About
57
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Introduction
I am a bioinformatician and evolutionary biologist, serving as a researcher at the Institute of Biochemistry, Biological Research Centre in Szeged and a habilitated university assistant professor at the Dept. of Genetics, Eötvös Loránd University, Budapest, Hungary. My research focuses on genomics, antibiotic resistance, and transcriptional regulation. I teach bioinformatics, omics studies, and R programming to master and graduate students. Group website: https://genet.elte.hu/bioinformatics.
Current institution
Additional affiliations
May 2016 - present
Biological Research Centre Szeged Inst. Biochemistry
Position
- Researcher
Description
- Teaching bioinformtaics, OMIC studies and advanced R programming to biology master and PhD students. / Investigating the barriers of horizontal gene transfer of bacterial antibiotic resistance genes.
January 2009 - August 2019
May 2016 - present
Biological Research Centre
Position
- PostDoc Position
Description
- Bioinformatician, metagenomics
Education
June 2017 - June 2017
Field of study
- 8th International Course in Microbial Ecology: Microbiome Metagenome Analysis: Hands-on Taining
August 2016 - August 2016
June 2012 - June 2012
Field of study
- Meeting of Advances and Challenges of RNA-Seq Analysis
Publications
Publications (57)
Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of...
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 a progress...
Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phylogeographic analysis with high-throughput phage ty...
Phage therapy is gaining increasing interest in the fight against critically resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here we combine large-scale phylogeographical analysis with high-throughput phage typing to gu...
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 innov...
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...
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 w...
Despite the ongoing development of new antibiotics, the future evolution of bacterial resistance may render them ineffective. We demonstrate that antibiotic candidates currently under development are as prone to resistance evolution in Gram-negative pathogens as clinically employed antibiotics. Resistance generally stems from both genomic mutations...
Background
In patients with inflammatory bowel disease (IBD), Crohn’s disease (CD), and ulcerative colitis (UC), numerous cases of exacerbations could be observed after colonoscopy, raising the possible pathogenetic effect of colonic microbiota alterations in IBD flare.
Objectives
We aimed to investigate the changes in the fecal microbiota composi...
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...
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 r...
In this study we report 21 ancient shotgun genomes from present-day Western Hungary (3530-1620 cal BCE), from previously understudied Late Copper Age Baden, and Bronze Age Somogyvar-Vinkovci, Kisapostag, and Encrusted Pottery archaeological cultures. Our results indicate the presence of high steppe ancestry in Somogyvar-Vinkovci culture that was re...
Background
Bowel preparation prior to colonoscopy is a routine procedure and supposed to be safe. However, the exacerbation of the complaints could be observed in numerous cases after colonoscopy in patients with inflammatory bowel disease (IBD, Crohn’s disease CD, ulcerative colitis UC). Therefore, our study aimed to investigate the short- and lon...
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 value...
A koronavírus-fertőzés terjedési láncának visszakövetésében és a klinikai fejlesztés alatt álló vakcinajelöltek várható hosszú távú hatékonyságának előrejelzésében is segíthet az a vírusgenom-kutatási program, amely konzorciális együttműködéssel, szegedi, pécsi, debreceni és budapesti kutatóintézetek és klinikák közreműködésével valósul meg, és bek...
Gut microbial composition alters in some special situations, such as in ulcerative colits (UC) after total proctocolectomy and ileal pouch-anal anastomosis (IPAA) surgery. The aim of our study was to determine the composition of the intestinal microbiome in UC patients after IPAA surgery, compared with UC patients, familial adenomatous polyposis (F...
Antimicrobial peptides (AMPs) are key effectors of the innate immune system and promising therapeutic agents. Yet, knowledge on how to design AMPs with minimal cross-resistance to human host-defense peptides remains limited. Here, we systematically assess the resistance determinants of Escherichia coli against 15 different AMPs using chemical-genet...
Due to the critical role played by autophagy in pathogen clearance, pathogens have developed diverse strategies to subvert it. Despite previous key findings of bacteria-autophagy interplay, asystems-level insight into selective targeting by the host and autophagy modulation by the pathogens is lacking. We predicted potential interactions between hu...
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 antibiot...
Antimicrobial peptides (AMPs) are key effectors of the innate immune system and promising therapeutic agents. Yet, knowledge on how to design AMPs with minimal cross-resistance to human host-defense peptides remains limited. Here, with a chemical-genetic approach, we systematically assessed the resistance determinants of Escherichia coli against 15...
The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs) that are ancient components of immune defence. Despite important medical relevance, 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- and antibiotic-resis...
Significance
Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. By building on multiplex automated genome engineering, we developed a method that enables precise mutagenesis of multiple, long genomic segments in multiple...
Salmonella enterica is a prominent bacterial pathogen with implications on human and animal health. Salmonella serovars could be classified as gastro-intestinal or extra-intestinal. Genome-wide comparisons revealed that extra-intestinal strains are closer relatives of gastro-intestinal strains than to each other indicating a parallel evolution of t...
Biomarkers with high reproducibility and accurate prediction performance can contribute to comprehending the underlying pathogenesis of related complex diseases and further facilitate disease diagnosis and therapy. Techniques integrating gene expression profiles and biological networks for the identification of network-based disease biomarkers are...
Study focussing in the molecular warfare between bacterial pathogens and host autophagy investigated using a combination of computational and experimental techniques.
The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylo...
Autophagy (cellular self-eating) is a highly regulated degradation process of the eukaryotic cell during which parts of the cytoplasm are delivered into, and broken down within, the lysosomal compartment. The process serves as a main route for the elimination of superfluous and damaged cellular constituents, thereby mediating macromolecular and org...
Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in...
Previous morphological studies showed that the description of the Cyclotella genus was too general and according to new morphological criteria new genera were established based on both recent and fossil taxa (e.g. Discostella, Handmannia, Puncticulata, Tertiarius). Furthermore, previous molecular biological investigations proved that the Cyclotella...
A discrete mathematical method, Boolean analysis (or BOOL-AN), was used for evaluating of functional relationships within and between the families of transfer RNA sequences. The binary encoded sequence information of each transfer RNA was transformed into a compact analytical form, called the Iterative Canonical Form (ICF) of Boolean functions. Thi...
Autophagy, the lysosome-mediated self-degradation process, is implicated in survival during starvation in yeast, Dictyostelium and animals. In these eukaryotic taxa (collectively called Unikonts), autophagy is induced primarily through the Atg1/ULK1 complex in response to nutrient depletion. Autophagy has also been well-studied in non-unikont paras...
Supplementary Dataset
Hox genes play a central role in axial patterning during animal development. They are clustered in the genome and specify cell fate in sequential domains along the anteroposterior (A-P) body axis in a conserved order that is co-linear with their relative genomic position. In the soil worm Caenorhabditis elegans, this striking rule of co-linearity i...
Same species of genus Fridericia (Oligochaeta: Enchytraeidae) collected from different localities, can have small differences in their morphology, for example, the number of nephridia or length and width of the spermathecal ectal duct. During the identification of enchytraeid worms, several characteristics were investigated at the same time but pre...
A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar...
Questions
Questions (8)
Please suggest a website, API, or other solutions to sequence similarity searches on many (all available) metagenomic libraries without downloading the metagenomic reads or assemblies.
Thank you
We would like to analyse thousands of E. coli genomes and identify orthologous genes. Before this we would like to filter the bad quality genomes by BUSCO (https://busco.ezlab.org/). What % of BUSCO genes should we accept to consider the genome as "good quality"?
I have a large phylogenetic tree and a list of tip names for which I would like to know their closest relatives (based on the tree). The tree has polytomic nodes as well. Can you help me to solve this problem? I prefer R. Thanks
Here you are: http://crowdfightcovid19.org/volunteers PLEASE JOIN!
I think all biological and/or medical researchers who can should contribute to save our asses from this corona crisis. Do you know any organization who tries to coordinate a kind of home office research for this purpose?
Dear Community,
I would like to reconstruct the phylogeny of 16,000 E. coli strains based on their genome sequences. What do you think about the following concept?
1. ORF prediction in all genomes. (Prodigal)
2. Identification of the core genes based on reciprocal BLAST of the proteins of the reference E. coli strain to all proteomes. (Diamond)
3. Align the core genes. (MAFFT)
4. Keep SNV sites only and concatenate them to a "super" alignment.
5. Calculate a maximum likelihood tree based on the "super" alignment. (PhyML)
My questions are the following:
A) Should we use only those core genes that we found in all genomes? This is impossible since the overlap contains 0 genes. (We didn't find a single common gene.) Then should I exclude some strains to gain common core genes or can I use genes that are not common in all strains but represented at least in 15,000 strains?
B) Is it a good idea to concatenate SNV sites and infer a tree based on them?
C) How should I choose nucleotide substitution model for such a long and multitaxa alignment?
Cheers,
Eszter
The canonical way is to find the differentially expressed genes and than do gene set enrichment analysis. But is there a solution to include the pathway information before calculating differential expression? My dataset contains two different treatments, therefore I would like to use Generalized Linear Model and not a simple pairwise analysis. Many thanks for the help!
At least I cannot find them on Ensembl or USCS. I know some specific databases for tRNAs like tRNAdb and GtRNAdb. But I am really suprised that there are no tRNAs in the reference human genome annotation. Does anyone know the reason?
