Publication Records

JAIN, Akanksha, Vladimír ULMAN, Argo MUKHERJEE, Mangal PRAKASH, Lokesh PIMPALE, Stefan MÜNSTER, Panfilio KRISTEN, Florian JUG, Stephan GRILL, Pavel TOMANCAK and Anastasios PAVLOPOULOS. Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation. Online. Nature Communications. Springer, 2020, vol. 11, p. 1-13. Available from: https://dx.doi.org/10.1038/s41467-020-19356-x.

HANDBERG-THORSAGER, Mette, Vladimír ULMAN, Pavel TOMANČÁK, D. ARENDT and M. SCHUBERT. A Behavioral Assay to Study Effects of Retinoid Pharmacology on Nervous System Development in a Marine Annelid. In Swapan K. Ray. Retinoid and Rexinoid Signaling. Springer, 2019, p. 193-207. ISBN 978-1-4939-9584-4. Available from: https://dx.doi.org/10.1007/978-1-4939-9585-1_14.

SOROKIN, Dmitry, Igor PETERLÍK, Marco TEKTONIDIS, Karl ROHR and Pavel MATULA. Non-rigid Contour-Based Registration of Cell Nuclei in 2-D Live Cell Microscopy Images Using a Dynamic Elasticity Model. IEEE Transactions on Medical Imaging. IEEE, 2018, vol. 37, No 1, p. 173-184. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2017.2734169.

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.

ANOSHINA, Nadezhda A., Andrey S. KRYLOV and Dmitry SOROKIN. Correlation-based 2D Registration Method for Single Particle Cryo-EM Images. Online. In Seventh International Conference on Image Processing Theory, Tools and Applications (IPTA), 2017. Montreal: IEEE, 2017, p. 1-6. ISBN 978-1-5386-1842-4. Available from: https://dx.doi.org/10.1109/IPTA.2017.8310125.

SVOBODA, David and Vladimír ULMAN. MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy. IEEE Transactions on Medical Imaging. IEEE Engineering in Medicine and Biology Society, 2017, vol. 36, No 1, p. 310-321. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2016.2606545.

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA and Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia. Online. In 14th IEEE International Symposium on Biomedical Imaging. Melbourne: IEEE, 2017, p. 822-826. ISBN 978-1-5090-1172-8. Available from: https://dx.doi.org/10.1109/ISBI.2017.7950644.

FRANEK, Michal, Jana SUCHÁNKOVÁ, Petra ŘEZNÍČKOVÁ-PODLOUČKOVÁ, Jana KREJČÍ, Soňa LEGARTOVÁ, Stanislav KOZUBEK, J VEČEŘA, Dmitry SOROKIN and Eva BÁRTOVÁ. Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections. Microscopy and Microanalysis. Saarbrücken: Cambridge University Press, 2016, vol. 22, No 2, p. 326-341. ISSN 1431-9276. Available from: https://dx.doi.org/10.1017/S1431927616000052.

KONDRAT'EV, Alexandr and Dmitry SOROKIN. Automatic Detection of Laser-Induced Structures in Live Cell Fluorescent Microscopy Images Using Snakes with Geometric Constraints. Online. In IEEE 23rd International Conference on Pattern Recognition (ICPR). Not specified: IEEE, 2016, p. 326-331. ISBN 978-1-5090-4846-5. Available from: https://dx.doi.org/10.1109/ICPR.2016.7899655.

LEGARTOVÁ, Soňa, Petra ŘEZNÍČKOVÁ-PODLOUČKOVÁ, Barbora MALYŠKOVÁ, Thomas KÜNTZIGER, Philippe COLLAS, Dušan CMARKO, Ivan RAŠKA, Dmitry SOROKIN, Stanislav KOZUBEK and Eva BÁRTOVÁ. Localized Movement and Levels of 53BP1 Protein Are Changed by gamma-irradiation in PML Deficient Cells. Journal of Cellular Biochemistry [IF=2.778 (1990)]. Wiley-Liss, 2016, vol. 117, No 11, p. 2583-2596. ISSN 0730-2312. Available from: https://dx.doi.org/10.1002/jcb.25551.

MUSINOVA, Yana R., Olga M. LISITSYNA, Dmitry SOROKIN, Eugene A. ARIFULIN, Tatiana A. SMIRNOVA, Roman A. ZINOVKIN, Daria M. POTASHNIKOVA, Yegor S. VASSETZKY and Eugene V. SHEVAL. RNA-dependent disassembly of nuclear bodies. Journal of Cell Science. The Company of Biologists Ltd., 2016, vol. 129, No 24, p. 4509-4520. ISSN 0021-9533. Available from: https://dx.doi.org/10.1242/jcs.189142.

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.

ULMAN, Vladimír, David SVOBODA, Matti NYKTER, Michal KOZUBEK and Pekka RUUSUVUORI. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry Part A. John Wiley & Sons, 2016, 89A, No 12, p. 1057-1072. ISSN 1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.23031.

SOROKIN, Dmitry, Lenka STIXOVÁ, Petra SEHNALOVÁ, Soňa LEGARTOVÁ, Jana SUCHÁNKOVÁ, Pavel ŠIMARA, Stanislav KOZUBEK, Pavel MATULA, Magdalena SKALNÍKOVÁ, Ivan RAŠKA and Eva BÁRTOVÁ. Localized movement and morphology of UBF1-positive nucleolar regions are changed by gamma-irradiation in G2 phase of the cell cycle. Nucleus. 2015, vol. 6, No 4, p. 301-313. ISSN 1949-1034. Available from: https://dx.doi.org/10.1080/19491034.2015.1075111.

SVOBODA, David, Vladimír ULMAN and Igor PETERLÍK. On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy. In Proceedings of 2015 IEEE International Symposium on Biomedical Imaging. Stoughton (WI, USA): Engineering in Medicine and Biology Society, 2015, p. 712-716. ISBN 978-1-4799-2374-8. Available from: https://dx.doi.org/10.1109/ISBI.2015.7163972.

ULMAN, Vladimír, Zoltán ORÉMUŠ and David SVOBODA. TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells. In Vittorio Murino, Enrico Puppo, Gianni Vernazza. Proceedings of 18th International Conference on Image Analysis and Processing. Heidelberg, Německo: Springer International Publishing, 2015, p. 623-634. ISBN 978-3-319-23230-0. Available from: https://dx.doi.org/10.1007/978-3-319-23231-7_56.

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.

BÁRTOVÁ, Eva, Veronika FOLTÁNKOVÁ, Soňa LEGARTOVÁ, Petra SEHNALOVÁ, Dmitry SOROKIN, Jana SUCHÁNKOVÁ and Stanislav KOZUBEK. Coilin is rapidly recruited to UVA-induced DNA lesions and gamma-radiation affects localized movement of Cajal bodies. Nucleus. Landes Bioscience, 2014, vol. 5, No 3, p. 269-277. ISSN 1949-1034. Available from: https://dx.doi.org/10.4161/nucl.29229.

STIXOVÁ, Lenka, Petra SEHNALOVÁ, Soňa LEGARTOVÁ, Jana SUCHÁNKOVÁ, Tereza HRUŠKOVÁ, Stanislav KOZUBEK, Dmitry SOROKIN, Pavel MATULA, Ivan RAŠKA, Aleš KOVAŘÍK, Jaroslav FULNEČEK and Eva BÁRTOVÁ. HP1B-dependent recruitment of UBF1 to irradiated chromatin occurs simultaneously with CPDs (HP1B-dependent recruitment of UBF1 to 3 irradiated chromatin occurs simultaneously with 4 CPDs). Epigenetics & Chromatin. BioMed Central, 2014, vol. 7, No 39, p. 1-17. ISSN 1756-8935. Available from: https://dx.doi.org/10.1186/1756-8935-7-39.

SOROKIN, Dmitry, Marco TEKTONIDIS, Karl ROHR and Pavel MATULA. NON-RIGID CONTOUR-BASED TEMPORAL REGISTRATION OF 2D CELL NUCLEI IMAGES USING THE NAVIER EQUATION. Online. In IEEE International Symposium on Biomedical Imaging: Nano to Macro. Beijing: IEEE, 2014, p. 746-749. ISBN 978-1-4673-1959-1. Available from: https://dx.doi.org/10.1109/ISBI.2014.6867978.

SVOBODA, David, Vladimír ULMAN, Luděk MATYSKA, Martin MAŠKA, Ján BELLA and Stanislav STEJSKAL. On Proper Simulation of Phenomena Influencing Image Formation in Fluorescence Microscopy. In 2014 IEEE International Conference on Image Processing. Neuveden: IEEE Signal Processing Society, 2014, p. 3944-3948. ISBN 978-1-4799-5750-7. Available from: https://dx.doi.org/10.1109/ICIP.2014.7025801.

SUCHÁNKOVÁ, Jana, Soňa LEGARTOVÁ, Petra SEHNALOVÁ, Stanislav KOZUBEK, Sergio VALENTE, Donatella LABELLA, Antonello MAI, Carmen ECKERICH, Frank O. FACKELMAYER, Dmitry SOROKIN and Eva BÁRTOVÁ. PRMT1 arginine methyltransferase accumulates in cytoplasmic bodies that respond to selective inhibition and DNA damage. European Journal of Histochemistry. Pavia, Italy: PAGEPress, 2014, vol. 58, No 2, p. 139-151. ISSN 1121-760X. Available from: https://dx.doi.org/10.4081/ejh.2014.2389.

SOROKIN, Dmitry, Jana SUCHÁNKOVÁ, Eva BÁRTOVÁ and Pavel MATULA. Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation. Folia biologica. Univerzita Karlova, 2014, vol. 60, (Suppl 1), p. 45-49. ISSN 0015-5500.

FOLTÁNKOVÁ, Veronika, Pavel MATULA, Dmitry SOROKIN, Stanislav KOZUBEK and Eva BÁRTOVÁ. Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body co-localization in DNA lesions. Microscopy and Microanalysis. Saarbrücken: Cambridge University Press, 2013, Volume 19, Issue 2, p. 360-369. ISSN 1431-9276. Available from: https://dx.doi.org/10.1017/S1431927612014353.

SVOBODA, David and Vladimír ULMAN. Towards a Realistic Distribution of Cells in Synthetically Generated 3D Cell Populations. In Alfredo Petrosino. 17th International Conference on Image Analysis and Processing - ICIAP 2013. LNCS 8157, Part II. Berlin, Heidelberg: Springer-Verlag, 2013, p. 429-438. ISBN 978-3-642-41183-0. Available from: https://dx.doi.org/10.1007/978-3-642-41184-7_44.

SVOBODA, David and Vladimír ULMAN. Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy. In Campilho, Aurélio; Kamel, Mohamed. Proceedings of 9th International Conference on Image Analysis and Recognition. LNCS 7325, Part II. Heidelberg: Springer-Verlag, 2012, p. 473-482. ISBN 978-3-642-31297-7. Available from: https://dx.doi.org/10.1007/978-3-642-31298-4_56.

ULMAN, Vladimír. Boundary Treatment for Young-van Vliet Recursive Zero-Mean Gabor Filtering. EURASIP Journal on Advances in Signal Processing. NEW YORK (USA): HINDAWI PUBLISHING CORPORATION, 2011, vol. 2011, ID 234090, p. 1-9. ISSN 1687-6172. Available from: https://dx.doi.org/10.1155/2011/234090.

ULMAN, Vladimír. Fast Anisotropic Filtering and Performance Evaluation Tool for Optical Flow in Biomedical Image Analysis. Brno: Masarykova Univerzita, 2011, 210 pp.

ULMAN, Vladimír and David SVOBODA. Tool for Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy. In 11th European Light Microscopy Initiative (ELMI) meeting. 2011.

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

ULMAN, Vladimír. Improving Accuracy of Optical Flow of Heeger's Original Method on Biomedical Images. In Proceedings of the 7th International Conference on Image Analysis and Recognition, ICIAR 2010. Povoa de Varzim (Portugal): Springer, 2010, p. 263-273. ISBN 978-3-642-13771-6. Available from: https://dx.doi.org/10.1007/978-3-642-13772-3_27.

VAŘECHA, Miroslav, Vladimír ULMAN, Pavel MATULA and 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 and Michal KOZUBEK. Prediction of localization and interactions of apoptotic proteins. Journal of Biomedical Science. BioMed website: BioMed Central, London, England, 2009, vol. 16, No 59, p. 1-14. ISSN 1021-7770.

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

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

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN and 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 and 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.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Emilie LUKÁŠOVÁ and 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, vol. 12, No 7, p. 1155-1171. ISSN 1360-8185.

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

HUBENÝ, Jan, Vladimír ULMAN and Pavel MATULA. Estimating Large Local Motion in Live-Cell Imaging Using Variational Optical Flow. In VISAPP 2007 Second International Conference On Computer Vision Theory And Applications, Proceedings. Portugal: INSTICC PRESS, 2007, p. 542-548. ISBN 978-972-8865-74-0.

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

ULMAN, Vladimír and Jan HUBENÝ. On Generating Ground-truth Time-lapse Image Sequences and Flow Fields. In Proceedings of the Fourth International Conference on Informatics in Control, Automation and Robotics. RA-1. Angers: INSTICC, 2007, p. 234-239. ISBN 978-972-8865-83-2.

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

ULMAN, Vladimír. Automatic Detection of Histones on Chromosome X in Images of Cell Nuclei. Clinician and Technology (Lékař a technika). Praha: Czech Medical Association J.E.Purkyne, 2006, roč. 36, No 2, p. 160-164. ISSN 0301-5491.

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.

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.

ULMAN, Vladimír. Mosaicking of High-resolution Biomedical Images Acquired from Wide-field Optical Microscope. In Proceedings of the 3rd European Medical and Biological Engineering Conference EMBEC'05. Praha: IFMBE Proceedings Series, vol. 11, 2005, p. 1-5. ISSN 1727-1983.

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

FEIT, Josef, Vladimír ULMAN, Werner KEMPF and Hana JEDLIČKOVÁ. Pořizování obrazů o velmi vysokém rozlišení metodou skládání (Acquiring Microscopic Images of Very High Resolution by a Method of Composing). Čes-slov. Patologie. 2004, vol. 40, No 2, p. 78-82. ISSN 1210-7875.