Masaryk University Publications (2016 - 2018)

MUNI, CEITEC, CF CELLIM

- Up to 5 core publications recommended in MEDLINE format (including IF) produced by facility users

Robert HS, Park C, Gutièrrez CL, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nat Plants. 2018 Aug;4(8):548-553. doi: 10.1038/s41477-018-0204-z. IF= 11.5

Tereza Renzova,1 Dasa Bohaciakova,1 Milan Esner,1,2 Veronika Pospisilova,1 Tomas Barta,1 Ales Hampl,1,3
and Lukas Cajanek. Inactivation of PLK4-STIL Module Prevents Self-Renewal and Triggers p53-Dependent Differentiation in Human Pluripotent Stem Cells, - accepted in Stem Cells Reports. IF= 7.3

RŮŽIČKA, Kamil, M. ZHANG, A. CAMPILHO, Z. BODI, M. KASHIF, Mária SALEH, D. EECKHOUT, S. EL-SHOWK, H.Y. LI, S.L. ZHONG, G. DE JAEGER, N.P. MONGAN, Jan HEJÁTKO, Y. HELARIUTTA a R.G. FRAY. Identification of factors required for m(6)A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytologist, HOBOKEN: WILEY-BLACKWELL, 2017, roč. 215, č. 1, s. 157-172. ISSN 0028-646X. doi:10.1111/nph.14586. IF=7,433

Kania U, Nodzyński T, Lu Q, Hicks GR , Nerinckx W, Mishev K, Peurois F, Cherfils J, De Rycke R, Grones P, Robert S, Russinova E, Friml J. The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Subcellular Trafficking in Eukaryotes. Plant Cell. 2018 Oct;30(10):2553-2572. IF=8.228

Dzatko S, Krafcikova M, Hänsel-Hertsch R, Fessl T, Fiala R, Loja T, Krafcik D, Mergny JL, Foldynova-Trantirkova S, Trantirek L. Evaluation of the Stability of DNA i-Motifs in the Nuclei of Living Mammalian Cells. Angew Chem Int Ed Engl. 2018 Feb 19;57(8):2165-2169. doi: 10.1002/anie.201712284. Epub 2018 Jan 29. PubMed PMID: 29266664; PubMed Central PMCID: PMC5820743. IF=12.102

- Up to 5 most important technical / methodological publications (including IF) created by the members of the CzBI team at your facility

Renzova, Tereza; Bohaciakova, Dasa; Esner, Milan; et al. (2018) Inactivation of PLK4-STIL Module Prevents Self-Renewal and Triggers p53-Dependent Differentiation in Human Pluripotent Stem Cells. STEM CELL REPORTS   Volume: 11   Issue: 4   Pages: 959-972, IF2017 = 6.537

Samadder, Pounami; Suchankova, Tereza; Hylse, Ondrej; et al. Synthesis and Profiling of a Novel Potent Selective Inhibitor of CHK1 Kinase Possessing Unusual N-trifluoromethylpyrazole Pharmacophore Resistant to Metabolic N-dealkylation. MOLECULAR CANCER THERAPEUTICS Volume: 16 Issue: 9 Pages: 1831-1842. IF2017 = 5.365

Dobisová, T, Hrdinová, V., Žádníková, P., Cuestad, C., Skoupa, S., Urbankova, I., Hejátková, R., Pernisova, M., Benková, E andHejátko, J. (2017) Light-regulated expression of sensor histidine kinase CKI1 controls cytokinin-related development of Arabidopsis. Plant Physiology, 174: 387-404. IF2014 = 6.280

NOVAKOVA, L; KOVACOVICOVA, K; DANG-NGUYEN, TQ; SODEK, M; SKULTETY, M; ANGER, M, 2016:A Balance between Nuclear and Cytoplasmic Volumes Controls Spindle Length. PLOS ONE 11 (2) IF=2.766

Ruzicka K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, Eeckhout D, El-Showk S, Li H, Zhong S, De Jaeger G, Mongan NP, Hejatko J, Helariutta Y, Fray RG (2017) Identification of factors required for m6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytologist, 215: 157-172, IF2014 = 6.545

MUNI, CEITEC, CF MAFIL

- Up to 5 core publications recommended in MEDLINE format (including IF) produced by facility users

Shaw D, Czekoova K, Gajdos M, Stanek R, Spalek J, Brazdil M. Social decision-making in the brain: Input-state-output modelling reveals patterns of effective connectivity underlying reciprocal choices. Human brain mapping; 2018; in press. DOI:10.1002/hbm.24446

In this paper, CF member Martin Gajdos implemented new method called behavioral DCM for the research team using fMRI hyperscanning. It is an example of implementation of new methods for data processing. This is the first paper with application of behavioral DCM to real study (previous papers were methodological). The HBM is top-level journal.

Anderkova L, Barton M, Rektorova I. Striato-cortical connections in Parkinson's and Alzheimer's diseases: Relation to cognition. Mov Disord. 2017 Jun;32(6):917-922. doi: 10.1002/mds.26956. Epub 2017 Mar 3. IF= 8.324

This paper is good example of results of research project in high-quality journal (probably top in the field of neurodegenerative disease like Parkinson). The research group headed by prof. Rektorova is one of the most important users of our facility (many projects, many results in high-quality journals, several international collaborations).

Nemcova Elfmarkova Nela, Gajdos Martin, Rektorova Irena, Marecek Radek and Steven Z. Rapcsak, Neural evidence for defective top-down control of visual processing in Parkinson´s and Alzheimer´s disease, Neuropsychologia, https://doi.org/10.1016/j.neuropsychologia.2017.09.034IF= 2.889

This paper is other example of outputs from the group of prof. Rektorova. It is example of one international collaboration with prof. Rapcsak. In this paper, the application of new cognitive task in neurodegenerative disease patients is presented, and this task was subsequently used in several other studies performed in our lab.

SVĚRÁK, Tomáš, Lenka ALBRECHTOVÁ, Martin LAMOŠ, Irena REKTOROVÁ a Libor USTOHAL. Intensive repetitive transcranial magnetic stimulation changes EEG microstates in schizophrenia: A pilot study. Schizophrenia Research, Elsevier, 2018, 193:451-452 ISSN 0920-9964. doi:10.1016/j.schres.2017.06.044. IF= 3.958

This is example of psychiatric research with electrophysiological methods in our lab, namely transcranial magnetic stimulation and EEG. This was probably one of first application of EEG microstates together with TMS in schizophrenia patients.

Rektor, Ivan; Svatkova, Alena; Vojtisek, Lubomir; et al. White matter alterations in Parkinson's disease with normal cognition precede grey matter atrophy. PLOS ONE Volume: 13 Issue: 1 Article Number: e0187939 Published: JAN 5 2018IF= 2.766

Example of results focused on morphological processing of structural MRI data.

- Up to 5 most important technical / methodological publications (including IF) created by the members of the CzBI team at your facility

Barton, Marek; Marecek, Radek; Krajcovicova, Lenka; Slavicek, Tomas; Kasparek, Tomas; Zemankova, Petra; Riha, Pavel; Mikl, Michal. Evaluation of different cerebrospinal fluid and white matter fMRI filtering strategies-Quantifying noise removal and neural signal preservation. Human brain mapping; 2018; DOI:10.1002/hbm.24433 IF=4.927

This paper is the result of our long-term effort to better understand noise structure in fMRI data and to optimize the processing pipeline. The results are relatively widely applicable. And the journal is one of the top journals with fMRI methodological scope.

Lamos, Martin; Marecek, Radek; Slavicek, Tomas; et al. Spatial-temporal-spectral EEG patterns of BOLD functional network connectivity dynamics. JOURNAL OF NEURAL ENGINEERING Volume: 15 Issue: 3 Article Number: 036025 Published: JUN 2018IF= 3.92

This paper describes the relationships between EEG and BOLD fMRI with respect to the dynamic processes in human brain. It is very hot topic and important for our facility because of the combination of two important modalities used in human brain mapping research.

Gajdos, Martin; Vytvarova, Eva; Fousek, Jan; et al.Robustness of Representative Signals Relative to Data Loss Using Atlas-Based Parcellations. BRAIN TOPOGRAPHY Volume: 31 Issue: 5 Pages: 767-779 Published: SEP 2018IF= 2.703

The paper is dealing with important topic of limited coverage of brain areas with good BOLD fMRI data (e.g. caused by dropouts and other MR artifacts). The topic is important for connectivity analyses based on regions of interest – typically created from anatomical atlases.

Latta, Peter; Starcuk, Zenon, Jr.; Gruwel, Marco L. H.; et al. Influence of k-space trajectory corrections on proton density mapping with ultrashort echo time imaging: Application for imaging of short T2 components in white matter. MAGNETIC RESONANCE IMAGING Volume: 51 Pages: 87-95 Published: SEP 2018IF= 2.564

This is good example of papers dealing with development of MRI pulse sequences and respective image processing. This shows our lab is participating on the methodological development not only in the field of data processing but also in the field of data acquisition.

Mareček R, Lamoš M, Labounek R, Bartoň M, Slavíček T, Mikl M, Rektor I, Brázdil M. Multiway Array Decomposition of EEG Spectrum: Implications of Its Stability for the Exploration of Large-Scale Brain Networks. Neural Comput. 2017 Apr;29(4):968-989. doi: 10.1162/NECO_a_00933. Epub 2017 Jan 17. IF= 1.651

This paper represent good example of development and implementation of new methods in the field of EEG data analysis with some implications for fusion of EEG and fMRI data

MUNI, Faculty of Informatics, CF Centre for Biomedical Image Analysis

- Up to 5 core publications recommended in MEDLINE format (including IF) produced by facility users

The choice was done based on IF, which correlates with the expected importance of the 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. IF=2,766

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. IF=4,963

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, ISSN 0021-9533. 2018. doi:10.1242/jcs.202416. IF=4,401

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, 2018, vol. 27, No 1, p. 10-22. ISSN 1547-3287. 2018. doi:10.1089/scd.2017.0132. IF=3,315

Castilla C, Maška M, Sorokin D, Meijering E, Ortiz-de-Solórzano C. Three-Dimensional Quantification of Filopodia in Motile Cancer Cells. IEEE Transactions on Medical Imaging, IEEE, 2018, p. in press. ISSN 0278-0062. 2018. doi:10.1109/TMI.2018.2873842. IF=6,131

- Up to 5 most important technical / methodological publications (including IF) created by the members of the CzBI team at your facility

The choice was done based on IF, which correlates with the expected importance of the papers.

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. IF=26,919

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. IF=6,131

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. IF=5,481

Sorokin D, Peterlík I, Tektonidis M, Rohr K, Matula P. Non-rigid Contour-Based Registration of Cell Nuclei in 2D 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. IF=6,131

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 3D 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. IF=6,131

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