@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}
}

@article{MTMT:33634821,
	title = {Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains},
	url = {https://m2.mtmt.hu/api/publication/33634821},
	author = {Apjok, Gábor and Számel, Mónika and Christodoulou, Chryso and Seregi, Viktória and Vásárhelyi, Bálint Márk and Stirling, Tamás and Eszenyi, Bálint Dénes and Sári , Tóbiás and Vidovics, Fanni and Nagrand, Erika and Kovács, Dorina and Szili, Petra and Lantos, Ildikó Ilona and Méhi, Orsolya Katinka and Jangir, Pramod Kumar and Herczeg, Róbert and Gálik, Bence and Urbán, Péter and Gyenesei, Attila and Draskovits, Gábor and Nyerges, Ákos and Fekete, Gergely and Bodai, László and Zsindely, Nóra and Dénes, Béla and Yosef, Ido and Qimron, Udi and Papp, Balázs and Pál, Csaba and Kintses, Bálint},
	doi = {10.1038/s41564-023-01320-2},
	journal-iso = {NAT MICROBIOL},
	journal = {NATURE MICROBIOLOGY},
	volume = {8},
	unique-id = {33634821},
	issn = {2058-5276},
	abstract = {Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.},
	year = {2023},
	eissn = {2058-5276},
	pages = {410-423},
	orcid-numbers = {Apjok, Gábor/0000-0002-8627-2378; Vásárhelyi, Bálint Márk/0000-0003-1782-8691; Stirling, Tamás/0000-0002-8964-6443; Méhi, Orsolya Katinka/0009-0004-7918-913X; Jangir, Pramod Kumar/0000-0001-8330-0655; Herczeg, Róbert/0000-0002-5903-0082; Gálik, Bence/0000-0002-3949-7005; Nyerges, Ákos/0000-0002-1581-490X; Bodai, László/0000-0001-8411-626X; Zsindely, Nóra/0000-0002-6189-3100; Dénes, Béla/0000-0002-9889-529X}
}

@article{MTMT:32813213,
	title = {Proteome-wide landscape of solubility limits in a bacterial cell},
	url = {https://m2.mtmt.hu/api/publication/32813213},
	author = {Györkei, Ádám and Daruka, Lejla and Balogh, Dávid and Őszi, Erika and Magyar, Zoltán and Szappanos, Balázs and Fekete, Gergely and Fuxreiter, Mónika and Horváth, Péter and Pál, Csaba and Kintses, Bálint and Papp, Balázs},
	doi = {10.1038/s41598-022-10427-1},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {12},
	unique-id = {32813213},
	issn = {2045-2322},
	abstract = {Proteins are prone to aggregate when expressed above their solubility limits. Aggregation may occur rapidly, potentially as early as proteins emerge from the ribosome, or slowly, following synthesis. However, in vivo data on aggregation rates are scarce. Here, we classified the Escherichia coli proteome into rapidly and slowly aggregating proteins using an in vivo image-based screen coupled with machine learning. We find that the majority (70%) of cytosolic proteins that become insoluble upon overexpression have relatively low rates of aggregation and are unlikely to aggregate co-translationally. Remarkably, such proteins exhibit higher folding rates compared to rapidly aggregating proteins, potentially implying that they aggregate after reaching their folded states. Furthermore, we find that a substantial fraction (similar to 35%) of the proteome remain soluble at concentrations much higher than those found naturally, indicating a large margin of safety to tolerate gene expression changes. We show that high disorder content and low surface stickiness are major determinants of high solubility and are favored in abundant bacterial proteins. Overall, our study provides a global view of aggregation rates and hence solubility limits of proteins in a bacterial cell.},
	keywords = {AGGREGATION; PROTEINS; ASSOCIATION; GENE-EXPRESSION; PREDICTION; RATES; INTRINSIC DISORDER; Expression levels; INCLUSION-BODIES},
	year = {2022},
	eissn = {2045-2322},
	orcid-numbers = {Őszi, Erika/0000-0002-0006-4683; Szappanos, Balázs/0000-0002-5075-1799}
}

@article{MTMT:32803914,
	title = {Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast},
	url = {https://m2.mtmt.hu/api/publication/32803914},
	author = {Farkas, Zoltán and Kovács, Károly and Sarkadi, Zsuzsa and Kalapis, Dorottya and Fekete, Gergely and Birtyik, Fanni and Ayaydin, Ferhan and Molnár, Csaba and Horváth, Péter and Pál, Csaba and Papp, Balázs},
	doi = {10.1038/s41559-022-01730-1},
	journal-iso = {NAT ECOL EVOL},
	journal = {NATURE ECOLOGY & EVOLUTION},
	volume = {6},
	unique-id = {32803914},
	issn = {2397-334X},
	year = {2022},
	eissn = {2397-334X},
	pages = {763-773},
	orcid-numbers = {Molnár, Csaba/0000-0002-6124-1209}
}

@article{MTMT:32106320,
	title = {Limited evolutionary conservation of multidrug resistance and collateral sensitivity (vol 36, pg 1601, 2019)},
	url = {https://m2.mtmt.hu/api/publication/32106320},
	author = {Apjok, Gábor and Boross, Gábor and Nyerges, Ákos and Fekete, Gergely and Lázár, Viktória and Papp, Balázs and Pál, Csaba and Csörgő, Bálint},
	doi = {10.1093/molbev/msab116},
	journal-iso = {MOL BIOL EVOL},
	journal = {MOLECULAR BIOLOGY AND EVOLUTION},
	volume = {38},
	unique-id = {32106320},
	issn = {0737-4038},
	keywords = {evolutionary biology; Biochemistry & Molecular Biology},
	year = {2021},
	eissn = {1537-1719},
	pages = {3029-3029},
	orcid-numbers = {Boross, Gábor/0000-0002-7208-5678; Nyerges, Ákos/0000-0002-1581-490X; Csörgő, Bálint/0000-0003-0397-6845}
}

@article{MTMT:31038930,
	title = {Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action},
	url = {https://m2.mtmt.hu/api/publication/31038930},
	author = {Kintses, Bálint and Jangir, Pramod Kumar and Fekete, Gergely and Számel, Mónika and Méhi, Orsolya Katinka and Spohn, Réka and Daruka, Lejla and Martins, Ana and Hosseinnia, A. and Gagarinova, A. and Kim, S. and Phanse, S. and Csörgő, Bálint and Györkei, Ádám and Ari, Eszter and Lázár, Viktória and Nagy, István and Babu, M. and Pál, Csaba and Papp, Balázs},
	doi = {10.1038/s41467-019-13618-z},
	journal-iso = {NAT COMMUN},
	journal = {NATURE COMMUNICATIONS},
	volume = {10},
	unique-id = {31038930},
	issn = {2041-1723},
	year = {2019},
	eissn = {2041-1723},
	orcid-numbers = {Jangir, Pramod Kumar/0000-0001-8330-0655; Méhi, Orsolya Katinka/0009-0004-7918-913X; Csörgő, Bálint/0000-0003-0397-6845; Ari, Eszter/0000-0001-7774-1067}
}

@article{MTMT:30703953,
	title = {Limited evolutionary conservation of the phenotypic effects of antibiotic resistance mutations},
	url = {https://m2.mtmt.hu/api/publication/30703953},
	author = {Apjok, Gábor and Boross, Gábor and Nyerges, Ákos and Fekete, Gergely and Lázár, Viktória and Papp, Balázs and Pál, Csaba and Csörgő, Bálint},
	doi = {10.1093/molbev/msz109},
	journal-iso = {MOL BIOL EVOL},
	journal = {MOLECULAR BIOLOGY AND EVOLUTION},
	volume = {36},
	unique-id = {30703953},
	issn = {0737-4038},
	year = {2019},
	eissn = {1537-1719},
	pages = {1601-1611},
	orcid-numbers = {Boross, Gábor/0000-0002-7208-5678; Nyerges, Ákos/0000-0002-1581-490X; Csörgő, Bálint/0000-0003-0397-6845}
}

@article{MTMT:30435652,
	title = {Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.},
	url = {https://m2.mtmt.hu/api/publication/30435652},
	author = {Kintses, Bálint and Méhi, Orsolya Katinka and Ari, Eszter and Számel, Mónika and Györkei, Ádám and Jangir, Pramod Kumar and Nagy, István and Pál, Ferenc and Fekete, Gergely and Tengölics, Roland and Nyerges, Ákos and Likó, István and Bálint, Anita and Molnár, Tamás and Bálint, Balázs and Vásárhelyi, Bálint Márk and Bustamante, Misshelle and Papp, Balázs and Pál, Csaba},
	doi = {10.1038/s41564-018-0313-5},
	journal-iso = {NAT MICROBIOL},
	journal = {NATURE MICROBIOLOGY},
	volume = {4},
	unique-id = {30435652},
	issn = {2058-5276},
	abstract = {The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.},
	year = {2019},
	eissn = {2058-5276},
	pages = {447-458},
	orcid-numbers = {Méhi, Orsolya Katinka/0009-0004-7918-913X; Ari, Eszter/0000-0001-7774-1067; Jangir, Pramod Kumar/0000-0001-8330-0655; Pál, Ferenc/0000-0002-0985-8578; Nyerges, Ákos/0000-0002-1581-490X; Likó, István/0000-0001-7668-4726; Bálint, Anita/0000-0002-3624-896X; Molnár, Tamás/0000-0002-4913-7599; Vásárhelyi, Bálint Márk/0000-0003-1782-8691}
}

@article{MTMT:3378998,
	title = {Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides},
	url = {https://m2.mtmt.hu/api/publication/3378998},
	author = {Lázár, Viktória and Martins, Ana and Spohn, Réka and Daruka, Lejla and Grézal, Gábor and Fekete, Gergely and Számel, Mónika and Jangir, Pramod Kumar and Kintses, Bálint and Csörgő, Bálint and Nyerges, Ákos and Györkei, Ádám and Kincses, András and Dér, András and Walter, Fruzsina and Deli, Mária Anna and Zsoldiné Urbán, Edit and Hegedüs, Zsófia and Olajos, Gábor and Méhi, Orsolya Katinka and Bálint, Balázs and Nagy, István and Martinek, Tamás and Papp, Balázs and Pál, Csaba},
	doi = {10.1038/s41564-018-0164-0},
	journal-iso = {NAT MICROBIOL},
	journal = {NATURE MICROBIOLOGY},
	volume = {3},
	unique-id = {3378998},
	issn = {2058-5276},
	abstract = {Antimicrobial peptides are promising alternative antimicrobial agents. However, little is known about whether resistance to small-molecule antibiotics leads to cross-resistance (decreased sensitivity) or collateral sensitivity (increased sensitivity) to antimicrobial peptides. We systematically addressed this question by studying the susceptibilities of a comprehensive set of 60 antibiotic-resistant Escherichia coli strains towards 24 antimicrobial peptides. Strikingly, antibiotic-resistant bacteria show a high frequency of collateral sensitivity to antimicrobial peptides, whereas cross-resistance is relatively rare. We identify clinically relevant multidrug-resistance mutations that increase bacterial sensitivity to antimicrobial peptides. Collateral sensitivity in multidrug-resistant bacteria arises partly through regulatory changes shaping the lipopolysaccharide composition of the bacterial outer membrane. These advances allow the identification of antimicrobial peptide-antibiotic combinations that enhance antibiotic activity against multidrug-resistant bacteria and slow down de novo evolution of resistance. In particular, when co-administered as an adjuvant, the antimicrobial peptide glycine-leucine-amide caused up to 30-fold decrease in the antibiotic resistance level of resistant bacteria. Our work provides guidelines for the development of efficient peptide-based therapies of antibiotic-resistant infections.},
	year = {2018},
	eissn = {2058-5276},
	pages = {718-731},
	orcid-numbers = {Grézal, Gábor/0000-0003-1685-4791; Jangir, Pramod Kumar/0000-0001-8330-0655; Csörgő, Bálint/0000-0003-0397-6845; Nyerges, Ákos/0000-0002-1581-490X; Walter, Fruzsina/0000-0001-8145-2823; Deli, Mária Anna/0000-0001-6084-6524; Zsoldiné Urbán, Edit/0000-0002-9602-7552; Hegedüs, Zsófia/0000-0002-5546-8167; Olajos, Gábor/0000-0002-2479-4891; Méhi, Orsolya Katinka/0009-0004-7918-913X; Martinek, Tamás/0000-0003-3168-8066}
}

@article{MTMT:3338278,
	title = {Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins},
	url = {https://m2.mtmt.hu/api/publication/3338278},
	author = {Natan, E and Endoh, T and Haim-Vilmovsky, L and Flock, T and Chalancon, G and Hopper, JTS and Kintses, Bálint and Horváth, Péter and Daruka, Lejla and Fekete, Gergely and Pál, Csaba and Papp, Balázs and Őszi, Erika and Magyar, Zoltán and Marsh, JA and Elcock, AH and Babu, MM and Robinson, CV and Sugimoto, N and Teichmann, SA},
	doi = {10.1038/s41594-018-0029-5},
	journal-iso = {NAT STRUCT MOL BIOL},
	journal = {NATURE STRUCTURAL & MOLECULAR BIOLOGY},
	volume = {25},
	unique-id = {3338278},
	issn = {1545-9993},
	abstract = {Cotranslational protein folding can facilitate rapid formation of functional structures. However, it can also cause premature assembly of protein complexes, if two interacting nascent chains are in close proximity. By analyzing known protein structures, we show that homomeric protein contacts are enriched toward the C termini of polypeptide chains across diverse proteomes. We hypothesize that this is the result of evolutionary constraints for folding to occur before assembly. Using high-throughput imaging of protein homomers in Escherichia coli and engineered protein constructs with N- and C-terminal oligomerization domains, we show that, indeed, proteins with C-terminal homomeric interface residues consistently assemble more efficiently than those with N-terminal interface residues. Using in vivo, in vitro and in silico experiments, we identify features that govern successful assembly of homomers, which have implications for protein design and expression optimization.},
	year = {2018},
	eissn = {1545-9985},
	pages = {279-288},
	orcid-numbers = {Őszi, Erika/0000-0002-0006-4683}
}