Publication Records

LUX, Filip and Petr MATULA. Cell Tracking based on Integer Linear Programming and Probability Scores. In Athens, Greece, IEEE 21th International Symposium on Biomedical Imaging. Athens: IEEE 21th International Symposium on Biomedical Imaging, 2024, p. 1-5. ISBN 979-8-3503-1334-5. Available from: https://dx.doi.org/10.1109/ISBI56570.2024.10635857.

MRÁZ, Radoslav, Karel ŠTĚPKA, Matěj PEKÁR, Petr MATULA and Stanislav PEKÁR. MAPHIS-Measuring arthropod phenotypes using hierarchical image segmentations. Methods in Ecology and Evolution. HOBOKEN: WILEY, 2024, vol. 15, No 1, p. 36-42. ISSN 2041-210X. Available from: https://dx.doi.org/10.1111/2041-210X.14250.

MRÁZ, Radoslav, Karel ŠTĚPKA, Matěj PEKÁR, Petr MATULA and Stanislav PEKÁR. MAPHIS - Measuring arthropod phenotypes using hierarchical image segmentations. 2023. Available from: https://dx.doi.org/10.1111/2041-210X.14250.

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 and Carlos ORTIZ-DE-SOLÓRZANO. The Cell Tracking Challenge: 10 years of objective benchmarking. Nature Methods. 2023, vol. 20, No 7, p. 1010-1020. ISSN 1548-7091. Available from: https://dx.doi.org/10.1038/s41592-023-01879-y.

KEŘKOVSKÝ, Miloš, Marek DOSTÁL, Tereza KOPŘIVOVÁ, Tomáš JŮZA, Václav VYBÍHAL, Eduard NEUMAN, Petr MATULA and 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 and Spyridon BAKAS. Federated learning enables big data for rare cancer boundary detection. Nature Communications. London: Nature Publishing Group, 2022, vol. 13, No 7346, p. 1-17. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-022-33407-5.

MELNIKOVA, Aleksandra and Petr MATULA. Topology Preserving Segmentation Fusion for Cells with Complex Shapes. Online. In The IEEE International Symposium on Biomedical Imaging. Nice: IEEE, 2021, p. 204-207. ISBN 978-1-6654-1246-9. Available from: https://dx.doi.org/10.1109/ISBI48211.2021.9433867.

FERKOVÁ, Zuzana, Petra URBANOVÁ, Dominik ČERNÝ, Marek ŽUŽI and Petr MATULA. Age and gender-based human face reconstruction from single frontal image. Multimedia Tools and Applications. Kluwer Academic Publishers, 2020, vol. 79, 5-6, p. 3217-3242. ISSN 1380-7501. Available from: https://dx.doi.org/10.1007/s11042-018-6869-5.

LUX, Filip and Petr MATULA. DIC Image Segmentation of Dense Cell Populations by Combining Deep Learning and Watershed. Online. In IEEE 16th International Symposium on Biomedical Imaging. Venice, Italy, Italy: IEEE 16th International Symposium on Biomedical Imaging, 2019, p. 236-239. ISBN 978-1-5386-3641-1. Available from: https://dx.doi.org/10.1109/ISBI.2019.8759594.

FERKOVÁ, Zuzana and Petr MATULA. Multimodal Point Distribution Model for Anthropological Landmark Detection. Online. In 26th IEEE International Conference on Image Processing (ICIP2019). Taipei, Taiwan: Springer, 2019, p. 2986-2990. ISBN 978-1-5386-6249-6. Available from: https://dx.doi.org/10.1109/ICIP.2019.8803252.

CORTESE, Mirko, Anil KUMAR, Petr MATULA, Lars KADERALI, Pietro SCATURRO, Holger ERFLE, Eliana Gisela ACOSTA, Sandra BUEHLER, Alessia RUGGIERI, Laurent CHATEL-CHAIX, Karl ROHR and Ralf BARTENSCHLAGER. Reciprocal Effects of Fibroblast Growth Factor Receptor Signaling on Dengue Virus Replication and Virion Production. Cell Reports. CAMBRIDGE, Spojené státy americké: Cell Press, 2019, vol. 27, No 9, p. 2579-2592,"e1"-"e6", 20 pp. ISSN 2211-1247. Available from: https://dx.doi.org/10.1016/j.celrep.2019.04.105.

DVOŘÁČKOVÁ, Martina, B. RAPOSO, Petr MATULA, J. FUCHS, V. SCHUBERT, Vratislav PEŠKA, B. DESVOYES, C. GUTIERREZ and Jiří FAJKUS. Replication of ribosomal DNA in Arabidopsis occurs both inside and outside the nucleolus during S phase progression. Journal of Cell Science. Cambridge: Company of Biologists Ltd., 2018, vol. 131, No 2, p. nestránkováno, 12 pp. ISSN 0021-9533. Available from: https://dx.doi.org/10.1242/jcs.202416.

ŠIMARA, Pavel, Lenka TESAŘOVÁ, Daniela ŘEHÁKOVÁ, Šimon FARKAŠ, Barbara ŠALINGOVÁ, Kateřina KUTÁLKOVÁ, Eva VAVREČKOVÁ, Pavel MATULA, Petr MATULA, Lenka VEVERKOVÁ and Irena KRONTORÁD KOUTNÁ. Reprogramming of Adult Peripheral Blood Cells into Human Induced Pluripotent Stem Cells as a Safe and Accessible Source of Endothelial Cells. Stem Cells and Development. Mary Ann Liebert, Inc. publishers, 2018, vol. 27, No 1, p. 10-22. ISSN 1547-3287. Available from: https://dx.doi.org/10.1089/scd.2017.0132.

ŠIMARA, Pavel, Lenka TESAŘOVÁ, Daniela ŘEHÁKOVÁ, Šimon FARKAŠ, Barbara ŠALINGOVÁ, Kateřina KUTÁLKOVÁ, Eva VAVREČKOVÁ, Pavel MATULA, Petr MATULA and Irena KRONTORÁD KOUTNÁ. Reprogramming of peripheral blood cells into hiPSCs as a source of endothelial cells. In SY-Stem symposium 2018. 2018.

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 and Carlos ORTIZ-DE-SOLORZANO. An objective comparison of cell-tracking algorithms. Nature Methods. Macmillan Publishers Limited, part of Springer Nature, 2017, vol. 14, No 12, p. 1141-1152. ISSN 1548-7091. Available from: https://dx.doi.org/10.1038/nmeth.4473.

WILLEMSEN, Joschka, Oliver WICHT, Julia WOLANSKI, Nina BAUR, Sandra BASTIAN, Darya HAAS, Petr MATULA, Bettina KNAPP, Laurene MEYNIEL-SCHICKLIN, Chen WANG, Ralf BARTENSCHLAGER, Volker LOHMANN, Karl ROHR, Holger ERFLE, Lars KADERALI, Joseph MARCOTRIGIANO, Andreas PICHLMAIR and Marco BINDER. Phosphorylation-Dependent Feedback Inhibition of RIG-I by DAPK1 Identified by Kinome-wide siRNA Screening. Molecular Cell. CAMBRIDGE: CELL PRESS, 2017, vol. 65, No 3, p. "403"-"415.e8", 21 pp. ISSN 1097-2765. Available from: https://dx.doi.org/10.1016/j.molcel.2016.12.021.

FERKOVÁ, Zuzana, Marek ŽUŽI, Petra URBANOVÁ and Petr MATULA. Single image reconstruction of human faces using database of depth images. Online. In 9th International Conference on Virtual Worlds and Games for Serious Applications (VS-Games 2017). Athens, Greece: IEEE Computer Society, 2017, p. 109-116. ISBN 978-1-5090-5812-9. Available from: https://dx.doi.org/10.1109/VS-GAMES.2017.8056578.

SVOBODA, David, Vladimír ULMAN, Peter KOVÁČ, Barbara ŠALINGOVÁ, Lenka TESAŘOVÁ, Irena KRONTORÁD KOUTNÁ and Petr MATULA. Vascular Network Formation in Silico Using the Extended Cellular Potts Model. In 2016 IEEE International Conference on Image Processing. Piscataway, NJ, USA: IEEE Signal Processing Society, 2016, p. 3180-3183. ISBN 978-1-4673-9961-6. Available from: https://dx.doi.org/10.1109/ICIP.2016.7532946.

STOKLASA, Roman, Lukáš BÁLEK, Pavel KREJČÍ and Petr MATULA. Automated Cell Segmentation in Phase-Contrast Images based on Classification and Region Growing. In Proceedings of 2015 IEEE International Symposium on Biomedical Imaging, 2015. Neuveden: Engineering in Medicine and Biology Society, 2015, p. 1447-1451. ISBN 978-1-4799-2374-8. Available from: https://dx.doi.org/10.1109/ISBI.2015.7164149.

MATULA, Pavel, Martin MAŠKA, Dmitry SOROKIN, Petr MATULA, Carlos ORTIZ-DE-SOLÓRZANO and Michal KOZUBEK. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE. 2015, vol. 10, No 12, p. "e0144959", 19 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0144959.

BUCHTOVÁ, marcela, Veronika ORALOVÁ, Anie AKLIAN, Jan MAŠEK, Iva VESELA, Zhufeng OUYANG, Tereza OBADALOVÁ, Žaneta KONEČNÁ, Tereza SPOUSTOVÁ, Tereza POSPÍŠILOVÁ, Petr MATULA, Miroslav VAŘECHA, Lukáš BÁLEK, Iva GUDERNOVÁ, Iva JELÍNKOVÁ, Ivan DURAN, Iveta ČERVENKOVÁ, Shunichi MURAKAMI, Alois KOZUBÍK, Petr DVOŘÁK, Vítězslav BRYJA and Pavel KREJČÍ. Fibroblast growth factor and canonical WNT/beta-catenin signaling cooperate in suppression of chondrocyte differentiation in experimental models of FGFR signaling in cartilage. Biochimica et Biophysica Acta - Molecular Basis of Disease. Amsterdam: ELSEVIER SCIENCE BV, 2015, vol. 1852, No 5, p. 839-850. ISSN 0925-4439. Available from: https://dx.doi.org/10.1016/j.bbadis.2014.12.020.

KARAS, Pavel, Vincent MORARD, Jan BARTOVSKÝ, Thierry GRANDPIERRE, Eva DOKLÁDALOVÁ, Petr MATULA and Petr DOKLÁDAL. GPU Implementation of Linear Morphological Openings with Arbitrary Angle. Journal of Real-Time Image Processing. Springer-Verlag, 2015, vol. 10, No 1, p. 27-41. ISSN 1861-8200. Available from: https://dx.doi.org/10.1007/s11554-012-0248-7.

ŠTĚPKA, Karel, Pavel MATULA, Petr MATULA, Stefan WOERZ, Karl ROHR and Michal KOZUBEK. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. Cytometry Part A. John Wiley & Sons, 2015, 87A, No 8, p. 759-772. ISSN 1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.22692.

HÖLSCHER, Christina, Florian SONNTAG, Katharina HENRICH, Qingxin CHEN, Jürgen BENEKE, Petr MATULA, Karl ROHR, Lars KADERALI, Nina BEIL, Holger ERFLE, Jürgen A KLEINSCHMIDT and Müller MARTIN. The SUMOylation Pathway Restricts Gene Transduction by Adeno-Associated Viruses. PLoS Pathogens. Public Library of Science, 2015, vol. 11, No 12, p. e1005281. ISSN 1553-7366. Available from: https://dx.doi.org/10.1371/journal.ppat.1005281.

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 and Carlos ORTIZ-DE-SOLORZANO. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics. 2014, vol. 30, No 11, p. 1609-1617. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btu080.

MOTL, Jason A., Petr MATULA, Mike A. LEPLEY, Li LI and Dan S. KAUFMAN. Use of Human Pluripotent Stem Cells to Derive and Quantify Endothelial Cell-Smooth Muscle Cell Interactions In Vitro. In 11th Annual Meeting of International Society for Stem Cell Research. 2013.

LISAUSKAS, Tautvydas, Petr MATULA, Christoph CLAAS, Susanne REUSING, Stefan WIEMANN, Holger ERFLE, Lars LEHMANN, Peter FISCHER, Roland EILS, Karl ROHR, Brian STORRIE and Vytaute STARKUVIENE. Live cell assays to identify regulators of ER to Golgi trafficking. Traffic. John Wiley & Sons, 2012, vol. 13, No 3, p. 416–432. ISSN 1398-9219. Available from: https://dx.doi.org/10.1111/j.1600-0854.2011.01318.x.

SERVA, Andrius, Bettina KNAPP, Yueh-Tso TSAI, Christoph CLASS, Tautvydas LISAUSKAS, Petr MATULA, Nathalie HARDER, Lars KADERALI, Karl ROHR, Holger ERFLE, Roland EILS, Vania BRAGA and Vytaute STARKUVIENE. miR-17-5p Regulates Endocytic Trafficking through Targeting TBC1D2/Armus. PLoS One. 2012, vol. 7, No 12, p. 52555-52569. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0052555.

STAIER, Florian, Heinz EIPEL, Petr MATULA, Alexei V EVSIKOV, Michal KOZUBEK, Christoph CREMER and 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, vol. 82, No 9, p. "093701-1"-"093701-8", 8 pp. ISSN 0034-6748.

KNAPP, Bettina, Ilka REBHAN, Anil KUMAR, Petr MATULA, Narsis A KIANI, Marco BINDER, Hoger ERFLE, Karl ROHR, Roland EILS, Ralf BARTENSCHLAGER and Lars KADERALI. Normalizing for Individual Cell Population Context in the Analysis of High-Content Cellular Screens. BMC Bioinformatics. BioMed Central, 2011, vol. 12, No 485, p. 1-14. ISSN 1471-2105.

MATULA, Petr, Tautvydas LISAUSKAS, Vytaute STARKUVIENE and Karl ROHR. 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 pp.

REISS, S., Ilka REBHAN, P. BACKES, I. ROMERO-BREY, Holger ERFLE, Petr MATULA, Lars KADERALI, Marion POENISCH, H. BLANKENBURG, M.S. HIET, T. LONGERICH, S. DIEHL, F. RAMIREZ, T. BALLA, Karl ROHR, A. KAUL, S. BÜHLER, Rainer PEPPERKOK, T. LENGAUER, M. ALBRECHT, Roland EILS, P. SCHIRMACHER, V. LOHMANN and Ralf BARTENSCHLAGER. Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host & Microbe. 2011, vol. 9, No 1, p. 32-45. ISSN 1931-3128. Available from: https://dx.doi.org/10.1016/j.chom.2010.12.002.

STOKLASA, Roman and Petr MATULA. Road Detection Using Similarity Search. In Roland Stelzer and Karim Jafarmadar. 2nd International Conference on Robotics in Education. Vienna: Neuveden, 2011, p. 95-102. ISBN 978-3-200-02273-7.

SURATANEE, Apichat, Ilka REBHAN, Petr MATULA, Anil KUMAR, Lars KADERALI, Karl ROHR, Ralf BARTENSCHLAGER, Roland EILS and Rainer KÖNIG. Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images. Bioinformatics. 2010, vol. 26, No 18, p. i653-i658, 6 pp. ISSN 1367-4803.

MATULA, Petr, Fatima VERISSIMO, Stefan WÖRZ, Roland EILS, Rainer PEPPERKOK and Karl ROHR. Quantification of Fluorescent Spots in Time Series of 3-D Confocal Microscopy Images Based on the HMAX Transform. 2010.

MATULA, Petr, Fatima VERISSIMO, Stefan WÖRZ, Roland EILS, Rainer PEPPERKOK and Karl ROHR. 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, 7 pp. ISBN 978-0-8194-8027-9.

MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA and 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, p. 1138-1141. ISBN 978-1-4244-3932-4.

MATULA, Petr, Anil KUMAR, Ilka WÖRZ, Holger ERFLE, Ralf BARTENSCHLAGER, Roland EILS and Karl ROHR. 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., 2009, 75A, No 4, p. 309-318. ISSN 1552-4922.

MATULA, Petr, Anil KUMAR, Ilka WÖRZ, Nathalie HARDER, Holger ERFLE, Ralf BARTENSCHLAGER, Roland EILS and Karl ROHR. Automated analysis of siRNA screens of cells infected by hepatitis C and dengue viruses based on immunofluorescence microscopy images. In Proceedings of SPIE. 6916th ed. 2008. ISSN 0277-786X.

MATULA, Petr, Anil KUMAR, Ilka WÖRZ, Nathalie HARDER, Holger ERFLE, Ralf BARTENSCHLAGER, Roland EILS and Karl ROHR. Automated Analysis of siRNA Screens of Virus Infected Cells Based on Immunofluorescence Microscopy Images. In Proc. Workshop Bildverarbeitung für die Medizin 2008 - Algorithmen, Systeme, Anwendungen. Berlin Heidelberg: Springer-Verlag, 2008, p. 453-457.

MATULA, Petr, Anil KUMAR, Ilka WÖRZ, Nathalie HARDER, Holger ERFLE, Ralf BARTENSCHLAGER, Roland EILS and Karl ROHR. Automated Single Cell Based Analysis of siRNA Screens of Human Cells Infected by Hepatitis C and Dengue Viruses Based on Immunofluorescence Microscopy Images. 2008.

MATULA, Petr, Anil KUMAR, Ilka WÖRZ, Holger ERFLE, Ralf BARTENSCHLAGER, Roland EILS and Karl ROHR. Evaluation of siRNA Screens of Cells Infected by Hepatitis C and Dengue Viruses based on Immunofluorescence Microscopy. In RITTSCHER, Jens, Stephen LOCKETT, Karl ROHR, Tolga TASDIZEN and Sean MEGASON. Proceedings of 3rd Workshop on Microscopic Image Analysis with Applications in Biology. 2008, 6 pp.

MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA, Stanislav STEJSKAL, Vladan ONDŘEJ and 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.

MATULA, Pavel, Martin MAŠKA, Ondřej DANĚK, Petr MATULA and 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.

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

SKALNÍKOVÁ, Magdalena, Eva BÁRTOVÁ, Vladimír ULMAN, Petr MATULA, David SVOBODA, Andrea HARNIČAROVÁ, Michal KOZUBEK and Stanislav KOZUBEK. Distinct patterns of histone methylation and acetylation in human interphase nuclei. Physiological Research. Prague: Czech Academy of Sciences, 2007, vol. 56, No 6, p. 797-806. ISSN 0862-8408.

MATULA, Petr, Michal KOZUBEK, Pavel MATULA, Miroslav VAŘECHA, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ and 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.

ONDŘEJ, Vladan, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Martin FALK, Pavel MATULA, Petr MATULA and Michal KOZUBEK. Directional motion of foreign plasmid DNA to nuclear HP1 foci. Chromosome Research. Dordrecht: Springer, 2006, vol. 14, No 5, p. 505-514. ISSN 0967-3849.

MATULA, Petr, Pavel MATULA, Michal KOZUBEK and Vladimír DVOŘÁK. Fast Point-Based 3D Alignment of Live Cells. IEEE Transactions on Image Processing. 2006, vol. 15, No 8, p. 2388-2396. ISSN 1057-7149.

KOZUBEK, Stanislav, Eva BÁRTOVÁ, Emilie LUKÁŠOVÁ, Martin FALK, Vladan ONDŘEJ, Kozubek M Kroupová J, Pavel MATULA and Petr MATULA. High-Resolution cytometry represents the main technology used in the laboratory of molecular cytology and cytometry. In Cytomics Emerging from Cytometry 16th Annual Meeting of the German Society for Cytometry, 18. – 21. října, 2006, Leipziger Kubus, Leipzig, Německo.In: Cell Proliferation 39, p. 341. 2006.

HUBENÝ, Jan, Pavel MATULA, Petr MATULA and 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, p. 163-173, 10 pp. ISBN 3-540-33266-9.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Pavel MATULA, Petr MATULA and 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.

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

KOZUBEK, Michal, Pavel MATULA, Petr MATULA and 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, p. 24-27. ISBN 80-01-03239-6.

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

JANSOVÁ, Eva, Petr KRONTORÁD, Irena KOUTNÁ, Stanislav STEJSKAL, Petr MATULA, David SVOBODA, Michal KOZUBEK and 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.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ, Vladimír ULMAN, Petr MATULA, Michal KOZUBEK and 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.

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

MATULA, Petr, Michal KOZUBEK and 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, p. 376-384. ISBN 3-540-22675-3.

KOZUBEK, Michal, Petr MATULA, Pavel MATULA and Stanislav KOZUBEK. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. Microscopy research and technique. USA: Wiley-Liss, 2004, vol. 64, No 2, p. 164-175. ISSN 1059-910X.

KOZUBEK, Michal, Petr MATULA and 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 and 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, p. 69-72. ISBN 0-7803-8389-3.

KOZUBEK, Michal, Petr MATULA, Pavel MATULA, David SVOBODA, Jan HUBENÝ and 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, p. 44-46. ISBN 80-210-3560-9.

ONDŘEJ, Vladan, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Pavel MATULA, Petr MATULA and 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, p. 66-71. ISBN 80-210-3560-9.

MATULA, Pavel, Petr MATULA, Michal KOZUBEK and 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, p. 580-583. ISBN 0-7695-2223-8.

MATULA, Petr, Vladan ONDŘEJ and Stanislav KOZUBEK. Image analysis of the movement of sub-cellular structures. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, p. 62-65. ISBN 80-210-3560-9.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ, Stanislav KOZUBEK, Pavel MATULA, Petr MATULA and 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, p. 76-82. ISBN 80-210-3560-9.

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

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

MATULA, Petr, Michal KOZUBEK, Florian STAIER and Michael HAUSMANN. Precise 3D image alignment in micro-axial tomography. Journal of Microscopy. Oxford: Blackwell Science, 2003, vol. 209, No 2, p. 126-142. ISSN 0022-2720.

MEJZLÍK, Petr, Petr MATULA and Pavel MATULA. Algorithms and data representation in the FISH 3.0 image processing system. In Biophysics of the genome and its interactions. Brno: Masaryk University, 2002, p. 80-81. ISBN 80-210-2853-X.

KOZUBEK, Michal, Magdalena SKALNÍKOVÁ, Petr MATULA, Eva BÁRTOVÁ, Joachim RAUCH, Friedrich NEUHAUS, Heinz EIPEL and Michael HAUSMANN. Automated micro axial tomography of cell nuclei after specific labelling by fluorescence in situ hybridisation. Micron. Amsterdam: Elsevier, 2002, vol. 33, No 7, p. 655-665. ISSN 0968-4328.

KOZUBEK, Michal, Petr MATULA, Heinz EIPEL and 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, p. 91-98. ISBN 0-7695-1521-5.

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

MATULA, Petr, Pavel MATULA, Petr MEJZLÍK and 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, p. 77-79. ISBN 80-210-2853-X.

KOZUBEK, Michal, Petr MATULA, Pavel MATULA and 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, p. 99-106. ISBN 0-7695-1521-5.

SKALNÍKOVÁ, Magdalena, Michal KOZUBEK, Petr MATULA, Eva BÁRTOVÁ, Heinz EIPEL and 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, p. 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 and 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.

KOZUBEK, Michal, Petr MATULA and Pavel MATULA. The power of computerized light microscopy. Imaging & Microscopy. Darmstadt: GIT Verlag, 2002, vol. 4, No 2, p. 25-28. ISSN 1439-4243.

KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ, Pavel MATULA, Petr MATULA, Pavla JIRSOVÁ, Alena GAŇOVÁ and Irena KOUTNÁ. Combined confocal and wide-field high-resolution cytometry of FISH-stained cells. Cytometry. New York: International Society for Analytical Cyt, 2001, vol. 45, No 1, p. 1-12. ISSN 0196-4763.

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 and 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.

KOZUBEK, Michal, Pavel MATULA, Petr MATULA and Stanislav KOZUBEK. Využití počítačové analýzy obrazu v moderní cytometrii (Application of computer image analysis in modern cytometry). Ed. Alois Kozubík. In Analytická cytometrie I. 2001. ISBN 80-238-6833-0.

KOZUBEK, Michal, Stanislav KOZUBEK, Emilie LUKÁŠOVÁ, Eva BÁRTOVÁ, Magdalena SKALNÍKOVÁ, Pavel MATULA, Petr MATULA, Pavla JIRSOVÁ, Alena GAŇOVÁ and 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 and 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 and Petr MATULA. An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy. Journal of Microscopy. Oxford: Blackwell Science, 2000, vol. 200, No 3, p. 206-217. ISSN 0022-2720.

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

MATULA, Petr. Rozpoznávání českého textu psaného rukou (Recognition of Czech hand-written text). In Sborník z letní školy Informační systémy a jejich aplikace Ruprechtov. Brno: Fakulta stavební VUT, 1998, p. 144-153. ISBN 80-214-1205-4.