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Hungarian Centre for Genomics and Bioinformatics

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The Genomics and Bioinformatics Core Facility is the first Hungarian core facility with special emphasis of providing services on both next generation sequencing (NGS) and bioinformatics.

Located in the Szentágothai Research Centre at the University of Pécs, it offers a broad range of NGS services, including Illumina sequencing (NextSeq, MiSeq, MiniSeq and iSeq), nanopore long-read sequencing (MinION), and full-service protocols for genome, transcriptome, epigenome and metagenome sequencing. The facility also offers advice on study design and provide bioinformatics and biostatistical data analysis services on NGS as well as other biomedical data.

Services

Library preparation and quality control

Tapestation 4200

The Genomics and Bioinformatics Facility offers a broad range of library preparation methods from DNA and RNA samples depending on the sequencing technology, sample source, and biological question of interest. At each step there is a careful quality check of each sequencing library prepared either by our facility staff members or the users. The major steps include:

  • Measurement of concentration (Fluorescence Qubit 4.0)
  • Measurement of size (Bioanalyzer 2100, TapeStation 4200)


Next generation sequencing

Sequencing is performed on Illumina (NextSeq 550, MiSeq, MiniSeq, iSeq) and Nanopore (MinION) sequencing instruments depending on the application and biological question. The available instruments cover short (Illumina technology) and long sequencing (Oxford Nanopore technology) as well as a broad range of output, from a few million to hundrends of millions reads.

NextSeq 550


Bioinformatics and data analyis

The facility provides bioinformatics services covering all the major steps of NGS data analysis, including data preprocessing (demultiplexing and transfer of unaligned BAM file), standard bioinformatic analysis (alignment and genome browser visualization of BAM file), downstream bioinformatic analysis (e.g. differential expression or genotype calling) as well as assistance with publication-related data sharing requirements (e.g. GEO submission).



Equipments

Covaris M220 Ultrasonicator

Covaris M220

M220 Focused-ultrasonicator is designed for Next Generation Sequencing applications requiring fragment sizes between 150bp and 5kb. Covaris AFA transmits acoustic energy at ultrasonic frequencies and very short wavelengths and is uniquely able to focus the energy into your sample. AFA controls the shearing forces that fragment nucleic acids to the selected size.



Illumina iSeq 100

The iSeq destkop sequencer utilizes Illumina’s one-channel sequencing by synthesis technology to give extraordinarily fast sequencing turnaround while maintaining high data quality. Even as the smallest Illumina sequencer to-date, it is still able to produce over 1.2 billion base pairs in as little as 9 hours for a 50-bp single-read run. The iSeq is a flexible system with a wide range of applications that is ideal small genome sequencing, targeted and amplicon sequencing, and viral and microbial sequencing.

iSeq


Illumina MiniSeq

MiniSeq

The MiniSeq System provides high-quality sequencing technology with the cost-effective desktop system. It enables small genome, amplicon, targeted enrichment, and RNA sequencing using low library volume. It is ideal for targeted research applications like cancer sequencing and gene expression profiling.



Illumina MiSeq

The MiSeq benchtop instrument utilizes a double-sided, single-lane flow cell and reagent cartridge supplied in kit form. It performs both single- and paired-end runs with adjustable read lengths from 1 x 36 base pairs to 2 x 300 base pairs. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing or target enrichment), metagenomics, and gene expression studies.

MiSeq


Illumina NextSeq 550 NGS

NextSeq 550

The NextSeq 550 System offers the right sequencer for various project sizes and sequencing throughputs, providing users with optimal operational efficiency. This fast, flexible, high-throughput benchtop sequencer enables transcriptome and targeted resequencing applications with the accuracy of Illumina sequencing technology. With the ability to switch between lower and higher run configurations based on a project’s needs, the NextSeq 550 is the ideal platform for small to medium sequencing projects that range in output requirements.



Illumina Novaseq 6000

NovaSeq 6000 Sequencing System is designed to do it all. The system allows to sequence up to 48 genomes in ~2 days for the most comprehensive coverage. The workflow could be scalable up and down effortlessly with the improved economics so it is cost effective even for the small project. The NovaSeq 6000 sequencer is ideal for transciptomic, metagenomic, targeted and whole genome sequencing.

 



Oxford Nanopore MinION sequencer

Nanopore MinIon

MinION is a portable, real-time device for DNA and RNA sequencing, putting you in control of your sequence data. Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the fragmentation, the need for PCR amplification or chemical labeling of the sample. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length.



TapeStation 4200 system

 

The Agilent 4200 TapeStation system is intended to separate nucleic acids by means of electrophoresis. This instrument is a complete solution for true end-to-end sample QC within any NGS workflow covering the full DNA and RNA sizing range. Depending on your application, the software automatically determines size, quantity, purity, RNA and DNA integrity.

 

Tapestation 4200


ABI Prism 310 Genetic Analyzer

The ABI PRISM® 310 sequencer is an automated single-capillary genetic analyzer designed for a wide range of sequencing and fragment analysis applications. Perform comparative sequencing, linkage analysis, STR analysis, SNP detection, discovery and validation, mutation detection, and many other applications. The sequencer detect five dyes simultaneously to increase throughput. The average test time for a sample is one and a half hours.



Applied Biosystems StepOnePlus™

The StepOnePlus™ Real-Time PCR System is a 96-well Real-Time PCR instrument perfect for both first-time and experienced users. The StepOnePlus™ Real-Time PCR System can be setup in a variety of configurations and comes ready to use, out of the box, with intuitive data analysis and instrument control software. Utilizing robust LED based 4-color optical recording, the StepOnePlus™ Real-Time PCR System is designed to deliver precise, quantitative Real-Time PCR results for a variety of genomic research applications. The StepOnePlus™ Real-Time PCR System has an innovative Applied Biosystems VeriFlex Block for convenient PCR optimization.

www.thermofisher.com/hu/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/step-one-real-time-pcr-systems.html#

 



Bio-Rad CFX96 Touch DeepWell Real Time PCR

Bio-Rad cfx96

CFX Real-Time PCR Detection Systems are powerful and flexible instruments, featuring 2–5 color multiplexing, advanced optical technology, and precise temperature control with thermal gradients. These systems deliver sensitive, reliable detection of both singleplex and multiplex real-time PCR reactions. Paired with CFX Maestro Analysis Software, CFX Instruments provide superior data collection, statistical analysis, and data visualization capabilities.



Hitachi CR22GIII centrifuga

With the high capacity floor standing Hitachi centrifuge, maximum 6 L (4x1500 ml) can be centrifuged. The centrifuge can be operated easily with the help of an LCD touchscreen, and all the important parameter can be controlled and followed during centrifugation. Maximum speed is 22.000 rpm.

http://www.ibiotech.cz/media/files/product_pdf/cn22n.pdf

 



nCounter SPRINT Profiler

The nCounter SPRINT Profiler employs a novel digital barcode technology that hybridizes to target molecules. Each unique digital barcode is then directly counted using a single molecule imaging technique to yield precise and sensitive quantification. Up to 800 targets can be measured simultaneously in a single sample, and up to 12 samples can be assayed in a single run.

https://www.nanostring.com/products/ncounter-systems-overview/ncounter-sprint-profiler

The following nCounter applications are supported on the SPRINT Profiler:

  • Gene expression (mRNA)
  • miRNA
  • DNA copy number variation (CNV)
  • lncRNA
  • DNA enriched by chromatin-immunoprecipitation (ChIP-String)
  • Protein
  • Gene fusions


Useful Information

Usage policy and facility access

The Genomics and Bioinformatics facility offers access to its services to all Hungarian academic and industrial research groups. Free capacity is offered to other external users (academic and industry) of other countries. To estimate feasibility and allocable resources, we strongly recommend contacting our team when planning a sequencing experiment or bioinformatics data analysis task.

 

Acknowledging the facility

Continuation of funding for the Genomics and Bioinformatics facility by the University of Pécs as well as the Hungarian and European funding agencies depends on documented evidence of contribution to scientific output. We therefore require acknowledgement of use of the facility in published work. A simple statement is sufficient and can either be placed in the Materials and Methods section or at the end of your manuscript (acknowledgements) depending on the journal format, such as:

“Next generation sequencing and/or bioinformatics data analysis services were performed by the Genomics and Bioinformatics Core Faciity of the Szentágothai Research Centre at the University of Pécs.” Your publication will be also listed on our website.

Dr Attila Gyenesei
senior research fellow
gyenesei.attila@pte.hu
Dr. József Kun
research fellow
kun.jozsef@pte.hu
29021, 29202
Dr. Róbert Herczeg
research fellow
herczeg.robert@pte.hu
Péter Urbán
assistant research fellow
urban.peter@pte.hu
29291
Bence Gálik (ImPress MSCA PhD student at the Medical University of Bialystok)
PhD student
galik.bence@pte.hu
Witold Bauer
assistant research fellow
bauer.witold@pte.hu
Mónika Mátyás
project assistant
matyas.monika@pte.hu
29202
Réka Zsiborás
laboratory assistant
zsiboras.reka@pte.hu
29291
Adrienn Harangozó-Dimák
laboratory assistant
dimak.adrienn@pte.hu
29291
Fanni Géczi
laboratory assistant
geczi.fanni@pte.hu
29291

2023

2023

 

  • Charkiewicz, R.; Sulewska, A.; Charkiewicz, A.; Gyenesei, A.; Galik, B.; Ramlau, R.; Piwkowski, C.; Stec, R.; Biecek, P.; Karabowicz, P.; et al. miRNA-Seq Tissue Diagnostic Signature: A Novel Model for NSCLC Subtyping. Int. J. Mol. Sci. 2023, 24, 13318. https://doi.org/10.3390/ijms241713318

  • Zsolt Datki, Zsuzsanna Darula, Viktor Vedelek, Eva Hunyadi-Gulyas, Brian J. Dingmann, Balazs Vedelek, Janos Kalman, Peter Urban, Attila Gyenesei, Zita Galik-Olah, Bence Galik, Rita Sinka: Biofilm formation initiating rotifer-specific biopolymer and its predicted components, International Journal of Biological Macromolecules, Volume 253, Part 5, 2023,127157, ISSN 0141-8130, https://doi.org/10.1016/j.ijbiomac.2023.127157

  • Balikó A, Szakács Z, Kajtár B, Ritter Z, Gyenesei A, Farkas N, Kereskai L, Vályi-Nagy I, Alizadeh H and Pajor L (2023) Clinicopathological analysis of diffuse large B-cell lymphoma using molecular biomarkers: a retrospective analysis from 7 Hungarian centers. Front. Oncol., 2023 13:1224733. doi: 10.3389/fonc.2023.1224733

  • Margot Otto, József Geml, Ádám I. Hegyi, Júlia Hegyi-Kaló, József Kun, Attila Gyenesei, Kálmán Z. Váczy: Metatranscriptomic analyses of grapes reveal differences in expressed functional genes of filamentous and yeast fungi during noble rot and grey rot, Fungal Ecology, Volume 65,2023,101277,ISSN 1754-5048, https://doi.org/10.1016/j.funeco.2023.101277.

  • Champramary S, Indic B, Szűcs A, Tyagi C, Languar O, Hasan KMF, Szekeres A, Vágvölgyi C, Kredics L and Sipos G (2023) The mycoremediation potential of the armillarioids: a comparative genomics analysis. Front. Bioeng. Biotechnol. 11:1189640. doi: 10.3389/fbioe.2023.1189640

  • Sahu, N., Indic, B., Wong-Bajracharya, J. et al. Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria. Nat Microbiol 8, 1668–1681 (2023). https://doi.org/10.1038/s41564-023-01448-

  • Felső R, Lányi É, Erhardt É, Laufer Z, Kardos D, Herczeg R, Gyenesei A, Hollódy K, Molnár D. Total sleep deprivation decreases saliva ghrelin levels in adolescents. J Sleep Res. 2023 Apr;32(2):e13746. doi: 10.1111/jsr.13746. Epub 2022 Oct 11. PMID: 36217837

  • Denes V, Lukats A, Szarka G, Subicz R, Mester A, Kovacs-Valasek A, Geck P, Berta G, Herczeg R, Postyeni E, Gyenesei A, Gabriel R. Long-term Effects of the pituitary-adenylate cyclase-activating Polypeptide (PACAP38) in the Adult Mouse Retina: Microglial Activation and Induction of Neural Proliferation. Neurochem Res. 2023 Jul 19. doi: 10.1007/s11064-023-03989-7. Epub ahead of print. PMID: 37466802.

  • Pajor L.,Kun J.,Herczeg R.,Gálik B., Ritter Zs.,Baliko A.,Hegedűs G.,Barna T.,Czifra J.,Pálvölgyi A.,Östör G.,Babarczi E.,Ligeti E.,Kránitz N.,Bali O.,Bodor A.,Tiszlavicz L.,Pajor G.,Kajtár B,Kereskai L.,Tornóczki T.,Alizadeh H.,Gyenesei A,Vályi-Nagy I.: A diffúz nagy B-sejtes limfóma fenotipikus, citogenetikai és expressziós profil heterogenitása – Magyarországi multicentrikus tanulmány. Hematológia–Transzfuziológia, 55 (2022) 4, 154–163, https://doi.org/10.1556/2068.2023.00157
  • Horváth, M.; Kovács, T.; Kun, J.; Gyenesei, A.; Damjanova, I.; Tigyi, Z.; Schneider, G. Virulence Characteristics and Molecular Typing of Carbapenem-Resistant ST15 Klebsiella pneumoniae Clinical Isolates, Possessing the K24 Capsular Type. Antibiotics 2023, 12, 479. https://doi.org/10.3390/antibiotics12030479.
  • Apjok, G., Számel, M., Christodoulou, C. et al. Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains. Nat Microbiol (2023). https://doi.org/10.1038/s41564-023-01320-2 

  • Friston, Dominic Anthony; Cuddihy, Joshua; Souza Luiz, Jessica; Truong, An Hoai; Ho, Laptin; Basra, Meirvaan; Santha, Peter; Oszlacs, Orsolya; de Sousa Valente, Joao; Marczylo, Time; Junttila, Sini; Laycock, Helen; Collins, Declan; Vizcaychipi, Marcela; Gyenesei, Attila; Takats, Zoltan; Jancso, Gabor; Want, Elizabeth; Nagy, Istvan: Elevated 18:0 lysophosphatidylcholine contributes to the development of pain in tissue injury. PAIN 164(2):p e103-e115, February 2023. | DOI: 10.1097/j.pain.0000000000002709

2022

2022

  • Neparáczki E, Kis L, Maróti Z, Kovács B, Varga GIB, Makoldi M, Horolma P, Éva Teiszler, Tihanyi B, Nagy PL, Maár K, Gyenesei A, Schütz O, Dudás E, Török T, Pascuttini-Juraga V, Peharda I, Vizi LT, Horváth-Lugossy G, Kásler M.: The genetic legacy of the Hunyadi descendants . Heliyon. 2022 Nov 17;8(11):e11731. doi: 10.1016/j.heliyon.2022.e11731 

  • Felső R., Lányi,E., Erhardt,E., Laufer,Z., Kardos, D., Herczeg, R., Gyenesei, A., Hollódy, K., & Molnár,D. (2022). Total sleep deprivation decreases saliva ghrelinlevels in adolescents.Journal of Sleep Research, e13746. https://doi.org/10.1111/jsr.137468of8 

  • Kiss F, Kormos V, Szőke É, Kecskés A, Tóth N, Steib A, Szállási Á, Scheich B, Gaszner B, Kun J, Fülöp G, Pohóczky K, Helyes Z. Functional Transient Receptor Potential Ankyrin 1 and Vanilloid 1 Ion Channels Are Overexpressed in Human Oral Squamous Cell Carcinoma. Int J Mol Sci. 2022 Feb 8;23(3):1921. doi: 10.3390/ijms23031921. PMID: 35163843; PMCID: PMC8836603.

  • Datki Z, Balazs E, Galik B, Sinka R, Zeitler L, Bozso Z, Kalman J, Hortobagyi T, Galik-Olah Z. The interacting rotifer-biopolymers are anti- and disaggregating agents for human-type beta-amyloid in vitro. Int J Biol Macromol. 2022 Mar 15;201:262-269. doi: 10.1016/j.ijbiomac.2021.12.184. Epub 2022 Jan 7. PMID: 34999044.

  • Datki Z, Sinka R, Galik B, Galik-Olah Z. Particle-dependent reproduction and exogenic biopolymer secretion of protozoa co-cultured rotifers. Int J Biol Macromol. 2022 Jun 30;211:669-677. doi: 10.1016/j.ijbiomac.2022.05.020. Epub 2022 May 16. PMID: 35588974.

  • Hamar Á, Filipánits K, Váradi A, Váradi-Rácz R, Gellén HO, Futács K, Urbán P, Kovacs GL, Gombos K. Diagnostic accuracy of SARS-CoV-2 Panbio™ rapid antigen diagnostic tests in a 4,440-case clinical follow-up. Front Med (Lausanne). 2022 Aug 2;9:908127. doi: 10.3389/fmed.2022.908127. PMID: 35983094; PMCID: PMC9380887.

  • Kurucz K, Zeghbib S, Arnoldi D, Marini G, Manica M, Michelutti A, Montarsi F, Deblauwe I, Van Bortel W, Smitz N, Pfitzner WP, Czajka C, Jöst A, Kalan K, Šušnjar J, Ivović V, Kuczmog A, Lanszki Z, Tóth GE, Somogyi BA, Herczeg R, Urbán P, Bueno-Marí R, Soltész Z, Kemenesi G. Aedes koreicus, a vector on the rise: Pan-European genetic patterns, mitochondrial and draft genome sequencing. PLoS One. 2022 Aug 1;17(8):e0269880. doi: 10.1371/journal.pone.0269880. PMID: 35913994; PMCID: PMC9342712.

  • Aczél T, Benczik B, Ágg B, Körtési T, Urbán P, Bauer W, Gyenesei A, Tuka B, Tajti J, Ferdinandy P, Vécsei L, Bölcskei K, Kun J, Helyes Z. Disease- and headache-specific microRNA signatures and their predicted mRNA targets in peripheral blood mononuclear cells in migraineurs: role of inflammatory signalling and oxidative stress. J Headache Pain. 2022 Sep 2;23(1):113. doi: 10.1186/s10194-022-01478-w. PMID: 36050647; PMCID: PMC9438144.

  • Boros Á, Albert M, Urbán P, Herczeg R, Gáspár G, Balázs B, Cságola A, Pankovics P, Gyenesei A, Reuter G. Unusual "Asian-origin" 2c to 2b point mutant canine parvovirus (Parvoviridae) and canine astrovirus (Astroviridae) co-infection detected in vaccinated dogs with an outbreak of severe haemorrhagic gastroenteritis with high mortality rate in Hungary. Vet Res Commun. 2022 Sep 21:1–7. doi: 10.1007/s11259-022-09997-2. Epub ahead of print. PMID: 36129562; PMCID: PMC9490711.

  • Jia X, Bene J, Balázs N, Szabó K, Berta G, Herczeg R, Gyenesei A, Balogh P. Age-Associated B Cell Features of the Murine High-Grade B Cell Lymphoma Bc.DLFL1 and Its Extranodal Expansion in Abdominal Adipose Tissues. J Immunol. 2022 Jun 15;208(12):2866-2876. doi: 10.4049/jimmunol.2100956. Epub 2022 Jun 3. PMID: 35867673.

  • Pohóczky K, Kun J, Szentes N, Aczél T, Urbán P, Gyenesei A, Bölcskei K, Szőke É, Sensi S, Dénes Á, Goebel A, Tékus V, Helyes Z. Discovery of novel targets in a complex regional pain syndrome mouse model by transcriptomics: TNF and JAK-STAT pathways. Pharmacol Res. 2022 Aug;182:106347. doi: 10.1016/j.phrs.2022.106347. Epub 2022 Jul 9. PMID: 35820612.

  • Majláth I, Éva C, Hamow KÁ, Kun J, Pál M, Rahman A, Palla B, Nagy Z, Gyenesei A, Szalai G, Janda T. Methylglyoxal induces stress signaling and promotes the germination of maize at low temperature. Physiol Plant. 2022 Jan;174(1):e13609. doi: 10.1111/ppl.13609. Epub 2021 Dec 15. PMID: 34851527.

  • Vokó Z, Kiss Z, Surján G, Surján O, Barcza Z, Pályi B, Formanek-Balku E, Molnár GA, Herczeg R, Gyenesei A, Miseta A, Kollár L, Wittmann I, Müller C, Kásler M. Nationwide effectiveness of five SARS-CoV-2 vaccines in Hungary-the HUN-VE study. Clin Microbiol Infect. 2022 Mar;28(3):398-404. doi: 10.1016/j.cmi.2021.11.011. Epub 2021 Nov 25. PMID: 34838783; PMCID: PMC8612758.

  • Pham D, Polgar B, Toth T, Jungling A, Kovacs N, Balas I, Pal E, Szabo D, Fulop BD, Reglodi D, Szanto Z, Herczeg R, Gyenesei A, Tamas A. Examination of pituitary adenylate cyclase-activating polypeptide in Parkinson's disease focusing on correlations with motor symptoms. Geroscience. 2022 Apr;44(2):785-803. doi: 10.1007/s11357-022-00530-6. Epub 2022 Feb 26. PMID: 35220508; PMCID: PMC9135934.

  • Maasz A, Hadzsiev K, Ripszam R, Zsigmond A, Maka E, Knezy K, Lesch B, Nemeth A, Bene J, Galik B, Gyenesei A, Melegh B. TUBB4B gene mutation in Leber phenotype of congenital amaurosis syndrome associated with early-onset deafness. Eur J Med Genet. 2022 Apr;65(4):104471. doi: 10.1016/j.ejmg.2022.104471. Epub 2022 Feb 28. PMID: 35240325.

  • Komlósi K, Gyenesei A and Bene J (2022) Editorial: Copy Number Variation in Rare Disorders. Front. Genet. 13:898059. doi: 10.3389/fgene.2022.898059

  • Tompa, M.; Kraboth, Z.; Galik, B.; Kajtar, B.; Gyenesei, A.; Kalman, B. Epigenetic Suppression of the IL-7 Pathway in Progressive Glioblastoma. Biomedicines 2022, 10, 2174. https://doi.org/10.3390/ biomedicines10092174

  • Mutuku, C.; Melegh, S.; Kovacs, K.; Urban, P.; Virág, E.; Heninger, R.; Herczeg, R.; Sonnevend, Á.; Gyenesei, A.; Fekete, C.; et al. Characterization of β-Lactamases and Multidrug Resistance Mechanisms in Enterobacterales from Hospital Effluents and Wastewater Treatment Plant. Antibiotics 2022, 11, 776. https://doi.org/10.3390/ antibiotics11060776

  • Hegyi, Á.I.; Otto, M.; Geml, J.; Hegyi-Kaló, J.; Kun, J.; Gyenesei, A.; Pierneef, R.; Váczy, K.Z. Metatranscriptomic Analyses Reveal the Functional Role of Botrytis cinerea in Biochemical and Textural Changes during Noble Rot of Grapevines. J. Fungi 2022, 8, 378. https://doi.org/10.3390/jof8040378
  • Otto, M., Geml, J., Hegyi, Á. I., Hegyi-Kaló, J., Pierneef, R., Pogány, M., Kun, J., Gyenesei, A., Váczy, K. Z. Botrytis cinerea expression profile and metabolism differs between noble and grey rot of grapes. Food Microbiology, 2022, 104037. https://doi.org/10.1016/j.fm.2022.104037
  • Gervain J, Sz. Bartha K, B. Hodovánszky E, Kadlecsik L, Herczeg R, Gyenesei A, Simon J. : Monitoring of anti- SARS-CoV-2 IgG antibody immune responses in two cohorts of Hungarian healthcare workers following infection or immunization Orv Hetil. 2022; 163(12): 455–46
  • Takács-Lovász, K.; Kun, J.; Aczél, T.; Urbán, P.; Gyenesei, A.; Bölcskei, K.; Szőke, É.; Helyes, Z. PACAP-38 Induces Transcriptomic Changes in Rat Trigeminal Ganglion Cells Related to Neuroinflammation and Altered Mitochondrial Function Presumably via PAC1/VPAC2 Receptor-Independent Mechanism. Int. J. Mol. Sci. 2022, 23, 2120. https://doi.org/10.3390/ijms23042120

2021

Publications

 

  • Zeghbib, S.; Somogyi, B.A.; Zana, B.; Kemenesi, G.; Herczeg, R.; Derrar, F.; Jakab, F. The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Viruses 2021, 13, 1525. https://doi.org/10.3390/v13081525

  • Sawicka-Smiarowska,E.; Bondarczuk, K.; Bauer, W.; Niemira, M.; Szalkowska, A.; Raczkowska, J.; Kwasniewski, M.; Tarasiuk, E.; Dubatowka, M.; Lapinska, M.; et al. Gut Microbiome in Chronic Coronary Syndrome Patients. J. Clin. Med. 2021, 10,5074. https://doi.org/10.3390/ jcm10215074

  • Aczél, T., Körtési, T., Kun, J. et al. Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis. J Headache Pain 22, 117 (2021). https://doi.org/10.1186/s10194-021-01285-9 

  • Bauer W.; Gyenesei A.; Krętowski A. : Review: The Multifactorial Progression from the Islet Autoimmunity to Type 1 Diabetes in Children. Int. J. Mol. Sci. 2021, 22(14), 7493; doi:10.3390/ijms22147493

  • Schvarcz, C.A.; Danics, L.; Krenács, T.; Viana, P.; Béres, R.; Vancsik, T.; Nagy, Á.; Gyenesei, A.; Kun, J.; Fonović, M.; Vidmar, R.; et al.: Repeated Modulated Electro‐Hyperthermia Induces a Prominent Local Stress Response and Growth Inhibition in Triple Negative Mouse Breast Cancer Isografts. Cancers 2021, 13, 1744. https://doi.org/10.3390/ cancers13071744

  • Kraboth, Z.; Kajtár, B.; Gálik, B.; Gyenesei, A.; Miseta, A.; Kalman, B. Involvement of the Catecholamine Pathway in Glioblastoma Development. Cells 2021, 10, 549. https://doi.org/10.3390/cells10030549
  • Szabo, D.; Sarszegi, Z.; Polgar, B.; Saghy, É.; Nemeth, A.; Reglodi, D.; Makkos, A.; Gorbe, A.; Helyes, Z.; Ferdinandy, P.; et al.: PACAP-38 in Acute ST-Segment Elevation Myocardial Infarction in Humans and Pigs: A Translational Study. International Journal of Moecular  Sciences 2021, 22, 2883. https://doi.org/10.3390/ijms22062883 

  • Gombos K., Gálik B.,Kalács K.I., Gödöny K., Várnagy Á., Bódis J., Alpár D., Gyenesei A., Kovács. L.G. : NGS-based pipeline for routine non-invasive pre-implantation genetic assessment in IVF, International Journal of Molecular Sciences, 2021, 22, 2443  https://doi.org/10.3390/ijms22052443

  • Steffen PA, Altmutter C, Dworschak E, Junttila S, Gyenesei A, Zhu X, Kockmann T, Ringrose L.: The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival. Chromosoma. 2021 Sep;130(2-3):215-234. doi: 10.1007/s00412-021-00762-z.
  • Garai K, Adam Z, Herczeg R, Banfai K, Gyebrovszki A, Gyenesei A, Pongracz JE, Wilhelm M, Kvell K.: Physical Activity as a Preventive Lifestyle Intervention Acts Through Specific Exosomal miRNA Species-Evidence From Human Short- and Long-Term Pilot Studies. Front Physiol. 2021 Aug 2;12:658218. doi: 10.3389/fphys.2021.658218
  • Tamás A, Tóth D, Pham D, Loibl C, Rendeki S, Csontos C, Rozanovic M, Bogár L, Polgár B, Németh J, Gyenesei A, Herczeg R, Szántó Z, Reglődi D.: Changes of pituitary adenylate cyclase activating polypeptide (PACAP) level in polytrauma patents in the early post-traumatic period. Peptides. 2021 Sep 1;146:170645. doi: 10.1016/j.peptides.2021.170645
  • Gombos K, Földi M, Kiss S, Herczeg R, Gyenesei A, Geiger L, Csabai D, Futács K, Nagy T, Miseta A, Somogyi BA, Hegyi P, Szentesi A.: Analysis of COVID-19-Related RT-qPCR Test Results in Hungary: Epidemiology, Diagnostics, and Clinical Outcome. Front. Med. 2021 Jan 26;7:625673. doi: 10.3389/fmed.2020.625673.
  • Tompa M, Kajtar B, Galik B, Gyenesei A, Kalman B.:  DNA methylation and protein expression of Wnt pathway markers in progressive glioblastoma. Pathol Res Pract. 2021 Apr 5;222:153429. doi: 10.1016/j.prp.2021.153429.
  • Balazs E, Galok-Olah Z, Galik B, Somogyvari F, Kalman J, Datki Zs. : External modulation of Rotimer exudate secretion in monogonantrotifers. Ecotoxicology and Environmental safety 220 Paper: 112399, 8p. (2021)
  • Bence Galik, Jonathan J.M. Landry, Joanna M. Kirkpatrick, Markus Hsi-Yang Fritz, Bianka Baying, Jonathon Blake, Bettina Haase, Paul G. Collier, Rajna Hercog, Dinko Pavlinic, Peggy Stolt-Bergner, Hüseyin Besir, Kim Remans, Attila Gyenesei, Vladimir Benes. Extensive OMICS resource for Sf21 and Tni cell lines. bioRxiv 2021.04.06.438574; doi: https://doi.org/10.1101/2021.04.06.438574
  • N Turić, M Temunović, I Szivák, R Herczeg, G Vignjević, Z Csabai: Importance of floodplains for water beetle diversity: a crucial habitat for the endangered beetle Graphoderus bilineatus in Southeastern Europe Biodiversity and Conservation 30 (6), 1781-1801
  • M Madai, G Horváth, R Herczeg, B Somogyi, B Zana, F Földes: Effectiveness Regarding Hantavirus Detection in Rodent Tissue Samples and Urine,Viruses 13 (4), 570
  • V Temesfői, R Herczeg, Z Lőcsei, K Sebestyén, Z Sebestyén, L Mangel: Should We Reconsider the Necessity of a Refinement of Prostate Cancer Risk Classification and Radiotherapy Treatment Strategy? Experiences from a Retrospective Analysis of Data. Journal of Clinical Medicine 10 (1), 110

2020

Publications

  • Gombos K., Földi M., Kiss Sz., herczeg R., Gyenesei A., Geiger L., Csabai D., Futács K., Nagy T., Miseta A., Somogyi B.A., hegyi P., Szentesi A. : Analysis of COVID-19-related RT-qPCR test results in Hungary: Epidemology, dianostics and clinical outcome . Frontiers in Medicine, 2020
  • Kemenesi, G.; Zeghbib, S.; Somogyi, B.A.; Tóth, G.E.; Bányai, K.; Solymosi, N.; Szabo, P.M.; Szabó, I.; Bálint, Á.; Urbán, P.; Herczeg, R.; Gyenesei, A.; Nagy, Á.; Pereszlényi, C.I.; Babinszky, G.C.; Dudás, G.; Terhes, G.; Zöldi, V.; Lovas, R.; Tenczer, S.; Kornya, L.; Jakab, F.: Multiple SARS-CoV-2 Introductions Shaped the Early Outbreak in Central Eastern Europe: Comparing Hungarian Data to a Worldwide Sequence Data-Matrix. Viruses 2020, 12, 1401.
  • Gombos K, Herczeg R, Erőss B, Kovács S Zs, Uzzoli A, Nagy T, Kiss Sz, Szakács Zs, Imrei M, Szentesi A, Nagy A, Fábián A, Hegyi P, Gyenesei A : Translating Scientific Knowledge to Government Decision Makers Has Crucial Importance in the Management of the COVID-19 Pandemic. Population Health Management 2020 SEP 2 doi: 10.1089/pop.2020.0159
  • Kecskés A, Pohóczky  K, Kecskés  M, , Varga  V.Z, Kormos V, Szőke É, Henn-Mike N, Fehér M, Kun J, Gyenesei A, Renner É, Palkovits M, Ferdinandy P, Ámrahám M. I, Gaszner B, Helyes Zs: Characterization of Neurons Expressing the Novel Analgesic Drug Target Somatostatin Receptor 4 in Mouse and Human Brains. International Journal of Molecular Sciences, 2020, 21(20), 7788; https://doi.org/10.3390/ijms21207788 
     
  • Salgado D, Armean IM, Baudis M et al.:  The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: awaiting peer review]. F1000Research 2020, 9(ELIXIR):1229 (https://doi.org/10.12688/f1000research.24887.1)
     
  • Krabóth Z., Gálik B.,Tompa M., Kajtár B., Urbán P., Gyenesei, A., Miseta, A., Kálmán, B. : DNA CpG methylation in sequential glioblastoma specimens. Journal of Cancer Research and Clinical Oncology 2020 Aug 10. https://doi.org/10.1007/s00432-020-03349-w
  • Gángó A, Alpár D, Galik B, Marosvári D, Kiss R, Fésüs V, Aczél D, Eyüpoglu E, Nagy N, Nagy Á, Krizsán S, Reiniger L, Farkas P, Kozma A, Ádám E, Tasnády S, Réti M, Matolcsy A, Gyenesei A, Mátrai Z, Bödör C. Dissection of subclonal evolution by temporal mutation profiling in chronic lymphocytic leukemia patients treated with ibrutinib. Int J Cancer. 2020 Jan 1;146(1):85-93. doi: 10.1002/ijc.32502.
     
  • Montgomery SA, Tanizawa Y, Galik B, Wang N, Ito T, Mochizuki T, Akimcheva S, Bowman JL, Cognat V, Maréchal-Drouard L, Ekker H, Hong SF, Kohchi T, Lin SS, Liu LD, Nakamura Y, Valeeva LR, Shakirov EV, Shippen DE, Wei WL, Yagura M, Yamaoka S, Yamato KT, Liu C, Berger F. :Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Current Biology 2020 Feb 24;30(4):573-588.e7. doi: 10.1016/j.cub.2019.12.015. 
     
  • Bödör C, Alpár D, Marosvári D, Galik B, Rajnai H, Bátai B, Nagy Á, Kajtár B, Burján A, Deák B, Schneider T, Alizadeh H, Matolcsy A, Brandner S, Storhoff J, Chen N, Liu M, Ghali N, Csala I, Bagó AG, Gyenesei A, Reiniger L. : Molecular Subtypes and Genomic Profile of Primary Central Nervous System Lymphoma. Journal of Neuropathology & Experimental Neurology 2020 Feb 1;79(2):176-183. doi:10.1093/jnen/nlz125.
     
  • Csepregi R, Temesfői V, Das S, Alberti Á, Tóth CA, Herczeg R, Papp N, Kőszegi T. :Cytotoxic, Antimicrobial, Antioxidant Properties and Effects on Cell Migration of Phenolic Compounds of Selected Transylvanian Medicinal Plants. Antioxidants (Basel). 2020 Feb 18;9(2):166. doi: 10.3390/antiox9020166. 
     
  • Paczkowska-Abdulsalam M, Niemira M, Bielska A, Szałkowska A, Raczkowska BA, Junttila S, Gyenesei A, Adamska-Patruno E, Maliszewska K, Citko A, Szczerbiński Ł, Krętowski A. : Evaluation of Transcriptomic Regulations behind Metabolic Syndrome in Obese and Lean Subjects. International Journal of Molecular Sciences 2020 Feb 20;21(4):1455. doi:10.3390/ijms21041455.
     
  • Fodor, István ; Zrinyi, Zita ; Urbán, Péter ; Herczeg, Robert ; Büki, Gergely ; M. Koene, Joris ; Tsai, Pei-San ; Pirger, Zsolt: Identification, presence, and possible multifunctional regulatory role of invertebrate gonadotropin-releasing hormone/corazonin molecule in the great pond snail (Lymnaea stagnalis)2020 doi: 10.1101/2020.03.01.971697
     
  • Madai M, Németh V, Oldal M, Horváth G, Herczeg R, Kelemen K, Kemenesi G, Jakab F. :Temporal Dynamics of Two Pathogenic Hantaviruses Among Rodents in Hungary. Vector-Borne and Zoonotic Diseases. 2020 Mar;20(3):212-221. doi: 10.1089/vbz.2019.2438.
     
  • Aczél T, Kecskés A, Kun J, Szenthe K, Bánáti F, Szathmary S, Herczeg R, Urbán P, Gyenesei A, Gaszner B, Helyes Z, Bölcskei K. : Hemokinin-1 Gene Expression Is Upregulated in Trigeminal Ganglia in an Inflammatory Orofacial Pain Model: Potential Role in Peripheral Sensitization. International Journal of Molecular Sciences 2020 Apr 22;21(8):2938. doi: 10.3390/ijms21082938. 
     
  • Papp H, Zeghbib S, Földes F, Banfai K, Madai M, Kemenesi G, Urbán P, Kvell K, Jakab F. :Crimean-Congo hemorrhagic fever virus infection triggers the upregulation of the Wnt signaling pathway inhibitor genes. Virus Genes 2020 Apr 25. doi: 10.1007/s11262-020-01759-z. 
     
  • Friston D, Junttila S, Lemes JBP, Laycock H, Torres-Perez JV, Want E, Gyenesei A, Nagy I.:  Leptin and fractalkine: novel subcutaneous cytokines in burn injury. Disease Models & Mechanisms 2020 Apr 29;13(4):dmm042713. doi: 10.1242/dmm.042713.
     
  • Kemenesi G, Kornya L, Tóth GE, Kurucz K, Zeghbib S, Somogyi BA, Zöldi V, Urbán P, Herczeg R, Jakab F. :Nursing homes and the elderly regarding the COVID-19 pandemic: situation report from Hungary. Geroscience. 2020 May 18:1-7. doi: 10.1007/s11357-020-00195-z. 
     
  • Fodor I, Urbán P, Kemenes G, Koene JM, Pirger Z. :Aging and disease-relevant gene products in the neuronal transcriptome of the great pond snail (Lymnaea stagnalis): a potential model of aging, age-related memory loss, and neurodegenerative diseases. Invertebrate Neuroscience 2020 May 24;20(3):9. doi: 10.1007/s10158-020-00242-6. 
     
  • Bodis J, Gödöny K, Várnagy Á, Kovács K, Koppán M, Nagy B, Erostyák J, Herczeg R, Szekeres-Barthó J, Gyenesei A, Kovács GL.:  How to reduce the potential harmful effects of light on blastocyst development during IVF. Medical Principles and Practice 2020 May 29. doi: 10.1159/000509016. 
  • Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D; WHO European Region sequencing laboratories and GISAID EpiCoV group; WHO European Region sequencing laboratories and GISAID EpiCoV group. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Euro Surveill. 2020 Aug;25(32):2001410. doi: 10.2807/1560-7917.ES.2020.25.32.2001410.
  • Balazs E., Galik-Olah Z, Galik B, Bozso Z, Kalman J, Datki Z: Neurodegeneration-related beta-amyloid as autocatabolism-attenuator in micro-in vivo system. IBRO Reports 9 pp. 319-323, 5 p. (2020)
  • Gál R, Deres L, Horváth O, Erős K, Sándor B, Urbán P, Soós Sz, Marton Zs, Sümegi B, Tóth K et al: Resveratrol Improves Heart Function by Moderating Inflammatory Processes in Patients with Systolic Heart Failure. Antioxidants 9: 11 Paper: 1108, 19 p (2020)
  • Fodor I, Urbán P, Scott A. P, Pirger Zs : A critical evaluation of some of the recent so-called ‘evidence’ for the involvement of vertebrate-type sex steroids in the reproduction of mollusks. Molecular and cellular endocrinology 516, paper: 110949, 10p (2020)
  • Fodor I, Svigruha R, Molnar E, Urbán P, Joris M. K., Pirger Zs: Progesztogének indukálta hatások a nagy mocsári csiga (Lymnaea stagnalis) neuroendokrin és reprodukciós rendszerében. Ökotoxikológia 2: 2 pp. 9-10, 2 p. (2020)

2019

Publications

  • Marik T, Tyagi C, Balázs D, Urbán P, Szepesi Á, Bakacsy L, Endre G, Rakk D, Szekeres A, Andersson M A, Salonen H, Druzhinina I S, Vágvölgyi Cs, Kredics L. Structural Diversity and Bioactivities of Peptaibol Compounds From the Longibrachiatum Clade of the Filamentous Fungal Genus Trichoderma. Frontiers in Microbiology, 2019. Accepted for publication. Doi: 10.3389/fmicb.2019.01434. IF: 4.26
     
  • Garai K, Ádam Z, Herczeg R, Katai E, Nagy T, Pál Sz., Gyenesei A, Pongracz J, Wilhelm M, Kvell K. Artificial neural network correlation and biostatistics evaluation of physiological and molecular parameters in healthy young individuals performing regular exercise. Frontiers in Physiology, 2019. Accepted for publication. IF: 3.2
     
  • Péterfalvi A, Németh N, Herczeg R, Tényi T, Miseta A, Czéh B, Simon M. Examining the Influence of Early Life Stress on Serum Lipid Profiles and Cognitive Functioning in Depressed Patients. Frontiers in Psychology 2019. Accepted for publication. https://doi.org/10.3389/fpsyg.2019.01798, IF: 2.13
     
  • Macsai L, Olah Z, Bush AI, Galik B, Onody R, Kalman J, Datki Z. :Redox Modulating Factors Affect Longevity Regulation in Rotifers.  The Journals of Gerontology Series A Biological Sciences and Medical Sciences 2019 May 16;74(6):811-814. doi: 10.1093/gerona/gly193.
     
  • Gángó A*, Alpár D*, Gálik B*, Marosvári D, Kiss R, Fésüs V, Aczél D, Eyüpoglu E, Nagy N, Nagy Á, Krizsán S, Reiniger L, Farkas P, Kozma A, Ádám E, Tasnády S, Réti M, Matolcsy A, Gyenesei A, Mátrai Z, Bödör C. Dissection of Subclonal Evolution by Temporal Mutation Profiling in Chronic Lymphocytic Leukemia Patients Treated With Ibrutinib. International Journal of Cancer 2019 Jun 10. Doi: 10.1002/ijc.32502. IF: 7.36
     
  • Bauer W, Veijola R, Lempainen J, Kiviniemi M, Härkönen T, Toppari J, Knip M, Gyenesei A*, Ilonen J*. Age at Seroconversion, HLA Genotype and Specificity of Autoantibodies in Progression of Islet Autoimmunity in Childhood. Journal of Clinical Endocrinology & Metabolism 2019 May 23. pii: jc.2019-00421. doi: 10.1210/jc.2019-00421. IF: 5.79
     
  • Zana B, Geiger L, Kepner A, Földes F, Urbán P, Herczeg R, Kemenesi G, Jakab F. First molecular detection of Apis mellifera filamentous virus in honey bees ( Apis mellifera ) in Hungary, Acta Veterinaria 2019, 67:1 pp. 151-157. IF: 1.04
     
  • Montskó, G ; Gödöny, K ; Herczeg, R ; Várnagy, Á ; Bódis, J ; Kovács, GL Alpha-1 chain of human haptoglobin as viability marker of in vitro fertilized human embryos: information beyond morphology. System Biology in Reproductive Medicine 2019, 65: 2 pp. 174-180, IF: 1.58
  • Datki Z, Galik-Olah Z, Bohar Z, Zadori D, Fulop F, Szatmari I, Galik B, Kalman J, Vecsei L. : Kynurenic Acid and Its Analogs Are Beneficial Physiologic Attenuators in Bdelloid Rotifers. Molecules. 2019 Jun 10;24(11):2171. doi.:10.3390/molecules24112171. 
  • Aczél T, Kun J, Szőke É, Rauch T, Junttila S, Gyenesei A, Bölcskei K, Helyes Zs. Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. Frontiers in Molecular Neuroscience 2018. Doi: 10.3389/fnmol.2018.00219. IF: 3.90
  • Zana B, Kemenesi G, Buzás D, Csorba G, Görföl T, Khan FAA, Tahir NFDA,Zeghbib S, Madai M, Papp H, Földes F, Urbán P, Herczeg R, Tóth GE, Jakab F.: Molecular Identification of a Novel Hantavirus in Malaysian Bronze Tube-Nosed Bats (Murina aenea) Viruses. 2019 Sep 21;11(10):887. doi:10.3390/v11100887. 
  • Földes F, Madai M, Németh V, Zana B, Papp H, Kemenesi G, Bock-Marquette I,Horváth G, Herczeg R, Jakab F. : Serologic survey of the Crimean-Congo haemorrhagic fever virus infection among wild rodents in Hungary. Ticks Tick-borne Diseases. 2019 Oct;10(6):101258. doi: 10.1016/j.ttbdis.2019.07.002.
  • Zeghbib S, Herczeg R, Kemenesi G, Zana B, Kurucz K, Urbán P, Madai M, Földes F, Papp H, Somogyi B, Jakab F.: Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses. Scientific Reports 2019 Oct 31;9(1):15706. doi: 10.1038/s41598-019-52209-2.
  • Bödör C, Alpár D, Marosvári D, Galik B, Rajnai H, Bátai B, Nagy Á, Kajtár B, Burján A, Deák B, Schneider T, Alizadeh H, Matolcsy A, Brandner S, Storhoff J, Chen N, Liu M, Ghali N, Csala I, Bagó AG, Gyenesei A, Reiniger L. Molecular Subtypes and Genomic Profile of Primary Central Nervous System Lymphoma. J Neuropathol Exp Neurol. 2019 Nov 28. doi: 10.1093/jnen/nlz125. 
  • Rosser J, Bachmann B, Jordan C, Ribitsch I, Haltmayer E, Gueltekin S, Junttila S, Galik B, Gyenesei A, Haddadi B, Harasek M, Egerbacher M, Ertl P, Jenner F. Microfluidic nutrient gradient-based three-dimensional chondrocyte culture-on-a-chip as an in vitro equine arthritis model. Materials To Mater Today Bio. day Bio. 2019; 4:100023. doi: 10.1016/j.mtbio.2019.100023.
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Dr Attila Gyenesei
Core Facility Leader
 gyenesei.attila@pte.hu
 
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2023

 

  • Charkiewicz, R.; Sulewska, A.; Charkiewicz, A.; Gyenesei, A.; Galik, B.; Ramlau, R.; Piwkowski, C.; Stec, R.; Biecek, P.; Karabowicz, P.; et al. miRNA-Seq Tissue Diagnostic Signature: A Novel Model for NSCLC Subtyping. Int. J. Mol. Sci. 2023, 24, 13318. https://doi.org/10.3390/ijms241713318

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2022

  • Neparáczki E, Kis L, Maróti Z, Kovács B, Varga GIB, Makoldi M, Horolma P, Éva Teiszler, Tihanyi B, Nagy PL, Maár K, Gyenesei A, Schütz O, Dudás E, Török T, Pascuttini-Juraga V, Peharda I, Vizi LT, Horváth-Lugossy G, Kásler M.: The genetic legacy of the Hunyadi descendants . Heliyon. 2022 Nov 17;8(11):e11731. doi: 10.1016/j.heliyon.2022.e11731 

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