Publications

Bioinformatics lab

Nagy, Á., Pongor, S., Győrffy, B., 2021. Different mutations in SARS-CoV-2 associate with severe and mild outcome. Int J Antimicrob Agents 57, 106272. https://doi.org/10.1016/j.ijantimicag.2020.106272 Cite Download
Mansour, B., Monyók, Á., Makra, N., Gajdács, M., Vadnay, I., Ligeti, B., Juhász, J., Szabó, D., Ostorházi, E., 2020. Bladder cancer-related microbiota: examining differences in urine and tissue samples. Scientific Reports 10, 11042. https://doi.org/10.1038/s41598-020-67443-2 Cite Download
Juhász, J., Pongor, S., Ligeti, B., 2020. Toward a Systematic Genomic Survey of Bacterial Quorum Sensing Genes: Cross Cutting Regulatory and Genomic Concepts, in: Rai, V.R., Bai, J.A. (Eds.), Trends in Quorum Sensing and Quorum Quenching: New Perspectives and Applications. CRC Press - Taylor and Francis Group, Boca Raton (FL), USA, pp. 31–45. https://doi.org/10.1201/9780429274817-3 Cite
Juhász, J., Gáspári, Z., Pongor, S., 2020. Structure and Oxidative Folding of AAI, the Major Alfa-Amylase Inhibitor From Amaranth Seeds. Front. Chem. 8. https://doi.org/10.3389/fchem.2020.00180 Cite Download
Kiss-Tóth, A., Dobson, L., Péterfia, B., Ángyán, A.F., Ligeti, B., Lukács, G., Gáspári, Z., 2019. Occurrence of Ordered and Disordered Structural Elements in Postsynaptic Proteins Supports Optimization for Interaction Diversity. Entropy 21, 761. https://doi.org/10.3390/e21080761 Cite Download
Pap, D., Kiss, Z., Veres-Székely, A., Sziksz, E., Szebeni, B., Takács, I., Pajtók, C., Jármi, L., Ligeti, B., Szabó, A., Vannay, Ád., 2019. Novel integrative methods to identify therapeutic targets and compounds for treating kidney fibrosis. Nephrol Dial Transplant 34, i463–i464. https://doi.org/10.1093/ndt/gfz103.SP307 Cite Download
Juhász, J., Makove, B., Pesti, D., Pillér, B., Gaizler, T., Csikász-Nagy, A., 2019. In-silico Modelling of Yeast Colony Growth, in: Programme and Books of Abstracts - Hungarian Molecular Life Sciences. Presented at the Hungarian Molecular Life Sciences Conference, Diamond Congress Ltd., Budapest, p. 329. Cite
Ligeti, B., Kistóth, É.M., Kalcsevszki, R., Stellek, B.S., Juhász, J., Pongor, S., 2019. Fast and sensitive detection of pathogens from high throughput sequencing data, in: Programme and Books of Abstracts - Hungarian Molecular Life Sciences 2019. Presented at the Hungarian Molecular Life Sciences 2019, Diamond Congress Ltd., Eger, Hungary, pp. 91–92. Cite
Lázár, B., Brenner, G.B., Makkos, A., Balogh, M., László, S.B., Al-Khrasani, M., Hutka, B., Bató, E., Ostorházi, E., Juhász, J., Kemény, Á., László, T., Tiszlavicz, L., Bihari, Z., Giricz, Z., Szabó, D., Helyes, Z., Ferdinandy, P., Gyires, K., Zádori, Z.S., 2019. Lack of Small Intestinal Dysbiosis Following Long-Term Selective Inhibition of Cyclooxygenase-2 by Rofecoxib in the Rat. Cells 8, 251. https://doi.org/10.3390/cells8030251 Cite Download
Ábrahám, D., Fehér, J., Scuderi, G.L., Szabó, D., Dobolyi, Á., Cservenák, M., Juhász, J., Ligeti, B., Pongor, S., Gomez-Cabrera, M.C., Vina, J., Higuchi, M., Suzuki, K., Boldogh, I., Radak, Z., 2019. Exercise and probiotics attenuate the development of Alzheimer’s disease in transgenic mice: Role of microbiome. Experimental Gerontology 115, 122–131. https://doi.org/10.1016/j.exger.2018.12.005 Cite
Domokos, J., Damjanova, I., Kristóf, K., Ligeti, B., Kocsis, B., Szabó, D., 2019. Multiple Benefits of Plasmid-Mediated Quinolone Resistance Determinants in Klebsiella pneumoniae ST11 High-Risk Clone and Recently Emerging ST307 Clone. Front. Microbiol. 10. https://doi.org/10.3389/fmicb.2019.00157 Cite Download
Ligeti, B., Hőnich, Á.K., Juhász, J., Pongor, S., 2019. Surveying bacteriophages of the human gut. Jedlik Laboratories Reports Vii, 79. Cite
Kiss, Z., Makra, N., 2019. Characteristics of the Microbiome Under Biological Theraphy in Pediatric Patients With Inflammatory Bowel Disease. Journal of Pediatric Gastroenterology and Nutrition 68, 556. Cite
Juhász, J., Kistóth, É.M., Nagy, Z., Szolgay, P., Pongor, S., Ligeti, B., 2019. Towards a systematic census of bacterial quorum sensing genes in public databases. Jedlik Laboratories Reports Vii, 72–74. Cite
Ligeti, B., Menyhárt, O., Juhász, J., Pongor, S., Győrffy, B., 2019. Network-based prediction of drug-combination efficiency based on expression data on off target genes. Jedlik Laboratories Reports 7, 75–76. Cite
Juhász, J., Ligeti, B., Pongor, S., 2019. Modelling genomic and metabolic responses of microbial communities to antibiotics. Jedlik Laboratories Reports Vii, 77–78. Cite
Juhász, J., Gaizler, T., 2019. Designing synthetic yeast colonies via in silico and in vitro methods. International Workshop on Control Engineering and Synthetic Biology, Oxford. Cite
Kocsis, B., Tóth, Á., Gulyás, D., Ligeti, B., Katona, K., Rókusz, L., Szabó, D., 2019. Acquired qnrVC1 and blaNDM-1 resistance markers in an international high-risk Pseudomonas aeruginosa ST773 clone. J Med Microbiol 68, 336–338. https://doi.org/10.1099/jmm.0.000927 Cite
Kiss-Tóth, A., Péterfia, B., Ángyán, A.F., Ligeti, B., Lukács, G., Gáspári, Z., 2018. Multiple polyvalency provided by intrinsically disordered segments is a key feature of postsynaptic scaffold proteins. bioRxiv 2018, 448100. https://doi.org/10.1101/448100 Cite Download
Juhász, J., Jády, A., Ligeti, B., 2018. Horizontal gene transfer can facilitate the formation of stable and diverse microbial communities: an in silico agent-based model, in: Benjamin, J.R. (Ed.), Research in Computational Molecular Biology, Lecture Notes in Bioinformatics. Presented at the 22nd Annual International Conference, RECOMB 2018, Springer International Publishing, Paris, France. https://doi.org/10.1007/978-3-319-89929-9 Cite Download
Pap, D., Kiss, Z., Szebeni, B., Veres-Székely, A., Takács, I.M., Pajtók, C., Jármi, L., Ligeti, B., Szabó, A., Vannay, Á., 2018. Novel integrative framework to identify therapeutic targets and compounds for treating kidney fibrosis. Hypertonia Nephrologia 22, 33. Cite
Juhász, J., Jády, A., Ligeti, B., 2018. Horizontal gene transfer can facilitate the formation of stable and diverse microbial communities: an in silico agent-based model, in: Proceeding of Computational Molecular Biology. 22nd Annual International Conference, RECOMB 2018. Presented at the Computational Molecular Biology. 22nd Annual International Conference, RECOMB 2018. Cite
Kiss, Z., Makra, N., 2018. A TNF gátló biológiai terápia hatása a bél mikrobiom funkcionális összetételére Crohn-beteg gyermekekben. Gyermekgyógyászat 69, 359. Cite
Juhász, J., Bihary, D., Pongor, S., Ligeti, B., 2017. Differential signal sensitivities can contribute to the stability of multispecies bacterial communities. Biology Direct 12, 10. https://doi.org/10.1186/s13062-017-0192-3 Cite Download Download
Ligeti, B., Menyhart, O., Petric, I., Győrffy, B., Pongor, S., 2016. Propagation on Molecular Interaction Networks: Prediction of Effective Drug Combinations and Biomarkers in Cancer Treatment. Current pharmaceutical design 22, 5–28. https://doi.org/10.2174/1381612822666161021162727 Cite Download
Nagy, G., Czipa, E., Steiner, L., Nagy, T., Pongor, S., Nagy, L., Barta, E., 2016. Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA. BMC Genomics 17, 637. https://doi.org/10.1186/s12864-016-2940-7 Cite Download
Ligeti, B., Vera, R., Juhász, J., Pongor, S., 2016. CX, DPX and PCW (2016): Web servers for the visualization of interior and protruding regions of protein structures in 3D and 1D, in: Zhou, Y., Kloczkowski, A. (Eds.), Prediction of Protein Secondary Structure, Methods in Molecular Biology. Springer Science+Business Media, Humana Press, New York, p. Chapter 20, 301?310. Cite
Ligeti, B., Pénzváltó, Z., Vera, R., Győrffy, B., Pongor, S., 2015. A Network-Based Target Overlap Score for Characterizing Drug Combinations: High Correlation with Cancer Clinical Trial Results. PLoS One 10, e0129267. https://doi.org/10.1371/journal.pone.0129267 Cite Download
Marini, B., Kertesz-Farkas, A., Ali, H., Lucic, B., Lisek, K., Manganaro, L., Pongor, S., Luzzati, R., Recchia, A., Mavilio, F., Giacca, M., Lusic, M., 2015. Nuclear architecture dictates HIV-1 integration site selection. Nature 521, 227–231. https://doi.org/10.1038/nature14226 Cite Download
Hudaiberdiev, S., Choudhary, K.S., Vera Alvarez, R., Gelencsér, Z., Ligeti, B., Lamba, D., Pongor, S., 2015. Census of solo LuxR genes in prokaryotic genomes. Front. Cell. Infect. Microbiol. 5. https://doi.org/10.3389/fcimb.2015.00020 Cite Download
Bihary, D., Tóth, M., Kerényi, Á., Venturi, V., Pongor, S., 2014. Modeling bacterial quorum sensing in open and closed environments: potential discrepancies between agar plate and culture flask experiments. J Mol Model 20, 2248. https://doi.org/10.1007/s00894-014-2248-y Cite Download
Reiz, B., P. Myers, M., Pongor, S., Kertész-Farkas, A., 2014. Precursor Mass Dependent Filtering of Mass Spectra for Proteomics Analysis. Protein and Peptide Letters 21, 858–863. Cite
Petrič, I., Ligeti, B., Győrffy, B., Pongor, S., 2014. Biomedical Hypothesis Generation by Text Mining and Gene Prioritization. Protein and Peptide Letters 21, 847–857. Cite Download
Dogsa, I., Choudhary, K.S., Marsetic, Z., Hudaiberdiev, S., Vera, R., Pongor, S., Mandic-Mulec, I., 2014. ComQXPA Quorum Sensing Systems May Not Be Unique to Bacillus subtilis: A Census in Prokaryotic Genomes. PlosOne 9, e96122. https://doi.org/10.1371/journal.pone.0096122 Cite Download
Juhász, J., Kertész-Farkas, A., Szabó, D., Pongor, S., 2014. Emergence of Collective Territorial Defense in Bacterial Communities: Horizontal Gene Transfer Can Stabilize Microbiomes. PlosOne 9, e95511. https://doi.org/10.1371/journal.pone.0095511 Cite Download
Kertész-Farkas, A., Reiz, B., Vera, R., Myers, M.P., Pongor, S., 2014. PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. Bioinformatics 30, 234–241. https://doi.org/10.1093/bioinformatics/btt642 Cite Download
Popovic, M., Wienk, H., Coglievina, M., Boelens, R., Pongor, S., Pintar, A., 2014. The basic helix–loop–helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA. Proteins 82, 537–545. https://doi.org/10.1002/prot.24507 Cite Download
Ligeti, B., Vera, R., Lukács, G., Győrffy, B., Pongor, S., 2013. Predicting effective drug combinations via network propagation, in: 2013 IEEE Biomedical Circuits and Systems Conference (BioCAS). Presented at the 2013 IEEE Biomedical Circuits and Systems Conference (BioCAS), pp. 378–381. https://doi.org/10.1109/BioCAS.2013.6679718 Cite Download
Choudhary, K.S., Hudaiberdiev, S., Gelencsér, Z., Gonçalves Coutinho, B., Venturi, V., Pongor, S., 2013. The Organization of the Quorum Sensing luxI/R Family Genes in Burkholderia. Int. J. Mol. Sci. 14, 13727–13747. https://doi.org/10.3390/ijms140713727 Cite Download
Reiz, B., Busa-Fekete, R., Pongor, S., Kovács, I., 2013. Closure enhancement in a model network with orientation tuned long-range connectivity. Learning & Perception 5, 119–148. https://doi.org/10.1556/lp.5.2013.suppl2.8 Cite Download
Luo, J., Nijveen, H., Attwood, T., Judge, D., Pongor, S., Landsman, D., Bishop, M., 2013. Obituary: In memory of Jack Leunissen. Brief Bioinform 14, 261–262. https://doi.org/10.1093/bib/bbt036 Cite Download
Reiz, B., Kertész-Farkas, A., Pongor, S., Myers, M.P., 2013. Chemical rule-based filtering of MS/MS spectra. Bioinformatics 29, 925–932. https://doi.org/10.1093/bioinformatics/btt061 Cite Download
Coglievina, M., Guarnaccia, C., Zlatev, V., Pongor, S., Pintar, A., 2013. Jagged-1 juxtamembrane region: biochemical characterization and cleavage by ADAM17 (TACE) catalytic domain. Biochem. Biophys. Res. Commun. 432, 666–671. https://doi.org/10.1016/j.bbrc.2013.02.022 Cite Download
Kerényi, Á., Bihary, D., Venturi, V., Pongor, S., 2013. Stability of Multispecies Bacterial Communities: Signaling Networks May Stabilize Microbiomes. Plos One 8, e57947. https://doi.org/10.1371/journal.pone.0057947 Cite Download
Kuznetsov, V., Lee, H.K., Maurer-Stroh, S., Molnár, M.J., Pongor, S., Eisenhaber, B., Eisenhaber, F., 2013. How bioinformatics influences health informatics: usage of biomolecular sequences, expression profiles and automated microscopic image analyses for clinical needs and public health. Health Inf Sci Syst 1, 2. https://doi.org/10.1186/2047-2501-1-2 Cite Download
Vera, R., Perez-Riverol, Y., Perez, S., Ligeti, B., Kertész-Farkas, A., Pongor, S., 2013. JBioWH: an open-source Java framework for bioinformatics data integration. Database (Oxford) 2013, bat051. https://doi.org/10.1093/database/bat051 Cite Download
Popovic, M., Zlatev, V., Hodnik, V., Anderluh, G., Felli, I.C., Pongor, S., Pintar, A., 2012. Flexibility of the PDZ-binding motif in the micelle-bound form of Jagged-1 cytoplasmic tail. Biochimica et Biophysica Acta (BBA) - Biomembranes 1818, 1706–1716. https://doi.org/10.1016/j.bbamem.2012.03.012 Cite Download
Reiz, B., Kertész-Farkas, A., Pongor, S., Myers, M.P., 2012. Data Preprocessing and Filtering in Mass Spectrometry Based Proteomics. Current Bioinformatics 7, 212–220. https://doi.org/10.2174/157489312800604363 Cite Download
Gelencsér, Z., Choudhary, K.S., Coutinho, B.G., Hudaiberdiev, S., Galbáts, B., Venturi, V., Pongor, S., 2012. Classifying the Topology of AHL-Driven Quorum Sensing Circuits in Proteobacterial Genomes. Sensors 12, 5432–5444. https://doi.org/10.3390/s120505432 Cite Download
Gelencsér, Z., Galbáts, B., Gonzalez, J.F., Choudhary, K.S., Hudaiberdiev, S., Venturi, V., Pongor, S., 2012. Chromosomal Arrangement of AHL-Driven Quorum Sensing Circuits in Pseudomonas. ISRN Microbiology 2012, 6. https://doi.org/10.5402/2012/484176 Cite Download