Welcome to the website of the Evolutionary Bioinformatics Research Group

2021

We are a research lab in bioinformatics at Eötvös Loránd University, Institute of Biology, Department of Genetics, Budapest, Hungary. Our primary research interests include:

• Bioinformatics and computational biology
• Evolutionary genomics and phylogenetics
• Microbial genomics and the evolution of antibiotic resistance
• Development of databases and packages for gene expression analysis and regulation

We created the TFLink transcription factor - target gene interaction database, the BacCurate standardized sequencing-metadata database for ESKAPEE bacterial isolates, and developed the mulea R package, and the treetune packages for bioinformatics analyses.

For detailed information, please navigate through the tabs.

News

TipNew manuscript 📃 (July 2026)

A new preprint of a collaborative work is available on BioRXiv. In this research, the standardised sequencing metadata we created was applied:

• Szili P, Czikkely MS, Farkas Z, Daruka L, Toldi B, Kurkó E, Vonyó AZ, Csernyák M, Kámán R, Maharramov E, Daraba A, Benedek B, Imre G, Lantos II, Mészáros L, Somogyi Á, Nagy D, Nagy ZF, Grézal G, Ari E, Kada N, Papp B, Csenki-Bakos Z, Kaszab E, Kriszt B, Szabó I, Balogh G, Péter M, Gombos I, Pilbat A, Török Z, Varga Z, Czimmerer Z, Csörgő B, Adamecz D, Papp CG, Szilovics Z, Veres É, Gácser A, Madácsy T, Maléth J, Ayaydin F, Farkas A, Tengölics R, Kintses B, Varga V, Haracska L, Juhász S, Pál C (2026) A preclinical resistance framework discovers the virulence risks of antibiotics in development BioRXiv.

TipBacCurate database is now online! 🦠 (June 2026)

Explore standardised, confidence-scored metadata for ~1.4 million public ESKAPEE pathogen bacterial BioSample records, and the AllTheBacteria collection.

Search, compare, and export curated metadata for genomic epidemiology and One Health research: https://baccurate.org/

TipCsenge Gazsó has defended her master thesis 🎓 (June 2026)

We are pleased to share that Csenge Gazsó, a master’s student in the EvoBioinfo group, has successfully defended her master’s thesis, entitled Investigation of transposable element gene expression regulation using bioinformatics methods, at ELTE.

TipEszter Ari awarded the MTA Bolyai Research Fellowship ⭐ (June 2026)

We are delighted to announce that Eszter Ari, the PI of the EvoBioinfo group, has been awarded the prestigious MTA Bolyai János Research Fellowship.

TipSummer university application is open 👩 🏫 (March 2026)

Eszer Ari and her colleagues (Orsoly Pipek, Ágoston Hunya from ELTE, Marco Trevisan-Herraz from Newcastle University) are organizing an English-language, practice-oriented summer school at ELTE, Budapest, on the Analysis of omics data PR. Description of the two-week course is available here. Further details are available on the website of the organizer, Budapest Summer University 2026.

TipTwo conferences 🇩🇪 🇬🇧 (March 2026)

Eszter Ari presented our work on standardizing sequencing metadata with LLMs at the EMBL Symposium: AI and Biology in Heidelberg, D. Huge credit to Norbert Kada, ELTE MSc student, who did the work, and sincere thanks to Balázs Papp at Synthetic and Systems Biology Unit, Biological Research Centre HUN-REN BRC for the support. The reception was incredibly warm, and it was exciting to see such strong interest to our work and tools.

Eszter also presented our work on standardizing sequencing metadata with LLMs at the Wellcome Connecting Science conference Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies in Hinxton, UK.

TipNew manuscript 📃 (March 2026)

New preprint about the PhD work of András Asbóth is available on BioRXiv:

• Asbóth A, Stirling T, Méhi O, Apjok G, De Sousa VK, Taylor NMI, Mehdi HH, Papp B, Ari E, Kintses B (2026) A global map of receptor-binding protein compatibility for the programmable design of Klebsiella and Acinetobacter phages BioRXiv.

TipInternational guest lecturer 👨 (Feb 2026)

We are delighted to welcome Marco Trevisan-Herraz from Newcastle University as a new international guest lecturer in our Analysis of OMICS Data Practical course. His contribution brings valuable international expertise to the teaching of omics data analysis.

TipTeaching 🎓 (Feb 2026)

We started the new semester of teaching at ELTE:

• Analysis of OMICS Data Practical for Master students. The course has also been included in the CHARM-EU Course Catalogue.

• Phylogenetics Lecture+Practical for Master students

Coordinating the Bioinformatics specialisation

TipCoordinating the Bioinformatics specialisation az ELTE (Feb 2026)

Eszter Ari became the coordinator of the Bioinformatics Specialisation within the Biology Master’s programme at ELTE.

TipNew collaborative publications 🍾 (Fall 2025)

Two collaborative publications have been accepted recently:

• Balogh GM, Koncz B, Asztalos L, Ari E, Papp B, Szebeni GJ, Gémes N, Pál C & Manczinger M (2025) C>U mutations generate immunogenic peptides in SARS-CoV-2. Nature Communications, 16: 10156. D1, IF: 15.70

• Zsichla L, Adravecz L, Müller D, Lemey P, Lakatos Á, Ari E, Kusejko K, Kouyos R, Szlávik J, Lakatos B, Áy É & Müller V (2025) Molecular epidemiology of HIV-1 in Hungary: an evolving contact zone of colliding virus subtypes. Frontiers in Microbiology, Q1, IF: 4.5

TipConference (13 Nov 2025)

Eszter Ari and Norbert Kada gave an invited conference talk about the Application of large language models for the standardization of DNA sequencing metadata on the 2nd National HUN-REN Cloud Meeting, 13 Nov 2025, Budapest, H; Recorded video (in Hungarian)

TipMentorship (Fall 2025)

Eszter Ari became a mentor at Szent-Györgyi Mentoring Program

TipMSCA PF Hosting Offer (2025)

The Evolutionary Bioinformatics Research Group offers postdoctoral supervision for the Marie-Skłodowska Curie Postdoctoral Fellow 2025 call