VU Gyvybės mokslų centro autoriaus 'Aleksej Železniak' publikacijų sąrašas

2025
1 Johnson, Sean R.; Fu, Xiaozhi; Viknander, Sandra; Goldin, Clara; Monaco, Sarah; Železniak, Aleksej; Yang, Kevin K. Computational scoring and experimental evaluation of enzymes generated by neural networks // Nature biotechnology. Berlin : Springer Nature. ISSN 1087-0156. eISSN 1546-1696. 2025, vol. 43, iss. 3, p. 396-405. DOI: 10.1038/s41587-024-02214-2. [DB: Science Citation Index Expanded (Web of Science), Scopus]
2 Buric, Filip; Viknander, Sandra; Fu, Xiaozhi; Lemke, Oliver; Carmona, Oriol Gracia; Zrimec, Jan; Szyrwiel, Lukasz; Mülleder, Michael; Ralser, Markus; Železniak, Aleksej. Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost // Protein science : John Wiley and Sons Inc. ISSN 0961-8368. eISSN 1469-896X. 2025, vol. 34, iss. 1, art. no. e5239, p. [1-25]. DOI: 10.1002/pro.5239. [DB: Science Citation Index Expanded (Web of Science), Scopus]
3 Ventimiglia, Leandro N.; Železniak, Aleksej. Programming of synthetic regulatory DNA for cell-type targeting in humans // Molecular cell: Focus on patterns in molecular biology. Cambridge : Cell Press. ISSN 1097-2765. eISSN 1097-4164. 2025, vol. 85, iss. 2, p. 205-207. DOI: 10.1016/j.molcel.2024.12.019. [DB: Science Citation Index Expanded (Web of Science), Scopus]
4 Lindell, Anna E.; Grießhammer, Anne; Michaelis, Lena; Papagiannidis, Dimitrios; Ochner, Hannah; Kamrad, Stephan; Guan, Rui; Blasche, Sonja; Ventimiglia, Leandro N.; Ramachandran, Bini; Ozgur, Hilal; Železniak, Aleksej; Beristain-Covarrubias, Nonantzin; Yam-Puc, Juan Carlos; Roux, Indra; Barron, Leon P.; Richardson, Alexandra K.; Martin, Maria Guerra; Benes, Vladimir; Morone, Nobuhiro; Thaventhiran, James E. D.; Bharat, Tanmay A. M.; Savitski, Mikhail M.; Maier, Lisa; Patil, Kiran R. Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances // Nature microbiology : Springer Nature. eISSN 2058-5276. 2025, vol. 10, iss. 7, p. 1630-1647. DOI: 10.1038/s41564-025-02032-5. [DB: Science Citation Index Expanded (Web of Science), Scopus]
5 Lemke, Oliver; Heineike, Benjamin Murray; Viknander, Sandra; Cohen, Nir; Li, Feiran; Steenwyk, Jacob Lucas; Spranger, Leonard; Agostini, Federica; Lee, Cory Thomas; Aulakh, Simran Kaur; Berman, Judith; Rokas, Antonis; Nielsen, Jens; Gossmann, Toni Ingolf; Železniak, Aleksej; Ralser, Markus. The role of metabolism in shaping enzyme structures over 400 million years // Nature : Springer Nature. ISSN 0028-0836. eISSN 1476-4687. 2025, vol. 644, p. 280-289. DOI: 10.1038/s41586-025-09205-6. [DB: Science Citation Index Expanded (Web of Science), Scopus]
6 Lyu, Bingxue; Wu, Ke; Huang, Yuanyuan; Anton, Mihail; Li, Xiongwen; Viknander, Sandra; Anwer, Danish; Yang, Yunfeng; Lu, Diannan; Kerkhoven, Eduard; Železniak, Aleksej; Gao, Dan; Chen, Yu; Li, Feiran. GotEnzymes2: expanding coverage of enzyme kinetics and thermal properties // Nucleic acids research. Oxford : Oxford University Press (OUP). ISSN 0305-1048. eISSN 1362-4962. 2025, Early Access, p. [1-10]. DOI: 10.1093/nar/gkaf1053. [DB: Science Citation Index Expanded (Web of Science)]

2024
1 Abrusán, György; Železniak, Aleksej. Cellular location shapes quaternary structure of enzymes // Nature communications. Berlin : Springer Nature. eISSN 2041-1723. 2024, vol. 15, iss. 1, art. no. 8505, p. [1-16]. DOI: 10.1038/s41467-024-52662-2. [DB: Science Citation Index Expanded (Web of Science), Scopus]
2 Coleman, Tom; Viknander, Sandra; Kirk, Alicia M.; Sandberg, David; Caron, Elise; Železniak, Aleksej; Krenske, Elizabeth; Larsbrink, Johan. Structure-based clustering and mutagenesis of bacterial tannases reveals the importance and diversity of active site-capping domains // Protein science. Hoboken : John Wiley and Sons Inc. ISSN 0961-8368. eISSN 1469-896X. 2024, vol. 33, iss. 12, art. no. e5202, p. [1-20]. DOI: 10.1002/pro.5202. [DB: Science Citation Index Expanded (Web of Science), Scopus] [IF: 5.200; AIF: 5.300; Q1 (2024 InCities JCR SCIE)]

2023
1 Vernardis, Spyros I.; Demichev, Vadim; Lemke, Oliver; Grüning, Nana-Maria; Messner, Christoph; White, Matt; Pietzner, Maik; Peluso, Alina; Collet, Tinh-Hai; Henning, Elana; Gille, Christoph; Campbell, Archie; Hayward, Caroline; Porteous, David J.; Marioni, Riccardo E.; Mülleder, Michael; Železniak, Aleksej; Wareham, Nicholas J.; Langenberg, Claudia; Farooqi, I Sadaf; Ralser, Markus. The impact of acute nutritional interventions on the plasma proteome // The journal of clinical endocrinology and metabolism. Washington : Oxford University Press. ISSN 0021-972X. eISSN 1945-7197. 2023, vol. 108, iss. 8, p. 2087-2098. DOI: 10.1210/clinem/dgad031. [DB: Science Citation Index Expanded (Web of Science), Scopus] [IF: 5.000; AIF: 4.300; Q1 (2023 InCities JCR SCIE)]
2 Correia-Melo, Clara; Kamrad, Stephan; Tengölics, Roland; Messner, Christoph B.; Trebulle, Pauline; Townsend, StJohn; Jayasree Varma, Sreejith; Freiwald, Anja; Heineike, Benjamin M.; Campbell, Kate; Herrera-Dominguez, Lucía; Kaur Aulakh, Simran; Szyrwiel, Lukasz; Yu, Jason S.L.; Železniak, Aleksej; Demichev, Vadim; Mülleder, Michael; Papp, Balázs; Alam, Mohammad Tauqeer; Ralser, Markus. Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan // Cell. Cambridge : Elsevier B.V. ISSN 0092-8674. eISSN 1097-4172. 2023, vol. 186, iss. 1, p. 63-79. DOI: 10.1016/j.cell.2022.12.007. [DB: Science Citation Index Expanded (Web of Science), Scopus] [IF: 45.600; AIF: 5.900; Q1 (2023 InCities JCR SCIE)]
3 Cao, Zhejian; Fu, Xiaozhi; Li, Hao; Pandit, Santosh; Amombo Noa, Francoise M.; Öhrström, Lars; Železniak, Aleksej; Mijakovic, Ivan. Synthesis of metal-organic frameworks through enzymatically recycled polyethylene terephthalate // ACS Sustainable Chemistry and Engineering. Washington : American Chemical Society. eISSN 2168-0485. 2023, vol. 11, iss. 43, p. 15506-15512. DOI: 10.1021/acssuschemeng.3c05222. [DB: Science Citation Index Expanded (Web of Science), Scopus]

2022
1 Zrimec, Jan; Fu, Xiaozhi; Muhammad, Azam Sheikh; Skrekas, Christos; Jauniškis, Vykintas; Speicher, Nora K; Börlin, Christoph S; Verendel, Vilhelm; Chehreghani, Morteza Haghir; Dubhashi, Devdatt; Siewers, Verena; David, Florian; Nielsen, Jens; Železniak, Aleksej. Controlling gene expression with deep generative design of regulatory DNA // Nature communications. Berlin : Nature Portfolio. eISSN 2041-1723. 2022, vol. 13, iss. 1, art. no. 5099, p. [1-17]. DOI: 10.1038/s41467-022-32818-8. [DB: Science Citation Index Expanded (Web of Science), Scopus]
2 Li, Gang; Buric, Filip; Zrimec, Jan; Viknander, Sandra; Nielsen, Jens; Železniak, Aleksej; Engqvist, Martin Km. Learning deep representations of enzyme thermal adaptation // Protein science. Hoboken : Wiley. ISSN 0961-8368. eISSN 1469-896X. 2022, vol. 31, no. 12, art. no. e4480, p. [1-14]. DOI: 10.1002/pro.4480. [DB: Science Citation Index Expanded (Web of Science), Scopus, MEDLINE] [IF: 8.000; AIF: 5.900; Q1 (2022 InCities JCR SCIE)]

2021
1 Zorrilla, Francisco; Buric, Filip; Patil, Kiran R; Železniak, Aleksej. metaGEM: reconstruction of genome scale metabolic models directly from metagenomes // Nucleic acids research. Oxford : Oxford University Press. ISSN 0305-1048. eISSN 1362-4962. 2021, vol. 49, iss. 21, art. no. e126, p. [1-12]. DOI: 10.1093/nar/gkab815. [DB: Science Citation Index Expanded (Web of Science), Scopus, PubMed] [IF: 19.160; AIF: 6.490; Q1 (2021 InCities JCR SCIE)]
2 Zrimec, Jan; Kokina, Mariia; Jonasson, Sara; Zorrilla, Francisco; Železniak, Aleksej. Plastic-degrading potential across the global microbiome correlates with recent pollution trends // mBio. Washington : American Society for Microbiology. eISSN 2150-7511. 2021, vol. 12, iss. 5, art. no. e02155-21, p. [1-15]. DOI: 10.1128/mBio.02155-21. [DB: Science Citation Index Expanded (Web of Science), Scopus, PubMed, Current Contents, BIOSIS Previews]