@misc{MTMT:34718081,
	title = {mulea - an R package for enrichment analysis using multiple ontologies and empirical FDR correction},
	url = {https://m2.mtmt.hu/api/publication/34718081},
	author = {Turek, Cezary and Olbei, Marton and Stirling, Tamás and Fekete, Gergely and Tasnádi, Ervin Áron and Gul, Leila and Bohár, Balázs and Papp, Balázs and Jurkowski, Wiktor and Ari, Eszter},
	unique-id = {34718081},
	abstract = {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.},
	year = {2024},
	orcid-numbers = {Stirling, Tamás/0000-0002-8964-6443; Ari, Eszter/0000-0001-7774-1067}
}

@misc{MTMT:34158052,
	title = {Antibiotics of the future are prone to resistance in Gram-negative pathogens},
	url = {https://m2.mtmt.hu/api/publication/34158052},
	author = {Daruka, Lejla and Márton, Simon Czikkely and Petra, Szili and Farkas, Zoltán and Dávid, Balogh and Elvin, Maharramov and Thu-Hien, Vu and Levente, Sipos and Botond, Dávid Vincze and Gábor, Grézal and Szilvia, Juhász and Anett, Dunai and Andreea, Daraba and Mónika, Számel and Tóbiás, Sári and Tamás, Stirling and Vásárhelyi, Bálint Márk and Ari, Eszter and Chryso, Christodoulou and Máté, Manczinger and Márton, Zsolt Enyedi and Gábor, Jaksa and Stineke, van Houte and Elizabeth, Pursey and Csaba, Gergő Papp and Zóra, Szilovics and Lajos, Pintér and Lajos, Haracska and Attila, Gácser and Bálint, Kintses and Balázs, Papp and Csaba, Pál},
	unique-id = {34158052},
	year = {2023},
	orcid-numbers = {Vásárhelyi, Bálint Márk/0000-0003-1782-8691; Ari, Eszter/0000-0001-7774-1067}
}

@article{MTMT:33549439,
	title = {Interdisciplinary analyses of Bronze Age communities from Western Hungary reveal complex population histories},
	url = {https://m2.mtmt.hu/api/publication/33549439},
	author = {Gerber, Dániel and Szeifert, Bea and Székely, Orsolya and Egyed, Balázs and Gyuris, Balázs and Giblin, Julia I. and Horváth, Anikó and Köhler, Kitti and Kulcsár, Gabriella and Kustár, Ágnes and Major, István and Molnár, Mihály and Palcsu, László and Szeverényi, Vajk and Fábián, Szilvia and Mende, Balázs Gusztáv and Bondár, Mária (Ködmönné) and Ari, Eszter and Kiss, Viktória and Szécsényi-Nagy, Anna},
	doi = {10.1093/molbev/msad182},
	journal-iso = {MOL BIOL EVOL},
	journal = {MOLECULAR BIOLOGY AND EVOLUTION},
	volume = {182},
	unique-id = {33549439},
	issn = {0737-4038},
	abstract = {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.},
	year = {2023},
	eissn = {1537-1719},
	orcid-numbers = {Egyed, Balázs/0000-0003-3960-2052; Major, István/0000-0003-4675-9875; Bondár, Mária (Ködmönné)/0000-0002-6526-0570; Ari, Eszter/0000-0001-7774-1067; Szécsényi-Nagy, Anna/0000-0003-2095-738X}
}

@article{MTMT:34014839,
	title = {Effects of bowel cleansing on the composition of the gut microbiota in inflammatory bowel disease patients and healthy controls},
	url = {https://m2.mtmt.hu/api/publication/34014839},
	author = {Bacsur, Péter and Rutka, Mariann and Asbóth, András and Resál, Tamás and Szántó, Kata Judit and Jójárt, Boldizsár and Bálint, Anita and Ari, Eszter and Ajibola, Walliyulahi and Kintses, Bálint and Fehér, Tamás and Pigniczki , Daniella and Bor, Renáta and Fábián, Anna and Maléth, József and Szepes, Zoltán and Farkas, Klaudia and Molnár, Tamás},
	doi = {10.1177/17562848231174298},
	journal-iso = {THER ADV GASTROENTER},
	journal = {THERAPEUTIC ADVANCES IN GASTROENTEROLOGY},
	volume = {16},
	unique-id = {34014839},
	issn = {1756-283X},
	year = {2023},
	eissn = {1756-2848},
	orcid-numbers = {Bacsur, Péter/0000-0002-8534-0068; Rutka, Mariann/0000-0003-2360-7836; Resál, Tamás/0000-0002-3842-9094; Szántó, Kata Judit/0000-0003-0749-5061; Jójárt, Boldizsár/0000-0002-2764-3925; Bálint, Anita/0000-0002-3624-896X; Ari, Eszter/0000-0001-7774-1067; Fehér, Tamás/0000-0001-9318-3640; Pigniczki , Daniella/0000-0001-6395-2576; Bor, Renáta/0000-0001-9393-5240; Fábián, Anna/0000-0002-0824-7476; Maléth, József/0000-0001-5768-3090; Szepes, Zoltán/0000-0002-9466-8719; Farkas, Klaudia/0000-0003-0599-182X; Molnár, Tamás/0000-0002-4913-7599}
}

@article{MTMT:34119363,
	title = {Downregulation of transposable elements extends lifespan in Caenorhabditis elegans},
	url = {https://m2.mtmt.hu/api/publication/34119363},
	author = {Sturm, Ádám and Saskői, Éva and Hotzi, Bernadette and Tarnóci, Anna and Barna, János and Bodnár, Ferenc and Sharma, Himani and Kovács, Tibor and Ari, Eszter and Weinhardt, Nóra and Kerepesi, Csaba and Perczel, András and Ivics, Zoltán and Vellai, Tibor},
	doi = {10.1038/s41467-023-40957-9},
	journal-iso = {NAT COMMUN},
	journal = {NATURE COMMUNICATIONS},
	volume = {14},
	unique-id = {34119363},
	issn = {2041-1723},
	abstract = {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.},
	year = {2023},
	eissn = {2041-1723},
	orcid-numbers = {Sturm, Ádám/0000-0002-9515-8761; Saskői, Éva/0000-0001-6691-8576; Hotzi, Bernadette/0000-0003-1433-6843; Barna, János/0000-0002-9242-0939; Bodnár, Ferenc/0000-0001-9630-1315; Sharma, Himani/0000-0001-6947-9281; Kovács, Tibor/0000-0002-0632-9128; Ari, Eszter/0000-0001-7774-1067; Kerepesi, Csaba/0000-0001-9541-246X; Perczel, András/0000-0003-1252-6416; Ivics, Zoltán/0000-0002-7803-6658; Vellai, Tibor/0000-0002-3520-2572}
}

@article{MTMT:33040340,
	title = {A Single Early Introduction Governed Viral Diversity in the Second Wave of SARS-CoV-2 Epidemic in Hungary},
	url = {https://m2.mtmt.hu/api/publication/33040340},
	author = {Ari, Eszter and Vásárhelyi, Bálint Márk and Kemenesi, Gábor and Tóth, Gábor Endre and Zana, Brigitta and Somogyi, Balázs Antal and Lanszki, Zsófia and Röst, Gergely and Jakab, Ferenc and Papp, Balázs and Kintses, Bálint},
	doi = {10.1093/ve/veac069},
	journal-iso = {VIRUS EVOL},
	journal = {VIRUS EVOLUTION},
	volume = {8},
	unique-id = {33040340},
	abstract = {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.},
	year = {2022},
	eissn = {2057-1577},
	orcid-numbers = {Ari, Eszter/0000-0001-7774-1067; Vásárhelyi, Bálint Márk/0000-0003-1782-8691; Kemenesi, Gábor/0000-0001-9775-3065; Tóth, Gábor Endre/0000-0002-7201-9646; Lanszki, Zsófia/0000-0003-3116-4633; Röst, Gergely/0000-0001-9476-3284}
}

@article{MTMT:32352175,
	title = {SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks},
	url = {https://m2.mtmt.hu/api/publication/32352175},
	author = {Csabai, Luca and Fazekas, Dávid and Kadlecsik, Tamás and Szalay-Bekő, Máté and Bohár, Balázs and Madgwick, Matthew and Módos, Dezső and Ölbei, Márton and Gul, Lejla and Sudhakar, Padhmanand and Kubisch, János and James Oyeyemi, Oyebode and Liska, Orsolya and Ari, Eszter and Hotzi, Bernadette and Billes, Viktor András and Molnár, Eszter and Földvári-Nagy, László and Csályi, Kitti and Demeter, Amanda and Pápai, Nóra and Koltai, Mihály and Varga, Máté and Földvári-Nagy Lászlóné Lenti, Katalin and J Farkas, Illés and Türei, Dénes and Csermely, Péter and Vellai, Tibor and Korcsmáros, Tamás},
	doi = {10.1093/nar/gkab909},
	journal-iso = {NUCLEIC ACIDS RES},
	journal = {NUCLEIC ACIDS RESEARCH},
	volume = {50},
	unique-id = {32352175},
	issn = {0305-1048},
	abstract = {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.},
	year = {2022},
	eissn = {1362-4962},
	pages = {701-709},
	orcid-numbers = {Fazekas, Dávid/0000-0001-7605-592X; Módos, Dezső/0000-0001-9412-6867; Ari, Eszter/0000-0001-7774-1067; Hotzi, Bernadette/0000-0003-1433-6843; Billes, Viktor András/0000-0003-0030-6221; Földvári-Nagy, László/0000-0002-3954-721X; Varga, Máté/0000-0003-4289-1705; Földvári-Nagy Lászlóné Lenti, Katalin/0000-0002-1252-822X; Csermely, Péter/0000-0001-9234-0659; Vellai, Tibor/0000-0002-3520-2572}
}

@article{MTMT:33101945,
	title = {TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species},
	url = {https://m2.mtmt.hu/api/publication/33101945},
	author = {Liska, Orsolya and Bohár, Balázs and Hidas, András and Korcsmáros, Tamás and Papp, Balázs and Fazekas, Dávid and Ari, Eszter},
	doi = {10.1093/database/baac083},
	journal-iso = {DATABASE-OXFORD},
	journal = {DATABASE-JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
	volume = {2022},
	unique-id = {33101945},
	issn = {1758-0463},
	abstract = {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.},
	year = {2022},
	eissn = {1758-0463},
	orcid-numbers = {Hidas, András/0000-0002-6030-8459; Fazekas, Dávid/0000-0001-7605-592X; Ari, Eszter/0000-0001-7774-1067}
}

@CONFERENCE{MTMT:32681011,
	title = {Uncanny genetic proportions from Hungary suggest a long lasting Hunter-Gatherer ancestry in Central Europe at the Bronze Age},
	url = {https://m2.mtmt.hu/api/publication/32681011},
	author = {Gerber, Dániel and Ari, Eszter and Szeifert, Bea and Kiss, Viktória and Fábián, Szilvia and Kustár, Ágnes and Köhler, Kitti and Mende, Balázs Gusztáv and Szécsényi-Nagy, Anna},
	booktitle = {9th International Symposium on Biomolecular Archaeology : ISBA9},
	unique-id = {32681011},
	year = {2021},
	pages = {121-121},
	orcid-numbers = {Ari, Eszter/0000-0001-7774-1067; Szécsényi-Nagy, Anna/0000-0003-2095-738X}
}

@misc{MTMT:32476999,
	title = {A COVID-19 PANDÉMIÁHOZ TÁRSULÓAN ELŐFORDULT MULTIREZISZTENS ACINETOBACTER BAUMANNII TÖRZSEK MOLEKULÁRIS JELLEMZÉSE},
	url = {https://m2.mtmt.hu/api/publication/32476999},
	author = {Visnyovszki, Ádám and Orosz, László and Kintses, Bálint and Stirling, Tamás and Vásárhelyi, Bálint Márk and Ari, Eszter and Kiss, Enikő and Papp, Balázs and Apjok, Gábor and Vidovics, Fanni and Lakatos, Lóránt and Lengyel, György and Ánosi, Noel and Sóki, József and Baaity, Zain and Hajdú, Edit and Burián, Katalin},
	unique-id = {32476999},
	year = {2021},
	orcid-numbers = {Stirling, Tamás/0000-0002-8964-6443; Vásárhelyi, Bálint Márk/0000-0003-1782-8691; Ari, Eszter/0000-0001-7774-1067; Lengyel, György/0000-0002-0534-5935; Sóki, József/0000-0001-9230-8907; Baaity, Zain/0000-0001-6411-382X; Burián, Katalin/0000-0003-1300-2374}
}