Curriculum Vitae of Eszter Ari

Bioinformatic Researcher, University Teacher

arieszter@gmail.com

Websites

Positions

Present

Assistant professor – Eötvös Loránd University (ELTE), Department of Genetics

H-1117, Pázmány Péter stny. 1/C, Budapest, Hungary

  • 2019 - : Role: Teaching various bioinformatics courses to biology master and graduate students. Supervising undergraduate and graduate students. Coordinating the Molecular Genetics, Cell- and Developmental Biology specialisation.
  • 2009 - 2019: assistant lecturer
  • 2007 - 2009: scientific research associate

Research fellow – HUN-REN1 Biological Research Centre (BRC), Institute of Biochemistry, Szeged

H-6726, Temesvári krt. 62, Szeged, Hungary

  • 2016 - : Investigating the evolution of antibiotic resistance and virulence using phylogenetic and comparative genomics approaches in Balázs Papp’s Lab, from 2020 as a project leader.

Research fellow – Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Metabolic Systems Biology Research Group, Szeged

  • 2019 -

Formerly

Postdoctoral researcher – Univ. of Veterinary Medicine (Vet-Med Uni), Institut für Populationsgenetik, Vienna, A

  • 2012 - 2014: Analysing the RNA-seq data of thermal adapted fruit fly populations in Christian Schlötterer’s Lab.

Diplomas & Degrees

  • Habilitation: ELTE, Budapest, H, 2023
  • PhD: Biology Doctoral School, Theoretical and Evolutionary Biology Doctoral Programme, ELTE, Budapest, H, 2012
  • Bachelor and Master: Majoring in Applied Zoology, Faculty of Veterinary Sciences2, Szent István University, Budapest, H, 1999 - 2004

Awards & Scholarships

  • Outstanding scientific publication award from Excellence Fund of Eötvös Loránd University, 2024 and 2022, Budapest, H
  • Junior fellowship at Collegium Budapest – Institute for Advanced Study, 2009, Budapest, H
  • Scholarship of the Fac. Veterinary Sci., Szent István Univ., 2003 - 2004, Budapest, H
  • 2nd Prize of the Conference for Student Scientists at Fac. Veterinary Sci., Szent István Univ., 2003, Budapest, H

Grants

  • Supported Research Groups Programme 2025 - 2028: Role: co-applicant; Title: Genomic surveillance for precision therapies against antibiotic-resistant bacteria; PI: Papp Balázs; Number: TKCS-2024/66; amount awarded to ELTE: 30,000,000 HUF
  • ELTE international online courses 2025: the “Analysis of OMICS Data PR” was selected as a course in CHARM-EU; 500 000 HUF
  • Hungarian National Research Fund Grant – Postdoctoral Excellence Programme 2020 - 2023: Role: Principal investigator; Title: How do ‘superbugs’ emerge? - A systematic study of the mobility of resistance and virulence genes in human microbiota and pathogenic bacteria; Nr. 131839; 25,500,000 HUF
  • Promoting Excellence in Education, ELTE 2020: Role: Principal investigator; Title: Development of the infrastructure of the computer practical room; 4,000,000 HUF
  • Visegrad 4 Eastern Partnership (V4Eap) 2014 - 2015; Role: Supervisor; Connected to the fellowship of Zeljko Popovic; Title: DORMANCYbase – developing a database on gene and protein expression during dormancy in animals; 3,000 EUR

Teaching Activities

Present

Formerly

  • Introduction to Bioinformatics (L; HU) – for Bachelor students
  • Genetic lab. practices (selected P; EN, HU) – for Bachelor students
  • Genomics (selected L; EN, HU) – for Master students
  • Molecular evolution (selected L; HU) – for Master students
  • Evolutionary biology (selected L; HU) – for Master students
  • Discrete mathematical methods in biology (L, P; HU) – for Master and PhD students

Course Book

  • Genetics Exercises: Chapter 7 – Bioinformatics: Genetic Disease Recognition and Detection (HU)

Supervising & Mentoring

  • The personal site at the website of Hungarian Doctoral Council
  • Graduated students: 2 co-supervised PhD, 6 Master, 12 Bachelor, and 6 Scientific Student Association students
  • At present: Co-supervising 4 PhD students, supervising 2 Master, 2 Bachelor, and 3 Scientific Student Association students
  • Mentoring visiting student: 1 (with Support for summer internships for Hungarian students studying abroad grant)

Main Workshops

As Lecturer

As Participant

  • EMBO Training: Laboratory Leadership Course, 2024, Budapest, H
  • An R Reproducibility Toolkit for the practical researcher, 2022, online
  • 8th International Course in Microbial Ecology – Microbiome Metagenome Analysis, 2017, CNR-ISE, Verbania, I
  • EMBO course: Bioinformatics and Comparative Genome Analyses, 2011, Inst. Pasteur Paris, F
  • Computational Phyloinformatics Course, 2008, Duke Univ., Durham, NC, USA
  • Workshop on Molecular Evolution, 2006, Marine Biological Lab., Woods Hole, MA, USA

Memberships

Languages

  • Hungarian – mother tongue
  • English – C1 level
  • Italian – A1 level

Areas of Interest

  • Bioinformatics
  • Evolutionary Biology
  • Antibiotic Resistance
  • Comparative genomics
  • Molecular phylogenetics
  • Metagenomics
  • Transcriptomics
  • Transcriptional regulation
  • Data analysis

Professional Skills

  • Developing and using different bioinformatic methods, software and pipelines.
  • R programming language – professional level
  • Linux Shell scripting – intermediate level

Editing & Reviewing

  • Topic editor in Frontiers in Systems Biology
  • Reviewer in journals: Brief. Bioinformatics (3); Evol. Biol. (1); Genome Biol. Evol. (1); J. Math. Chem. (4); Mol. Ecol. (1); Mol. Phylogenetics Evol. (1); Sci. Rep. (1); Opusc. Zool. (1); Plos One (2)
  • Reviewing: PhD Theses (4), Grant proposals: Hungarian Scientific Research Fund Grant (3)

Popularising Science

  • Presenting at the Festival of ELTE: Global map of evolutionary dependencies between antibiotic resistance and virulence genes in E. coli. 2022, Budapest, H
  • Creating a website for The genomic epidemiology of SARS-CoV-2 in Hungary
  • Presenting at Capital of Science “Tudományok Fővárosa”: The genomic epidemiology of SARS-CoV-2 in Hungary, 2020, Budapest, H
  • Presenting at Night of Scientists “Kutatók Éjszakája”, 2018 and 2020

Scientific Websites

  • Supervising the creation of the TFLink, a transcription factor - target gene database.
  • Supervising the creation of the mulea and the muleaData R packages for functional enrichment analysis and dataset.

Publications

  • Google Scholar MTMT
  • Nr. of published papers: 27 (D1: 17 + Q1: 5)
  • Nr. of first, last or corresponding author publications: 8
  • Cumulative impact factor of first, last or corresponding author publications: 47.22
  • Cumulative impact factor of all publications (IF): 218.56
  • Independent citations of all publications (IC): 562
  • h-index: 16

Preprints

  • Balogh GM, Koncz B, Asztalos L, Ari E, Papp B, Szebeni GJ, Gémes N, Pál C & Manczinger M (2025) APOBEC3-associated mutations generate immunogenic peptides in SARS-CoV-2. Nature Communications, under review.

Published

Oral Presentations in Conferences

  • Nr. of international conference talks: 9
  • Nr. of national conference talks: 6
  • As an invited speaker*: 3
  • Ari E, et al. (2024) mulea - an R package for enrichment analysis using multiple ontologies and empirical false discovery rate. Bioinformatika, a Magyar Tudomány Ünnepén, 8 Nov, Budapest, H
  • Ari E, et al. (2024) mulea - an R package for enrichment analysis using multiple ontologies and empirical false discovery rate. SciComp24 Conference, 17-19 Oct, Szeged, H
  • Ari E, et al. (2023) Global map of evolutionary dependencies between antibiotic resistance and virulence genes in E. coli. 3rd HCEMM PhD-POSTDOC Symposium, 8-9 Nov, Keszthely, H
  • Ari E, et al. (2022) Global map of evolutionary dependencies between antibiotic resistance and virulence genes in E. coli. 1st Bioinformatics and Data Science in Genomic Studies (BDG2022) online conference, 25 Nov, University of Debrecen, H
  • Ari E, et al. (2022) Global map of evolutionary dependencies between antibiotic resistance and virulence genes in E. coli. Bioinformatics, Celebrating the Hungarian Science, 11 Nov, HAS, Research Centre for Natural Sciences, Budapest, H
  • Ari E*, Kintses B (2020) Methods to investigate the microbiome and understand the results. Meeting of Hungarian Society for Gastroenterology, Section Colon, 6-7 Mar, Visegrád, H
  • Ari E, et al. (2019) Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota. EvolBiol Day, 17 Apr, Szeged, H
  • Ari E*, et al. (2018) How well do the antimicrobial peptide resistance genes spread? Bioinformatics, Celebrating the Hungarian Science, 16 Nov, HAS, Research Centre for Natural Sciences, Budapest, H
  • Ari E: (2017) MulEA – A tool for multi-enrichment analysis. 2nd Interdisciplinary Signaling Workshop, 17-21 Jul, Visegrád, H
  • Ari E*: (2012) Molecular phylogenetic reconstructions with a discrete mathematical method, the Boolean analysis. International Congress, Hungarian Society for Microbiology, 24-26 Oct, Keszthely, H
  • Ari E & Jakó É (2012) Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes. 9th Joint Conference on Mathematics and Computer Science, 9-12 Feb, Siófok, H
  • Ari E, et al. (2007) Boolean analysis: A new discrete mathematical method for phylogenetic reconstruction. From Molecular Informatics to Bioinformatics – International Symposium, 19-21 Apr, Collegium Budapest, H
  • Ari E & Jakó É (2007) Testing a new discrete mathematical method for phylogenetic reconstruction. Evolution 2007 Conference, 16-20 Jun, Christchurch, NZ
  • Ari E & Jakó É (2007) Testing a new discrete mathematical method for phylogenetic reconstruction. The Dumont D’Urville Workshop on Applied Evolutionary Bioinformatics, 24-27 Jun, Kaikoura, NZ
  • Ari E, et al. (2007) Phylogenetic tree reconstruction with a new discrete mathematical method. Molecular taxonomic, phylogenetic and phylogeographic researches in Hungary, Meeting in memory of Sámuel Diószegi, 17 Nov, Debrecen, H
  • Ari E (2006) Reconstructing the phylogenetic tree of great apes by using a new discrete mathematical method. 12th Annual European Meeting of PhD students in Evolutionary Biology, 4-9 Sep, St. Andrews, UK

Other Invited Talks

  • Ari E* (2017) Investigating the antimicrobial peptide resistome in the human gut microbiome: a metagenomic approach. University of Graz, Institute of Zoology, 15 Nov, Graz, A
  • Ari E*: (2015) Rapid evolution of phenotypic plasticity during experimental evolution of Drosophila. The Genome Analysis Centre, 23 Feb, Norwich, UK

Poster Presentations in Conferences

  • Nr. of international conference posters: 9

Footnotes

  1. Formal names: Research Network of the Hungarian Academy of Science (HAS); Eötvös Loránd Research Network (ELKH)↩︎

  2. Formal and actual name: University of Veterinary Medicine↩︎