, Jarmila NAVRÁTILOVÁ, Markéta MACHÁLKOVÁ, Jan MICHÁLEK, Karel ŠTĚPKA, Adam PRUŠKA, Michal KOZUBEK, Petr BENEŠ, Jan ŠMARDA a Jan PREISLER. Combined therapy of perifosine and ABT-737 results in higher cytotoxic effect but also induces expression of EMT markers in colon cancer cell lines. In Spetses Summer School: Molecular Mechanisms in Signal Transduction and Cancer, Greece. 2019.

WIESNER, David, David SVOBODA, Martin MAŠKA a Michal KOZUBEK. CytoPacq: A web-interface for simulating multi-dimensional cell imaging. Bioinformatics. Oxford University Press, 2019, roč. 35, č. 21, s. 4531-4533. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btz417.

MACHÁLKOVÁ, Markéta, Barbora PAVLATOVSKÁ, Jan MICHÁLEK, Adam PRUŠKA, Karel ŠTĚPKA, Tereza NEČASOVÁ, Katarzyna Anna RADASZKIEWICZ, Michal KOZUBEK, Jan ŠMARDA, Jan PREISLER a Jarmila NAVRÁTILOVÁ. Drug Penetration Analysis in 3D Cell Cultures Using Fiducial-Based Semiautomatic Coregistration of MALDI MSI and Immunofluorescence Images. Analytical Chemistry. American Chemical Society, 2019, roč. 91, č. 21, s. 13475-13484. ISSN 0003-2700. Dostupné z: https://dx.doi.org/10.1021/acs.analchem.9b02462.

NAVRÁTILOVÁ, Jarmila, Markéta MACHÁLKOVÁ, Barbora PAVLATOVSKÁ, Jan MICHÁLEK, Adam PRUŠKA, Karel ŠTĚPKA, Katarzyna Anna RADASZKIEWICZ, Jan PREISLER, Jan ŠMARDA a Michal KOZUBEK. Fiducial-based semi-automatic coregistration and analysis of multimodal MALDI MS and immunofluorescent data. In Imaging Principles of Life 2019. 2019.

MICHÁLEK, Jan, Karel ŠTĚPKA, Michal KOZUBEK, Jarmila NAVRÁTILOVÁ, Barbora PAVLATOVSKÁ, Markéta MACHÁLKOVÁ, Jan PREISLER a Adam PRUŠKA. Quantitative Assessment of Anti-Cancer Drug Efficacy From Coregistered Mass Spectrometry and Fluorescence Microscopy Images of Multicellular Tumor Spheroids. Microscopy and Microanalysis. Cambridge University Press, 2019, roč. 25, č. 6, s. 1311-1322. ISSN 1431-9276. Dostupné z: https://dx.doi.org/10.1017/S1431927619014983.

PAVLATOVSKÁ, Barbora, Jarmila NAVRÁTILOVÁ, Markéta MACHÁLKOVÁ, Petra BRISUDOVÁ, Jan MICHÁLEK, Karel ŠTĚPKA, Adam PRUŠKA, Michal KOZUBEK, Petr BENEŠ, Jan ŠMARDA a Jan PREISLER. Tumor-specific microenvironment contributes to the perifosine resistance in 3D colorectal cancer (CRC) models. In Goodbye Flat Biology: Advancing 3D-based Models for Cancer Biology and Drug Discovery, Berlin, Germany. 2019.

REINKE, Annika, Matthias EISENMANN, Sinan ONOGUR, Marko STANKOVIC, Patrick SCHOLZ, Peter M FULL, Hrvoje BOGUNOVIC, Bennett A LANDMAN, Oskar MAIER, Bjoern MENZE, Gregory C SHARP, Korsuk SIRINUKUNWATTANA, Stefanie SPEIDEL, Fons VAN DER SOMMEN, Guoyan ZHENG, Henning MÜLLER, Michal KOZUBEK, Tal ARBEL, Andrew P BRADLEY, Pierre JANNIN, Annette KOPP-SCHNEIDER a Lena MAIER-HEIN. How to Exploit Weaknesses in Biomedical Challenge Design and Organization. In Alejandro F. Frangi, Julia A. Schnabel, Christos Davatzikos, Carlos Alberola-López, Gabor Fichtinger. Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. LNCS 11073. Cham (Switzerland): Springer, 2018, s. 388-395. ISBN 978-3-030-00936-6. Dostupné z: https://dx.doi.org/10.1007/978-3-030-00937-3_45.

PAVLATOVSKÁ, Barbora, Jarmila NAVRÁTILOVÁ, Markéta MACHÁLKOVÁ, Adam PRUŠKA, Jan MICHÁLEK, Karel ŠTĚPKA, Michal KOZUBEK, Jan ŠMARDA a Jan PREISLER. The effect and distribution of the drug perifosine in 2D and 3D colorectal cell cultures. In Summer School in Translational Cancer Research 2018. 2018.

PAVLATOVSKÁ, Barbora, Jarmila NAVRÁTILOVÁ, Markéta MACHÁLKOVÁ, Adam PRUŠKA, Jan MICHÁLEK, Karel ŠTĚPKA, Michal KOZUBEK, Jan ŠMARDA a Jan PREISLER. The effect and distribution of the drug perifosine in 2D and 3D colorectal cell cultures. In XIX. Meeting of Biochemists and Molecular Biologists. 2018.

MAIER-HEIN, Lena, Matthias EISENMANN, Annika REINKE, Sinan ONOGUR, Marko STANKOVIC, Patrick SCHOLZ, Tal ARBEL, Hrvoje BOGUNOVIC, Andrew BRADLEY, Aaron CARASS, Carolin FELDMANN, Alejandro FRANGI, Peter FULL, Bram VAN GINNEKEN, Allan HANBURY, Katrin HONAUER, Michal KOZUBEK, Bennett LANDMAN, Keno MÄRZ, Oskar MAIER, Klaus MAIER-HEIN, Bjoern MENZE, Henning MÜLLER, Peter NEHER, Wiro NIESSEN, Nasir RAJPOOT, Gregory SHARP, Korsuk SIRINUKUNWATTANA, Stefanie SPEIDEL, Christian STOCK, Danail STOYANOV, Abdel Aziz TAHA, Fons VAN DER SOMMEN, Ching-Wei WANG, Marc-André WEBER, Guoyan ZHENG, Pierre JANNIN a Annette KOPP-SCHNEIDER. Why rankings of biomedical image analysis competitions should be interpreted with care. Nature Communications. Nature Publishing Group, 2018, roč. 9, č. 5217, s. 1-13. ISSN 2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-018-07619-7.

ULMAN, Vladimír, Martin MAŠKA, Klas E G MAGNUSSON, Olaf RONNEBERGER, Carsten HAUBOLD, Nathalie HARDER, Pavel MATULA, Petr MATULA, David SVOBODA, Miroslav RADOJEVIC, Ihor SMAL, Karl ROHR, Joakim JALDÉN, Helen M BLAU, Oleh DZYUBACHYK, Boudewijn LELIEVELDT, Pengdong XIAO, Yuexiang LI, Siu-Yeung CHO, Alexandre C DUFOUR, Jean-Christophe OLIVO-MARIN, Constantino C REYES-ALDASORO, Jose A SOLIS-LEMUS, Robert BENSCH, Thomas BROX, Johannes STEGMAIER, Ralf MIKUT, Steffen WOLF, Fred A HAMPRECHT, Tiago ESTEVES, Pedro QUELHAS, Ömer DEMIREL, Lars MALMSTRÖM, Florian JUG, Pavel TOMANCAK, Erik MEIJERING, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLORZANO. An objective comparison of cell-tracking algorithms. Nature Methods. Macmillan Publishers Limited, part of Springer Nature, 2017, roč. 14, č. 12, s. 1141-1152. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/nmeth.4473.

ANGUIANO, María, Carlos CASTILLA, Martin MAŠKA, Cristina EDERRA, Rafael PELÁEZ, Xabier MORALES, Gorka MUÑOZ-ARRIETA, Maite MUJIKA, Michal KOZUBEK, Arrate MUÑOZ-BARRUTIA, Ana ROUZAUT, Sergio ARANA, José Manuel GARCIA-AZNAR a Carlos ORTIZ-DE-SOLORZANO. Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis. PLoS ONE. 2017, roč. 12, č. 2, s. 1-24. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0171417.

POPOVICI, Vlad, Eva BUDINSKÁ, Ladislav DUŠEK, Michal KOZUBEK a Fred BOSMAN. Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. Bioinformatics. Oxford: Oxford University Press, 2017, roč. 33, č. 13, s. 2002-2009. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btx027.

SVOBODA, David a Michal KOZUBEK. Multimodal Simulations in Live Cell Imaging. In Tsaftaris S., Gooya A., Frangi A., Prince J. Simulation and Synthesis in Medical Imaging. LNCS 10557. Neuveden: Springer, 2017, s. 89-98. ISBN 978-3-319-68126-9. Dostupné z: https://dx.doi.org/10.1007/978-3-319-68127-6_10.

KOZUBEK, Michal. Challenges and Benchmarks in Bioimage Analysis. Online. In DeVos WH, Munck S, Timmermans JP. Focus on Bio-Image Informatics. Berlin: Springer, 2016, s. 231-262. Advances in Anatomy, Embryology and Cell Biology 219. ISBN 978-3-319-28547-4. Dostupné z: https://dx.doi.org/10.1007/978-3-319-28549-8_9.

ULMAN, Vladimír, David SVOBODA, Matti NYKTER, Michal KOZUBEK a Pekka RUUSUVUORI. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry Part A. John Wiley & Sons, 2016, roč. 89A, č. 12, s. 1057-1072. ISSN 1552-4922. Dostupné z: https://dx.doi.org/10.1002/cyto.a.23031.

MATULA, Pavel, Martin MAŠKA, Dmitry SOROKIN, Petr MATULA, Carlos ORTIZ-DE-SOLÓRZANO a Michal KOZUBEK. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE. 2015, roč. 10, č. 12, s. "e0144959", 19 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0144959.

ANGUIANO, María, Carlos CASTILLA, Martin MAŠKA, Cristina EDERRA, Javier FERNÁNDEZ-MARQUÉS, Rafael PELÁEZ, Ana ROUZAUT, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. Characterization of the Role of Collagen Network Structure and Composition in Cancer Cell Migration. Online. In 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Milano: IEEE, 2015, s. 8139-8142. ISBN 978-1-4244-9271-8. Dostupné z: https://dx.doi.org/10.1109/EMBC.2015.7320283.

ŠTĚPKA, Karel, Pavel MATULA, Petr MATULA, Stefan WOERZ, Karl ROHR a Michal KOZUBEK. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. Cytometry Part A. John Wiley & Sons, 2015, roč. 87A, č. 8, s. 759-772. ISSN 1552-4922. Dostupné z: https://dx.doi.org/10.1002/cyto.a.22692.

MAŠKA, Martin, Cristina EDERRA, Javier FERNÁNDEZ-MARQUÉS, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy. Online. In 22nd IEEE International Conference on Image Processing. Québec City: IEEE, 2015, s. 1791-1794. ISBN 978-1-4799-8339-1. Dostupné z: https://dx.doi.org/10.1109/ICIP.2015.7351109.

ORTIZ-DE-SOLÓRZANO, Carlos, Arrate MUÑOZ-BARRUTIA, Erik MEIJERING a Michal KOZUBEK. Toward a Morphodynamic Model of the Cell. IEEE Signal Processing Magazine. New York: IEEE, 2015, roč. 32, č. 1, s. 20-29. ISSN 1053-5888. Dostupné z: https://dx.doi.org/10.1109/MSP.2014.2358263.

MAŠKA, Martin, Vladimír ULMAN, David SVOBODA, Pavel MATULA, Petr MATULA, Cristina EDERRA, Ainhoa URBIOLA, Tomás ESPAÑA, Subramanian VENKATESAN, Deepak M W BALAK, Pavel KARAS, Tereza BOLCKOVÁ, Markéta ŠTREITOVÁ, Craig CARTHEL, Stefano CORALUPPI, Nathalie HARDER, Karl ROHR, Klas E G MAGNUSSON, Joakim JALDÉN, Helen M BLAU, Oleh DZYUBACHYK, Pavel KŘÍŽEK, Guy M HAGEN, David PASTOR-ESCUREDO, Daniel JIMENEZ-CARRETERO, Maria J LEDESMA-CARBAYO, Arrate MUÑOZ-BARRUTIA, Erik MEIJERING, Michal KOZUBEK a Carlos ORTIZ-DE-SOLORZANO. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics. 2014, roč. 30, č. 11, s. 1609-1617. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btu080.

KOZUBEK, Michal. Člen panelu P202 Informatika. GAČR, 2012 - 2016.

VAŘECHA, Miroslav, Michaela POTĚŠILOVÁ, Pavel MATULA a Michal KOZUBEK. Endonuclease G interacts with histone H2B and DNA topoisomerase II alpha during apoptosis. Mol Cell Biochem. 2012, roč. 363, 1-2, s. 301-307. ISSN 0300-8177. Dostupné z: https://dx.doi.org/10.1007/s11010-011-1182-x.

VAŘECHA, Miroslav, Daniela PÁCLOVÁ, Jiřina PROCHÁZKOVÁ, Pavel MATULA, Dušan CMARKO a Michal KOZUBEK. Knockdown of apoptosis-inducing factor disrupts function of respiratory complex I. BIOCELL. Argentina: National Council of Scientific and Techn, 2012, roč. 36, č. 3, s. 121-126. ISSN 0327-9545.

DANĚK, Ondřej, Pavel MATULA, Martin MAŠKA a Michal KOZUBEK. Smooth Chan-Vese Segmentation via Graph Cuts. Pattern recognition letters : an official publication of the International Association for Pattern Recognition. Amsterdam: Elsevier, 2012, roč. 33, č. 10, s. 1405-1410. ISSN 0167-8655. Dostupné z: https://dx.doi.org/10.1016/j.patrec.2012.03.013.

VAŘECHA, Miroslav, Michaela POTĚŠILOVÁ, Pavel MATULA a Michal KOZUBEK. Endonuclease G interacts with histone H2B, AIF, and DNA topoisomerase II alpha during apoptosis as revealed by FRET analysis of living cells. In 19th Euroconference on Apoptosis - Metabolism, Epigenetics and Death. 2011.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Image Division Technique in Pre-acquisition Analysis of Information Content for Automated Microscopy. Journal of Microscopy. Oxford: Blackwell Science, 2011, roč. 242, č. 3, s. 279-289. ISSN 0022-2720. Dostupné z: https://dx.doi.org/10.1111/j.1365-2818.2010.03465.x.

VAŘECHA, Miroslav, Michaela POTĚŠILOVÁ, Pavel MATULA a Michal KOZUBEK. Interaction of endonuclease G with histone H2B, AIF, and DNA topoisomerase II alpha during apoptosis as revealed by FRET imaging of living cells. In Analytická Cytometrie VI. 2011. ISBN 978-80-260-0676-3.

STAIER, Florian, Heinz EIPEL, Petr MATULA, Alexei V EVSIKOV, Michal KOZUBEK, Christoph CREMER a Michael HAUSMANN. Micro axial tomography: A miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy. Rev. Sci. Instrum. USA: American Institute of Physica, 2011, roč. 82, č. 9, s. "093701-1"-"093701-8", 8 s. ISSN 0034-6748.

KRONTORÁD KOUTNÁ, Irena, Martina PETERKOVÁ, Pavel ŠIMARA, Stanislav STEJSKAL, Lenka TESAŘOVÁ a Michal KOZUBEK. Proliferation and differentiation potential of CD133+ and CD34+ populations from the bone marrow and mobilized peripheral blood. Annals of hematology. Germany: Springer, 2011, roč. 90, (2), s. 127-137. ISSN 0939-5555.

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

MATYSKA, Luděk, Michal KOZUBEK, Tomáš VOJNAR, Pavel ZEMČÍK a David ANTOŠ. Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS'10) -- Selected Papers. Dagstuhl, Germany: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2011. ISBN 978-3-939897-22-4.

MAŠKA, Martin, Pavel MATULA, Ondřej DANĚK a Michal KOZUBEK. A Fast Level Set-Like Algorithm for Region-Based Active Contours. Online. In 6th International Symposium on Visual Computing. Berlin, Heidelberg: Springer-Verlag, 2010, s. 387-396. ISBN 978-3-642-17276-2. Dostupné z: https://dx.doi.org/10.1007/978-3-642-17277-9_40.

STEJSKAL, Stanislav, Pavel MATULA, Ondřej DANĚK, Martin MAŠKA, Irena KRONTORÁD KOUTNÁ a Michal KOZUBEK. 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, s. 39-41. ISBN 978-80-210-5312-0.

MATULA, Pavel, Ondřej DANĚK, Martin MAŠKA, Marek VINKLER a Michal KOZUBEK. Acquiarium: Free Software For Image Acquisition And Image Analysis In Cytometry. In Mikroskopie 2010. 2010.

VAŘECHA, Miroslav, Daniela PÁCLOVÁ, Jiřina PROCHÁZKOVÁ, Pavel MATULA a Michal KOZUBEK. Alteration in mitochondrial superoxide production by shRNA gene silencing of AIF in various cell line. In Advances in Molecular and Cancer Bilogy. 2010. ISBN 978-80-210-5312-0.

VAŘECHA, Miroslav, Daniela PÁCLOVÁ, Jiřina PROCHÁZKOVÁ, Pavel MATULA a Michal KOZUBEK. Alteration in mitochondrial superoxide production by shRNA gene silencing of AIF in various cell lines. In 18th Euroconference on Apoptosis. 2010.

VAŘECHA, Miroslav, Pavel MATULA a Michal KOZUBEK. Automated spinning disk confocal microscopy in 3D live cell imaging. In Mikroskopie 2010. 2010.

KOZUBEK, Michal. Centre for Biomedical Image Analysis. In International industry - academia brokerage event in the fields of biotechnologies, bioinformatics, nanotechnologies and materials and health. 2010.

KOZUBEK, Michal, David SVOBODA a Stanislav STEJSKAL. CytoPacq: A web-based toolbox for simulation of 3D cell imaging and quality control of related image analysis. In Mikroskopie 2010. 2010.

ŠIMARA, Pavel, Stanislav STEJSKAL, Martina PETERKOVÁ, Jiří MAYER, Zdeněk RÁČIL, Irena KRONTORÁD KOUTNÁ a Michal KOZUBEK. Dasatinib suppresses MEK/ERK pathway activity without sustained BCR-ABL inhibition and promotes BIM dependent apoptosis in chronic myeloid leukaemia cells. In XXIV. Olomoucké hematologické dny s mezinárodní účastí. 2010. ISSN 1213-5763.

KOZUBEK, Michal. Digital phantoms of cell nuclei and the use of simulations in nuclear studies. In Functional Organization of the Cell Nucleus Symposium. 2010.

KOZUBEK, Michal a Silvie Luisa BRÁZDILOVÁ. From autofocusing to automatic 3D information content analysis. In Informatics Colloquium. 2010.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Image Division Technique in Automated Fluorescence Microscopy. In MEMICS. 2010. ISBN 978-80-87342-10-7.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. 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. 2010. vyd. Freiburg, Germany: International Association for Development of the Information Society, 2010, s. 176-183. ISBN 978-972-8939-22-9.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Information content analysis in automated microscopy imaging using modified autofocusing approach. In EMBO Workshop Advanced Light Microscopy - 10th International ELMI Meeting. 2010.

MATYSKA, Luděk, Michal KOZUBEK, Tomáš VOJNAR, Pavel ZEMČÍK a David ANTOŠ. MEMICS 2010: Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS s.r.o., 2010, 213 s. ISBN 978-80-87342-10-7.

KOZUBEK, Michal. Panel Member. Data analysis review panel, Academy of Finland, 2010.

MAŠKA, Martin, Pavel MATULA a Michal KOZUBEK. 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, s. 117-125. ISBN 978-80-87342-10-7.

STEJSKAL, Stanislav, Irena KRONTORÁD KOUTNÁ, Pavel MATULA, Zdeněk RUČKA, Ondřej DANĚK, Martin MAŠKA a Michal KOZUBEK. The role of chromatin condensation during granulopoiesis in the regulation of gene cluster expression. Epigenetics. USA: Landes Bioscience, 2010, roč. 5, č. 8, s. 759-767. ISSN 1559-2294. Dostupné z: https://dx.doi.org/10.4161/epi.5.8.13183.

KOZUBEK, Michal. Využití laseru ve světelné mikroskopii při studiu prostorového uspořádání a dynamiky buněčných struktur. In LASER 50. 2010. ISBN 978-80-87441-01-5.

MAŠKA, Martin, Ondřej DANĚK, Carlos ORTIZ-DE-SOLÓRZANO, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Ignacio FERNÁNDEZ GARCÍA. A Two-Phase Segmentation of Cell Nuclei Using Fast Level Set-Like Algorithms. Online. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009, s. 390-399. ISBN 978-3-642-02229-6. Dostupné z: https://dx.doi.org/10.1007/978-3-642-02230-2_40.

MATULA, Pavel, Ondřej DANĚK, Martin MAŠKA, Marek VINKLER a Michal KOZUBEK. Acquiarium: Free image acquisition and analysis software for image cytometry. In Analytical Cytometry V. 2009.

MATULA, Pavel, Ondřej DANĚK, Martin MAŠKA, Marek VINKLER a Michal KOZUBEK. Acquiarium: Free Software For Image Acquisition And 3D Analysis Of Fluorescently Labeled Cells. In Focus On Microscopy. 2009.

MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA a Michal KOZUBEK. Acquiarium: Free Software for the Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy. Online. In IEEE International Symposium on Biomedical Imaging. Boston: IEEE, 2009, s. 1138-1141. ISBN 978-1-4244-3932-4.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Autofocusing software issues in automated fluorescence microscopy. In Mikroskopia 2009. 2009. ISBN 978-80-7399-739-7.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Automated search for information content in fluorescence microscopy images using modified autofocusing approach. In Focus on Microscopy 2009. 2009.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Pavel MATULA a Michal KOZUBEK. Automated spinning disk confocal microscopy in 3D live cell imaging. In Funkční organizace buněčného jádra. 2009.

ŠIMARA, Pavel, Irena KOUTNÁ, Stanislav STEJSKAL, Petr KRONTORÁD, Zdeněk RUČKA, Martina PETERKOVÁ a Michal KOZUBEK. Combination of mRNA and protein microarray analysis in complex cell profiling. Neoplasma. Bratislava, Slovensko: AEPress, s.r.o., 2009, roč. 2/2009, č. 56, s. 141-149. ISSN 0028-2685.

SVOBODA, David, Michal KOZUBEK a Jaromír COUFAL. CytoPacq. 2009.

SVOBODA, David a Michal KOZUBEK. CytoPacq – On-line Framework for Simulating Fluorescence Microscopy Images. In Hands-on Image Processing, Robotiker-Tecnalia, Bilbao, Spain. 2009.

KOZUBEK, Michal. Free tools for automated cell image acquisition and analysis. In Workshop on Optical Techniques in Cell and Developmental Biology. 2009.

SVOBODA, David, Michal KOZUBEK a Stanislav STEJSKAL. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry. Cytometry Part A. John Wiley & Sons, Inc., 2009, roč. 75A, č. 6, s. 494-509. ISSN 1552-4922. Dostupné z: https://dx.doi.org/10.1002/cyto.a.20714.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions. Journal of Microscopy. Oxford: Blackwell Science, 2009, roč. 236, č. 3, s. 194-202. ISSN 0022-2720. Dostupné z: https://dx.doi.org/10.1111/j.1365-2818.2009.03280.x.

KOZUBEK, Michal. Member of Program Committee. Program Committee of the 4th International Conference on Computer Vision Theory and Applications, 2009.

PETERKOVÁ, Martina, Irena KOUTNÁ, Lenka TESAŘOVÁ, Michaela POTĚŠILOVÁ, Michal KOZUBEK, Viera HRABČÁKOVÁ, Martin KLABUSAY, Michael DOUBEK a Jiří MAYER. Microarray analysis using limited amount of cells. Folia Biologica (Praha). 2009, roč. 2009, č. 55, s. 53-60. ISSN 0015-5500.

VAŘECHA, Miroslav, Vladimír ULMAN, Pavel MATULA a Michal KOZUBEK. Prediction of localization and interactions of apoptotic proteins. In Analytical Cytometry V. 2009. ISBN 978-80-254-2561-9.

VAŘECHA, Miroslav, Michal ZIMMERMANN, Jana AMRICHOVÁ, Vladimír ULMAN, Pavel MATULA a Michal KOZUBEK. Prediction of localization and interactions of apoptotic proteins. Journal of Biomedical Science. BioMed website: BioMed Central, London, England, 2009, roč. 16, č. 59, s. 1-14. ISSN 1021-7770.

VAŘECHA, Miroslav, Daniela PÁCLOVÁ, Jiřina PROCHÁZKOVÁ, Pavel MATULA a Michal KOZUBEK. Prediction of localization and interactions of proteins involved in caspase-independent apoptosis. In Abstract Book of 17th ECDO Euroconference. 2009.

DANĚK, Ondřej, Pavel MATULA, Carlos ORTIZ-DE-SOLÓRZANO, Arrate MUÑOZ-BARRUTIA, Martin MAŠKA a Michal KOZUBEK. Segmentation of Touching Cell Nuclei using a Two-Stage Graph Cut Model. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009, s. 410-419. ISBN 978-3-642-02229-6. Dostupné z: https://dx.doi.org/10.1007/978-3-642-02230-2_42.

POTĚŠILOVÁ, Michaela, Miroslav VAŘECHA, Stanislav STEJSKAL, Irena KOUTNÁ a Michal KOZUBEK. Time-lapse living cells microscopy of cell line K562 for study of CML-associated proteins dynamics - immobilization of suspension cultured cells. In Analytical cytometry V. 2009. ISBN 978-80-254-2561-9.

SVOBODA, David, Michal KOZUBEK a Stanislav STEJSKAL. Towards Proper Evaluation of Image Analysis Methods Used in Biomedical Research. In Analytical Cytometry V, International Conference. 2009. ISBN 978-80-254-2561-5.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. An Adaptive Algorithm for Multimodal Focus Functions in Automated Fluorescence Microscopy. In Medical Imaging Conference. Dresden: IEEE, 2008, s. 1-5. ISBN 978-1-4244-2714-7.

ZIMMERMANN, Michal, Miroslav VAŘECHA, Jana AMRICHOVÁ, Vladimír ULMAN, Pavel MATULA a Michal KOZUBEK. Bioinformatic prediction, molecular modelling and image analysis of localization and interactions of apoptotic proteins endonuclease G, AIF, and AMID. In Apoptosis World 2008. 2008.

KOUTNÁ, Irena. Gene Expression differences in bone marrow hematoietic stem cell subpopulation. In KOUTNÁ, Irena, Martin KLABUSAY, Martina PETERKOVÁ, Viera HRABČÁKOVÁ, Michaela POTĚŠILOVÁ, Petr KRONTORÁD a Michal KOZUBEK. 3rd ESF functional genomics conference. 2008.

MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA, Stanislav STEJSKAL, Vladan ONDŘEJ a Michal KOZUBEK. High-Resolution Image Cytometry of a Large Number of 3D Confocal FISH and Immunofluorescence Stained Cells. In 13. LEIPZIGER WORKSHOP Cytomics and NanoBioengineering. 2008.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN a Michal KOZUBEK. Image analysis of localization and translocation of apoptotic proteins in living cells. In European Light Microscopy Initiative. 2008.

VAŘECHA, Miroslav, Michal ZIMMERMANN, Jana AMRICHOVÁ, Vladimír ULMAN a Michal KOZUBEK. Interactions of apoptotic proteins AIF and endonuclease G analyzed by bioinformatic predictions, molecular docking, and fluorescent microscopy. In 16th Euroconference on Apoptosis an 5th Swiss Apoptosis Meeting. 2008.

KOZUBEK, Michal. Member of Program Committee. Program Committee of the XXIV International Congress of International Society for Analytical Cytology, 2008.

KOZUBEK, Michal. Member of Program Committee. Program Committee of the 3rd International Conference on Computer Vision Theory and Applications, 2008.

VAŘECHA, Miroslav, Pavel MATULA a Michal KOZUBEK. New approaches to automated cell image acquisition and analysis using fluorescence microscopy. In XIX. Biologické Dny - International Symposium "The Functional Organization of the Cell Nucleus". 2008. ISBN 978-80-7399-545-4.

MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA a Michal KOZUBEK. Processing of a Large Number of FISH and Immunofluorescence Stained Cells on Confocal Spinning Disk Systems. In European light microscopy initiative meeting. 2008.

KOZUBEK, Michal, David SVOBODA, Marek KAŠÍK, Martin MAŠKA, Jan HUBENÝ, Stanislav STEJSKAL, Michal SEEMAN a Pavel ZEMČÍK. Simulation of fluorescence image formation in 3D image cytometry. In XXIV International Congress of International Society for Analytical Cytology. 2008.

KOZUBEK, Michal, David SVOBODA, Marek KAŠÍK, Martin MAŠKA, Jan HUBENÝ, Stanislav STEJSKAL, Michal SEEMAN a Pavel ZEMČÍK. Simulation of fluorescence image formation in 3D light microscopy. In 8th Meeting of European Light Microscopy Initiative. 2008.

SVOBODA, David, Martin MAŠKA, Jan SKALICKÝ, Michal KOZUBEK a Stanislav STEJSKAL. 3D AcquiGen 0.2. 2008.

SVOBODA, David, Martin MAŠKA, Jan SKALICKÝ, Michal KOZUBEK a Stanislav STEJSKAL. 3D CytoGen 0.2. 2008.

SVOBODA, David, Martin MAŠKA, Jan SKALICKÝ, Michal KOZUBEK a Stanislav STEJSKAL. 3D OptiGen 0.2. 2008.

MAŠKA, Martin, Jan HUBENÝ, David SVOBODA a Michal KOZUBEK. A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy. Online. In 3rd International Symposium on Visual Computing. Berlin, Heidelberg: Spinger-Verlag, 2007, s. 571-581. ISBN 978-3-540-76855-5.

MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA, Michal KOZUBEK a Petr KRONTORÁD. Acquiarium 1.0. 2007.

KOZUBEK, Michal. Automation of biomedical image acquisition and analysis in optical microscopy. In Seminar of the Centre for Image Analysis. 2007.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Emilie LUKÁŠOVÁ a Michal KOZUBEK. Bioinformatic and image analyses of cellular localization of apoptotic proteins endonuclease G, AIF, and AMID. In Symposium "Structure and Function of Cell Nucleus". 2007.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Emilie LUKÁŠOVÁ a Michal KOZUBEK. 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, 2007, roč. 12, č. 7, s. 1155-1171. ISSN 1360-8185.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Pavel MATULA a Michal KOZUBEK. Bioinformatic predictions and image analysis of localization and interactions of endonuclease G, AIF, and AMID in human cells. In Book of Abstracts for 15th Euroconference on Apoptosis. 2007.

SKALNÍKOVÁ, Magdalena, Eva BÁRTOVÁ, Vladimír ULMAN, Petr MATULA, David SVOBODA, Andrea HARNIČAROVÁ, Michal KOZUBEK a Stanislav KOZUBEK. Distinct patterns of histone methylation and acetylation in human interphase nuclei. Physiological Research. Prague: Czech Academy of Sciences, 2007, roč. 56, č. 6, s. 797-806. ISSN 0862-8408.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Marek KAŠÍK a Michal KOZUBEK. Fluorescent microscopy of living cells. In Analytical Cytometry IV: Book of Abstracts. 2007. ISBN 978-80-239-9591-6.

KOUTNÁ, Irena, Petr KRONTORÁD, Zbyněk SVOBODA, Eva BÁRTOVÁ, Michal KOZUBEK a Stanislav KOZUBEK. New insights into gene positional clustering and its properties supported by large-scale analysis of various differentiation pathways. Genomics. United States: Elsevier Science Inc, 2007, roč. 89, č. 1, s. 81-88. ISSN 0888-7543.

KOZUBEK, Michal a Jakub KULAVIAK. Optimizing light throughput in image cytometry. In Analytical Cytometry IV: Book of Abstracts. 2007. ISBN 978-80-239-9591-6.

KOZUBEK, Michal a Jakub KULAVIAK. Optimizing light throughput in image cytometry. In Analytical Cytometry IV: International Conference. 2007.

KOZUBEK, Michal. Precise simulation of 3D fluorescence microscope image formation. In Pattern Recognition and Computer Vision Colloquium. 2007.

KOZUBEK, Michal. Simulace degradace obrazu v optické mikroskopii. In Informatics Colloquium. 2007.

AMRICHOVÁ, Jana, Miroslav VAŘECHA, Daša MEDŘÍKOVÁ, Emilie LUKÁŠOVÁ, Jiří FAJKUS, Stanislav KOZUBEK a Michal KOZUBEK. Spatial Organization, Dynamics, and Associations of Telomeres in Healthy, Telomerase-Positive and ALT Human Cell Lines. In The Role of Telomeres and Telomerase in Cancer Research. 2007.

KLABUSAY, Martin, Viera HRABČÁKOVÁ, Irena KOUTNÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Michal KOZUBEK a Jiří MAYER. Srovnání metod CD34+ a Lin– selekce buněk ze štěpu periferních kmenových buněk pacientů s lymfomy a vyhodnocení jejich ex vivo diferenciace pomocí cDNA microarrays. In XXXI. Brněnské onkologické dny s XXI. konferencí pro sestry a laboranty. 1. vyd. Brno: Masarykův onkologický ústav, 2007, s. 182-183, 410 s. ISBN 978-9780-86793-09-2.

SVOBODA, David, Martin MAŠKA, Marek KAŠÍK, Jan HUBENÝ, Michal KOZUBEK, Michal ZIMMERMANN a Stanislav STEJSKAL. 3D AcquiGen 0.1. 2007.

SVOBODA, David, Martin MAŠKA, Marek KAŠÍK, Jan HUBENÝ, Michal KOZUBEK, Michal ZIMMERMANN a Stanislav STEJSKAL. 3D CytoGen 0.1. 2007.

SVOBODA, David, Martin MAŠKA, Marek KAŠÍK, Jan HUBENÝ, Michal KOZUBEK, Michal ZIMMERMANN a Stanislav STEJSKAL. 3D OptiGen 0.1. 2007.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Michal KOZUBEK a Stanislav KOZUBEK. Analýza lokalizace a interakce fluorescenčně značených molekul v živých i fixovaných lidských buňkách. In Sborník konference Mikroskopie 2006. 2006.

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, s. 465-476. ISBN 80-7015-037-8.

KOZUBEK, Michal. Automated analysis of multi-dimensional biomedical image data acquired using optical microscopy. In 6th International Conference on Stereology, Spatial Statistics and Stochastic Geometry. 2006.

MATULA, Petr, Michal KOZUBEK, Pavel MATULA, Miroslav VAŘECHA, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ a Stanislav KOZUBEK. Automated confocal live cell microscopy based on spinning disks. In 6th International ELMI Meeting and Workshop on Advanced Light Microscopy: Abstract Book. 2006.

KOZUBEK, Michal. Automation of biomedical image acquisition and processing in optical microscopy: Exploring the structure and function of human genome. In Seminar of the Centre for Applied Medical Research. 2006.

JANSOVÁ, Eva, Irena KOUTNÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Silvie KŘIVÁNKOVÁ, Jan ŽALOUDÍK, Michal KOZUBEK a Stanislav KOZUBEK. Comparative transcriptome maps: a new approach to the diagnosis of colorectal carcinoma patients using cDNA microarrays. Clinical Genetics. Denmark: Blackwell Munksgaard, 2006, roč. 69, č. 3, s. 218-227. ISSN 0009-9163.

ONDŘEJ, Vladan, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Martin FALK, Pavel MATULA, Petr MATULA a Michal KOZUBEK. Directional motion of foreign plasmid DNA to nuclear HP1 foci. Chromosome Research. Dordrecht: Springer, 2006, roč. 14, č. 5, s. 505-514. ISSN 0967-3849.

KOUTNÁ, Irena, Martin KLABUSAY, Viera HRABČÁKOVÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Michal KOZUBEK a Jiří MAYER. 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, 2006, roč. 34, č. 7, s. 832-840, 10 s. ISSN 0301-472X.

MATULA, Petr, Pavel MATULA, Michal KOZUBEK a Vladimír DVOŘÁK. Fast Point-Based 3D Alignment of Live Cells. IEEE Transactions on Image Processing. 2006, roč. 15, č. 8, s. 2388-2396. ISSN 1057-7149.

HUBENÝ, Jan, Pavel MATULA, Petr MATULA a Michal KOZUBEK. 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, s. 163-173, 10 s. ISBN 3-540-33266-9.

TASLEROVÁ, Renata, Stanislav KOZUBEK, Eva BÁRTOVÁ, Pavla GAJDUŠKOVÁ, Roman KODET a Michal KOZUBEK. 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, 2006, roč. 155, č. 3, s. 493-504. ISSN 1047-8477.

FALK, Martin, Emilie LUKÁŠOVÁ, Barbora GABRIELOVÁ, Vladan ONDŘEJ, Michal KOZUBEK a Iva KROUPOVÁ. Nuclear organization and dynamics of the DSB-repair. In COST P9 Action ‘Radiation Damage to Biomolecules’, Working Group 5 Meeting RISC-RAD Work Package 5 Meeting, Workshop on Challenges for Modelling of Radiation Damage in Biological Systems. 17.–19. října, 2006, Physik-Zentrum Bad Honnef, Německo (Invited ). 2006.

JEŽEK, Jan, Miroslav VAŘECHA, Jana AMRICHOVÁ, Michal KOZUBEK, Tomáš ČIŽMÁR a Pavel ZEMÁNEK. Optical tracking of microobjects within living cells. In Proceedings of SPIE. 6180. vyd. Bellingham, USA: International Society for Optical Engineering, 2006, s. 618025-1, 6 s. ISBN 0-8194-6236-5.

KOZUBEK, Michal a Jakub KULAVIAK. Optimizing light throughput in fluorescence microscopy. In 6th International ELMI Meeting and Workshop on Advanced Light Microscopy: Abstract Book. 2006.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Pavel MATULA, Petr MATULA a Michal KOZUBEK. Single-cell image analysis of cellular localization and colocalization of endonuclease G, AIF and AMID in living cells. In Book of Abstracts for 14th Euroconference on Apoptosis. 2006.

KOUTNÁ, Irena, Petr KRONTORÁD, Lenka TESAŘOVÁ, Martin KLABUSAY, Viera HRABČÁKOVÁ a Michal KOZUBEK. Transcription density map as a new tool for evaluation of various expression profiles: Ex vivo differentiation of CD34+ cells. In ISREC Conference on Cancer Research. 2006.

KOUTNÁ, Irena, Petr KRONTORÁD, Zbyněk SVOBODA a Michal KOZUBEK. Vybrané aplikace technologie cDNA microarrays v onkologickém výzkumu. Klinická onkologie. Czech Republic: ApS BRNO, 2006, roč. 19, č. 2, s. 338 - 341. ISSN 0862-495X.

KOZUBEK, Michal, Pavel MATULA, Petr MATULA a David SVOBODA. Analysis of biomedical image data acquired using optical microscopy. In 1st International Summer School on Computational Biology. 2005.

KOZUBEK, Michal, Pavel MATULA, Petr MATULA a David SVOBODA. Analysis of biomedical image data acquired using optical microscopy. In DUŠEK, Ladislav, Jiří HŘEBÍČEK a Jiří JARKOVSKÝ. Proceedings of the 1st International Summer School on Computational Biology. Brno: Masaryk University, 2005, s. 21-28. ISBN 80-210-3907-8.

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

KRONTORÁD, Petr, Zbyněk SVOBODA, Irena KOUTNÁ, Eva JANSOVÁ a Michal KOZUBEK. Analýza obrazů získaných snímáním microarrays. In Analytická cytometrie III. 2005. ISBN 80-239-5155-6.

PAVLÍK, Tomáš, Eva JANSOVÁ, Petr KRONTORÁD, Zbyněk SVOBODA a Michal KOZUBEK. Aplikace FDR a FWER testovacích procedur na data ze studie kolorektálního karcinomu. In Analytická cytometrie III. 2005. ISBN 80-239-5155-6.

KOZUBEK, Michal, Petr MATULA, Pavel MATULA, Miroslav VAŘECHA, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ a Stanislav KOZUBEK. Automated confocal in vivo microscopy based on spinning disks. In Focus on Microscopy: Program and Abstract Book. 2005.

KOUTNÁ, Irena, Eva JANSOVÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Michal KOZUBEK a Stanislav KOZUBEK. cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases. In Prague Post Genome Technology Workshop. Prague, Czech Republic: Czech Pattern Recognition Society, 2005, s. 69-72. ISBN 80-01-03239-6.

JANSOVÁ, Eva, Petr KRONTORÁD, Irena KOUTNÁ, Stanislav STEJSKAL, Petr MATULA, David SVOBODA, Michal KOZUBEK a Stanislav KOZUBEK. Combination of cDNA microarray technology and fluorescence leads to better understanding of relationships between gene expression and epigenetic regulation. In MGED8 Abstract book. 2005.

KOUTNÁ, Irena, Petr KRONTORÁD, Eva JANSOVÁ, Zbyněk SVOBODA, Michal KOZUBEK a Stanislav KOZUBEK. Důkaz klastrování genů na chromosomových doménách studiem diferenciací buněčných nádorových linií. In Analytická cytometrie III. 2005. ISBN 80-239-5155-6.

FALK, Martin, Emilie LUKÁŠOVÁ, Mario FARETTA, Ivan DELLINO, Stanislav KOZUBEK, Pier Giuseppe PELICCI, Michal KOZUBEK a Mario ROCCHI. Changes of nuclear architecture and chromatin structure induced by PML/RARa fusion protein in APL leukemic cells. In 3rd Conference on Analytic Cytometry, 21. - 25. June 2005, Červenohorské sedlo, Czech Republic.In: Sborník abstraktů konference se zahraniční účastí. Analytická cytometrie III. Česká společnost pro analytickou cytologii, 2005. 2005. ISBN 80-239-5155-6.

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

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ, Vladimír ULMAN, Petr MATULA, Michal KOZUBEK a Stanislav KOZUBEK. Imaging of mitochondrial apoptogenic proteins released during apoptosis in living and fixed cells. In Book of Abstracts for 13th Euroconference on Apoptosis. 2005. ISBN 963-219-273-7.

LUKÁŠOVÁ, Emilie, Zdeněk KOŘÍSTEK, Martin FALK, Stanislav KOZUBEK, Sergei GRIGORYEV, Michal KOZUBEK, Vladan ONDŘEJ a Iva KROUPOVÁ. Methylation of histones in myeloid leukemias as a potential marker of granulocyte abnormalities. Journal of Leukocyte Biology. New York: Society for Leukocyte Biology, 2005, roč. 77, č. 1, s. 100-111. ISSN 0741-5400.

KRONTORÁD, Petr, Zbyněk SVOBODA, Irena KOUTNÁ, Eva JANSOVÁ a Michal KOZUBEK. New practical tools for microarray data analysis. In MGED8 Abstract book. 2005.

SVOBODA, Zbyněk, Petr KRONTORÁD, Eva JANSOVÁ, Irena KOUTNÁ a Michal KOZUBEK. Normalizační metody ve zpracování dat z DNA Microarrays. In Analytická cytometrie III. 2005. ISBN 80-239-5155-6.

BÁRTOVÁ, Eva, J. PACHERNÍK, Andrea HARNIČAROVÁ, A. KOVAŘÍK, M. KOVAŘÍKOVÁ, Jiřina HOFMANOVÁ, Magdalena SKALNÍKOVÁ, Michal KOZUBEK a Stanislav KOZUBEK. Nuclear levels and patterns of histone H3 modification and HP1 proteins after inhibition of histone deacetylases. Journal of Cell Science. Cambridge: Company of Biologists Ltd., 2005, roč. 118, č. 21, s. 5035-5046. ISSN 0021-9533.

JANSOVÁ, Eva, Irena KOUTNÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Michal KOZUBEK a Stanislav KOZUBEK. Sledování změn genové exprese u pacientů s kolorektálním karcinomem pomocí cDNA microarrays technologie a jejich diagnostika pomocí transkripčních map. In Analytická cytometrie III. 2005. ISBN 80-239-5155-6.

KOUTNÁ, Irena, Jiří MAYER, Martin KLABUSAY, Petr KRONTORÁD, Eva JANSOVÁ, Michal KOZUBEK a Stanislav KOZUBEK. Transcriptional profiling of human CD34+ cells during in vitro differentiation. In MGED8 Abstract book. 2005.

HUBENÝ, Jan, David SVOBODA, Pavel MATULA a Michal KOZUBEK. Využití deformabilních modelů v obrazové cytometrii. 2005.

KOZUBEK, Michal. Zpracování nových typů obrazových dat v optické mikroskopii. In Informatics Colloquium. 2005.

HUBENÝ, Jan, Pavel MATULA, Petr MATULA a Michal KOZUBEK. 3D Reconstruction of Interphase Chromosomes. In 1st Doctoral Workshop on Mathematical and Engeneering methods in Computer Science. 2005.

MATULA, Petr, Michal KOZUBEK a Pavel MATULA. Applications of Image Registration in Human Genome Research. In Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis. Berlin: Springer-Verlag, 2004, s. 376-384. ISBN 3-540-22675-3.

KOZUBEK, Michal, Petr MATULA, Pavel MATULA a Stanislav KOZUBEK. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. Microscopy research and technique. USA: Wiley-Liss, 2004, roč. 64, č. 2, s. 164-175. ISSN 1059-910X.

KOZUBEK, Michal, Petr MATULA a Pavel MATULA. Automated confocal microscopy: The way of achieving both quality and quantity in 3D image cytometry. In International Symposium on Biomedical Imaging. 2004.

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

KOZUBEK, Michal, Petr MATULA, Pavel MATULA, David SVOBODA, Jan HUBENÝ a Petr KRONTORÁD. Automated image analysis in fluorescence microscopy: From isolated cells to tissues and microarray images. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, s. 44-46. ISBN 80-210-3560-9.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK a Michal KOZUBEK. Automated in vivo imaging of cell interior using fluorescent proteins. In Abstracts of the Congress of International Society for Analytical Cytology, Cytometry 59A, p.107. 2004. ISSN 0196-4763.

KOZUBEK, Stanislav a Michal KOZUBEK. Biophysics of the Genome. Brno: Masaryk University, 2004, 82 s. ISBN 80-210-3560-9.

KOZUBEK, Stanislav a Michal KOZUBEK. Biophysics of the Genome. 2004.

KOUTNÁ, Irena, Eva JANSOVÁ, Petr KRONTORÁD, Zbyněk SVOBODA, Tomáš PAVLÍK, Eva BÁRTOVÁ, Michal KOZUBEK a Stanislav KOZUBEK. Clustering of genes with similar regulation patterns during monocyte and granulocyte differentiation of HL-60 cells. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, s. 38-43. ISBN 80-210-3560-9.

FALK, Martin, E LUKÁŠOVÁ, M FARETTA, I DELLINO, Stanislav KOZUBEK, Pelicci G I, Michal KOZUBEK a M ROCCHI. Colocalization of PML bodies and PML/RARa microspeckles with up- and down-regulated loci and changes of chromatin structure in APL leukemia cells. In Biophysics of the Genome. Brno: Masarykova Univerzita, 2004, s. 8-23. ISBN 80-210-3560-9.

FALK, Martin, Emilie LUKÁŠOVÁ, M FARETTA, I DELLINO, Stanislav KOZUBEK, Pelicci G I, Michal KOZUBEK a M ROCCHI. Colocalization of PML bodies and PML/RARa microspeckles with up and downregulated loci and changes of chromatin structure in APL leukemia cells. In Third Workshop on Biophysics of the Genome, 12. – 13. října, 2004, Brno, Česká republika. In: Book of Abstracts. 2004.

FALK, Martin, Emilie LUKÁŠOVÁ, Mario FARETTA, Ivan DELLINO, Stanislav KOZUBEK, Giuseppe PELICCI, Michal KOZUBEK a Mariano ROCHI. 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. First Edition 2004. Brno: Masaryk University, 2004, s. 8-23. ISBN 80-210-3560-9.

SKALNÍKOVÁ, Magdalena, Eva BÁRTOVÁ, Stanislav KOZUBEK a Michal KOZUBEK. Cytological study of DNA methylation and histone methylation patterns in human cell lines. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, s. 72-75. ISBN 80-210-3560-9.

ONDŘEJ, Vladan, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Pavel MATULA, Petr MATULA a Michal KOZUBEK. Dynamics of HP1 transgene loci movement and silencing in living cells. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, s. 66-71. ISBN 80-210-3560-9.

MATULA, Pavel, Jan HUBENÝ a Michal KOZUBEK. Fast Marching 3D Reconstruction of Interphase Chromosomes. In Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis. Berlin: Springer-Verlag, 2004, s. 385-394. ISBN 3-540-22675-3.

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

JANSOVÁ, Eva, Petr KRONTORÁD, Zbyněk SVOBODA, Irena KOUTNÁ, Tomáš PAVLÍK, Michal KOZUBEK, Marie JAROŠOVÁ, Jan ŽALOUDÍK a Stanislav KOZUBEK. Gene expression in colorectal carcinoma determined by cDNA microarrays using a combination of several evaluation approaches. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, s. 29-37. ISBN 80-210-3560-9.

MATULA, Pavel, Petr MATULA, Michal KOZUBEK a Petr MEJZLÍK. 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. Los Alamitos: IEEE Computer Society, 2004, s. 580-583. ISBN 0-7695-2223-8.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK, Pavel MATULA, Petr MATULA a Michal KOZUBEK. In vivo imaging of cell interior using automated high-resolution cytometry. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, s. 76-82. ISBN 80-210-3560-9.

LUKÁŠOVÁ, Emilie, Martin FALK, Zdeněk KOŘISTEK, Stanislav KOZUBEK, Sergei GRIGORYEV, Michal KOZUBEK, Vladan ONDŘEJ a Iva KROUPOVÁ. Methylation of histone H3K9 in human blood cells and in granulocytes of patients with myeloid leukemia. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, s. 53-57. ISBN 80-210-3560-9.

LUKÁŠOVÁ, E, Martin FALK, Z KOŘISTEK, Stanislav KOZUBEK, S GRIGORYEV, Michal KOZUBEK, V ONDŘEJ a I KROUPOVÁ. Methylation of histone H3K9 in human blood cells and in granulocytes of patients with myeloid leukemia. In Biophysics of the Genome. Brno: Masarykova univerzita, 2004, s. 53-57. ISBN 80-210-3560-9.

LUKÁŠOVÁ, Emilie, Martin FALK, Zdeněk KOŘÍSTEK, Stanislav KOZUBEK, S GRIGORYEV, Michal KOZUBEK, Vladan ONDŘEJ a Iva KROUPOVÁ. Methylation of histone H3K9 on lysine 9 distinguishes granulocytes of healthy individuals and patients with myeloid leukemia. In Third Workshop on Biophysics of the Genome, 12. - 13. října, 2004, Brno, Česká republika. In: Book of Abstracts. 2004.

JANSOVÁ, Eva, Petr KRONTORÁD, Zbyněk SVOBODA, Tomáš PAVLÍK, Irena KOUTNÁ, Michal KOZUBEK, Jan ŽALOUDÍK a Stanislav KOZUBEK. Nové možnosti v diagnostice kolorektálního karcinomu s využitím technologie cDNA mikročipů. Klinická onkologie. Brno: ApS Brno, spol.s.r.o., 2004, roč. 6/17, č. 6, s. 203-207. ISSN 0862-495X.

MATULA, Pavel, Michal KOZUBEK, Stanislav KOZUBEK a Vladan ONDŘEJ. Rapid Image Acquisition of Living Cells and its Limits. In Biophysics of the Genome. Brno, Czech Republic: Masaryk University, 2004, s. 58-61. ISBN 80-210-3560-9.

AMRICHOVÁ, Jana, Emilie LUKÁŠOVÁ, Miroslav VAŘECHA, Stanislav KOZUBEK, Vladan ONDŘEJ a Michal KOZUBEK. Topographic characterization of telomeres in healthy and various tumor cell lines determined in situ and in vivo. In Abstracts of the Congress of International Society for Analytical Cytology, Cytometry 59A, p.91. 2004. ISSN 0196-4763.

LUKÁŠOVÁ, Emilie, Stanislav KOZUBEK, Martin FALK, Michal KOZUBEK, Jan ŽALOUDÍK, Václav VAGUNDA a Zdeněk PAVLOVSKÝ. Topography of genetic loci in the nuclei of cells of colorectal carcinoma and adjacent tissue of colonic epithelium. Chromosoma. Berlin: Springer-Verlag, 2004, roč. 112, č. 5, s. 221-230. ISSN 0009-5915.

KOZUBEK, Michal, Petr MATULA, Pavel MATULA a Petr MEJZLÍK. A network solution for high-resolution image cytometry. In Biophysics of the Genome. Brno: Masaryk University, 2003, s. 30-36. ISBN 80-210-3226-X.

SKALNÍKOVÁ, Magdalena, Eva BÁRTOVÁ, Pavla GAJDUŠKOVÁ, Stanislav KOZUBEK a Michal KOZUBEK. Analysis of DNA methylation status of cell nuclei using high-resolution. In Biophysics of the Genome. Brno: Masaryk University, 2003, s. 59-61. ISBN 80-210-3226-X.

TASLEROVÁ, Renata, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Pavla JIRSOVÁ, Eva BÁRTOVÁ a Michal KOZUBEK. 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. 2003, roč. 112, č. 2, s. 143-155. ISSN 0340-6717.

KOZUBEK, Stanislav a Michal KOZUBEK. Biophysics of the Genome. Brno: Masaryk University, 2003, 94 s. ISBN 80-210-3226-X.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Hana GAJOVÁ, Pavla JIRSOVÁ, Jitka ŽLŮVOVÁ, Renata TASLEROVÁ, Irena KOUTNÁ a Michal KOZUBEK. Cytogenetics and cytology of retinoblastomas. J Cancer Res. Clin.Oncol. Berlin: Springer-Verlag, 2003, roč. 129, č. 2, s. 89-99. ISSN 0171-5216.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Michal KOZUBEK a Okumura KATSUZUMI. Detailed studies of the human genome 3D structure. In Biophysics of the Genome. Brno: Masaryk University, 2003, s. 37-41. ISBN 80-210-3226-X.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Michal KOZUBEK, Jana AMRICHOVÁ, Martin FALK a Vladan ONDŘEJ. Detailed studies of the 3D structure of chromosome territories. In 4th European Cytogenetics Conference, 6. – 19. září, 2003, Bologna, ItálieIn: Ann. Genet. - Paris, 46, 2003, p. 77-78. 2003.

FALK, Martin, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK, Michal KOZUBEK, Pellici P G a M FARETTA. Functional topology of genes regulated by fusion protein PML/RARa. In Second Workshop on Biophysics of the Genome, 2. – 4. dubna, 2003, Hlohovec, Česká republika.In: Scientific Programme and Book of Abstracts, p. 18-19. 2003.

FALK, Martin, E LUKASOVA, Stanislav KOZUBEK, Pellici G I, M FARETTA, Michal KOZUBEK a M ROCCHI. Changes in gene expression induced by PML/RARa fusion protein correlate with the degree of chromatin compaction. In International Conference on Applied Genomics, 9th ESACP/ 16th ISDQP Meeting, 1. – 4. října, 2003, Amsterdam, Holandsko. In: Proceedings, p. 72-73, Published in Analytical Cellular Pathology, 2003. 2003.

MATULA, Petr, Magdalena SKALNÍKOVÁ, Michal KOZUBEK a Michael HAUSMANN. Improving measurement precision using automated micro-axial tomography. In Biophysics of the Genome. Brno: Masaryk University, 2003, s. 51-53. ISBN 80-210-3226-X.

KOZUBEK, Stanislav, Eva BÁRTOVÁ, Emilie LUKÁŠOVÁ, Michal KOZUBEK, Jana AMRICHOVÁ, Renata TASLEROVÁ, Martin FALK a Vladan ONDŘEJ. Large-scale organization of human genome and chromosomal territories in the nucleus of normal and cancer cells and its functional implications. In International Conference on Applied Genomics, 9th ESACP/ 16th ISDQP Meeting, 1. – 4. října, 2003, Amsterdam, Holandsko. In: Proceedings, p. 73, Published in Analytical Cellular Pathology, 2003. 2003.

AMRICHOVÁ, Jana, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK a Michal KOZUBEK. Nuclear and territorial topography of chromosome telomeres in human lymphocytes. Experimental Cell Research. Elsevier Science, USA, 2003, roč. 289, č. 1, s. 11-26. ISSN 0014-4827.

LUKÁŠOVÁ, Emilie, Stanislav KOZUBEK, Martin FALK, Michal KOZUBEK, Jan ŽALOUDÍK, Václav VAGUNDA, M ROCCHI a Zdeněk PAVLOVSKÝ. Organization of selected loci of chromosomes 7,11, and 20 in cells colorectal carcinoma and adjacent colonic tissue. In Conference on Biophysics of the Genome, 2. – 4. dubna, 2003, Hlohovec, Česká republika.In: Scientific Programme and Book of Abstracts, p. 30. 2003.

KOZUBEK, Michal. Počítačové zpracování 2D a 3D obrazů buněk, buněčných jader, chromosomů a genů pomocí automatizované optické mikroskopie. In External seminar. 2003.

MATULA, Petr, Michal KOZUBEK, Florian STAIER a Michael HAUSMANN. Precise 3D image alignment in micro-axial tomography. Journal of Microscopy. Oxford: Blackwell Science, 2003, roč. 209, č. 2, s. 126-142. ISSN 0022-2720.

VAŘECHA, Miroslav, Martin JABUREK, Lubomi DVORAK, Petr JEZEK, Petr PAUČEK, Keith GARLID, Stanislav KOZUBEK a Michal KOZUBEK. Structural and functional characterization of uncoupling proteins: Alkylsulfonates as probes of UCP transport mechanism. In Biophysics of the Genome. Brno: Masaryk University, 2003, s. 74-81. ISBN 80-210-3226-X.

AMRICHOVÁ, Jana, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ a Michal KOZUBEK. Topography of telomeres and structure of chromosome territories in human lymphocytes. In Biophysics of the Genome. Brno: Masaryk University, 2003, s. 1-11. ISBN 80-210-3226-X.

KOZUBEK, Michal, Magdalena SKALNÍKOVÁ, Petr MATULA, Eva BÁRTOVÁ, Joachim RAUCH, Friedrich NEUHAUS, Heinz EIPEL a Michael HAUSMANN. Automated micro axial tomography of cell nuclei after specific labelling by fluorescence in situ hybridisation. Micron. Amsterdam: Elsevier, 2002, roč. 33, č. 7, s. 655-665. ISSN 0968-4328.

KOZUBEK, Michal, Petr MATULA, Heinz EIPEL a Michael HAUSMANN. Automated multi-view 3D image acquisition in human genome research. In 3D data processing, visualization and transmission. Los Alamitos: IEEE Computer Society, 2002, s. 91-98. ISBN 0-7695-1521-5.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Michal KOZUBEK, P JIRSOVÁ, Alena GAŇOVÁ a Martin FALK. Backbone radial looping model of interphase chromosome. In XIV International Biophysics Congress, 27. dubna - 1. května, 2002, Buenos Aires, Argentina.In: Abstracts, p. 44. 2002.

KOZUBEK, Stanislav a Michal KOZUBEK. Biophysics of the Genome and Its Interactions. Brno: Masaryk University, 2002, 91 s. ISBN 80-210-2853-X.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Hana GAJOVÁ, Pavla JIRSOVÁ, Rudolf AUTRATA a Michal KOZUBEK. Cytogenetics of Retinoblastoma. In Biophysics of the genome and its interactions. Brno: Masaryk University, 2002, s. 7-11. ISBN 80-210-2853-X.

KOZUBEK, Michal, Magdalena SKALNÍKOVÁ, Petr MATULA, Eva BÁRTOVÁ, Heinz EIPEL a Michael HAUSMANN. Development of software for automated micro-axialtomography. In Biophysics of the genome and its interactions. Brno: Masaryk University, 2002, s. 45-53. ISBN 80-210-2853-X.

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

KOZUBEK, Michal, Petr MATULA, Pavel MATULA a Petr MEJZLÍK. 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. Los Alamitos: IEEE Computer Society, 2002, s. 99-106. ISBN 0-7695-1521-5.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Hana GAJOVÁ, Pavla JIRSOVÁ, Gabriela GALIOVÁ a Michal KOZUBEK. Chromatin modifications determined in retinoblastoma. In 8th European Workshop on Cytogenetics and Molecular Genetics of Human Solid Tumours. 2002.

FALK, Martin, E LUKÁŠOVÁ, Michal KOZUBEK a Stanislav KOZUBEK. Model of chromosome structure in interphase nuclei of human lymphocytes. In Conference on New Models and Nuclear Methods in Biophysics and Biochemistry, Joint Institute for Nuclear Research, Russian Academy of Sciences, 24.–25. ledna, 2002, Dubna, Rusko (Invited Lecture). 2002.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Pavla JIRSOVÁ, Michal KOZUBEK, Hana GAJOVÁ, Emilie LUKÁŠOVÁ, Magdalena SKALNÍKOVÁ, Alena GAŇOVÁ, Irena KOUTNÁ a Michael HAUSMANN. Nuclear structure and gene activity in human differentiated cells. Journal of Structural Biology. San Diego,USA: Academic Press, 2002, roč. 139, č. 2, s. 76-89. ISSN 1047-8477.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Pavla JIRSOVÁ, Michal KOZUBEK, Emilie LUKÁŠOVÁ, Magdalena SKALNÍKOVÁ, Alena GAŇOVÁ, Irena KOUTNÁ a Renata PASEKOVÁ. Nuclear topography and gene activity. In Biophysics of the genome and its interactions. Brno: Masaryk University, 2002, s. 13-17. ISBN 80-210-2853-X.

SKALNÍKOVÁ, Magdalena, Michal KOZUBEK, Petr MATULA, Eva BÁRTOVÁ, Heinz EIPEL a Michael HAUSMANN. 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. Brno: Masaryk University, 2002, s. 82-85. ISBN 80-210-2853-X.

AMRICHOVÁ, Jana, Michal KOZUBEK, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Martin FALK, Renata TASLEROVÁ, Pavel MATULA, Petr MATULA, P JIRSOVÁ, Magdalena SKALNÍKOVÁ, Eva BÁRTOVÁ a Irena KRONTORÁD KOUTNÁ. Repeated fluorescence in situ hybridization and its applications in human genome studies. In 2nd Elmau Conference on Nuclear Organisation, Gene Regulation and Nuclear Structure, 6. - 9. října, 2002, Schloss Elmau, Německo. (in English)In: Conference Program, p. 13. 2002.

LUKASOVA, E, Stanislav KOZUBEK, Michal KOZUBEK, Martin FALK, P JIRSOVA a E BARTOVA. Spatial Arrangement of Chromosome 17 Territory in the Interphase Nucleus of Human Lymphocytes. In Biophysics of the genome and its interactions. Brno: Masarykova univerzita, 2002, s. 68-73. ISBN 80-210-2853-X.

AMRICHOVÁ, Jana, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK, Pavla JIRSOVÁ a Michal KOZUBEK. 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. Brno: Masaryk University, 2002, s. 1-6. ISBN 80-210-2853-X.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Irena KOUTNÁ, Pavla JIRSOVÁ, Michal KOZUBEK, Alena GAŇOVÁ, Renata PASEKOVÁ, Jana AMRICHOVÁ, Martin FALK a Pavel HLOŽEK. Structure of the human genome: Experimental results and models. In Biophysics of the genome and its interactions. Brno: Masaryk University, 2002, s. 54-67. ISBN 80-210-2853-X.

KOZUBEK, Michal, Petr MATULA a Pavel MATULA. The power of computerized light microscopy. Imaging & Microscopy. Darmstadt: GIT Verlag, 2002, roč. 4, č. 2, s. 25-28. ISSN 1439-4243.

LUKÁŠOVÁ, Emilie, Stanislav KOZUBEK, Michal KOZUBEK, Martin FALK a Jana AMRICHOVÁ. The 3D structure of human chromosomes in cell nuclei. Chromosome Research. Dordrecht: Kluwer Academic, 2002, roč. 10, č. 7, s. 535-548. ISSN 0967-3849.

FALK, Martin, E LUKASOVA, Stanislav KOZUBEK, Michal KOZUBEK a Krasavin E A. Topography of Dystrophin Exons Relative to the Cell Nucleus and to the Active and Inactive Chromosome X Territory Determined for Human Lymphocytes. In Biophysics of the genome and its interactions. Brno: Masarykova univerzita, 2002, s. 18-27. ISBN 80-210-2853-X.

FALK, Martin, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK a Michal KOZUBEK. Topography of genetic elements of X-chromosome relative to the cell nucleus and to the chromosome X territory determined for human lymphocytes. Gene. Amsterdam: Elsevier, 2002, roč. 292, č. 1, s. 13-24. ISSN 0378-1119.

FALK, Martin, E LUKÁŠOVÁ, Stanislav KOZUBEK a Michal KOZUBEK. Topography of genetic elements of X-chromosome relative to the cell nucleus and to the chromosome X territory determined for human lymphocytes. In 2nd Elmau Conference on Nuclear Organization, Gene Regulation and Nuclear Structure, 6. - 9. října, 2002, Schloss Elmau, Německo. (in English)In: Conference Program, p. 20. 2002.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Pavla JIRSOVÁ, Irena KOUTNÁ, Michal KOZUBEK, Alena GAŇOVÁ, Eva BÁRTOVÁ, Martin FALK a Renata TASLEROVÁ. 3D Structure of the human genome: Order in randomness. Chromosoma. Berlin: Springer-Verlag, 2002, roč. 111, č. 5, s. 321-331. ISSN 0009-5915.

KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ, Pavel MATULA, Petr MATULA, Pavla JIRSOVÁ, Alena GAŇOVÁ a Irena KOUTNÁ. Combined confocal and wide-field high-resolution cytometry of FISH-stained cells. Cytometry. New York: International Society for Analytical Cyt, 2001, roč. 45, č. 1, s. 1-12. ISSN 0196-4763.

BÁRTOVÁ, Eva, Hana GAJOVÁ, Stanislav KOZUBEK, Pavla JIRSOVÁ a Michal KOZUBEK. Cytogenetics of Retinoblastoma. In Biophysics of the Genome and Its Interactions. 2001.

VORÁČEK, Jan, Michal KOZUBEK, Eva BÁRTOVÁ a Markus MANNIO. Deterministic modeling of the chromatin organization in human cell nuclei. In Shaping future with simulation. Delft: TU Delft, 2001, s. 1-7. ISBN 90-806441-1-0.

GAŇOVÁ, Alena, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK, Michal KOZUBEK, Raisa GOVORUN, Irena KOUTNÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ, Pavla JIRSOVÁ, Renata PASEKOVÁ a Evgenij KRASAVIN. Exchange aberrations among 11 chromosomes of human lymphocytes induced by gamma-rays. International Journal of Radiation Biology. 2001, roč. 77, č. 4, s. 419-429. ISSN 0955-3002.

GAŇOVÁ, Alena, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK, Michal KOZUBEK, Eva BÁRTOVÁ, P JIRSOVÁ, Magdalena SKALNÍKOVÁ, Irena KRONTORÁD KOUTNÁ, R PASEKOVÁ a Martin FALK. Exchange aberrations among 11 chromosomes of human lymphocytes induced by gamma-rays. In Mezinárodní radiobiologické symposium, 15. - 16. června, 2001, Hradec Králové, Česká republika. In: Acta Radiobiologica 1, 2001, p. 21. 2001.

KOZUBEK, Michal. FISH Imaging. In Confocal and two-photon microscopy: Foundations, applications, and advances. New York: Wiley-Liss, 2001, s. 389-429. ISBN 0-471-40920-0. Dostupné z: https://dx.doi.org/10.1007/1-4020-3616-7_13.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Pavla JIRSOVÁ, Michal KOZUBEK, Emilie LUKÁŠOVÁ, Magdalena SKALNÍKOVÁ, Alena GAŇOVÁ, Irena KOUTNÁ a Renata PASEKOVÁ. Higher-order chromatin structure of human granulocytes. Chromosoma. Berlin: Springer-Verlag, 2001, roč. 110, č. 5, s. 360-370. ISSN 0009-5915.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Michal KOZUBEK, Magdalena SKALNÍKOVÁ, Irena KRONTORÁD KOUTNÁ, P JIRSOVÁ, Alena GAŇOVÁ, R PASEKOVÁ, J AMRICHOVÁ, Pavel MATULA, Petr MATULA, P MEJZLÍK, Martin FALK a S PALŠA. Induction of chronic myeloid leukemia by ionizing radiation: experimental basis for risk estimation. In VIIth International Workshop Radiation Damage to DNA, 2. - 7. září, 2001, Orléans Nouan-le-Fuzelier, Francie. In: Abstracts, nestr. 2001.

JIRSOVÁ, Pavla, Stanislav KOZUBEK, Eva BÁRTOVÁ, Michal KOZUBEK, Emilie LUKÁŠOVÁ, Alena GAŇOVÁ, Irena KOUTNÁ a Magdalena SKALNÍKOVÁ. Spatial distribution of selected genetic loci in nuclei of human leukemia cells after irradiation. Radiation Research. 2001, roč. 155, č. 2, s. 311-319. ISSN 0033-7587.

LUKÁŠOVÁ, E, Stanislav KOZUBEK, Michal KOZUBEK, Martin FALK, J AMRICHOVÁ, P JIRSOVÁ a E BÁRTOVÁ. Spatial structure of chromosome 17 territory in the interphase nucleus of human lymphocytes. In Conference on Biophysics of the Genome and Its Interactions, Hlohovec, 15. - 17. 10. 2001In: Scientific Programme and Book of Abstracts, p. 35. 2001.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Irena KRONTORÁD KOUTNÁ, P JIRSOVÁ, Michal KOZUBEK, A GAŇOVÁ, R PASEKOVÁ, J AMRICHOVÁ, Martin FALK a P HLOŽEK. Structure of the human genome: Experimental results and models. In Conference on Biophysics of the Genome and Its Interactions, 15. – 17. října, 2001, Hlohovec, Česká republika. (in English). In: Book of Abstracts. 2001.

KOZUBEK, Michal. Theoretical versus experimental resolution in optical microscopy. Microscopy research and technique. USA: Wiley-Liss, 2001, roč. 53, č. 2, s. 157-166. ISSN 1059-910X. Dostupné z: https://dx.doi.org/10.1002/jemt.1080.

FALK, Martin, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK a Michal KOZUBEK. Topography of dystrophin exons relative to the cell nucleus and to the active and inactive chromosome X territory determined for human lymphocytes. In Conference on Biophysics of the Genome and Its Interactions, 15. – 17. října, 2001, Hlohovec, Česká republika. (in English)In: In: Scientific Programme and Book of Abstracts, p. 18. 2001.

KOZUBEK, Michal, Pavel MATULA, Petr MATULA a Stanislav KOZUBEK. Využití počítačové analýzy obrazu v moderní cytometrii. Ed. Alois Kozubík. In Analytická cytometrie I. 2001. ISBN 80-238-6833-0.

KOZUBEK, Stanislav a Michal KOZUBEK. Způsob stanovení vlastností buněk metodou cytometrie s vysokým rozlišením a zařízení pro jeho provádění. 2001. Patent. Číslo: 288693. Vydavatel: Úřad průmyslového vlastnictví ČR. Místo vydání: Praha. Název vlastníka: Biofyzikální ústav AV ČR. Datum registrace: 14. 10. 1998. Datum přijetí: 20. 6. 2001.

KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ, Pavel MATULA, Petr MATULA, Pavla JIRSOVÁ, Alena GAŇOVÁ a Irena KOUTNÁ. Advances in high-resolution cytometry of FISH dots in interphase cell nuclei. In Cytokinematics 2000. 2000.

KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ, Pavel MATULA, Petr MATULA, Pavla JIRSOVÁ, Alena GAŇOVÁ a Irena KOUTNÁ. Advances in high-resolution cytometry of FISH dots in interphase cell nuclei. In The XX Congress of the International Society for Analytical Cytology. 2000.

KOZUBEK, Michal a Petr MATULA. An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy. Journal of Microscopy. Oxford: Blackwell Science, 2000, roč. 200, č. 3, s. 206-217. ISSN 0022-2720.

LUKÁŠOVÁ, Emilie, Stanislav KOZUBEK, Michal KOZUBEK, Václav KROHA, Andrea MAREČKOVÁ, Magdalena SKALNÍKOVÁ a Eva BÁRTOVÁ. Chromosomes participating in translocations typical of malignant haemoblastoses are also involved in frequent interchanges induced by densely ionising radiation. In The XX Congress of the International Society for Analytical Cytology. 2000.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Jana AMRICHOVÁ, Michal KOZUBEK, Andrea LIŠKOVÁ a Jana ŠLOTOVÁ. Influence of cell fixation on chromatin topography. Analytical Biochemistry. San Diego: Academic Press, 2000, roč. 282, č. 1, s. 29-38. ISSN 0003-2697.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Michal KOZUBEK, Pavla JIRSOVÁ, Emilie LUKÁŠOVÁ, Magdalena SKALNÍKOVÁ, Alena CAFOURKOVÁ a Irena KOUTNÁ. Nuclear topography of the c-myc gene in human leukemic cells. Gene. Amsterdam: Elsevier, 2000, roč. 244, č. 1, s. 1-11. ISSN 0378-1119.

SKALNÍKOVÁ, Magdalena, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Pavla JIRSOVÁ, Alena CAFOURKOVÁ, Irena KOUTNÁ a Michal KOZUBEK. 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. Dordrecht: Kluwer Academic, 2000, roč. 8, č. 6, s. 487-499. ISSN 0967-3849.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Michal KOZUBEK, Pavla JIRSOVÁ, Emilie LUKÁŠOVÁ, Magdalena SKALNÍKOVÁ a Kateřina BUCHNÍČKOVÁ. 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. 2000, roč. 24, č. 3, s. 233-241. ISSN 0145-2126.

KOUTNÁ, Irena, Stanislav KOZUBEK, Jan ŽALOUDÍK, Michal KOZUBEK, Emilie LUKÁŠOVÁ, Pavel MATULA, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ, Alena CAFOURKOVÁ a Pavla JIRSOVÁ. Topography of genetic loci in tissue samples: towards new diagnostic tool using interphase FISH and high-resolution image analysis techniques. Analytical Cellular Pathology. Amsterdam: IOS Press, 2000, roč. 20, č. 4, s. 173-185. ISSN 0921-8912.

MATULA, Petr, Pavel MATULA a Michal KOZUBEK. Ways to the High-Resolution Cytometry Network. Brno: Faculty of Informatics, Masaryk University, 2000.

LUKÁŠOVÁ, Emilie, Stanislav KOZUBEK, Raisa GOVORUN, Michail REPIN, Leonard RÝZNAR, Evgenij KRASAVIN, Michal KOZUBEK a Václav KROHA. Aberrations induced in chromosome 1, 2 and Y of human lymphocytes by three types of radiation of different LET value as detected by FISH. edited by C.Baumstark-Khan, S.Kozubek, G.Horneck. In Fundamentals for the assesment of risks from environmental radiation. Dordrecht: Kluwer Academic Publishers, 1999, s. 195-202. ISBN 0-7923-5667-5.

KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Leonard RÝZNAR, Andrea LIŠKOVÁ, Jana AMRICHOVÁ a Gerda HORNECK. Advances in computer analysis of radiation-induced changes in human genome. edited by C.Baumstark-Khan, S.Kozubek, G.Horneck. In Fundamentals for the assesment of risks from environmental radiation. Dordrecht: Kluwer Academic Publishers, 1999, s. 243-248. ISBN 0-7923-5667-5.

KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Andrea MAREČKOVÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ a Adriana JERGOVÁ. High-resolution cytometry of FISH dots in interphase cell nuclei. Cytometry. New York: International Society for Analytical Cyt, 1999, roč. 36, č. 4, s. 279-293. ISSN 0196-4763.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Leonard RÝZNAR, Michal KOZUBEK, Andrea LIŠKOVÁ a Václav KROHA. Chromatin structure and its cell cycle kinetics in intact and irradiated cell nuclei. edited by C.Baumstark-Khan, S.Kozubek, G.Horneck. In Fundamentals for the assesment of risks from environmental radiation. Dordrecht: Kluwer Academic Publishers, 1999, s. 231-242. ISBN 0-7923-5667-5.

LUKÁŠOVÁ, Emilie, Stanislav KOZUBEK, Michal KOZUBEK, Václav KROHA, Andrea MAREČKOVÁ, Magdalena SKALNÍKOVÁ, Eva BÁRTOVÁ a Jana ŠLOTOVÁ. Chromosomes participating in translocations typical of malignant hemoblastoses are also involved in exchange aberrations induced by fast neutrons. Radiation Research. 1999, roč. 151, č. 4, s. 375-384. ISSN 0033-7587.

BÁRTOVÁ, Eva, Stanislav KOZUBEK, Markus DURM, Michael HAUSMANN, Michal KOZUBEK, Emilie LUKÁŠOVÁ, Magdalena SKALNÍKOVÁ, Pavla JIRSOVÁ, Alena CAFOURKOVÁ a Kateřina BUCHNÍČKOVÁ. The position of centromeres in interphase nuclei of human leukemic cells during myeloid differentiation and after gamma-irradiation. edited by A.Kotyk. In Fluorescence microscopy and fluorescent probes. vol.3. Ústí nad Labem: Espero Publishing, 1999, s. 347-354. ISBN 80-238-4668-X.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Andrea MAREČKOVÁ, Magdalena SKALNÍKOVÁ, Michal KOZUBEK, Eva BÁRTOVÁ, Václav KROHA, Eva KRAHULCOVÁ a Jana ŠLOTOVÁ. 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. Berlin: Springer-Verlag, 1999, roč. 108, č. 7, s. 426-435. ISSN 0009-5915.

SKALNÍKOVÁ, Magdalena, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Michal KOZUBEK, Eva BÁRTOVÁ, Andrea MAREČKOVÁ, Pavla JIRSOVÁ a Alena CAFOURKOVÁ. Topography of some genes and chromosomes in interphase nuclei of human cells. edited by A.Kotyk. In Fluorescence microscopy and fluorescent probes. vol.3. Ústí nad Labem: Espero Publishing, 1999, s. 259-266. ISBN 80-238-4668-X.

KOZUBEK, Michal. High-resolution cytometry : Hardware approaches, image analysis techniques and applications. Brno: Masaryk University, 1998, 122 s.

KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Jana AMRICHOVÁ, Leonard RÝZNAR a Andrea LIŠKOVÁ. Semi-automated FISH-stained interphase nuclei analysis in human genome studies. edited by J.Slavík. In Fluorescence Microscopy and Fluorescent Probes. vol.2. New York: Plenum, 1998, s. 173-179. ISBN 0-306-46021-1.

WILSON, Tony, Rimas JUŠKAITIS, Mark NEIL a Michal KOZUBEK. An aperture correlation approach to confocal microscopy. edited by Cogswell CJ, Conchello JA, Wilson T. In Three-Dimensional Microscopy: Image Acquisition and Processing IV. Bellingham: SPIE, 1997, s. 21-24. ISBN 0-8194-2395-5.

KOZUBEK, Stanislav, Emilie LUKÁŠOVÁ, Leonard RÝZNAR, Michal KOZUBEK, Raisa GOVORUN, Evgenij KRASAVIN a Gerda HORNECK. Distribution of ABL and BCR genes in cell nuclei of normal and irradiated lymphocytes. Blood. 1997, roč. 89, č. 12, s. 4537-4545. ISSN 0006-4971.

LUKÁŠOVÁ, Emilie, Stanislav KOZUBEK, Michal KOZUBEK, Jana KJERONSKÁ, Leonard RÝZNAR, Jana HORÁKOVÁ, Eva KRAHULCOVÁ a Gerda HORNECK. 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. 1997, roč. 100, 5/6, s. 525-535. ISSN 0340-6717.

SCHRADER, Martin, Michal KOZUBEK, Stefan HELL a Tony WILSON. Optical transfer functions of 4Pi confocal microscopes : theory and experiment. Optics Letters. 1997, roč. 22, č. 7, s. 436-438. ISSN 0146-9592.

WILSON, Tony, Rimas JUŠKAITIS, Mark NEIL a Michal KOZUBEK. Confocal microscopy by aperture correlation. Optics Letters. 1996, roč. 21, č. 23, s. 1879-1881. ISSN 0146-9592.

JUŠKAITIS, Rimas, Tony WILSON, Mark NEIL a Michal KOZUBEK. Efficient real-time confocal microscopy with white light sources. Nature. 1996, roč. 383, č. 6603, s. 804-806. ISSN 0028-0836.

WILSON, Tony, Rimas JUŠKAITIS, Mark NEIL a Michal KOZUBEK. SCAM - a new form of confocal microscope. In 3D Imaging Sciences in Microscopy. 1996.

KOZUBEK, Michal. Analýza obrazu pořízeného při fluorescenční in situ hybridizaci. Brno: Masarykova univerzita, 1995, 64 s.

OCHRANOVÁ, Renata a M. KOZUBEK. Objektově orientované programování (v Pascalu). In PŘÍSPĚVEK K VÝUCE informatiky a výpočetní techniky na středních školách. prvni. Praha: Ústav pro informace a vzdělávání, 1993, s. 5-29. ISBN 80-211-0164-4.

OCHRANOVÁ, Renata a M. KOZUBEK. Objektově orientované programování v TURBO PASCALU. 1. vyd. Brno: Masarykova univerzita, 1993, 117 s. ISBN 80-210-0659-5.