Selected Publications (Last 10 Years)

2019

Journal Papers

Castilla C, Maška M, Sorokin D, Meijering E, Ortiz-de-Solórzano C. 3-D Quantification of Filopodia in Motile Cancer Cells. IEEE Transactions on Medical Imaging, IEEE, 2019, vol. 38, No 3, p. 862-872. ISSN 0278-0062. 2019. doi:10.1109/TMI.2018.2873842.

Kotrbová A, Štěpka K, Maška M, Pálenik J, Ilkovics L, Klemová D, Kravec M, Hubatka F, Dave Z, Hampl A, Bryja V, Matula P, Pospíchalová V. TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images. Journal of Extracellular Vesicles, 2019, vol. 8, No 1, p. 1-13. ISSN 2001-3078. 2019. doi:10.1080/20013078.2018.1560808.

Michálek J, Hanzlíková P, Trinh T, Pacík D. Fast and accurate compensation of signal offset for T2 mapping. Magnetic Resonance Materials in Physics, Biology and Medicine, Springer International Publishing, 2019, Neuveden, February 2019, p. 1-14. ISSN 0968-5243. 2019. doi:10.1007/s10334-019-00737-3.

Wiesner D, Svoboda D, Maška M, Kozubek M. CytoPacq: A web-interface for simulating multi-dimensional cell imaging. Bioinformatics, Oxford University Press, 2019. ISSN 1367-4803. 2019. doi:10.1093/bioinformatics/btz417.

Conference Papers

Akbaş CE, Ulman V, Maška M, Jug F, Kozubek M. Automatic Fusion of Segmentation and Tracking Labels. In Laura Leal-Taixé, Stefan Roth. Computer Vision – ECCV 2018 Workshops. LNCS 11134., Switzerland: Springer Nature, 2019. p. 446-454, 9 pp., ISBN 978-3-030-11023-9. doi:10.1007/978-3-030-11024-6_34.

Lux F, Matula P. DIC Image Segmentation of Dense Cell Populations by Combining Deep Learning and Watershed. In IEEE 16th International Symposium on Biomedical Imaging. IEEE 16th International Symposium on Biomedical Imaging, 2019. p. 236-239, 4 pp., ISBN 978-1-5386-3640-4.

Maška M, Nečasová T, Wiesner D, Sorokin D, Peterlík I, Ulman V, Svoboda D. Toward Robust Fully 3D Filopodium Segmentation and Tracking in Time-Lapse Fluorescence Microscopy. In 26th IEEE International Conference on Image Processing. Taipei: IEEE, in press, 2019.

Nečasová T, Svoboda D. Visual and Quantitative Comparison of Real and Simulated Biomedical Image Data. In Laura Leal-Taixé, Stefan Roth. Computer Vision – ECCV 2018 Workshops. LNCS 11134., Munich, Germany: Springer, 2019. p. 385-394, 10 pp., ISBN 978-3-030-11023-9. doi:10.1007/978-3-030-11024-6_28.

Wiesner D, Nečasová T, Svoboda D. On Generative Modeling of Cell Shape Using 3D GANs. In 20th International Conference on Image Analysis and Processing. LNCS 11752., Trento: Springer, in press, 2019.

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2018

Journal Papers

Dvořáčková M, Raposo B, Matula P, Fuchs J, Schubert V, Peška V, Desvoyes B, Gutierrez C, Fajkus J. 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. ISSN 0021-9533. 2018. doi:10.1242/jcs.202416.

Maier-Hein L, Eisenmann M, Reinke A, Onogur S, Stankovic M, Scholz P, Arbel T, Bogunovic H, Bradley A, Carass A, Feldmann C, Frangi A, Full P, van Ginneken B, Hanbury A, Honauer K, Kozubek M, Landman B, März K, Maier O, Maier-Hein K, Menze B, Müller H, Neher P, Niessen W, Rajpoot N, Sharp G, Sirinukunwattana K, Speidel S, Stock Ch, Stoyanov D, Taha AA, van der Sommen F, Wang Ch, Weber M, Zheng G, Jannin P, Kopp-Schneider A. Why rankings of biomedical image analysis competitions should be interpreted with care. Nature Communications, Nature Publishing Group, 2018, vol. 9, No 5217, p. 1-13. ISSN 2041-1723. 2018. doi:10.1038/s41467-018-07619-7.

Sorokin D, Peterlík I, Tektonidis M, Rohr K, Matula P. 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. 2018. doi:10.1109/TMI.2017.2734169.

Sorokin D, Peterlík I, Ulman V, Svoboda D, Nečasová T, Morgaenko K, Eiselleová L, Tesařová L, Maška M. FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia. IEEE Transactions on Medical Imaging, IEEE, 2018, vol. 37, No 12, p. 2630-2641. ISSN 0278-0062. 2018. doi:10.1109/TMI.2018.2845884.

Šimara P, Tesařová L, Řeháková D, Farkaš Š, Šalingová B, Kutálková K, Vavrečková E, Matula P, Matula P, Veverková L, Krontorád Koutná I. 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. 2018. doi:10.1089/scd.2017.0132.

Conference Papers

Castilla C, Maška M, Sorokin D, Meijering E, Ortiz-de-Solorzano C. Segmentation of Actin-Stained 3D Fluorescent Cells with Filopodial Protrusions using Convolutional Neural Networks. In 15th IEEE International Symposium on Biomedical Imaging. Washington: IEEE, 2018. p. 413-417, 5 pp., ISBN 978-1-5386-3636-7. doi:10.1109/ISBI.2018.8363605.

Peterlík I, Svoboda D, Ulman V, Sorokin D, Maška M. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia. In Simulation and Synthesis in Medical Imaging. Cham: Springer, 2018. p. 71-79, 9 pp., ISBN 978-3-030-00535-1. doi:10.1007/978-3-030-00536-8_8.

Reinke A, Eisenmann M, Onogur S, Stankovic M, Scholz P, Full PM, Bogunovic H, Landman BA, Maier O, Menze B, Sharp GC, Sirinukunwattana K, Speidel S, van der Sommen F, Zheng G, Müller H, Kozubek M, Arbel T, Bradley AP, Jannin P, Kopp-Schneider A, Maier-Hein L. 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. p. 388-395, 8 pp., ISBN 978-3-030-00936-6. doi:10.1007/978-3-030-00937-3_45.

Svoboda D, Nečasová T, Tesařová L, Šimara P. Tubular Network Formation Process Using 3D Cellular Potts Model. In Gooya A., Goksel O., Oguz I., Burgos N.. Simulation and Synthesis in Medical Imaging. LNCS 11037., Springer, 2018. p. 90-99, 10 pp., ISBN 978-3-030-00535-1. doi:10.1007/978-3-030-00536-8_10.

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2017

Journal Papers

Anguiano M, Castilla C, Maška M, Ederra C, Peláez R, Morales X, Muñoz-Arrieta G, Mujika M, Kozubek M, Muñoz-Barrutia A, Rouzaut A, Arana S, Garcia-Aznar JM, Ortiz-de-Solorzano C. Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis. PLoS ONE, 2017, vol. 12, No 2, p. e0171417. ISSN 1932-6203. 2017. doi:10.1371/journal.pone.0171417.

Popovici V, Budinská E, Dušek L, Kozubek M, Bosman F. Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. Bioinformatics, Oxford: Oxford University Press, 2017, vol. 33, No 13, p. 2002-2009. ISSN 1367-4803. 2017. doi:10.1093/bioinformatics/btx027.

Sečkář P, Svoboda D. FTutor: An Interactive Guide to the Fundamentals of Frequency Analysis. Computer Applications in Engineering Education, Wiley, 2017, vol. 25, No 3, p. 508-520. ISSN 1061-3773. 2017. doi:10.1002/cae.21817.

Svoboda D, Ulman V. 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. 2017. doi:10.1109/TMI.2016.2606545.

Tesařová L, Šimara P, Stejskal S, Krontorád Koutná I. Hematopoietic developmental potential of human pluripotent stem cell lines is accompanied by the morphology of embryoid bodies and the expression of endodermal and hematopoietic markers. Cellular Reprogramming, 2017, vol. 19, No 4, p. 270-284. ISSN 2152-4971. 2017. doi:10.1089/cell.2016.0042.

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho S, Dufour AC, Olivo-Marin J, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C. 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. 2017. doi:10.1038/nmeth.4473.

Šimara P, Tesařová L, Řeháková D, Matula P, Stejskal S, Hampl A, Krontorád Koutná I. DNA double-strand breaks in human induced pluripotent stem cell reprogramming and long-term in vitro culturing. Stem Cell Research & Therapy, Springer Nature, 2017, vol. 8, No 73, p. 1-13. ISSN 1757-6512. 2017. doi:10.1186/s13287-017-0522-5.

Conference Papers

Anoshina NA, Krylov AS, Sorokin D. Correlation-based 2D Registration Method for Single Particle Cryo-EM Images. In Seventh International Conference on Image Processing Theory, Tools and Applications (IPTA), 2017. Montreal: IEEE, 2017. p. 1-6, 6 pp., ISBN 978-1-5386-1842-4. doi:10.1109/IPTA.2017.8310125.

Maška M, Matula P. Particle Tracking Accuracy Measurement Based on Comparison of Linear Oriented Forests. In 16th IEEE International Conference on Computer Vision Workshops. Venice: IEEE, 2017. p. 11-17, 7 pp., ISBN 978-1-5386-1034-3. doi:10.1109/ICCVW.2017.8.

Sorokin D, Peterlík I, Ulman V, Svoboda D, Maška M. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia. In 14th IEEE International Symposium on Biomedical Imaging. Melbourne: IEEE, 2017. p. 822-826, 5 pp., ISBN 978-1-5090-1172-8. doi:10.1109/ISBI.2017.7950644.

Svoboda D, Kozubek M. Multimodal Simulations in Live Cell Imaging. In Tsaftaris S., Gooya A., Frangi A., Prince J.. Simulation and Synthesis in Medical Imaging. LNCS 10557., Springer, 2017. p. 89-98, 10 pp., ISBN 978-3-319-68126-9. doi:10.1007/978-3-319-68127-6_10.

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2016

Journal Papers

Franek M, Suchánková J, Řezníčková-Podloučková P, Krejčí J, Legartová S, Kozubek S, Večeřa J, Sorokin D, Bártová E. 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. 2016. doi:10.1017/S1431927616000052.

Kratochvílová K, Moráň L, Paďourová S, Stejskal S, Tesařová L, Šimara P, Hampl A, Krontorád Koutná I, Vaňhara P. The role of the endoplasmic reticulum stress in stemness, pluripotency and development. European Journal of Cell Biology, Jena: Elsevier GMBH, 2016, vol. 95, 3-5, p. 115-123. ISSN 0171-9335. 2016. doi:10.1016/j.ejcb.2016.02.002.

Legartová S, Řezníčková-Podloučková P, Malyšková B, Küntziger T, Collas P, Cmarko D, Raška I, Sorokin D, Kozubek S, Bártová E. 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. 2016. doi:10.1002/jcb.25551.

Musinova YR, Lisitsyna OM, Sorokin D, Arifulin EA, Smirnova TA, Zinovkin RA, Potashnikova DM, Vassetzky YS, Sheval EV. 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. 2016. doi:10.1242/jcs.189142.

Tesařová L, Šimara P, Stejskal S, Krontorád Koutná I. The Aberrant DNA Methylation Profile of Human Induced Pluripotent Stem Cells Is Connected to the Reprogramming Process and Is Normalized During In Vitro Culture. PLOS ONE, Public Library of Science, 2016, vol. 11, No 6, p. nestránkováno. ISSN 1932-6203. 2016. doi:10.1371/journal.pone.0157974.

Ulman V, Svoboda D, Nykter M, Kozubek M, Ruusuvuori P. 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. 2016. doi:10.1002/cyto.a.23031.

Conference Papers

Kondrat'ev A, Sorokin D. Automatic Detection of Laser-Induced Structures in Live Cell Fluorescent Microscopy Images Using Snakes with Geometric Constraints. In IEEE 23rd International Conference on Pattern Recognition (ICPR). Not specified: IEEE, 2016. p. 326-331, 6 pp., ISBN 978-1-5090-4846-5. doi:10.1109/ICPR.2016.7899655.

Stoklasa R, Majtner T. Texture Analysis of 3D Fluorescence Microscopy Images Using RSurf 3D Features. In International Symposium on Biomedical Imaging (ISBI'16). Los Alamitos, California: IEEE Computer Society, 2016. p. 1212-1216, 5 pp., ISBN 978-1-4799-2350-2. doi:10.1109/ISBI.2016.7493484.

Svoboda D, Ulman V, Kováč P, Šalingová B, Tesařová L, Krontorád Koutná I, Matula P. 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, 4 pp., ISBN 978-1-4673-9961-6. doi:10.1109/ICIP.2016.7532946.

Štěpka K, Maška M, Pálenik JJ, Pospíchalová V, Kotrbová A, Ilkovics L, Klemová D, Hampl A, Bryja V, Matula P. Automatic Detection and Segmentation of Exosomes in Transmission Electron Microscopy. In Gang Hua, Hervé Jégou. Computer Vision -- ECCV 2016 Workshops: Amsterdam, The Netherlands, October 8-10 and 15-16, 2016, Proceedings, Part I. Cham, Switzerland: Springer International Publishing, 2016. p. 318-325, 8 pp., ISBN 978-3-319-46603-3. doi:10.1007/978-3-319-46604-0_23.

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2015

Journal Papers

Karas P, Morard V, Bartovský J, Grandpierre T, Dokládalová E, Matula P, Dokládal P. 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. 2015. doi:10.1007/s11554-012-0248-7.

Matula P, Maška M, Sorokin D, Matula P, Ortiz-de-Solórzano C, Kozubek M. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE, 2015, vol. 10, No 12, p. e0144959. ISSN 1932-6203. 2015. doi:10.1371/journal.pone.0144959.

Ortiz-de-Solórzano C, Muñoz-Barrutia A, Meijering E, Kozubek M. Toward a Morphodynamic Model of the Cell. IEEE Signal Processing Magazine, New York: IEEE, 2015, vol. 32, No 1, p. 20-29. ISSN 1053-5888. 2015. doi:10.1109/MSP.2014.2358263.

Sorokin D, Stixová L, Sehnalová P, Legartová S, Suchánková J, Šimara P, Kozubek S, Matula P, Skalníková M, Raška I, Bártová E. 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. 2015. doi:10.1080/19491034.2015.1075111.

Stejskal S, Štěpka K, Tesařová L, Stejskal K, Matějková M, Šimara P, Zdráhal Z, Krontorád Koutná I. Cell cycle-dependent changes in H3K56ac in human cells.. Cell Cycle, Philadelphia: Taylor&Francis Inc, 2015, vol. 14, No 24, p. 3851-3863. ISSN 1538-4101. 2015. doi:10.1080/15384101.2015.1106760.

Svoboda D. Next Step Toward the Automation of Screening for Cervical Cancer. Cytometry Part A, John Wiley & Sons, 2015, 87a, No 3, p. 195-196. ISSN 1552-4922. 2015. doi:10.1002/cyto.a.22564.

Štěpka K, Matula P, Matula P, Woerz S, Rohr K, Kozubek M. 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. 2015. doi:10.1002/cyto.a.22692.

Conference Papers

Anguiano M, Castilla C, Maška M, Ederra C, Fernández-Marqués J, Peláez R, Rouzaut A, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solórzano C. Characterization of the Role of Collagen Network Structure and Composition in Cancer Cell Migration. In 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Milano: IEEE, 2015. p. 8139-8142, 4 pp., ISBN 978-1-4244-9271-8. doi:10.1109/EMBC.2015.7320283.

Maška M, Ederra C, Fernández-Marqués J, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solórzano C. Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy. In 22nd IEEE International Conference on Image Processing. Québec City: IEEE, 2015. p. 1791-1794, 4 pp., ISBN 978-1-4799-8339-1. doi:10.1109/ICIP.2015.7351109.

Stoklasa R, Bálek L, Krejčí P, Matula P. Automated Cell Segmentation in Phase-Contrast Images based on Classification and Region Growing. In Proceedings of 2015 IEEE International Symposium on Biomedical Imaging, 2015. Engineering in Medicine and Biology Society, 2015. p. 1447-1451, 5 pp., ISBN 978-1-4799-2374-8. doi:10.1109/ISBI.2015.7164149.

Svoboda D, Ulman V, Peterlík I. 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, 5 pp., ISBN 978-1-4799-2374-8. doi:10.1109/ISBI.2015.7163972.

Ulman V, Orémuš Z, Svoboda D. 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, 12 pp., ISBN 978-3-319-23230-0. doi:10.1007/978-3-319-23231-7_56.

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2014

Journal Papers

Bártová E, Foltánková V, Legartová S, Sehnalová P, Sorokin D, Suchánková J, Kozubek S. 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. 2014. doi:10.4161/nucl.29229.

Chenouard N, Smal I, de Chaumont F, Maška M, Sbalzarini IF, Gong Y, Cardinale J, Carthel C, Coraluppi S, Winter M, Cohen AR, Godinez WJ, Rohr K, Kalaidzidis Y, Liang L, Duncan J, Shen H, Xu Y, Magnusson KEG, Jaldén J, Blau HM, Paul-Gilloteaux P, Roudot P, Kervrann Ch, Waharte F, Tinevez J, Shorte SL, Willemse J, Celler K, van Wezel GP, Dan H, Tsai Y, Ortiz-de-Solórzano C, Olivo-Marin J, Meijering E. Objective Comparison of Particle Tracking Methods. Nature Methods, 2014, vol. 11, No 3, p. 281-289. ISSN 1548-7091. 2014. doi:10.1038/nmeth.2808.

Jiang Y, Habibollah S, Tilgner K, Collin J, Bárta T, Al-Aama JY, Tesařová L, Hussain R, Trafford A, Kirkwood G, Sernagor E, Eleftheriou C, Przyborski S, Stojkovic M, Lako M, Keavney B, Armstrong L. An induced pluripotent stem cell model of hypoplastic left heart syndrome (HLHS) reveals multiple expression and functional differences in HLHS derived cardiac myocytes. Stem cells translational medicine, 2014, vol. 3, No 4, p. 416-423. ISSN 2157-6564. 2014. doi:10.5966/sctm.2013-0105.

Maška M, Ulman V, Svoboda D, Matula P, Matula P, Ederra C, Urbiola A, España T, Venkatesan S, Balak DMW, Karas P, Bolcková T, Štreitová M, Carthel C, Coraluppi S, Harder N, Rohr K, Magnusson KEG, Jaldén J, Blau HM, Dzyubachyk O, Křížek P, Hagen GM, Pastor-Escuredo D, Jimenez-Carretero D, Ledesma-Carbayo MJ, Muñoz-Barrutia A, Meijering E, Kozubek M, Ortiz-de-Solorzano C. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics, 2014, vol. 30, No 11, p. 1609-1617. ISSN 1367-4803. 2014. doi:10.1093/bioinformatics/btu080.

Ručka Z, Krontorád Koutná I, Tesařová L, Potěšilová M, Stejskal S, Šimara P, Vaňhara P, Doležel J, Zvoníček V, Coufal O, Čapov I. Intravenous insulin therapy during lung resection does not affect lung function or surfactant proteins. BMC Pulmonary Medicine, London, United Kingdom: BIOMED CENTRAL LTD, 2014, vol. 14, No 1, p. 155-163. ISSN 1471-2466. 2014. doi:10.1186/1471-2466-14-155.

Sorokin D, Suchánková J, Bártová E, Matula P. 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. 2014.

Stixová L, Sehnalová P, Legartová S, Suchánková J, Hrušková T, Kozubek S, Sorokin D, Matula P, Raška I, Kovařík A, Fulneček J, Bártová E. 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. 2014. doi:10.1186/1756-8935-7-39.

Stoklasa R, Majtner T, Svoboda D. Efficient k-NN based HEp-2 cells classifier. PATTERN RECOGNITION, OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2014, vol. 47, No 7, p. 2409-2418. ISSN 0031-3203. 2014. doi:10.1016/j.patcog.2013.09.021.

Suchánková J, Legartová S, Sehnalová P, Kozubek S, Valente S, Labella D, Mai A, Eckerich C, Fackelmayer FO, Sorokin D, Bártová E. 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. 2014. doi:10.4081/ejh.2014.2389.

Tesařová L, Stejskal S, Krontorád Koutná I. Driven hematopoietic differentiation of embryonic stem cells: Epigenetic perspectives. CURRENT PHARMACEUTICAL DESIGN, SHARJAH: BENTHAM SCIENCE PUBL LTD, 2014, vol. 20, No 11, p. 1674-1686. ISSN 1381-6128. 2014. doi:10.2174/13816128113199990524.

Tesařová L, Šimara P, Stejskal S, Krontorád Koutná I. Haematopoietic developmental potential of human pluripotent stem cell lines. Folia biologica, Praha: Univerzita Karlova, 2014, vol. 60, No 1, p. 90-94. ISSN 0015-5500. 2014.

Williams I, Bowring N, Svoboda D. A performance evaluation of statistical tests for edge detection in textured images. Computer Vision and Image Understanding, Elsevier, 2014, vol. 122, May 2014, p. 115-130. ISSN 1077-3142. 2014. doi:10.1016/j.cviu.2014.02.009.

Šalingová B, Madarásová M, Stejskal S, Tesařová L, Šimara P, Krontorád Koutná I. From Endothelial Progenitor Cells to Tissue Engineering: How Far Have We Come?. Journal of Stem Cell Research & Therapy, 5716 Corsa Ave, Los Angeles, USA: OMICS group, 2014, vol. 4, No 3, p. 185-195. ISSN 2157-7633. 2014. doi:10.4172/2157-7633.1000185.

Šimara P, Tesařová L, Paďourová S, Krontorád Koutná I. Generation of Human Induced Pluripotent Stem Cells Using Genome Integrating or Non-integrating Methods. Folia Biologica, Praha: Univerzita Karlova, 2014, vol. 60, S1, p. 85-89. ISSN 0015-5500. 2014.

Conference Papers

Majtner T, Stoklasa R, Svoboda D. RSurf - the Efficient Texture-Based Descriptor for Fluorescence Microscopy Images of HEp-2 Cells. In 22nd International Conference on Pattern Recognition. Los Alamitos, California: IEEE Computer Society, 2014. p. 1194-1199, 6 pp., ISBN 978-1-4799-5208-3. doi:10.1109/ICPR.2014.215.

Majtner T, Svoboda D. Texture Analysis Using 3D Gabor Features and 3D MPEG-7 Edge Histogram Descriptor in Fluorescence Microscopy. In 4th International Conference on 3D Imaging (IC3D). Los Alamitos, California: IEEE Computer Society, 2014. p. 1-7, 7 pp., ISBN 978-1-4799-8023-9. doi:10.1109/IC3D.2014.7032576.

Majtner T, Svoboda D. Comparison of 3D Texture-based Image Descriptors in Fluorescence Microscopy. In Reneta P. Barneva, Valentin E. Brimkov, Josef Šlapal. 16th International Workshop on Combinatorial Image Analysis (IWCIA) 2014. Switzerland: Springer International Publishing, 2014. p. 186-195, 10 pp., ISBN 978-3-319-07147-3. doi:10.1007/978-3-319-07148-0_17.

Sorokin D, Tektonidis M, Rohr K, Matula P. NON-RIGID CONTOUR-BASED TEMPORAL REGISTRATION OF 2D CELL NUCLEI IMAGES USING THE NAVIER EQUATION. In IEEE International Symposium on Biomedical Imaging: Nano to Macro. Beijing: IEEE, 2014. p. 746-749, 4 pp., ISBN 978-1-4673-1959-1. doi:10.1109/ISBI.2014.6867978.

Svoboda D, Ulman V, Matyska L, Maška M, Bella J, Stejskal S. On Proper Simulation of Phenomena Influencing Image Formation in Fluorescence Microscopy. In 2014 IEEE International Conference on Image Processing. IEEE Signal Processing Society, 2014. p. 3944-3948, 5 pp., ISBN 978-1-4799-5750-7. doi:10.1109/ICIP.2014.7025801.

Štěpka K, Falk M. Image Analysis of Gene Locus Positions within Chromosome Territories in Human Lymphocytes. In Petr Hliněný, Zdeněk Dvořák, Jiří Jaroš, Jan Kofroň, Jan Kořenek, Petr Matula, Karel Pala. Mathematical and Engineering Methods in Computer Science : Volume 8934 of the series Lecture Notes in Computer Science. Springer International Publishing, 2014. p. 125-134, 10 pp., ISBN 978-3-319-14895-3. doi:10.1007/978-3-319-14896-0_11.

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2013

Journal Papers

Foltánková V, Matula P, Sorokin D, Kozubek S, Bártová E. 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. 2013. doi:10.1017/S1431927612014353.

Maška M, Daněk O, Garasa S, Rouzaut A, Muñoz-Barrutia A, Ortiz-de-Solórzano C. Segmentation and Shape Tracking of Whole Fluorescent Cells Based on the Chan-Vese Model. IEEE Transactions on Medical Imaging, 2013, vol. 32, No 6, p. 995-1006. ISSN 0278-0062. 2013. doi:10.1109/TMI.2013.2243463.

Ručka Z, Vaňhara P, Krontorád Koutná I, Tesařová L, Potěšilová M, Stejskal S, Šimara P, Doležel J, Zvoníček V, Coufal O, Čapov I. Differential effects of insulin and dexamethasone on pulmonary surfactant-associated genes and proteins in A549 and H441 cells and lung tissue. INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, UNITED STATES: SPANDIDOS PUBL LTD, 2013, vol. 32, No 1, p. 211-218. ISSN 1107-3756. 2013. doi:10.3892/ijmm.2013.1363.

Šimara P, Motl J, Kaufman D. Pluripotent stem cells and gene therapy. Translational Research, 2013, vol. 161, No 4, p. 284-292. ISSN 1931-5244. 2013. doi:10.1016/j.trsl.2013.01.001.

Šimara P, Stejskal S, Krontorád Koutná I, Potěšil D, Tesařová L, Potěšilová M, Zdráhal Z, Mayer J. Apoptosis in chronic myeloid leukemia cells transiently treated with imatinib or dasatinib is caused by residual BCR-ABL kinase inhibition.. American Journal of Hematology, NJ 07030-577 United States: John Wiley & Sons, 2013, vol. 88, No 5, p. 385-393. ISSN 0361-8609. 2013. doi:10.1002/ajh.23419.

Conference Papers

Karas P, Kuderjavý M, Svoboda D. Deconvolution of huge 3-D images: Parallelization strategies on a multi-GPU system. In Kołodziej, Joanna and Martino, Beniamino and Talia, Domenico and Xiong, Kaiqi. Algorithms and Architectures for Parallel Processing. Springer International Publishing, 2013. p. 279-290, 12 pp., ISBN 978-3-319-03858-2. doi:10.1007/978-3-319-03859-9_24.

Maška M, Morales X, Muñoz-Barrutia A, Rouzaut A, Ortiz-de-Solórzano C. Automatic Quantification of Filopodia-Based Cell Migration. In 10th IEEE International Symposium on Biomedical Imaging. San Francisco: IEEE, 2013. p. 668-671, 4 pp., ISBN 978-1-4673-6454-6. doi:10.1109/ISBI.2013.6556563.

Svoboda D, Ulman V. 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, 10 pp., ISBN 978-3-642-41183-0. doi:10.1007/978-3-642-41184-7_44.

Štěpka K. Automated Cell Counting in Bürker Chamber. In J.-K. Kamarainen and M. Koskela. 18th Scandinavian Conference on Image Analysis, SCIA 2013. Espoo (Finland): Springer, 2013. p. 236-245, 10 pp., ISBN 978-3-642-38885-9. doi:10.1007/978-3-642-38886-6_23.

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2012

Journal Papers

Daněk O, Matula P, Maška M, Kozubek M. Smooth Chan-Vese Segmentation via Graph Cuts. Pattern recognition letters : an official publication of the International Association for Pattern Recognition., Amsterdam: Elsevier, 2012, vol. 33, No 10, p. 1405-1410. ISSN 0167-8655. 2012. doi:10.1016/j.patrec.2012.03.013.

Tesařová L, Krontorád Koutná I, Dvořáková M, Klabusay M. Relative expression of gammadelta T-cell receptor gene families detected by RT–PCR and capillary electrophoresis. International Journal of immunogenetics, Blackwell Publishing Ltd, 2012, vol. 39, No 5, p. 381-388. ISSN 1744-3121. 2012. doi:10.1111/j.1744-313X.2012.01114.x.

Vařecha M, Potěšilová M, Matula P, Kozubek M. Endonuclease G interacts with histone H2B and DNA topoisomerase II alpha during apoptosis. Mol Cell Biochem, 2012, vol. 363, 1-2, p. 301-307. ISSN 0300-8177. 2012. doi:10.1007/s11010-011-1182-x.

Šimara P, Peterková M, Stejskal S, Potěšilová M, Krontorád Koutná I, Ráčil Z, Rázga F, Jurček T, Dvořáková D, Mayer J. BCR-ABL activity measured by 50% inhibitory concentration for imatinib, p-CrkL/CrkL ratio or p-CrkL ratio in CD34+ cells of patients with chronic myeloid leukemia does not predict treatment response.. Leukemia & lymphoma, England: Informa Healthcare, 2012, vol. 53, No 8, p. 1627-1629. ISSN 1042-8194. 2012. doi:10.3109/10428194.2012.656104.

Conference Papers

Karas P, Svoboda D, Zemčík P. GPU Optimization of Convolution for Large 3-D Real Images. In Blanc-Talon, Jacques and Philips, Wilfried and Popescu, Dan and Scheunders, Paul and Zemcík, Pavel. Proceedings of the International Conference on Advanced Concepts for Intelligent Vision Systems (ACIVS’12). Springer Berlin / Heidelberg, 2012. p. 59-71, 13 pp., ISBN 978-3-642-33139-8. doi:10.1007/978-3-642-33140-4_6.

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

Maška M, Muñoz-Barrutia A, Ortiz-de-Solórzano C. Fast Tracking of Fluorescent Cells Based on the Chan-Vese Model. In 9th IEEE International Symposium on Biomedical Imaging. Barcelona: IEEE, 2012. p. 1316–1319, 4 pp., ISBN 978-1-4577-1857-1.

Svoboda D, Ulman V. 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, 10 pp., ISBN 978-3-642-31297-7. doi:10.1007/978-3-642-31298-4_56.

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2011

Journal Papers

Brázdilová SL, Kozubek M. Image Division Technique in Pre-acquisition Analysis of Information Content for Automated Microscopy. Journal of Microscopy, Oxford: Blackwell Science, 2011, vol. 242, No 3, p. 279-289. ISSN 0022-2720. 2011. doi:10.1111/j.1365-2818.2010.03465.x.

Karas P, Svoboda D. Convolution of Large 3D Images on GPU and its Decomposition. EURASIP Journal on Advances in Signal Processing, NEW YORK (USA): HINDAWI PUBLISHING CORPORATION, 2011, vol. 2011, No 120, p. 1-12. ISSN 1687-6172. 2011. doi:10.1186/1687-6180-2011-120.

Krontorád Koutná I, Peterková M, Šimara P, Stejskal S, Tesařová L, Kozubek M. Proliferation and differentiation potential of CD133+ and CD34+ populations from the bone marrow and mobilized peripheral blood. Annals of hematology, Germany: Springer, 2011, vol. 90, (2), p. 127-137. ISSN 0939-5555. 2011.

Pellicano F, Šimara P, Sinclair A, Helgason GV, Copland M, Grant S, Holyoake T. The MEK inhibitor PD184352 enhances BMS-214662-induced apoptosis in CD34+ CML stem/progenitor cells. Leukemia, London: Nature Publishing Group, 2011, vol. 25, No 7, p. 1159-1167. ISSN 0887-6924. 2011. doi:10.1038/leu.2011.67.

Staier F, Eipel H, Matula P, Evsikov AV, Kozubek M, Cremer Ch, Hausmann M. 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. ISSN 0034-6748. 2011.

Tesařová L, Krontorád Koutná I, Kořístek Z, Klabusay M. Multiple myeloma patients at peripheral blood stem cell harvest: restricted usage of TCR beta variable families. Clinical Immunology, Elsevier, 2011, vol. 138, No 1, p. 67-76. ISSN 1521-6616. 2011. doi:10.1016/j.clim.2010.09.007.

Ulman V. 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. 2011. doi:10.1155/2011/234090.

Conference Papers

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

Svoboda D, Homola O, Stejskal S. Generation of 3D Digital Phantoms of Colon Tissue. In M. Kamel and A. Campilho. Proceedings of 8th International Conference on Image Analysis and Recognition. LNCS 6754, Part II., Berlin, Heidelberg: Springer-Verlag, 2011. p. 31-39, 9 pp., ISBN 978-3-642-21595-7. doi:10.1007/978-3-642-21596-4_4.

Svoboda D. Efficient Computation of Convolution of Huge Images. In Giuseppe Maino; Gian Luca Foresti. Image Analysis and Processing - ICIAP 2011. LNCS 6978, Part I., Berlin, Heidelberg: Springer-Verlag, 2011. p. 453-462, 10 pp., ISBN 978-3-642-24084-3.

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2010

Journal Papers

Stejskal S, Krontorád Koutná I, Matula P, Ručka Z, Daněk O, Maška M, Kozubek M. The role of chromatin condensation during granulopoiesis in the regulation of gene cluster expression. Epigenetics, USA: Landes Bioscience, 2010, vol. 5, No 8, p. 759-767. ISSN 1559-2294. 2010. doi:10.4161/epi.5.8.13183.

Conference Papers

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

Maška M, Matula P, Daněk O, Kozubek M. A Fast Level Set-Like Algorithm for Region-Based Active Contours. In 6th International Symposium on Visual Computing. Berlin, Heidelberg: Springer-Verlag, 2010. p. 387-396, 10 pp., ISBN 978-3-642-17276-2. doi:10.1007/978-3-642-17277-9_40.

Maška M, Matula P, Kozubek M. 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. p. 117-125, 9 pp., ISBN 978-80-87342-10-7.

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

Ručka Z, Tesařová L, Potěšilová M, Stejskal S, Krontorád Koutná I, Vaňhara P, Doležel J. Dexamethasone and Insulin Affecting SFTPA1 and SFTPA2 mRNA Levels. In Advances in Molecular and Cancer Biology, 2010. Brno, Česká republika: muni PRESS, 2010. p. 36-38, 3 pp., ISBN 978-80-210-5312-0.

Tesařová L, Peterková M, Stejskal S, Potěšilová M, Krontorád Koutná I. Application of reverse transcription PCR and capillary electrophoresis in the analysis of T-cell receptor beta variable repertoire. In Advances in Molecular and Cancer Biology, 2010. Brno, Česká republika: muni PRESS, 2010. p. 46-51, 6 pp., ISBN 978-80-210-5312-0.

Ulman V. 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, 11 pp., ISBN 978-3-642-13771-6. doi:10.1007/978-3-642-13772-3_27.

Ulman V. 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, 10 pp., ISBN 978-0-88986-823-6.

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2009

Journal Papers

Brázdilová SL, Kozubek M. Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions. Journal of Microscopy, Oxford: Blackwell Science, 2009, vol. 236, No 3, p. 194-202. ISSN 0022-2720. 2009. doi:10.1111/j.1365-2818.2009.03280.x.

Peterková M, Koutná I, Tesařová L, Potěšilová M, Kozubek M, Hrabčáková V, Klabusay M, Doubek M, Mayer J. Microarray analysis using limited amount of cells. Folia Biologica (Praha), 2009, vol. 2009, No 55, p. 53-60. ISSN 0015-5500. 2009.

Svoboda D, Kozubek M, Stejskal S. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry. Cytometry Part A, John Wiley & Sons, Inc., 2009, 75A, No 6, p. 494-509. ISSN 1552-4922. 2009. doi:10.1002/cyto.a.20714.

Vařecha M, Zimmermann M, Amrichová J, Ulman V, Matula P, Kozubek M. 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. 2009.

Šimara P, Koutná I, Stejskal S, Krontorád P, Ručka Z, Peterková M, Kozubek M. Combination of mRNA and protein microarray analysis in complex cell profiling. Neoplasma, Bratislava, Slovensko: AEPress, s.r.o., 2009, 2/2009, No 56, p. 141-149. ISSN 0028-2685. 2009.

Conference Papers

Daněk O, Matula P, Ortiz-de-Solórzano C, Muñoz-Barrutia A, Maška M, Kozubek M. Segmentation of Touching Cell Nuclei using a Two-Stage Graph Cut Model. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009. p. 410-419, 10 pp., ISBN 978-3-642-02229-6. doi:10.1007/978-3-642-02230-2_42.

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

Maška M, Daněk O, Ortiz-de-Solórzano C, Muñoz-Barrutia A, Kozubek M, Fernández García I. A Two-Phase Segmentation of Cell Nuclei Using Fast Level Set-Like Algorithms. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009. p. 390-399, 10 pp., ISBN 978-3-642-02229-6. doi:10.1007/978-3-642-02230-2_40.

Maška M, Matula P. A Fast Level Set-Like Algorithm with Topology Preserving Constraint. In 13th International Conference on Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2009. p. 930-938, 9 pp., ISBN 978-3-642-03766-5. doi:10.1007/978-3-642-03767-2_113.

Peterková M, Koutná I, Šimara P, Stejskal S, Tesařová L. The in vitro proliferation potential and proportion of CD133+ versus CD34+ hematopoietic stem cells. In Experimental Hematology, Volume 37, Number 9. University of Nevada, USA: Elsevier, 2009. p. 35-36, 2 pp., ISSN 0301-472X.

Tesařová L, Koutná I, Peterková M, Potěšilová M, Dvořáková M, Stejskal S. Representation of T-cell receptor V beta families detected by reverse transcription PCR and capillary electrophoresis. In Experimental Hematology, Volume 37, Number 9. University of Nevada, USA: Elsevier, 2009. p. 72., ISSN 0301-472X.

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