TY - GEN AU - Turek, Cezary AU - Olbei, Marton AU - Stirling, Tamás AU - Fekete, Gergely AU - Tasnádi, Ervin Áron AU - Gul, Leila AU - Bohár, Balázs AU - Papp, Balázs AU - Jurkowski, Wiktor AU - Ari, Eszter TI - mulea - an R package for enrichment analysis using multiple ontologies and empirical FDR correction PY - 2024 UR - https://m2.mtmt.hu/api/publication/34718081 ID - 34718081 AB - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. mulea employs an innovative empirical false discovery rate (eFDR) correction method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, expanding its applicability across diverse research areas. Availability and Implementation: Software for the tools demonstrated in this article is available as an R package on GitHub: https://github.com/ELTEbioinformatics/mulea. LA - English DB - MTMT ER - TY - GEN AU - Daruka, Lejla AU - Márton, Simon Czikkely AU - Petra, Szili AU - Farkas, Zoltán AU - Dávid, Balogh AU - Elvin, Maharramov AU - Thu-Hien, Vu AU - Levente, Sipos AU - Botond, Dávid Vincze AU - Gábor, Grézal AU - Szilvia, Juhász AU - Anett, Dunai AU - Andreea, Daraba AU - Mónika, Számel AU - Tóbiás, Sári AU - Tamás, Stirling AU - Vásárhelyi, Bálint Márk AU - Ari, Eszter AU - Chryso, Christodoulou AU - Máté, Manczinger AU - Márton, Zsolt Enyedi AU - Gábor, Jaksa AU - Stineke, van Houte AU - Elizabeth, Pursey AU - Csaba, Gergő Papp AU - Zóra, Szilovics AU - Lajos, Pintér AU - Lajos, Haracska AU - Attila, Gácser AU - Bálint, Kintses AU - Balázs, Papp AU - Csaba, Pál TI - Antibiotics of the future are prone to resistance in Gram-negative pathogens PY - 2023 UR - https://m2.mtmt.hu/api/publication/34158052 ID - 34158052 LA - English DB - MTMT ER - TY - JOUR AU - Gerber, Dániel AU - Szeifert, Bea AU - Székely, Orsolya AU - Egyed, Balázs AU - Gyuris, Balázs AU - Giblin, Julia I. AU - Horváth, Anikó AU - Köhler, Kitti AU - Kulcsár, Gabriella AU - Kustár, Ágnes AU - Major, István AU - Molnár, Mihály AU - Palcsu, László AU - Szeverényi, Vajk AU - Fábián, Szilvia AU - Mende, Balázs Gusztáv AU - Bondár, Mária (Ködmönné) AU - Ari, Eszter AU - Kiss, Viktória AU - Szécsényi-Nagy, Anna TI - Interdisciplinary analyses of Bronze Age communities from Western Hungary reveal complex population histories JF - MOLECULAR BIOLOGY AND EVOLUTION J2 - MOL BIOL EVOL VL - 182 PY - 2023 PG - 18 SN - 0737-4038 DO - 10.1093/molbev/msad182 UR - https://m2.mtmt.hu/api/publication/33549439 ID - 33549439 AB - In this study we report 21 ancient shotgun genomes from present-day Western Hungary, from previously understudied Late Copper Age Baden, and Bronze Age Somogyvár-Vinkovci, Kisapostag, and Encrusted Pottery archaeological cultures (3530–1620 cal BCE). Our results indicate the presence of high steppe ancestry in the Somogyvár-Vinkovci culture. They were then replaced by the Kisapostag group, who exhibit an outstandingly high (up to ∼47%) Mesolithic hunter-gatherer ancestry, despite this component being thought to be highly diluted by the time of the Early Bronze Age. The Kisapostag population contributed the genetic basis for the succeeding community of the Encrusted pottery culture. We also found an elevated hunter-gatherer component in a local Baden culture associated individual, but no connections were proven to the Bronze Age individuals. The hunter-gatherer ancestry in Kisapostag is likely derived from two main sources, one from a Funnelbeaker or Globular Amphora culture related population and one from a previously unrecognised source in Eastern Europe. We show that this ancestry not only appeared in various groups in Bronze Age Central Europe, but also made contributions to Baltic populations. The social structure of Kisapostag and Encrusted pottery cultures is patrilocal, similarly to most contemporaneous groups. Furthermore, we developed new methods and method standards for computational analyses of ancient DNA, implemented to our newly developed and freely available bioinformatic package. By analysing clinical traits, we found carriers of aneuploidy and inheritable genetic diseases. Finally, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin. LA - English DB - MTMT ER - TY - JOUR AU - Bacsur, Péter AU - Rutka, Mariann AU - Asbóth, András AU - Resál, Tamás AU - Szántó, Kata Judit AU - Jójárt, Boldizsár AU - Bálint, Anita AU - Ari, Eszter AU - Ajibola, Walliyulahi AU - Kintses, Bálint AU - Fehér, Tamás AU - Pigniczki , Daniella AU - Bor, Renáta AU - Fábián, Anna AU - Maléth, József AU - Szepes, Zoltán AU - Farkas, Klaudia AU - Molnár, Tamás TI - Effects of bowel cleansing on the composition of the gut microbiota in inflammatory bowel disease patients and healthy controls JF - THERAPEUTIC ADVANCES IN GASTROENTEROLOGY J2 - THER ADV GASTROENTER VL - 16 PY - 2023 PG - 13 SN - 1756-283X DO - 10.1177/17562848231174298 UR - https://m2.mtmt.hu/api/publication/34014839 ID - 34014839 N1 - "Asbóth Andrásnál tévesen szerepel a publikáción az SZTE/TTIK/BI/Biokémiai és Molekuláris Biológiai Tanszék. (SE, SZTE admin5)" LA - English DB - MTMT ER - TY - JOUR AU - Sturm, Ádám AU - Saskői, Éva AU - Hotzi, Bernadette AU - Tarnóci, Anna AU - Barna, János AU - Bodnár, Ferenc AU - Sharma, Himani AU - Kovács, Tibor AU - Ari, Eszter AU - Weinhardt, Nóra AU - Kerepesi, Csaba AU - Perczel, András AU - Ivics, Zoltán AU - Vellai, Tibor TI - Downregulation of transposable elements extends lifespan in Caenorhabditis elegans JF - NATURE COMMUNICATIONS J2 - NAT COMMUN VL - 14 PY - 2023 IS - 1 PG - 18 SN - 2041-1723 DO - 10.1038/s41467-023-40957-9 UR - https://m2.mtmt.hu/api/publication/34119363 ID - 34119363 N1 - Department of Genetics, Eötvös Loránd University (ELTE), Budapest, 1117, Hungary Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, Budapest, 1117, Hungary HCEMM-BRC Metabolic Systems Biology Research Group, Szeged, 6726, Hungary Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári krt. 62, Szeged, 6726, Hungary Institute for Computer Science and Control (SZTAKI), Budapest, 1111, Hungary Brigham and Women’s Hospital & Harvard Medical School, Boston, MA 02115, United States Laboratory of Structural Chemistry and Biology & Hungarian Academy of Sciences (MTA)-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Budapest, 1117, Hungary Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, 63225, Germany Vellab Biotech Ltd., Szeged, 6722, Hungary Export Date: 12 September 2023 Correspondence Address: Vellai, T.; Department of Genetics, Hungary; email: vellai.tibor@ttk.elte.hu AB - Mobility of transposable elements (TEs) frequently leads to insertional mutations in functional DNA regions. In the potentially immortal germline, TEs are effectively suppressed by the Piwi-piRNA pathway. However, in the genomes of ageing somatic cells lacking the effects of the pathway, TEs become increasingly mobile during the adult lifespan, and their activity is associated with genomic instability. Whether the progressively increasing mobilization of TEs is a cause or a consequence of ageing remains a fundamental problem in biology. Here we show that in the nematode Caenorhabditis elegans , the downregulation of active TE families extends lifespan. Ectopic activation of Piwi proteins in the soma also promotes longevity. Furthermore, DNA N 6 -adenine methylation at TE stretches gradually rises with age, and this epigenetic modification elevates their transcription as the animal ages. These results indicate that TEs represent a novel genetic determinant of ageing, and that N 6 -adenine methylation plays a pivotal role in ageing control. LA - English DB - MTMT ER - TY - JOUR AU - Ari, Eszter AU - Vásárhelyi, Bálint Márk AU - Kemenesi, Gábor AU - Tóth, Gábor Endre AU - Zana, Brigitta AU - Somogyi, Balázs Antal AU - Lanszki, Zsófia AU - Röst, Gergely AU - Jakab, Ferenc AU - Papp, Balázs AU - Kintses, Bálint TI - A Single Early Introduction Governed Viral Diversity in the Second Wave of SARS-CoV-2 Epidemic in Hungary JF - VIRUS EVOLUTION J2 - VIRUS EVOL VL - 8 PY - 2022 IS - 2 PG - 12 SN - 2057-1577 DO - 10.1093/ve/veac069 UR - https://m2.mtmt.hu/api/publication/33040340 ID - 33040340 AB - Retrospective evaluation of past waves of the SARS-CoV-2 epidemic is key for designing optimal interventions against future waves and novel pandemics. Here we report on analysing genome sequences of SARS-CoV-2 from the first two waves of the epidemic in 2020 in Hungary, mirroring a suppression and a mitigation strategy, respectively. Our analysis reveals that the two waves markedly differed in viral diversity and transmission patterns. Specifically, unlike in several European areas or in the USA, we have found no evidence for early introduction and cryptic transmission of the virus in the first wave of the pandemic in Hungary. Despite the introduction of multiple viral lineages, extensive community spread was prevented by a timely national lockdown in March 2020. In sharp contrast, the majority of the cases in the much larger second wave can be linked to a single transmission lineage of the pan-European B.1.160 variant. This lineage was introduced unexpectedly early, followed by a two-month-long cryptic transmission before a soar of detected cases in September 2020. Epidemic analysis has revealed that the dominance of this lineage in the second wave was not associated with an intrinsic transmission advantage. This finding is further supported by the rapid replacement of B.1.160 by the alpha variant (B.1.1.7) that launched the third wave of the epidemic in February 2021. Overall, these results illustrate how the founder effect in combination with cryptic transmission, instead of repeated international introductions or higher transmissibility, can govern viral diversity. LA - English DB - MTMT ER - TY - JOUR AU - Csabai, Luca AU - Fazekas, Dávid AU - Kadlecsik, Tamás AU - Szalay-Bekő, Máté AU - Bohár, Balázs AU - Madgwick, Matthew AU - Módos, Dezső AU - Ölbei, Márton AU - Gul, Lejla AU - Sudhakar, Padhmanand AU - Kubisch, János AU - James Oyeyemi, Oyebode AU - Liska, Orsolya AU - Ari, Eszter AU - Hotzi, Bernadette AU - Billes, Viktor András AU - Molnár, Eszter AU - Földvári-Nagy, László AU - Csályi, Kitti AU - Demeter, Amanda AU - Pápai, Nóra AU - Koltai, Mihály AU - Varga, Máté AU - Földvári-Nagy Lászlóné Lenti, Katalin AU - J Farkas, Illés AU - Türei, Dénes AU - Csermely, Péter AU - Vellai, Tibor AU - Korcsmáros, Tamás TI - SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 50 PY - 2022 IS - D1 SP - 701 EP - 709 PG - 9 SN - 0305-1048 DO - 10.1093/nar/gkab909 UR - https://m2.mtmt.hu/api/publication/32352175 ID - 32352175 N1 - the first three authors should be regarded as joint First Authors AB - Signaling networks represent the molecular mechanisms controlling a cell's response to various internal or external stimuli. Most currently available signaling databases contain only a part of the complex network of intertwining pathways, leaving out key interactions or processes. Hence, we have developed SignaLink3 (http://signalink.org/), a valueadded knowledge-base that provides manually curated data on signaling pathways and integrated data from several types of databases (interaction, regulation, localisation, disease, etc.) for humans, and three major animal model organisms. SignaLink3 contains over 400 000 newly added human protein-protein interactions resulting in a total of 700 000 interactions for Homo sapiens, making it one of the largest integrated signaling network resources. Next to H. sapiens, SignaLink3 is the only current signaling network resource to provide regulatory information for the model species Caenorhabditis elegans and Danio rerio, and the largest resource for Drosophila melanogaster. Compared to previous versions, we have integrated gene expression data as well as subcellular localization of the interactors, therefore uniquely allowing tissue-, or compartment-specific pathway interaction analysis to create more accurate models. Data is freely available for download in widely used formats, including CSV, PSI-MI TAB or SQL. LA - English DB - MTMT ER - TY - JOUR AU - Liska, Orsolya AU - Bohár, Balázs AU - Hidas, András AU - Korcsmáros, Tamás AU - Papp, Balázs AU - Fazekas, Dávid AU - Ari, Eszter TI - TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species JF - DATABASE-JOURNAL OF BIOLOGICAL DATABASES AND CURATION J2 - DATABASE-OXFORD VL - 2022 PY - 2022 SN - 1758-0463 DO - 10.1093/database/baac083 UR - https://m2.mtmt.hu/api/publication/33101945 ID - 33101945 N1 - Funding Agency and Grant Number: National Research, Development and Innovation Office, Hungary (NKFIH) [131839]; NKFIH KKP [129814]; GINOP iChamber [2.3.215-2016-00026]; European Union [739593]; Biotechnology and Biological Sciences Research Council (BBSRC) Core Strategic Programme Grant [BB/CSP17270/1]; BBSRC ISP grant [BB/R012490/1] Funding text: This work was supported by the National Research, Development and Innovation Office, Hungary (NKFIH) grant PD [grant number 131839 to E.A.]; an NKFIH KKP [grant number 129814 to B.P.]; GINOP iChamber [grant number 2.3.215-2016-00026 to B.P.]; and The European Union's Horizon 2020 research and innovation programme under grant agreement [grant number 739593 to B.P.]; a Biotechnology and Biological Sciences Research Council (BBSRC) Core Strategic Programme Grant [grant number BB/CSP17270/1 to T.K.]; and a BBSRC ISP grant [grant number BB/R012490/1 to T.K.]. AB - Analysis of transcriptional regulatory interactions and their comparisons across multiple species are crucial for progress in various fields in biology, from functional genomics to the evolution of signal transduction pathways. However, despite the rapidly growing body of data on regulatory interactions in several eukaryotes, no databases exist to provide curated high-quality information on transcription factor–target gene interactions for multiple species. Here, we address this gap by introducing the TFLink gateway, which uniquely provides experimentally explored and highly accurate information on transcription factor–target gene interactions (∼12 million), nucleotide sequences and genomic locations of transcription factor binding sites (∼9 million) for human and six model organisms: mouse, rat, zebrafish, fruit fly, worm and yeast by integrating 10 resources. TFLink provides user-friendly access to data on transcription factor–target gene interactions, interactive network visualizations and transcription factor binding sites, with cross-links to several other databases. Besides containing accurate information on transcription factors, with a clear labelling of the type/volume of the experiments (small-scale or high-throughput), the source database and the original publications, TFLink also provides a wealth of standardized regulatory data available for download in multiple formats. The database offers easy access to high-quality data for wet-lab researchers, supplies data for gene set enrichment analyses and facilitates systems biology and comparative gene regulation studies. LA - English DB - MTMT ER - TY - CONF AU - Gerber, Dániel AU - Ari, Eszter AU - Szeifert, Bea AU - Kiss, Viktória AU - Fábián, Szilvia AU - Kustár, Ágnes AU - Köhler, Kitti AU - Mende, Balázs Gusztáv AU - Szécsényi-Nagy, Anna TI - Uncanny genetic proportions from Hungary suggest a long lasting Hunter-Gatherer ancestry in Central Europe at the Bronze Age T2 - 9th International Symposium on Biomolecular Archaeology : ISBA9 PY - 2021 SP - 121 EP - 121 PG - 1 UR - https://m2.mtmt.hu/api/publication/32681011 ID - 32681011 LA - English DB - MTMT ER - TY - GEN AU - Visnyovszki, Ádám AU - Orosz, László AU - Kintses, Bálint AU - Stirling, Tamás AU - Vásárhelyi, Bálint Márk AU - Ari, Eszter AU - Kiss, Enikő AU - Papp, Balázs AU - Apjok, Gábor AU - Vidovics, Fanni AU - Lakatos, Lóránt AU - Lengyel, György AU - Ánosi, Noel AU - Sóki, József AU - Baaity, Zain AU - Hajdú, Edit AU - Burián, Katalin TI - A COVID-19 PANDÉMIÁHOZ TÁRSULÓAN ELŐFORDULT MULTIREZISZTENS ACINETOBACTER BAUMANNII TÖRZSEK MOLEKULÁRIS JELLEMZÉSE PY - 2021 UR - https://m2.mtmt.hu/api/publication/32476999 ID - 32476999 LA - Hungarian DB - MTMT ER -