Publications by Jiří Kléma
Journals:
Saveleva, L., Sima, M., Klema, J., Krejcik, Z., Vartiainen, P., Sitnikova, V., Belaya, I., Malm, T., Jalava, P. I., Rössner, P., Kanninen, K. M.: Transcriptomic Alterations in the Olfactory Bulb Induced by Exposure to Air Pollution: Identification of Potential Biomarkers and Insights into Olfactory System Function. Environmental Toxicology and Pharmacology, Vol. 104, 104316, November 2023. (online).
Hruba, P., Klema, J., Le, A. V., Girmanova, E., Mrazova, P., Massart, A., Maixnerova, D., Voska, L., Piredda, G. B., Biancone, L., Puga, A. R., Seyahi, N., Sever, M. S., Weekers, L., Muhfeld, A., Budde, K., Watschinger, B., Miglinas, M., Zahradka, I., Abramowicz, M., Abramowicz, D., Viklicky, O.: Novel transcriptomic signatures associated with premature kidney allograft failure. EBioMedicine, Vol. 96, 104782, October 2023. (online).
Le, A. V., Vetrovsky, T., Barucic, D., Saraiva, J. P., Dobbler, P. T., Kohout, P., Pospisek, M., da Rocha, U. N., Klema, J., Baldrian, P.: Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns. Molecular Ecology Resources, 23(8), pp. 1800-1811, November 2023. (online).
Trsova, I., Hrustincova, A., Krejcik, Z., Kundrat, D., Holoubek, A., Staflova, K., Janstova, L., Vanikova, S., Szikszai, K., Klema, J., Rysavy, P., Belickova, M., Kaisrlikova, M., Vesela, J., Cermak, J., Jonasova, A., Dostal, J., Fric, J., Musil, J., Dostalova Merkerova, M: Expression of circular RNAs in myelodysplastic neoplasms and their association with mutations in the splicing factor gene SF3B1. Molecular Oncology, July 6, 2023. (online).
Rysavy P., Klema J., Dostalova Merkerova, M.: circGPA: circRNA functional annotation based on probability-generating functions. BMC Bioinformatics, 23(392), 2022. (online).
Iatsiuk, V., Malinka, F., Pickova, M., Tureckova, J., Klema, J., Spoutil, F., Novosadova, V., Prochazka, J., Sedlacek, R.: Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes ontology clusters with tissue expression patterns. BMC Gastroenterology, 22.1: 1-14, 2022. (online).
Kaisrlikova, M., Vesela, J., Kundrat, D., Votavova, H., Dostalova Merkerova, M., Krejcik, Z., Divoky, V., Jedlicka, M., Fric, J., Klema, J., Mikulenkova, D., Stastna Markova, M., Lauermannova, M., Mertova, J., Maalofouvá Soukupová, J., Jonasova, A., Cermak, J., Belickova, M.: RUNX1 mutations contribute to the progression of MDS due to disruption of antitumor cellular defense: A study on patients with lower-risk MDS. Leukemia, 1-9, 2022. (online).
Ambroz, A., Rossner, P., Rossnerova, A., Honkova, K., Milcova, A., Pastorkova, A., Klema, J., Pulkrabova, J., Parizek, O., Vondraskova, V., Zelenka, J., Vrzackova, N., Schmuczerova, J., Topinka, J., Sram, R.: Oxidative Stress and Antioxidant Response in Populations of the Czech Republic Exposed to Various Levels of Environmental Pollutants. International journal of environmental research and public health, 19(6), 3609, 2022. (online).
Dostalova Merkerova, M., Klema, J., Kundrat, D., Szikszai, K., Krejcik, Z., Hrustincova, A., Trsova, I., Le, A., V., Cermak, J., Jonasova, A., Belickova, M.: Noncoding RNAs and their response predictive value in azacitidine-treated patients with myelodysplastic syndromes and acute myeloid leukemia with myelodysplasia-related changes. Cancer Genomics and Proteomics, 19(2), pp. 205-228, 2022. (online).
Sima, M., Cervena, T., Elzeinova, F., Ambroz, A., Beranek, V., Vojtisek-Lom, M., Klema, J., Ciganek, M., Rossner, P.: The impact of extractable organic matter from gasoline and alternative fuel emissions on bronchial cell models (BEAS-2B, MucilAir). Toxicology in Vitro, Vol. 80, 105316, April 2022. (online).
Libalova, H., Zavodna, T., Vrbova, K., Sikorova, J., Vojtisek-Lom, M., Beranek, V., Pechout, M., Klema, J., Ciganek, M., Machala, M., Neca, J., Rossner, P., Topinka, J.: Transcription profiles in BEAS-2B cells exposed to organic extracts from particulate emissions produced by a port-fuel injection vehicle, fueled with conventional fossil gasoline and gasoline-ethanol blend. Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 872, 503414, 2021. (online).
Osickova, K., Hruba, P., Kabrtova, K., Klema, J., Maluskova, J., Slavcev, A., Slatinska, J., Marada, T., Böhmig, G., A., Viklicky, O.: Predictive Potential of Flow Cytometry Crossmatching in Deceased Donor Kidney Transplant Recipients Subjected to Peritransplant Desensitization. Frontiers in medicine, 2497, 2021. (online).
Kunc, V., Klema, J.: On Transformative Adaptive Activation Functions in Neural Networks for Gene Expression Inference. PLOS ONE, 16(1), pp. 1-27, 2021. (online).
Cervena, T., Lom, M., Vrbova, K., Ambroz, A., Novakova, Z., Elzeinova, F., Sima, M., Beranek, V., Pechout, M., Macoun, D., Klema, J., Rossnerova, A., Ciganek, M., Topinka, J., Rossner, P.: Ordinary Gasoline Emissions Induce a Toxic Response in Bronchial Cells Grown at Air-Liquid Interface. International Journal of Molecular Sciences, 22(1), 2021. (online).
Hyzdalova, M., Prochazkova, J., Strapacova, S., Svrzkova, L., Vacek, O., Fedr, R., Andrysik, Z., Hruba, E., Libalova, H., Klema, J., Topinka, J., Masek, J., Soucek, K., Vondracek, J., Machala, M.: A prolonged exposure of human lung carcinoma epithelial cells to benzo[a]pyrene induces p21-dependent epithelial-to-mesenchymal transition (EMT)-like phenotype. Chemosphere, Vol. 263, January 2021. (online).
Malinka, F., Zelezny, F., Klema, J.: Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator. BioData Mining, 13(1), pp. 1-22, 2020. (online).
Kunc, V., Klema, J.: On Tower and Checkerboard Neural Network Architectures for Gene Expression Inference. BMC Genomics, 21(5), pp. 1-11, 2020. (online).
Hruba, P., Madill-Thomsen, K., Mackova, M., Klema, J., Maluskova, J., Voska, L., Parikova, A., Slatinska, J., Halloran, P., Viklicky, O.: Molecular Patterns of Isolated Tubulitis Differ from Tubulitis with Interstitial Inflammation in Early Indication Biopsies of Kidney Allografts. Scientific Reports, 10(1), 2020. (online).
Szikszai, K., Krejcik, Z., Klema, J., Loudova, N., Hrustincova, A., Belickova, M., Hruba, M., Vesela, J., Stranecky, V., Kundrat, D., Pecherkova, P., Cermak, J., Jonasova, A., Dostalova Merkerova, M.: LncRNA profiling reveals that the deregulation of H19, WT1-AS, TCL6, and LEF1-AS1 is predictive of adverse outcomes in myelodysplastic syndrome. Cancers, 12(10), 2726, 2020. (online).
Sima, M., Vrbova, K., Zavodna, T., Honkova, K., Chvojkova, I., Ambroz, A., Klema, J., Rossnerova, A., Polakova, K., Malina, T., Belza, J., Topinka, J., Rossner, P.: The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and Dose. International Journal of Molecular Sciences, 21(13), 4763, 2020. (online).
Rossnerova, A., Honkova, K., Pelclova, D., Zdimal, V., Hubacek, J.A., Chvojkova, I., Vrbova, K., Rossner, P., Topinka, J., Vlckova, S., Fenclova, Z., Lischkova, L., Klusackova, P., Schwarz, J., Ondracek, J., Ondrackova, L., Kostejn, M., Klema, J., Dvorackova, S.: DNA methylation profiles in a group of workers occupationally exposed to nanoparticles. International Journal of Molecular Sciences, 21(7), 2420, 2020. (online).
Hrustincova, A., Krejcik, Z., Kundrat, D., Szikszai, K., Belickova, M., Pecherkova, P., Klema, J., Vesela, J., Hruba, M., Cermak, J., Hrdinova, T., Krijt, M., Valka, J., Jonasova, A., Dostalova-Merkerova, M.: Circulating Small Noncoding RNAs Have Specific Expression Patterns in Plasma and Extracellular Vesicles in Myelodysplastic Syndromes and Are Predictive of Patient Outcome. Cells, 9(4), 794, 2020. (online).
Hruba, P., Krejcik, Z., Dostalova-Merkerova, M., Klema, J., Stranecky, V., Slatinska, J., Maluskova, J., Honsova, E., Viklicky, O.: Molecular fingerprints of borderline changes in kidney allografts are influenced by donor category. Frontiers in Immunology, Vol. 11, pp. 423, 25 March 2020. (online).
Rossner, P., Vrbova, K., Rossnerova, A., Zavodna, J., Milcova, A., Klema, J., Vecera, Z., Mikuska, P., Coufalik, P., Capka, L., Krumal, K., Docekal, B., Holan, V., Machala, M., Topinka, J.: Gene Expression and Epigenetic Changes in Mice Following Inhalation of Copper(II) Oxide Nanoparticles. Nanomaterials, 10(3), 550, 2020. (online).
Svobodova, J., Prochazkova, J., Kabatkova, M., Krkoska, M., Smerdova, L., Libalova, H., Topinka, J., Klema, J., Kozubik, A., Machala, M., Vondracek, J.: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) disrupts control of cell proliferation and apoptosis in a human model of adult liver progenitors. Toxicological Sciences, Vol. 172, Issue 2, December 2019, pp. 368-384. (online).
Rossner, P., Cervena, T., Vojtisek-Lom, M., Vrbova, K., Ambroz, A., Novakova, Z., Elzeinova, F., Margaryan, H., Beranek, V., Pechout, M., Macoun, D., Klema, J., Rossnerova, A., Topinka, J.: The biological effects of complete gasoline engine emissions exposure in a 3D human airway model (MucilAirTM) and in human bronchial epithelial cells (BEAS-2B). International Journal of Molecular Sciences, 20(22), 5710, November 2019. (online).
Brzicova, T., Javorkova, E., Vrbova, K., Zajicova, A., Holan, V., Pinkas, D., Philimonenko, V., Sikorova, J., Klema, J., Topinka, J., Rossner, P.: Molecular Responses in THP-1 Macrophage-Like Cells Exposed to Diverse Nanoparticles. Nanomaterials, Vol. 9, Issue 5, Article 687, May 2019. (online).
Brzicova, T., Sikorova, J., Milcova, A., Vrbova, K., Klema, J., Pikal, P., Lubovska, Z., Philimonenko, V., Franco, F., Topinka, J., Rossner, P.: Nano-TiO2 stability in medium and size as important factors of toxicity in macrophage-like cells. Toxicology in Vitro, Vol. 54, pp. 178-188, February 2019. (online).
Rynning, I., Arlt, V., Vrbova, K., Neca, J., Rossner, P., Klema, J., Ulvestad, B., Petersen, E., Skare, Ø., Haugen, A., Phillips, D., Machala, M., Topinka, J., Mollerup, S.: Bulky DNA-adducts, miRNA profiles, and lipid biomarkers in Norwegian tunnel finishing workers occupationally exposed to diesel exhaust. Occupational and Environmental Medicine, 76(1):10-16, January 2019. (online).
Wohlfahrtova, M., Hruba, P., Klema, J., Novotny, M., Krejcik, Z., Stranecky, V., Honsova, E., Vichova, P., Viklicky, O.: Early isolated v-lesion may not truly represent rejection of the kidney allograft. Clinical Science, Vol. 132, Issue 20, pp. 2269-2284, Oct 29, 2018. (online).
Prochazkova, J., Strapacova, S., Svrzkova, L., Andrysik, Z., Hyzdalova, M., Hruba, E., Pencikova, K., Libalova, H., Topinka, J., Klema, J., Espinosa, J.M., Vondracek, J., Machala, M.: Adaptive changes in global gene expression profile of lung carcinoma A549 cells acutely exposed to distinct types of AhR ligands. Toxicology Letters, Vol. 292, August 2018, pp. 162-174. (online).
Honkova, K., Rossnerova, A., Pavlikova, J., Svecova, V., Klema, J., Topinka, J., Milcova, A., Libalova, H., Choi, H., Veleminsky, M., Sram, R., Rossner, P.: Gene expression profiling in healthy newborns from diverse localities of the Czech Republic. Environmental and Molecular Mutagenesis, Vol. 59, Issue 5, June 2018, pp 401-415. (online).
Libalova, H., Rossner, P., Vrbova, K., Brzicova, T., Sikorova, J., Vojtisek-Lom, M., Beranek, V., Klema, J., Ciganek, M., Neca, J., Machala, M., Topinka, J.: Transcriptional response to organic compounds from diverse gasoline and biogasoline fuel emissions in human lung cells. Toxicology In Vitro, 48:329-341, 2018. (online).
Klema, J., Malinka, F., Zelezny, F.: Semantic biclustering for finding local, interpretable and predictive expression patterns. BMC Genomics 18:752, 2017. (online).
Liskova, P., Dudakova, L., Krepelova, A., Klema, J. and Hysi, P. G.: Replication of SNP associations with keratoconus in a Czech cohort. PLOS ONE, February 16, 2017. (online).
Libalova, H., Rossner, P., Vrbova, K., Brzicova, T., Sikorova, J., Vojtisek-Lom, M., Beranek, V., Klema, J., Ciganek, M., Neca, J., Pencikova, K., Machala, M., Topinka, J.: Comparative Analysis of Toxic Responses of Organic Extracts from Diesel and Selected Alternative Fuels Engine Emissions in Human Lung BEAS-2B Cells. International Journal of Molecular Sciences, 17(11), 1833, 2016. (online).
Belickova, M., Dostalova-Merkerova, M., Votavova, H., Valka, J., Vesela, J., Pejsova, B., Hajkova, H., Klema, J., Cermak, J., Jonasova, A.: Up-regulation of ribosomal genes is associated with a poor response to azacitidine in myelodysplasia and related neoplasms. International Journal of Hematology, Nov, 104(5):566-573, 2016. (online).
Andel, M., Klema, J., Krejcik, Z.: Network-Constrained Forest for Regularized Classification of Omics Data. Methods, Vol. 83, pp. 88-97, 15 July 2015. (preprint pdf, online).
Krejcik, Z., Belickova, M., Mrhalkova, M., Klema, J., Zemanova, Z., Michalova, K., Cermak, J., Jonasova, A., Dostalova Merkerova, M.: Aberrant expression of miRNA cluster in 14q32 region is associated with del(5q) myelodysplastic syndrome and lenalidomide treatment. Cancer Genetics, Vol. 208, Issue 4 (April), pp. 156-161, 2015. (online).
Cellier, P., Charnois, T., Plantevit, M., Rigotti, C., Cremilleux, B., Gandrillon, O., Klema, J., Manguin, J. L.: Sequential Pattern Mining for Discovering Gene Interactions and their Contextual Information from Biomedical Texts. Journal of Biomedical Semantics, 6:27, 2015. (online).
Dostalova Merkerova, M., Krejcik, Z., Belickova, M., Hrustincova, A., Klema, J., Stara, E., Zemanova, Z., Michalova, K., Cermak, J. and Jonasova A.: Genome-wide miRNA profiling in myelodysplastic syndrome with del(5q) treated with lenalidomide. European Journal of Haematology, Vol. 95, Issue 1 (July), pp. 35-43, 2015. (online).
Libalova, H., Krckova, S., Uhlirova, K., Klema, J., Ciganek, M., Rossner, P., Sram, R., Vondracek, J., Machala, M., Topinka, J.: Analysis of gene expression changes in A549 cells induced by organic compounds from respirable air particles. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 770, pp. 94-105, 2014. (online).
Libalova, H., Krckova, S., Uhlirova, K., Milcova, A., Schmuczerova, J., Ciganek, M., Klema, J., Machala, M., Sram, R., Topinka, J.: Genotoxicity but not the AhR-mediated activity of PAHs is inhibited by other components of complex mixtures of ambient air pollutants. Toxicology Letters 225/3, pp. 350-357, 2014. (online).
Krejnik, M., Klema J.: Empirical Evidence of the Applicability of Functional Clustering through Gene Expression Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9:3, pp. 788-798, 2012. (online), (pdf).
Holec M., Klema J., Zelezny F., Tolar J.: Comparative Evaluation of Set-Level Techniques in Predictive Classification of Gene Expression Samples. BMC Bioinformatics, 13, Suppl. 10, S15, 2012. (online).
Girmanova, E., Brabcova, I., Klema, J., Hribova, P., Wohlfartova, M., Skibova, J., Viklicky, O.: Molecular Networks Involved in The Immune Control of BK Polyomavirus. Clinical and Developmental Immunology, Vol. 2012, Article ID 972102, 9 p., 2012. (online).
Libalova, H., Uhlirova, K., Klema, J., Machala, M., Sram, R., Ciganek, M. and Topinka, J.: Global Gene Expression Changes in Human Embryonic Lung Fibroblasts Induced by Organic Extracts from Respirable Air Particles. Particle and Fibre Toxicology, 9:1, 2012. (online).
Plantevit, M., Charnois, T., Klema, J., Rigotti, C., Cremilleux, B.: Combining Sequence and Itemset Mining to Discover Named Entities in Biomedical Texts: A New Type of Pattern. International Journal of Data Mining, Modelling and Management, Vol. 1, No. 2, pp. 119-148, 2009. (online).
Klema, J., Blachon, S., Soulet, A., Cremilleux, B., Gandrilon, O.: Constraint-Based Knowledge Discovery from SAGE Data. In Silico Biology, 8, 0014, 2008. (online1, pdf).
Klema, J., Novakova, L., Karel, F., Stepankova, O., Zelezny, F.: Sequential Data Mining: A Comparative Case Study in Development of Atherosclerosis Risk Factors. IEEE Transactions on Systems, Man, and Cybernetics: Part C: Applications and Reviews, Vol. 38, no. 1, pp. 3-15, 2008. (IEEE Trans. Sys Man Cyb C), (pdf).
Stryczek, K., Horacek, P., Klema, J., Castells, X., Stewart, B., Geoffroy, J.M.: Capitalizing on Aggregate Data for Gaining Process Understanding: Effect of Raw Material, Environmental and Process Conditions on the Dissolution Rate of a Sustained Release Product. Journal of Pharmaceutical Innovation, Vol. 2:1-2, pp. 6-17, 2007. (Springerlink), (pdf).
Klema, J., Almonayyes, A.: Automatic Categorization of Fanatic Texts Using Random Forests. Kuwait Journal of Science and Engineering. Vol. 33, no. 2, pp. 1-14, 2006.
Klema, J., Kubalik, J., Lhotska, L.: Optimized Model Tuning in Medical Systems. Computer Methods and Programs in Biomedicine. Vol. 80, no. 3, pp. 17-28, 2005. (online).
Kout, J., Vlcek, T., Klema, J.: Predictive System for Multivariate Time Series. Automa International - Trade Journal for Industrial Automation, no. 11, pp. 6-8, 2005. (pdf).
Novakova, L., Klema, J., Stepankova, O.: Anachronistic Attributes in Temporal Data: A Case Study. Neural Network World. Vol. 14, No. 5, pp. 421-434, 2004. (draft, pdf).
Book chapters:
Klema, J., Zahalka, J., Andel, M., Krejcik, Z.: Interaction-Based Aggregation of mRNA and miRNA Expression Profiles to Differentiate Myelodysplastic Syndrome. In Plantier, G., Schultz, T., Fred, A., Gamboa, H. (eds.): Biomedical Engineering Systems and Technologies, 7th International Joint Conference, BIOSTEC 2014, Angers, France, March 3–6, 2014, Revised Selected Papers, Communications in Computer and Information Science, Springer, pp. 165-180, 2015. (online), (pdf).
Zelezny, F., Klema, J.: Vyuzivani znalosti pro ziskavani znalosti. In Czech. In Marik, V., Stepankova, O., Lazansky, J. (eds.): Umela inteligence VI., Academia, 2013.
Klema, J., Zelezny, F., Trajkovski, I., Karel, F., Cremilleux, B., Tolar, J.: Gene Expression Mining Guided by Background Knowledge. In Berka, P., Rauch, J., Zighed, D.A. (eds.): Data Mining and Medical Knowledge Management: Cases and Applications, IGI Global Inc., pp. 268-292, 2009. (online).
Cremilleux, B., Soulet, A., Klema, J., Hebert, C., Gandrillon, O.: Discovering Knowledge from Local Patterns in SAGE Data. In Berka, P., Rauch, J., Zighed, D.A. (eds.): Data Mining and Medical Knowledge Management: Cases and Applications, IGI Global Inc., pp. 251-267, 2009. (online).
Soulet, A., Klema, J., Cremilleux, B.: Efficient Mining Under Rich Constraints Derived from Various Datasets. In Dzeroski, S., Struyf, J. (eds.): Knowledge Discovery in Inductive Databases, Lecture Notes in Computer Science Vol. 4747/2007, Springer Berlin / Heidelberg, pp. 223-239, 2007. (Springerlink), (pdf).
Zelezny, F., Klema, J., Stepankova, O.: Strojove uceni v dobyvani znalosti. In Czech. In Marik, V., Stepankova, O., Lazansky, J. (eds.): Umela inteligence IV., Academia, pp. 355-406, 2003.
Stepankova, O., Klema, J., Miksovsky, P.: Applying SumatraTT and RAMSYS: Prediction of Resources for a Health Farm. In Lavrac, N., Mladenic, D. (eds.): Data Mining and Decision Support:Integration and Collaboration, Kluwer Academic Press, pp. 215-226, 2003.
Editorials:
Marik, V., Jacovkis, P., Stepankova, O., Klema, J. (eds.): Interdisciplinary Aspects of Human-Machine Co-existence and Co-operation. Czech-Argentine Biennale "e-Golems", Czech Technical University Press, 366 p., 2005.
Conference papers:
Kunc, V., Klema, J.: On functional annotation with gene co-expression networks. In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Las Vegas, NV, USA, pp. 3055-3062, 2022. (online).
Zavodna, T., Libalova, H., Vrbova, K., Sikorova, J., Vojtisek, M., Beranek, V., Pechout, M., Klema, J., Ciganek, M., Machala, M., Neca, J., Rossner, P., Topinka, J.: Toxic responses in human lung epithelial cells (BEAS-2B) exposed to particulate matter exhaust emissions from gasoline and biogasoline. In: NANOCON Conference Proceedings -- International Conference on Nanomaterials. Ostrava: TANGER, pp. 453-458, 2021. (online).
Dvorakova, E., Kumar, S., Klema, J., Zelezny, F., Drbal, K., Song, M.: Evaluating Model-free Directional Dependency Methods on Single-cell RNA Sequencing Data with Severe Dropout. In Proceedings of the 6th International Conference on Bioinformatics Research and Applications (ICBRA 2019), 2019. (online).
Malinka, F., Zelezny, F., Klema, J.: Genomic single rule learning with an ontology-based refinement operator. In: SVOZIL, D. and P. CECH, eds. ENBIK2018 Conference proceedings. ENBIK - Narodni bioinformaticka konference, Bystrice nad Pernstejnem, 2018-06-11/2018-06-13. Praha: Vysoka skola chemicko-technologicka, 2018. s. 69.
Andel, M., Klema, J., Topinka, J.: Empirical Evaluation of QNTR Models Build on Physico-Chemical Characteristics. In Proceedings of the 8th International Conference on Nanomaterials -- Research and Application. Ostrava: Tanger, pp. 594-599, 2017.
Klema, J., Malinka, F., Zelezny, F.: Semantic Biclustering: a New Way to Analyze and Interpret Gene Expression Data. In Proceedings of The 12th International Symposium on Bioinformatics Research and Applications (ISBRA), Springer, LNBI 9683, pp. 332-3, 2016. (online).
Andel, M., Masri, F., Klema, J., Krejcik, Z., Belickova, M.: Sparse Omics-network Regularization to Increase Interpretability and Performance of Linear Classification Models. In Proceedings of The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 615-620, 2015. (online).
Kunc, V., Klema, J., Andel, M.: Increasing Weak Classifiers Diversity by Omics Networks. In Proceedings of the 2nd ECML/PKDD Workshop on Machine Learning in Life Sciences, Engine Center, Wroclaw University of Technology, Poland, pp. 28-39, 2015. (online). (pdf).
Andel, M., Klema, J., Krejcik, Z.: Network-Constrained Forest for Regularized Omics Data Classification. In Proceedings of The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 410-417, 2014. (online), (pdf).
Holec, M., Gologuzov, V., Klema, J.: miXGENE Tool for Learning from Heterogeneous Gene Expression Data Using Prior Knowledge. In Proceedings of 27th International Symposium on Computer-Based Medical Systems, Los Alamitos: IEEE Computer Society, pp. 247-250, 2014. (online), (pdf).
Klema, J., Zahalka, J., Andel, M., Krejcik, Z.: Knowledge-Based Subtractive Integration of mRNA and miRNA Expression Profiles to Differentiate Myelodysplastic Syndrome. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Porto: SciTePress - Science and Technology Publications, pp. 31-39, 2014. (pdf).
Andel, M., Klema, J., Krejcik, Z.: Integrating mRNA and miRNA expressions with interaction knowledge to predict myelodysplatic syndrome. In ITAT 2013: Information Technologies -- Applications and Theory, Workshop on Bioinformatics in Genomics and Proteomics, pp. 48-55, 2013. (pdf).
Klema, J.: Machine Learning Applications in Bioinformatics. In Proceedings of the Conference on Theory and Practice of Information Technologies, Institute of Computer Science, Faculty of Science, University Kosice, pp. 1-2, 2012. (Invited talk -- extended abstract).
Hrdlicka,J., Klema, J.: Schizophrenia Prediction with the Adaboost Algorithm. In Proceedings of 23th International Conference of the European Federation for Medical Informatics, IOS Press, pp. 574-578, 2011.
Klema, J., Holec, M., Zelezny, F., Tolar, J.: Comparative Evaluation of Set-Level Techniques in Microarray Classification. ISBRA 2011: 7th International Conference on Bioinformatics Research and Applications, Springer, Heidelberg, pp. 274-285, 2011. (pdf).
Vitovec, P., Klema, J.: Gene Interaction Extraction from Biomedical Texts by Sentence Skeletonization. In Znalosti 2011: VSB-TUO Ostrava, pp. 230-242, 2011. (pdf).
Holec, M., Zelezny, F., Klema, J., Tolar, J.: A Comparative Evaluation of Gene Set Analysis Techniques in Predictive Classification of Expression Samples. BCBGC 2010: International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, 2010. (pdf).
Holec, M., Zelezny, F., Klema, J., Tolar, J.: Integrating Multiple-Platform Expression Data through Gene Set Features. ISBRA 2009: 5th International Conference on Bioinformatics Research and Applications, 2009. (pdf).
Holec, M., Klema, J., Zelezny, F., Belohradsky, J., Tolar, J.: Cross-Genome Knowledge-Based Expression Data Fusion. BCBGC 2009: International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, 2009. (pdf).
Krejnik, M., Klema, J.: Knowledge-Based Feature Extraction in Genomics. In Znalosti 2009. Vydavatelstvo STU Bratislava, pp. 131-142, 2009. (ps).
Holec, M., Zelezny, F., Klema, J., Svoboda, J., Tolar, J.: Using Bio-Pathways in Relational Learning. In Late Breaking Papers of The 18th International Conference on Inductive Logic Programming, pp. 50-56, 2008.
Smrz, P., Silhava, J., Klema, J., Zelezny, F.: Gene expression data mining guided by genomic background knowledge. In: SOFSEM 2008: Theory and Practice of Computer Science, Novy Smokovec, SK, pp. 101-111, 2008. (draft, pdf).
Karel, F., Klema, J.: Quantitative Association Rule Mining in Genomics. In Berendt, B., Svatek, V. Zelezny, F. (eds.): Proc. of The ECML/PKDD Workshop On Prior Conceptual Knowledge in Machine Learning and Data Mining. University of Warsaw, Poland, pp. 53-64, 2007. (pdf).
Mares J., Szakacsova M., Zelezny F., Klema J., Soukup V., Duskova J., Babjuk M.: Differences in Gene Expression between Transitional Cell Carcinoma of The Human Bladder with Short and Prolonged Recurrence-Free Period Using Oligonucleotide Micorarrays. Poster Abstract In European Journal of Human Genetics, 15:157, 2007.
Karel, F., Klema, J.: Adaptivity in e-learning. In Current Developments in Technology-Assisted Education. Badajoz: Formatex, pp. 260-264, 2006. (pdf).
Klema, J., Almonayyes, A.: Classification of Fanatic Texts Using Random Forests. In Current Research in Information Sciences and Technologies - Multidisciplinary approaches to global information systems. Badajoz: Open Institute of Knowledge, vol. II., pp. 28-32, 2006.
Soulet, A., Klema J. and Cremilleux, B.: Efficient Mining under Flexible Constraints through Several Datasets. In Proceedings of 5th International Workshop on Knowledge Discovery in Inductive Databases, Humbolt Universitat Berlin, Germany, pp. 131-142, 2006, (pdf).
Charnois, T., Durand, N., Klema, J.: Automated Information Extraction from Gene Summaries. Humbolt Universitat Berlin, Germany, pp. 4-15, 2006, (pdf).
Klema, J., Soulet, A., Cremilleux, B., Blachon, S., Gandrilon, O.: Mining Plausible Patterns from Genomic Data. In Proceedings of Nineteenth IEEE International Symposium on Computer-Based Medical Systems. Los Alamitos: IEEE Computer Society Press, pp. 183-188, 2006.
Klema, J., Holas, T., Karel, F., Zelezny, F.: Mining the Strongest Patterns In Medical Sequential Data. In The 3rd European Medical and Biological Engineering Conference EMBEC05. Praha: Spolecnost biomedicinskeho inzenyrstvi a lekarske informatiky CLS JEP, vol. 11, 2005. (pdf).
Karel, F., Klema, J.: Dolovani ordinalnich asociacnich pravidel. In Czech. In Znalosti 2005. Ostrava: VSB-TUO, vol. 1, pp. 226-233, 2005. (pdf).
Klema, J., Almonayyes, A.: Categorizing Fanatic Documents Using Random Forest Classifier. In Workshop of Int. Conference on Computational Intelligence and Security (CIS'05). Xi'an, China, 2005. (draft, pdf).
Novakova, L., Klema, J., Stepankova, O.: Ziskavani znalosti z longitudinalnich studii. In Czech. In Telemedicina Brno 2005 [CD-ROM]. Brno: SYMMA agentura, 2005.
Kubalik, J., Klema, J., Kulich, M.: Application of Soft Computing Techniques to Rescue Operation Planning. In Artificial Intelligence and Soft Computing - ICAISC 2004. Berlin: Springer, vol. 1, pp. 897-902, 2004. (Springerlink).
Klema, J., Flek, O., Kout, J., Novakova, L.: Intelligent Diagnosis and Learning in Centrifugal Pumps. In Emerging Solutions for Future Manufacturing Systems. New York: Springer, pp. 513-522, 2004. (draft, pdf).
Kulich, M., Faigl, J., Klema, J., Kubalik, J.: Rescue Operation Planning by Soft Computing Techniques. In IEEE 4th International Conference on Intelligent Systems Design and Application. Piscataway: IEEE, vol. I,II, pp. 103-108, 2004.
Klema, J., Novakova, L., Karel, F., Stepankova, O.: Trend Analysis in Stulong Data. In Proceedings of the Discovery Challenge 2004, ECML/PKDD workshop - A Collaborative Effort in Knowledge Discovery from Databases. Prague: University of Economics, pp. 56-67, 2004. (pdf).
Novakova, L., Klema, J., Stepankova, O.: Anachronistic attributes and data mining. In MIPRO 2004 - Computers in Education. Chorvatsko: Mipro HU, pp. 153-156, 2004.
Klema, J., Kout, J., Vejmelka, M.: Predictive System for Multivariate Time Series. In Cybernetics and Systems 2004. Vienna: Austrian Society for Cybernetics Studies, vol. 1,2, pp. 723-728, 2004. (pdf).
Novakova, L., Klema, J., Stepankova, O.: Anachronicke atributy a dobyvani znalosti. In Czech. In Znalosti 2004. Ostrava: VSB-TUO, pp. 202-209, 2004. (pdf).
Kout, J., Klema, J.: Predikcni system pro distribucni spolecnosti. In Czech. In Riadenie v energetike `04. Bratislava: Slovenska technicka univerzita, pp. 228, 2004.
Novakova, L., Klema, J., Jakob, M., Rawles, S., Stepankova, O.: Trend Analysis and Risk Identification. In: Workshop Proceedings ECML/PKDD 2003. Cavtat, Croatia, 2003, (pdf).
Klema, J., Stepankova, O., Novakova, L.: Predictive Medical Data Mining: Case Study. In: Intelligent and Adaptive Systems in Medicine. Praha : CVUT FEL Praha, 2003, pp. 48-60. (pdf).
Stepankova, O., Klema, J., Lauryn, S., Miksovsky, P. and Novakova, L.: Data Mining for Resource Allocation: A Case Study. In proceedings of the 5th IEEE/IFIP International Conference on Information Technology for BALANCED AUTOMATION SYSTEMS In Manufacturing and Services (BASYS 2002), Cancun, Mexico, Kluwer Academic Publishers, pp.477-484, 2002. (draft, pdf).
Stepankova, O., Klema, J., Miksovsky, P.: Collaborative Data Mining and Data Exchange: A Case Study. In: Workshop Proceedings ECML/PKDD 2002. Helsinki: Helsinki University of Technology, 2002, vol. 1, p. 135-140.
Klema, J., Kubalik, J., Palous, J.: Optimized Model Tuning in Medical Systems. In: Proceedings: Computer-Based Medical Systems. New York : IEEE Computer Society Press, 2002, vol. 1, p. 59-64.
Klema, J.: Machine Learning in Diagnostics and Time Series Prediction. In: Intelligent Methods for Quality Improvement in Industrial Practice. Prague : CTU FEE, Department of Cybernetics, The Gerstner Laboratory, 2002, vol. 1, p. 85-92. (pdf).
Stepankova, O., Lauryn, S., Aubrecht, P., Klema, J., Miksovsky, P., Novakova, L., Palous, J.: Data Mining and Resource Allocation: A Case Study. In: Intelligent Methods for Quality Improvement in Industrial Practice. Prague : CTU FEE, Department of Cybernetics, The Gerstner Laboratory, 2002, vol. 1, p. 94-105. (pdf).
Klema, J., Palous, J.: iBARET - Instance-Based Reasoning Tool. In: Final Programme&Proceedings. Aachen : Verlag Mainz, 2001, vol. 1, p. 55-57. (online).
Sprogar, M., Kokol, P., Zorman, M., Podgorelec, V., Lhotska, L., Klema, J.: Notes on Medical Decision Model Creation. In: Medical Data Analysis. Heidelberg : Springer, 2001, vol. 1, p. 270-275.
Sprogar, M., Kokol, P., Zorman, M., Podgorelec, V., Lhotska, L., Klema, J.: Second Opinion Decision Trees. In: Adaptive Systems and Hybrid Computational Intelligence in Medicine. Aegean : University of the Aegean, 2001, vol. 1, p. 69-74.
Klema, J., Palous, J.: iBARET - Instance-Based Reasoning Tool. In Christophe Giraud-Carrier, Nada Lavrac, Steve Moyle, and Branko Kavsek, editors, ECML/PKDD'01 workshop on Integrating Aspects of Data Mining, Decision Support and Meta-Learning: Internal SolEuNet Session, pages 1-13. ECML/PKDD'01 workshop notes, September 2001.
Klema, J., Palous, J.: Pripadove rozhodovani a usuzovani. In Proceedings of Znalosti 2001, editors Jan Rauch a Olga Stepankova, poster, p. 231-238. (pdf).
Klema, J., Lhotska, L., Stepankova, O., Palous, J.: Instance-Based Modelling in Medical Systems. In: Cybernetics and Systems 2000. Vol. 2. Vienna: Austrian Society for Cybernetics Studies. 2000. pp. 365-370. (pdf).
Kout, J., Klema, J., Stepankova, O.: Fault Diagnostics of Intelligent Pump. In: Cybernetics and Systems 2000. Vol. 2. Vienna: Austrian Society for Cybernetics Studies. 2000. pp. 775-780. (pdf).
Klema, J., Kout, J.: Prediction of Gas Consumption. In: Systems Integration '99. Prague : Prague University of Economy, 1999, pp. 119-128. (pdf).
Klema, J., Kout, J., Marik, V., Stepankova, O.: Gas Take-off Analysis. In: Nostradamus Prediction Workshop. Brno : Technical University, 1998, pp. 7-18.
Lhotska, L., Klema, J., Stepankova, O.: Problems of Learning in Multi-Agent Systems. In: Intelligent Systems for Manufacturing: Multi-Agent Systems and Virtual Organizations. Norwell, Massachusetts : Kluwer Academic Publishers, 1998, p. 615-624. (draft, pdf).
Klema, J.: Use of Machine Learning Algorithms in Distributed Environment Discim. In: Artificial Intelligence Techniques 96. Brno: Technical University, 1996, p. 153-154.
Klema, J., Lhotska, L.: Machine Learning, Applications in Natural Language Processing. In: Artificial Intelligence Techniques. Brno : Technical University, 1995, p. 275-288.
Klema, J.: Machine Learning, Applications in Modelling of Dynamic Systems. In: Artificial Intelligence Techniques. Brno : Technical University, 1995, poster, p. 330.
Theses:
Klema, J.: Learning from Heterogeneous Genomic Data. Habilitation thesis, Czech Technical University, Faculty of Electrical Engineering, Department of Computer Science, 2013, (summary), (pdf).
Klema, J.: Prototype Applications of Instance-Based Reasoning. PhD. thesis, Czech Technical University, Faculty of Electrical Engineering, Department of Cybernetics, 2002, (abstract, pdf).
Klema, J.: Strojove uceni jako diagnosticky nastroj (Machine Learning as A Diagnostic Tool). In Czech, master thesis, Czech Technical University, Faculty of Electrical Engineering, Department of Computer Science, 1994.
Talks:
Klema, J.: Big data analytics: what the clinician needs to know. Seminar of the Clinic of Nephrology, Institute of Clinical and Experimental Medicine, Prague, 23.3.2022.
Klema, J.: Learning from large, complex and structured omics data. 2nd Workshop on Biomedical Information Management: Data-Driven Innovations, Hamburg University, Germany, invited talk, 30.8.2018.
Klema, J.: Klasifikace genomickych dat s bohatou apriorni znalosti. Seminar strojoveho uceni a modelovani, MFF UK, 10.10.2013.
Klema, J.: Aplikace strojoveho uceni v bioinformatice. Konference Informacni technologie -- aplikace a teorie (ITAT 2012), vyzvana prednaska, 17.9.2012. (pdf).
Zelezny, F., Klema, J.: Pokrocile metody analyzy dat genove exprese a nastroj XGENE.ORG. Oddeleni molekularni genetiky, Ustav hematologie a krevni transfuze, Praha, 15.09.2009.
Klema, J.: Proc vetsina publikovanych vedeckych tvrzeni neplati? Seminare skupin IDA a ATG, CVUT FEL Katedra kybernetiky, 11.06.2009 a 17.06.2009.
Klema, J.: Mining Patterns in Medical Sequential Data. Groupe de Recherche en Informatique, Image, Automatique et Instrumentation (GREYC), Caen University, France, 11.10.2005.
Enevoldsen, L., Kout, J., Klema, J.: Cooporation between Industry and Universities: Examples and Experience. CVUT FEL Katedra kybernetiky. 11.02.2002.
Klema, J.: Instance-Based Reasoning for Mortality Prediction. Portland, Oregon, USA, Health Data Research, Inc. 16.06.2000.
Kout, J., Klema, J.: Intelligent Pump Diagnostics and Control. Bjerringbro, Grundfos A/S. 16.05.2000.
Klema, J., Miksovsky, P.: Predikce odberu plynu a vody. Seminar Dobyvani znalosti z databazi. Laborator inteligentnich systemu FIS VSE Praha a GL FEL CVUT, Praha, 30.11.2000.
Klema, J., Stepankova, O., Palous, J., Vejmelka, M.: Vyuziti strojoveho uceni pro predikci mortality nad Sloucenym registrem srdecnich operaci strediska MEDICON. Seminar Simulace a modelovani jako prostredky podpory rozhodovacich procesu v lekarstvi. Praha, 30.10.2000.
Klema, J., Palous, J.: Modelovani v systemech pripadoveho usuzovani (pro lekarske aplikace). CVUT FEL Katedra kybernetiky. 10.04.2000.
Klema, J.: Case-Based Reasoning in Health Data Analysis. Portland, Oregon, USA: Health Data Research, Inc. 11.06.1999.
Klema, J.: Chybova diagnostika pomoci metod strojoveho uceni. Pripadova studie:chybova diagnostika cerpadla. Praha : CVUT FEL Katedra ridici techniky. 15.04.1998.
Klema, J., Kout, J.: Predikce spotreby plynu. CVUT FEL Katedra ridici techniky. 11.11.1998.
Klema, J., Kubalik, J., Lauryn, S.: Intelligent Pump Diagnostics Using Genetic Algorithms, Decision Trees and Neural Networks. Department of Electrical Engineering, University of Surrey, Guildford, UK. 20.03.1997.
Klema, J., Kout, J., Lauryn, S.: AI Methods for Intelligent Pump Diagnostics. CVUT FEL Katedra ridici techniky. 12.02.1997.
Czech journals:
Libalova, H., Uhlirova, K., Klema, J., Machala, M., Sram, R., Topinka, J.: Globalni zmeny genove exprese v lidskych embryonalnich plicnich fibroblastech indukovane organickymi extrakty prachovych castic z ovzdusi. In Czech. Ochrana ovzdusi, no. 5-6/2011, pp. 48-55, 2011.
Klema, J., Holas, T., Zelezny, F., Karel, F.: Dolovani silnych vzoru z lekarskych sekvencnich dat. In Czech. Lekar a technika, 38:4, Ceska lekarska spolecnost J. E. Purkyne, pp.87-94, 2008. (pdf).
Kout, J., Hejny, T., Klema, J.: Inteligentni rozhodovani a rizeni v distribucnich sitich. In Czech. Automa, no. 11, pp. 6-9, 2004. (pdf).
Hyankova-Svobodova, J., Klema, J., Hackajlo, D.: Dvoulete sledovani pacientu po kardiochirurgickych vykonech. In Czech. Kardiologicka revue [online], no. 5/1, pp. 23-27, 2004. (online).
Klema, J.: Vyuziti strojoveho uceni pro predikci mortality. In Czech. Lekar a technika, no.5, Ceska lekarska spolecnost J. E. Purkyne, pp.126-130, 2001. (pdf).
Research reports:
Vitovec, P., Klema, J.: Sequential Patterns for Extracting Protein-Protein Interactions From Biomedical Texts. [Research Report]. Praha : CVUT FEL, Katedra kybernetiky - Gerstnerova laborator, 2011. GL 226/11. 21 p. (pdf).
Holec, M., Zelezny, F., Klema, J., Tolar, J.: Towards Set Level Predictive Classification of Gene Expression Data. [Research Report]. Praha : CVUT FEL, Katedra kybernetiky - Gerstnerova laborator, 2011. GL 212/10. 15 p.
Kout, J., Klema, J., Marik, V.: Intelligent Pump Diagnostics and Control - Project Summary. [Research Report]. Praha : CVUT FEL, Katedra kybernetiky - Gerstnerova laborator, 2001. GL 145/01. 11 p.
Klema, J., Palous, J.: Sharing Models in Instance-Based Reasoning. [Research Report]. Praha : CVUT FEL, Katedra kybernetiky - Gerstnerova laborator, 2001. GL 135/01. 12 p.
Palous, J., Klema, J.: iBARET - Instance-Based Reasoning Tool. Technical Report of The Gerstner Lab CTU Prague & FAW Linz - Hagenberg - Praha - Wien, GL 113/00, 2000.
Klema, J., Stepankova, O., Vejmelka, M.: PreDO: Data Generator of Precisely Defined Objects for Machine Learning. [Research Report]. Praha : CVUT FEL, Katedra kybernetiky - Gerstnerova laborator, 1999. GL 88/99. 19 p.
Klema, J., Kout, J.: Predikce spotreby plynu. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1998. GLC 19/98. 8 s.
Klema, J., Kout, J., Stepankova, O., Flek, O., Unsworth, P., Vetcha, S.: Fault Diagnostics of Intelligent Pump. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1998. Gl 73/98. 19 p.
Hetmerova, A., Klema, J., Stepankova, O.: A Toolbox for Generation of Decision Trees from Data. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1997. GL 49/97. 17 p.
Klema, J., Miksovsky, P., Stepankova, O.: Predictive Model of Heart Operation Result-Built on Merged National Registry on Cardiovascular Interventions of MEDICON Center. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1998. GL 72/98. 11 p.
Klema, J., Kout, J., Stepankova, O.: Intelligent Pump Diagnostics by Means of Attribute Space Transformation. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1997. GL 39/97. 9 p.
Klema, J., Kout, J., Stepankova, O., Marik, V.: Gas Take-off Analysis. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1997. GL 42/97. 12 p.
Kout, J., Klema, J., Lauryn, S., Stepankova, O., Marik, V.: AI Methods for Intelligent Pump Diagnostics II. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1997. GL 27/97. 22 p.
Klema, J., Kout, J., Lauryn, S., Vetcha, S. B., Stepankova, O., Marik, V.: AI Methods for Intelligent Pump Diagnostics. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1996. 31 p.
Klema, J.: Use of Machine Learning Algorithms in Distributed Environment. [Research Report]. Praha : CVUT FEL, Katedra ridici techniky - Gerstnerova laborator, 1996. GL - 3/96. 26 p.
Klema, J.: Priklady pouziti metody PC-GUHA. [Research Report]. Praha : CVUT FEL, 1995. K335-1995-94. 21 s.
The last change: