Publications

Preprints

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, 2026.02.20.706991.

Published

2025

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, 16: 1732254. Q1, IF: 4.5, IC: 0
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: 15.7, IC: 1
Daruka L, Czikkely MS, Szili P, Farkas Z, Balogh D, Maharramov E, Vu TH, Sipos L, Vincze BD, Grézal G, Juhász Sz, Dunai A, Daraba A, Számel M, Sári T, Stirling T, Vásárhelyi BM, Ari E, Christodoulou C, Manczinger M, Enyedi MZs, Jaksa G, van Houte S, Pursey E, Papp CG, Szilovics Z, Pintér L, Haracska L, Gácser A, Kintses B, Papp B & Pál Cs (2025) ESKAPE pathogens rapidly develop resistance against antibiotics in development. Nature Microbiology, 10(2): 313-331. D1, IF: 20.5, IC: 71

2024

Koncz M, Stirling T, Mehdi HH, Méhi O, Eszenyi B, Asbóth A, Apjok G, Tóth Á, Orosz L, Vásárhelyi BM, Ari E, Daruka L, Polgár TF, Schneider Gy, Zalokh SA, Számel M, Fekete G, Bohár B, Nagy Varga K, Visnyovszki Á, Székely E, Licker MS, Izmendi O, Costache C, Gajic I, Lukovic B, Molnár Sz, Szőcs-Gazdi UO, Bozai Cs, Indreas M, Kristóf K, Van der Henst C, Breine A; Pál C, Papp B & Kintses B (2024) Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens. Cell, 187(21): 5901 - 5918.e28. D1, IF: 45.5, IC: 42
Turek C, Ölbei M, Stirling T, Fekete G, Tasnádi E, Gul L, Bohár B, Papp B, Jurkowski W & Ari E* (2024) mulea - an R package for enrichment analysis using various ontologies and empirical false discovery rate. BMC Bioinformatics, 25(1): 334. Q1, IF: 2.9, IC: 1 “Impactful paper” according to OOIR Observatory of International Research. (*corresponding author)

2023

Kiss V, Gerber D, Szeifert B, Székely O, Egyed B, Gyuris B, I Giblin J, Horváth A, Palcsu L, Köhler K, Kulcsár G, Kustár Á, Szeverényi V, Fábián S, Gusztáv Mende B, Ari E & Szécsényi-Nagy A (2023) Lifeway narratives of a Bronze Age community from Balatonkeresztúr (Western Hungary) based on bioarchaeological analyses. In: Meller, Harald; Krause, Johannes; Haak, Wolfgang; Risch, Roberto (ed.) Kinship, sex, and biological relatedness: the contribution of archaeogenetics to the understanding of social and biological relations, 15: Mitteldeutscher Archäologentag vom 6. bis 8. Oktober 2022 in Halle (Saale) Germany: Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt, Landesmuseum für Vorgeschichte 344 p. pp. 233-248. IC: 0 Book Chapter
Gerber D, Szeifert B, Székely O, Egyed B, Gyuris B, Giblin JI, Horváth A, Köhler K, Kulcsár G, Kustár Á, Major I, Molnár M, Palcsu L, Szeverényi V, Fábián S, Mende BG, Bondár M, Ari E*, Kiss V* & Szécsényi-Nagy A* (2023) Interdisciplinary analyses of Bronze Age communities from Western Hungary reveal complex population histories. Molecular Biology and Evolution, 40(9): msad182. D1, IF: 11, IC: 15 (*shared corresponding authorship)
Bacsur P, Rutka M, Resál T, Szántó K, Jójárt B, Bálint A, Ari E, Walliyulah A, Kintses B, Fehér T, Asbóth A, Pigniczki D, Bor R, Fábián A, Maléth J, Szepes Z, Farkas K & Molnár T (2023) Effects of bowel cleansing on the composition of the gut microbiome in inflammatory bowel disease patients and healthy controls. Therapeutic Advances in Gastroenterology, 16: 17562848231174298. Q1, IF: 3.9, IC: 18
Sturm Á, Saskői É, Hotzi B, Tarnóci A, Barna J, Bodnár F, Sharma H, Kovács T, Ari E, Weinhardt N, Kerepesi C, Perczel A, Ivics Z & Vellai T (2023) Downregulation of transposable elements extends lifespan in Caenorhabditis elegans. Nature Communications, 14(1): 5278. D1, IF: 14.7, IC: 33

2022

Ari E, Vásárhelyi BM, Kemenesi G, Tóth GE, Zana B, Somogyi B, Lanszki Z, Röst G, Jakab F, Papp B & Kintses B (2022) A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary. Virus Evolution, 8(2): veac069. D1, IF: 5.3, IC: 4
Csabai L, Fazekas D, Kadlecsik T, Szalay-Bekő M, Bohár B, Madgwick M, Módos D, Ölbei M, Gul L, Sudhakar P, Kubisch J, Oyeyemi OJ, Liska O, Ari E, Hotzi B, Billes VA, Molnár E, Földvári-Nagy L, Csályi K, Demeter A, Pápai N, Koltai M, Varga M, Lenti K, Farkas IJ, Türei D, Csermely P, Vellai T & Korcsmáros T (2022) SignaLink3: A multi-layered resource to uncover tissue-specific signaling networks. Nucleic Acids Research, 50(D1): 701-709. D1, IF: 14.9, IC: 37
Liska O, Bohár B, Hidas H, Korcsmáros T, Papp B, Fazekas D & Ari E* (2022) TFLink: An integrated gateway to access transcription factor - target gene interactions for multiple species. Database, 2022, baac083. D1, IF: 5.8, IC: 142 “High impact paper” according to scientometrics.org. (*corresponding author)

2020

Bálint A, Farkas K, Kintses B, Méhi O, Vásárhelyi BM, Ari E, Pál C, Madácsy T, Maléth J, Szántó KJ, Nagy I, Rutka M, Bacsur P, Szűcs D, Szepes Z, Nagy F, Fábián A, Bor R, Milassin Á & Molnár T (2020) Functional anatomical changes in ulcerative colitis patients determine their gut microbiota composition and consequently the possible treatment outcome. Pharmaceuticals, 13(11): 346-362. D1, IF: 5.68, IC: 27

2019

Kintses B, Jangir PK, Fekete G, Számel M, Méhi O, Spohn R, Daruka L, Martins A, Hosseinnia A, Gagarinova A, Kim S, Phanse S, Csörgö B, Györkei Á, Ari E, Lázár V, Faragó A, Nagy I, Babu M, Pál C & Papp B (2019) Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action. Nature Communications, 10(1): 5731. D1, IF: 12.12, IC: 44
Kintses B*, Méhi O*, Ari E*, Számel M, Györkei Á, Jangir PK, Nagy I, Pál F, Fekete G, Tengölics R, Nyerges Á, Likó I, Bálint A, Molnár T, Bálint B, Vásárhelyi BM, Bustamante M, Papp B & Pál C (2019) Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota. Nature Microbiology, 4(3): 447-458. D1, IF: 15.54, IC: 101 Craig MacLean recommended it in F1000Prime as being of special significance in its field. It was selected as a part of the Nature Gut Microbiota core collection. (*shared first authorship)
Sudhakar P, Claire-Jacomin A, Hautefort I, Samavedam S, Fatemian K, Ari E, Gul L, Demeter A, Jones E, Korcsmaros T & Nezis JP (2019) Targeted interplay between bacterial pathogens and host autophagy. Autophagy, 15(9): 1620-1633. D1, IF: 11.06, IC: 48
Sun D, Ren X, Ari E, Korcsmaros T, Csermely P & Wu L-Y (2019) Discovering cooperative biomarkers for heterogeneous complex disease diagnoses. Briefings in Bioinformatics, 20(1): 89-101. D1, IF: 9.1, IC: 20

2018

Nyerges Á, Csörgő B, Draskovits G, Kintses B, Szili P, Ferenc Gy, Révész T, Ari E, Nagy I, Bálint B, Vásárhelyi BM, Bihari P, Számel M, Balogh D, Papp H, Kalapis D, Papp B & Pál C (2018) Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. Proceedings of the National Academy of Sciences of the United States of America, 115(25): E5726-E5735. D1, IF: 9.58, IC: 95

2017

Fodor E, Sigmond T, Ari E, Lengyel K, Takács-Vellai K, Varga M & Vellai T (2017) Methods to study autophagy in zebrafish. Methods in Enzymology, 588: 467-96. Q1, IF: 1.48, IC: 22
Métris A, Sudhakar P, Fazekas D, Demeter A, Ari E, Ölbei M, Branchu P, Kingsley RA, Baranyi J & Korcsmáros T (2017) SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. Npj Systems Biology and Applications, 3(1): s41540-17-34-NaN-17. Q1, IF: 3.81, IC: 31
Ricotta C, Ari E, Bonanomi G, Giannino F, Heathfield D, Mazzoleni S & Podani J (2017) Spatial analysis of phylogenetic community structure: New version of a classical method. Community Ecology, 18(1): 37-46. Q2, IF: 0.98, IC: 2

2016

Ács É, Ari E, Duleba M, Dressler M, Genkal SI, Jakó É, Rimet F, Ector L & Kiss KT (2016) Pantocsekiella, a new centric diatom genus based on morphological and genetic studies. Fottea, 16(1): 56-78. Q2, IF: 0.6, IC: 61
Ari E* & Jakó É (2016) Classification of tRNA isoacceptor sequences by using graph-based molecular descriptors. Journal of Chemometrics, 30(1): 182-187. Q2, IF: 2.03, IC: 0 (*corresponding author)
Módos D, Brooks J, Fazekas D, Ari E, Vellai T, Csermely P, Korcsmáros T & Lenti K (2016) Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. Scientific Reports, 6: 38588. D1, IF: 4.62, IC: 7

2014

Földvári-Nagy L, Ari E, Csermely P, Korcsmáros T & Vellai T (2014) Starvation-response may not involve Atg1-dependent autophagy induction in non-unikont parasites. Scientific Reports, 4: 5829. D1, IF: 5.85, IC: 17

2012

Ari E*, Ittzés P, Podani J, Le Thi QC & Jakó É (2012) Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes. Molecular Phylogenetics and Evolution, 63(1): 193-202. D1, IF: 4.42, IC: 5 (*corresponding author)

2010

Boros G, Cech G, Ari E & Dózsa-Farkas K (2010) Extension of employing ITS region in the investigation of Hungarian Fridericia species (Oligochaeta: Enchytraeidae). Zoology in the Middle East, 51(sup2): 23-30. Q3, IF: 0.3, IC: 2
Tihanyi B, Vellai T, Regős Á, Ari E, Müller F & Takács-Vellai K (2010) The C. elegans Hox gene ceh-13 regulates cell migration and fusion in a non-colinear way. Implications for the early evolution of Hoxclusters. BMC Developmental Biology, 10(1): 78-92. Q1, IF: 2.78, IC: 27

2009

Jakó É, Ari E, Ittzés P, Horváth A & Podani J (2009) BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction. Molecular Phylogenetics and Evolution, 52(3): 887-897. D1, IF: 3.88, IC: 30

2008

Ari E, Ittzés P, Podani J & Jakó É (2008) Phylogenetic tree reconstruction with a new discrete mathematical method. Kitaibelia, 13: 209-211. Q2, IF: 0.23, IC: 0 (in Hungarian)