We have collaborated on the following publications

2021

56.

Maronek, M; Gromova, B; Liptak, R; Konecna, B; Pastorek, M; Cechova, B; Harsanyova, M; Budis, J; Smolak, D; Radvanszky, J; Szemes, T; Harsanyiova, J; Trancikova, A Kralova; Gardlik, R

Extracellular DNA Correlates with Intestinal Inflammation in Chemically Induced Colitis in Mice Journal Article

In: Cells, 10 (1), 2021, ISSN: 20734409.

Abstract | Links | BibTeX | Tags: Body fluids, Cell-free nucleic acids

55.

Pös, O; Radvanszky, J; Styk, J; Pös, Z; Buglyó, G; Kajsik, M; Budis, J; Nagy, B; Szemes, T

Copy number variation: Methods and clinical applications Journal Article

In: Applied Sciences (Switzerland), 11 (2), pp. 1-16, 2021, ISSN: 20763417.

Abstract | Links | BibTeX | Tags: Copy number variation, Review, Variant interpretation

54.

Misova, I; Pitelova, A; Budis, J; Gazdarica, J; Sedlackova, T; Jordakova, A; Benko, Z; Smondrkova, M; Mayerova, N; Pichlerova, K; Strieskova, L; Prevorovsky, M; Gregan, J; Cipak, L; Szemes, T; Polakova, S B

Repression of a large number of genes requires interplay between homologous recombination and HIRA Journal Article

In: Nucleic Acids Research, 49 (4), pp. 1914-1934, 2021, ISSN: 03051048.

Abstract | Links | BibTeX | Tags: Epigenetics, Transcriptomics

53.

Ženišová, K; Cabicarová, T; Sidari, R; Kolek, E; Pangallo, D; Szemes, T; Kuchta, T

Effects of co-fermentation with lachancea thermotolerans or metschnikowia pulcherrima on concentration of aroma compounds in pinot blanc wine Journal Article

In: Journal of Food and Nutrition Research, 60 (1), pp. 87-91, 2021, ISSN: 13368672.

Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Fungi

52.

Poláková, S Bágeľová; Lichtner, Ž; Szemes, T; Smolejová, M; Sulo, P

Mitochondrial DNA duplication, recombination, and introgression during interspecific hybridization Journal Article

In: Scientific Reports, 11 (1), 2021, ISSN: 20452322.

Abstract | Links | BibTeX | Tags: Fungi, Mitochondria

51.

Kucharík, M; Budiš, J; Hýblová, M; Minárik, G; Szemes, T

Copy number variant detection with low-coverage whole-genome sequencing represents a viable alternative to the conventional array-cgh Journal Article

In: Diagnostics, 11 (4), 2021, ISSN: 20754418.

Abstract | Links | BibTeX | Tags: Cell-free nucleic acids, Computational method, Copy number variation, Liquid biopsy, Non-invasive prenatal testing

50.

Pecimonova, M; Radvanszky, J; Smolak, D; Budis, J; Lichvar, M; Kristinova, D; Rozova, I; Turna, J; Szemes, T

Admixed phenotype of NEDD4L associated periventricular nodular heterotopia: A case report Journal Article

In: Medicine, 100 (22), pp. e26136, 2021, ISSN: 15365964.

Abstract | Links | BibTeX | Tags: Case study, Genetic testing, Single nucleotide variants, Variant interpretation

49.

Radvanszky, J; Hyblova, M; Radvanska, E; Spalek, P; Valachova, A; Magyarova, G; Bognar, C; Polak, E; Szemes, T; Kadasi, L

Characterisation of non-pathogenic premutation-range myotonic dystrophy type 2 alleles Journal Article

In: Journal of Clinical Medicine, 10 (17), 2021, ISSN: 20770383.

Abstract | Links | BibTeX | Tags: Non-invasive prenatal testing, Oncology, Single nucleotide variants

48.

Forgacova, N; Gazdarica, J; Budis, J; Radvanszky, J; Szemes, T

Repurposing non‑invasive prenatal testing data: Population study of single nucleotide variants associated with Colorectal Cancer and Lynch Syndrome Journal Article

In: Oncology Letters, 22 (5), 2021, ISSN: 17921074.

Abstract | Links | BibTeX | Tags: Non-invasive prenatal testing, Oncology, Population study

47.

Hekel, R.; Budis, J.; Kucharik, M.; Radvanszky, J.; Pös, Z.; Szemes, T.

Privacy-preserving storage of sequenced genomic data Journal Article

In: BMC Genomics, 22 (1), 2021, ISSN: 14712164.

Abstract | Links | BibTeX | Tags:

46.

Brejová, B.; Hodorová, V.; Boršová, K.; Čabanová, V.; Szemes, T.; Mišík, M.; Klempa, B.; Nosek, J.; Vinař, T.

Sequencing SARS-CoV-2 in Slovakia: An unofficial genomic surveillance report Conference

2962 , CEUR-WS, 2021, ISSN: 16130073.

Abstract | Links | BibTeX | Tags: Sars-cov-2

45.

Goga, A.; Böhmer, M.; Hekel, R.; Krampl, W.; Brejová, B.; Vinař, T.; Budiš, J.; Szemes, T.

SnakeLines workflow for SARS-CoV-2 variant detection from next-generation sequencing reads Conference

2962 , CEUR-WS, 2021, ISSN: 16130073.

Abstract | Links | BibTeX | Tags: Sars-cov-2, Variant calling

44.

Forgacova, N.; Gazdarica, J.; Budis, J.; Sekelska, M.; Szemes, T.

Identification and analyses of variants associated with COVID-19 from non-invasive prenatal testing in Slovak population Conference

2962 , CEUR-WS, 2021, ISSN: 16130073.

Abstract | Links | BibTeX | Tags: Non-invasive prenatal testing, Population study, Sars-cov-2, Variant calling

2020

43.

Böhmer, M; Ozdín, D; Račko, M; Lichvár, M; Budiš, J; Szemes, T

Identification of bacterial and fungal communities in the roots of orchids and surrounding soil in heavy metal contaminated area of mining heaps Journal Article

In: Applied Sciences (Switzerland), 10 (20), pp. 1-18, 2020, ISSN: 20763417.

Abstract | Links | BibTeX | Tags: Bacteria, Environmental microbiome, Metagenomics, Plants

42.

Böhmer, M; Smoľak, D; Ženišová, K; Čaplová, Z; Pangallo, D; Puškárová, A; Bučková, M; Cabicarová, T; Budiš, J; Šoltýs, K; Rusňáková, D; Kuchta, T; Szemes, T

Comparison of microbial diversity during two different wine fermentation processes Journal Article

In: FEMS microbiology letters, 367 (18), 2020, ISSN: 15746968.

Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Fungi, Metagenomics, Plants

41.

Hyblova, M; Harsanyova, M; Nikulenkov-Grochova, D; Kadlecova, J; Kucharik, M; Budis, J; Minarik, G

Validation of copy number variants detection from pregnant plasma using low-pass whole-genome sequencing in noninvasive prenatal testing-like settings Journal Article

In: Diagnostics, 10 (8), 2020, ISSN: 20754418.

Abstract | Links | BibTeX | Tags: Copy number variation, Fetal fraction, Non-invasive prenatal testing, Validation

40.

Kucharik, M; Gnip, A; Hyblova, M; Budis, J; Strieskova, L; Harsanyova, M; Pös, O; Kubiritova, Z; Radvanszky, J; Minarik, G; Szemes, T

Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions Journal Article

In: PLoS ONE, 15 (8 August), 2020, ISSN: 19326203.

Abstract | Links | BibTeX | Tags: Copy number variation, Fetal fraction, Non-invasive prenatal testing, Validation

39.

Šubr, Z; Predajňa, L; Šoltys, K; Bokor, B; Budiš, J; Glasa, M

Comparative transcriptome analysis of two cucumber cultivars with different sensitivity to cucumber mosaic virus infection Journal Article

In: Pathogens, 9 (2), 2020, ISSN: 20760817.

Abstract | Links | BibTeX | Tags: Plants, Transcriptomics, Viruses

38.

Bielik, V; Hric, I; BaláŽ, V; Penesová, A; Vávrová, S; Grones, J; Bokor, B; Budiš, J; Bohmer, M; Minárik, G; Augustovičová, D; Šoltys, K

Gut microbiota diversity in lean athletes is associated with positive energy balance Journal Article

In: Annals of Nutrition and Metabolism, 2020, ISSN: 02506807.

Abstract | Links | BibTeX | Tags: Bacteria, Gut microbiome, Metagenomics

37.

Kiani, A K; Paolacci, S; Scanzano, P; Michelini, S; Capodicasa, N; DÁgruma, L; Notarangelo, A; Tonini, G; Piccinelli, D; Farshid, K R; Petralia, P; Fulcheri, E; Buffelli, F; Chiurazzi, P; Terranova, C; Plotti, F; Angioli, R; Castori, M; Pös, O; Szemes, T; Bertelli, M

Prenatal genetic diagnosis: Fetal therapy as a possible solution to a positive test Journal Article

In: Acta bio-medica : Atenei Parmensis, 91 (13S), pp. e2020021, 2020, ISSN: 25316745.

Abstract | Links | BibTeX | Tags: Non-invasive prenatal testing, Prenatal diagnosis, Prenatal therapy, Review

36.

Pös, Z; Pös, O; Styk, J; Mocova, A; Strieskova, L; Budis, J; Kadasi, L; Radvanszky, J; Szemes, T

Technical and methodological aspects of cell‐free nucleic acids analyzes Journal Article

In: International Journal of Molecular Sciences, 21 (22), pp. 1-43, 2020, ISSN: 16616596.

Abstract | Links | BibTeX | Tags: Body fluids, Cell-free nucleic acids, Liquid biopsy, Non-invasive prenatal testing, Review

35.

Soltysova, A; Sedlackova, T; Dvorska, D; Jasek, K; Baradaran, P C; Kajabova, V H; Demkova, L; Buocikova, V; Kurucova, T; Lyskova, D; Furdova, A; Minarik, G; Babal, P; Dankova, Z; Smolkova, B

Monosomy 3 influences epithelial-mesenchymal transition gene expression in uveal melanoma patients; consequences for liquid biopsy Journal Article

In: International Journal of Molecular Sciences, 21 (24), pp. 1-24, 2020, ISSN: 16616596.

Abstract | Links | BibTeX | Tags: Aneuploidy, Body fluids, Circulating tumor cells, Liquid biopsy, Oncology

34.

Smolkova, B; Cierna, Z; Kalavska, K; Miklikova, S; Plava, J; Minarik, G; Sedlackova, T; Cholujova, D; Gronesova, P; Cihova, M; Majerova, K; Karaba, M; Benca, J; Pindak, D; Mardiak, J; Mego, M

Increased stromal infiltrating lymphocytes are associated with the risk of disease progression in mesenchymal circulating tumor cell-positive primary breast cancer patients Journal Article

In: International Journal of Molecular Sciences, 21 (24), pp. 1-16, 2020, ISSN: 16616596.

Abstract | Links | BibTeX | Tags: Body fluids, Circulating tumor cells, Liquid biopsy, Oncology

2019

33.

Sekelska, M; Izsakova, A; Kubosova, K; Tilandyova, P; Csekes, E; Kuchova, Z; Hyblova, M; Harsanyova, M; Kucharik, M; Budis, J; Szemes, T; Minarik, G

Result of prospective validation of the trisomy Test® for the detection of chromosomal trisomies Journal Article

In: Diagnostics, 9 (4), 2019, ISSN: 20754418.

Abstract | Links | BibTeX | Tags: Aneuploidy, Fetal fraction, Non-invasive prenatal testing, Validation

32.

Pös, O; Budis, J; Kubiritova, Z; Kucharik, M; Duris, F; Radvanszky, J; Szemes, T

Identification of structural variation from NGS-based non-invasive prenatal testing Journal Article

In: International Journal of Molecular Sciences, 20 (18), 2019, ISSN: 16616596.

Abstract | Links | BibTeX | Tags: Copy number variation, Non-invasive prenatal testing, Population study

31.

Pangallo, D; Kraková, L; Puškárová, A; Šoltys, K; Bučková, M; Koreňová, J; Budiš, J; Kuchta, T

Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation Journal Article

In: Food Microbiology, 82 , pp. 416-425, 2019, ISSN: 07400020.

Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Metagenomics, Transcriptomics

30.

Gazdarica, J; Hekel, R; Budis, J; Kucharik, M; Duris, F; Radvanszky, J; Turna, J; Szemes, T

Combination of fetal fraction estimators based on fragment lengths and fragment counts in non-invasive prenatal testing Journal Article

In: International Journal of Molecular Sciences, 20 (16), 2019, ISSN: 16616596.

Abstract | Links | BibTeX | Tags: Aneuploidy, Computational method, Fetal fraction, Non-invasive prenatal testing

29.

Planý, M; Czolderová, M; Kraková, L; Puškárová, A; Bučková, M; Šoltys, K; Budiš, J; Szemes, T; Mackulak, T; Wu, J -H; Pangallo, D

Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition Journal Article

In: Bioprocess and Biosystems Engineering, 42 (7), pp. 1151-1163, 2019, ISSN: 16157591.

Abstract | Links | BibTeX | Tags: Bacteria, Biogas production, Fungi, Metagenomics, Plants

28.

Gazdarica, J; Budis, J; Duris, F; Turna, J; Szemes, T

Adaptable model parameters in non-invasive prenatal testing lead to more stable predictions Journal Article

In: International Journal of Molecular Sciences, 20 (14), 2019, ISSN: 16616596.

Abstract | Links | BibTeX | Tags: Aneuploidy, Computational method, Non-invasive prenatal testing

27.

Strieskova, L; Gazdaricova, I; Kajsik, M; Soltys, K; Budis, J; Pos, O; Lickova, M; Klempa, B; Szemes, T

Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome Journal Article

In: Journal of Biotechnology, 299 , pp. 8-12, 2019, ISSN: 01681656.

Abstract | Links | BibTeX | Tags: Assembly, Mitochondria, Single nucleotide variants, Transcriptomics

26.

Budis, J; Gazdarica, J; Radvanszky, J; Harsanyova, M; Gazdaricova, I; Strieskova, L; Frno, R; Duris, F; Minarik, G; Sekelska, M; Nagy, B; Szemes, T

Non-invasive prenatal testing as a valuable source of population specific allelic frequencies Journal Article

In: Journal of Biotechnology, 299 , pp. 72-78, 2019, ISSN: 01681656.

Abstract | Links | BibTeX | Tags: Non-invasive prenatal testing, Population study, Single nucleotide variants, Variant calling

25.

Kubiritova, Z; Gyuraszova, M; Nagyova, E; Hyblova, M; Harsanyova, M; Budis, J; Hekel, R; Gazdarica, J; Duris, F; Kadasi, L; Szemes, T; Radvanszky, J

On the critical evaluation and confirmation of germline sequence variants identified using massively parallel sequencing Journal Article

In: Journal of Biotechnology, 298 , pp. 64-75, 2019, ISSN: 01681656.

Abstract | Links | BibTeX | Tags: Genetic testing, Single nucleotide variants, Validation, Variant calling

24.

Budiš, J; Kucharík, M; Duriš, F; Gazdarica, J; Zrubcová, M; Ficek, A; Szemes, T; Brejová, B; Radvanszky, J

Dante: Genotyping of known complex and expanded short tandem repeats Journal Article

In: Bioinformatics, 35 (8), pp. 1310-1317, 2019, ISSN: 13674803.

Abstract | Links | BibTeX | Tags: Computational method, Genetic testing, Short tandem repeats, Variant calling

23.

Sádecká, J; Čaplová, Z; Tomáška, M; Šoltys, K; Kopuncová, M; Budiš, J; Drončovský, M; Kolek, E I; Koreňová, J; Kuchta, T

Microorganisms and volatile aroma-active compounds in bryndza cheese produced and marketed in Slovakia Journal Article

In: Journal of Food and Nutrition Research, 58 (4), pp. 382-392, 2019, ISSN: 13368672.

Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Fungi, Metagenomics

22.

Tomáška, M; Čaplová, Z; Sádecká, J; Šoltys, K; Kopuncová, M; Budiš, J; Drončovský, M; Kolek, E; Koreňová, J; Kuchta, T

Microorganisms and volatile aroma-active compounds in “nite“and “vojky” cheeses Journal Article

In: Journal of Food and Nutrition Research, 58 (2), pp. 187-200, 2019, ISSN: 13368672.

Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Fungi, Metagenomics

21.

Budis, J; Gazdarica, J; Radvanszky, J; Szucs, G; Kucharik, M; Strieskova, L; Gazdaricova, I; Harsanyova, M; Duris, F; Minarik, G; Sekelska, M; Nagy, B; Turna, J; Szemes, T

Combining count- And length-based z-scores leads to improved predictions in non-invasive prenatal testing Journal Article

In: Bioinformatics, 35 (8), pp. 1284-1291, 2019, ISSN: 13674803.

Abstract | Links | BibTeX | Tags: Aneuploidy, Computational method, Fetal fraction, Non-invasive prenatal testing, Prenatal diagnosis

20.

Nagyova, E; Radvanszky, J; Hyblova, M; Simovicova, V; Goncalvesova, E; Asselbergs, F W; Kadasi, L; Szemes, T; Minarik, G

Targeted next-generation sequencing in Slovak cardiomyopathy patients Journal Article

In: Bratislava Medical Journal, 120 (1), pp. 46-51, 2019, ISSN: 00069248.

Abstract | Links | BibTeX | Tags: Genetic testing, Single nucleotide variants, Variant calling

2018

19.

Duris, F; Gazdarica, J; Gazdaricova, I; Strieskova, L; Budis, J; Turna, J; Szemes, T

Mean and variance of ratios of proportions from categories of a multinomial distribution Journal Article

In: Journal of Statistical Distributions and Applications, 5 (1), 2018, ISSN: 21955832.

Abstract | Links | BibTeX | Tags: Aneuploidy, Computational method, Non-invasive prenatal testing

18.

Kraková, L; Šoltys, K; Puškárová, A; Bučková, M; Jeszeová, L; Kucharík, M; Budiš, J; Orovčík, L; Szemes, T; Pangallo, D

The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment Journal Article

In: Environmental Microbiology, 20 (9), pp. 3294-3308, 2018, ISSN: 14622912.

Abstract | Links | BibTeX | Tags: Bacteria, Biodeterioration, Fungi, Metagenomics

17.

Soltys, K; Vavrova, S; Budis, J; Palkova, L; Minarik, G; Grones, J

Draft genome sequence of Escherichia coli KL53 Journal Article

In: Genome Announcements, 6 (13), 2018, ISSN: 21698287.

Abstract | Links | BibTeX | Tags: Assembly, Bacteria

2017

16.

Radvanszky, J; Hyblova, M; Durovcikova, D; Hikkelova, M; Fiedler, E; Kadasi, L; Turna, J; Minarik, G; Szemes, T

Complex phenotypes blur conventional borders between Say–Barber–Biesecker–Young–Simpson syndrome and genitopatellar syndrome Journal Article

In: Clinical Genetics, 91 (2), pp. 339-343, 2017, ISSN: 00099163.

Abstract | Links | BibTeX | Tags: Case study, Genetic testing, Single nucleotide variants, Variant calling

15.

Sulo, P; Szabóová, D; Bielik, P; Poláková, S; Soltys, K; Jatzová, K; Szemes, T

The evolutionary history of Saccharomyces species inferred fromcompleted mitochondrial genomes and revision in the 'yeast mitochondrial genetic code' Journal Article

In: DNA Research, 24 (6), pp. 571-583, 2017, ISSN: 13402838.

Abstract | Links | BibTeX | Tags: Assembly, Fungi, Mitochondria, Phylogeny

14.

Cierna, Z; Janega, P; Grochal, F; Ferianec, V; Braxatorisova, T; Strieskova, L; Malova, J; Jungova, P; Szemes, T

The first reported case of meckel-gruber syndrome associated with abnormal karyotype mosaic trisomy 17 Journal Article

In: Pediatric and Developmental Pathology, 20 (5), pp. 449-454, 2017, ISSN: 10935266.

Abstract | Links | BibTeX | Tags: Aneuploidy, Case study, Genetic testing

2016

13.

Kraková, L; Šoltys, K; Budiš, J; Grivalský, T; Ďuriš, F; Pangallo, D; Szemes, T

Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning Journal Article

In: Extremophiles, 20 (5), pp. 795-808, 2016, ISSN: 14310651.

Abstract | Links | BibTeX | Tags: Bacteria, Environmental microbiome, Metagenomics

2015

12.

Minarik, G; Repiska, G; Hyblova, M; Nagyova, E; Soltys, K; Budis, J; Duris, F; Sysak, R; Bujalkova, M G; Vlkova-Izrael, B; Biro, O; Nagy, B; Szemes, T

Utilization of benchtop next generation sequencing platforms ion torrent PGM and miseq in noninvasive prenatal testing for chromosome 21 trisomy and testing of impact of in silico and physical size selection on its analytical performance Journal Article

In: PLoS ONE, 10 (12), 2015, ISSN: 19326203.

Abstract | Links | BibTeX | Tags: Aneuploidy, Non-invasive prenatal testing, Size selection, Validation

11.

Repiská, G; Sedláčková, T; Szemes, T; Minárik, G

Effect of different DNA concentration methods on performance of non-invasive fetal y-chromosomal short tandem repeat profiling from maternal plasma Journal Article

In: Fetal Diagnosis and Therapy, 37 (1), pp. 58-64, 2015, ISSN: 10153837.

Abstract | Links | BibTeX | Tags: Fetal fraction, Non-invasive prenatal testing, Prenatal diagnosis, Short tandem repeats

10.

Radvánszky, J; Minárik, G; Szemeš, T; Konečný, M; Kádaši, L

Interpretation of clinical significance of sequence variants in molecular genetics [Interpretácia klinického významu sekvenčných variantov v molekulovej genetike] Journal Article

In: Lekarsky Obzor, 64 (11), pp. 418-427, 2015, ISSN: 04574214.

Abstract | Links | BibTeX | Tags: Genetic testing, Review, Single nucleotide variants, Variant interpretation

2014

9.

Sedlackova, T; Repiska, G; Minarik, G

Selection of an optimal method for co-isolation of circulating DNA and miRNA from the plasma of pregnant women Journal Article

In: Clinical Chemistry and Laboratory Medicine, 52 (11), pp. 1543-1548, 2014, ISSN: 14346621.

Abstract | Links | BibTeX | Tags: Cell-free nucleic acids, Liquid biopsy, Non-invasive prenatal testing

2013

8.

Repiská, G; Sedláčková, T; Szemes, T; Celec, P; Minárik, G

Selection of the optimal manual method of cell free fetal DNA isolation from maternal plasma Journal Article

In: Clinical Chemistry and Laboratory Medicine, 51 (6), pp. 1185-1189, 2013, ISSN: 14346621.

Abstract | Links | BibTeX | Tags: Liquid biopsy, Non-invasive prenatal testing, Validation

7.

Minárik, G; Plank, L; Lasabová, Z; Szemes, T; Burjanivová, T; Szépe, P; Buzalková, V; Porubský, D; Šufliarsky, J

Spectrum of mutations in gastrointestinal stromal tumor patients - a population-based study from Slovakia Journal Article

In: APMIS, 121 (6), pp. 539-548, 2013, ISSN: 09034641.

Abstract | Links | BibTeX | Tags: Oncology, Population study, Single nucleotide variants