About us

A Szentágothai János Kutatóközpont a PTE korszerű, nemzetközi tudományszervezési és menedzsment normák szerint kialakított új intézménye, amely az élettudományi, élettelen természettudományi, valamint környezettudományi oktatás...

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Bioinformatics Research Group

  • Research concept
  • Members
  • Publications
  • Awarded projects
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The main goal of the Bioinformatics Research Group is not only to concentrate and conduct research on a specific scientific problem but rather to develop and implement comprehensive bioinformatics pipelines, tools and strategy for the Szentágothai Research Centre and the University of Pécs.

The proposed strategy is based on four pillars:

 

  • bioinformatics research driving the development of new analysis methodologies,
  • bioinformatics core facility providing data analysis services for biomedical researchers,
  • bioinformatics education and training provided to students and researchers, and
  • bioinformatics infrastructure enabling the collection, storage and analysis of data. 

 

The group has established a number of research collaborations with local and international research groups, developed and implemented various data analysis algorithms and methods. Some of those have already been published or are currently under submission or review. 

The research group has also set up the Genomics and Bioinformatics Core Facility and started providing sequencing and data analysis collaboration-based services for its academic and industrial partners.

We are currently developing the curriculum of a Bioinformatics MSc program at the University. We have also successfully applied for an EU grant application under the ERASMUS+ program to develop bioinformatics and biostatistics competencies for biomedical students.



Péter Urbán
assistant research fellow
urban.peter@pte.hu
29291
Dr. József Kun
research fellow
kun.jozsef@pte.hu
29202
Dr. Róbert Herczeg
research fellow
herczeg.robert@pte.hu
Bence Gálik
assistant research fellow
galik.bence@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

2020

  • 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, Ábrahám M. I, GasznerB, Helyes Zs: Characterization of Neurons Expressing the Novel Analgesic Drug Target Somatostatin Receptor 4 in Mouse and Human Brains. International Journal os Molecular Sciences, 2020 Oct; 21(20): 7788. doi: 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)
  • 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
  • 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. International Journal of 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. 

2019

  • 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. 
  • 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. 
  • 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. Journal of Neuropathology & Experimental Neurology, 2019 Nov 28. doi:10.1093/jnen/nlzl125

2018

  • Mutti M, Sonnevend Á, Pál T, Junttila S, Ekker H, Galik B, Gyenesei A, Nagy G, Nagy E, Szijártó V. : Complete Genome Sequence of Escherichia coli 81009, a Representative of the Sequence Type 131 C1-M27 Clade with a Multidrug- Resistant Phenotype. Genome Announcements. 2018 doi: 10.1128/genomeA.00056-18. 
  • Aczél T, Kun J, Szőke É, Rauch T, Junttila S, Gyenesei A, Bölcskei K, Helyes Z. : 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. 
  • Datki Z, Olah Z, Hortobagyi T, Macsai L, Zsuga K, Fulop L, Bozso Z, Galik B, Acs E, Foldi A, Szarvas A, Kalman J. :Exceptional in vivo catabolism of neurodegeneration-related aggregates.  2018 Jan 29;6(1):6. doi: 10.1186/s40478-018-0507-3. 
  • Bán Á, Pintér E, Kun J. :A megfelelő szájegészség megvédhet a kalciumcsatorna- blokkoló készítmények okozta gingivahyperplasia kialakulásától [Proper oral health can protect from developing gingival hyperplasia induced by calcium channel blockers]. Orvosi Hetilap 2018 Jul;159(29):1183-1187. Hungarian. doi: 10.1556/650.2018.31088. 
  • Feller D, Kun J, Ruzsics I, Rapp J, Sarosi V, Kvell K, Helyes Z, Pongracz JE. : Cigarette Smoke-Induced Pulmonary Inflammation Becomes Systemic by Circulating Extracellular Vesicles Containing Wnt5a and Inflammatory Cytokines. Frontiers in Immunology. 2018 Jul 25;9:1724. doi: 10.3389/fimmu.2018.01724. 
  • Deutsch-Nagy L, Urbán P, Tóth Z, Bihari Z, Kocsis B, Fekete C, Kilár F. : Genome sequence of Shigella sonnei 4303. Gut Pathogens 2018 Oct 24;10:47. doi: 10.1186/s13099-018-0274-5.
  • H2020-CONVERGE-RIA-871075: “ELIXIR-CONVERGE - Connect and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services”
  • NKFIH 2020-2.1.1-ED-2020-00009: Több vizsgálati centrumban zajló, beavatkozással nem járó klinikai vizsgálat COVID-19 új típusú koronavírus által okozott fertőzés betegség lefolyását meghatározó genetikai tényezők azonosítására és farmakogenetikai alkalmazások előkészítésére (HUNGEN)
  • GINOP-2.3.4-15-2020-00010: Egészségügyi Adatelemző, Adathasznosítási, valamint Okoseszköz- és Technológia Fejlesztő Kompetencia Központ kialakítása a Pécsi Tudományegyetemen.
  • 2019-1-HU01-KA203-061251 (ERASMUS+): Educating Experts of the Future: Developing Bioinformatics and Biostatistics competencies of European Biomedical Students (BECOMING)
  • 2018-1-HU01-KA203-047811 (ERASMUS+): Curriculum Development of Human Clinical Trials for the Next Generation Biomedical Students (CONSCIOUS)
  • EURGINOP-2.3.2-15-2016-00021: „Chip-technológia alkalmazása a humán in vitro fertilizáció eredményességének javításában” (IVF GINOP project)
  • EFOP-3.6.2-16-2017-00009: „Klinikai kutatások tematikus hálózatának kialakítása és nemzetköziesítése” (HECRIN EFOP project)
  • GINOP-2.2.1-15-2017-00067: „Hálózatos analitikai és adathasznosítási lehetőségek az egészségügyben” (DataLake GINOP project)
CONTACT
Dr Attila Gyenesei
Research Group Leader